Portfolio EDEND: 2014-08-31

Publisher name: SPIE - International Society for Optical Engineering PY - 2014 Y1 - 2014 N2 - We report on the development of a pulsed high-power frequency doubled vertical-external-cavity surface-emitting laser (VECSEL) with a peak output power of 14 W and emission spectrum near 588 nm. The semiconductor gain chip was grown by molecular beam epitaxy and comprised 10 GaInAs quantum wells. The gain structure was designed to be antiresonant at 1180 nm. The fundamental wavelength was frequency doubled to the yellow-orange spectral range using a 10-mm long critically phase matched lithium triborate nonlinear crystal, situated at the mode waist of the V-shaped laser cavity. The emission spectrum was narrowed down to FWHM of < 0.2 nm by employing a 1.5 mm birefringent filter and a 100-μm-thick etalon inside the cavity. By directly modulating the pump laser of the VECSEL, we were able to produce pulse widths down to 570 ns with average and peak output power of 81 mW and 14 W, respectively. The repetition rate was kept constant at 10 kHz throughout the measurements. The maximum peak power obtained was pump power limited. In comparison, at the same coolant temperature, a maximum of 8.5 W was achieved in continuous wave. The maximum optical-to-optical conversion efficiency (absorbed peak pump power to peak output power) was calculated to be 20-21 %. © 2014 SPIE. AB - We report on the development of a pulsed high-power frequency doubled vertical-external-cavity surface-emitting laser (VECSEL) with a peak output power of 14 W and emission spectrum near 588 nm. The semiconductor gain chip was grown by molecular beam epitaxy and comprised 10 GaInAs quantum wells. The gain structure was designed to be antiresonant at 1180 nm. The fundamental wavelength was frequency doubled to the yellow-orange spectral range using a 10-mm long critically phase matched lithium triborate nonlinear crystal, situated at the mode waist of the V-shaped laser cavity. The emission spectrum was narrowed down to FWHM of < 0.2 nm by employing a 1.5 mm birefringent filter and a 100-μm-thick etalon inside the cavity. By directly modulating the pump laser of the VECSEL, we were able to produce pulse widths down to 570 ns with average and peak output power of 81 mW and 14 W, respectively. The repetition rate was kept constant at 10 kHz throughout the measurements. The maximum peak power obtained was pump power limited. In comparison, at the same coolant temperature, a maximum of 8.5 W was achieved in continuous wave. The maximum optical-to-optical conversion efficiency (absorbed peak pump power to peak output power) was calculated to be 20-21 %. © 2014 SPIE. KW - Frequency doubling KW - Gain modulation KW - High-efficiency KW - High-power KW - Pulsed KW - SHG KW - Yellow-orange VECSEL UR - http://www.scopus.com/inward/record.url?scp=84902438552&partnerID=8YFLogxK U2 - 10.1117/12.2054716 DO - 10.1117/12.2054716 M3 - Conference contribution SN - 978-1-6284-1090-7 VL - 9134 T3 - SPIE Conference Proceedings BT - Photonics Europe 2014, Semiconductor Lasers and Laser Dynamics VI, April 14-17, 2014, Brussels, Belgium. Proceedings of SPIE PB - SPIE ER - TY - GEN T1 - Ray-based evaluation of dual-polarized MIMO in (Ultra-)dense millimeter-wave urban deployments AU - Solomitckii, Dmitrii AU - Petrov, Vitaly AU - Nikopour, Hosein AU - Akdeniz, Mustafa AU - Orhan, Oner AU - Himayat, Nageen AU - Talwar, Shilpa AU - Andreev, Sergey AU - Koucheryavy, Yevgeni PY - 2018/7/20 Y1 - 2018/7/20 N2 - Dense deployments of millimeter-wave (mmWave) base stations (BSs) are being considered as the most feasible solution to meet the steadily growing data rate demands of mobile users. Accordingly, the achievable performance gains of mmWave-based dense networks in real deployments have to be studied carefully, since mmWave radio technology features specific transceiver, antenna, and propagation properties. In this paper, we contribute an accurate performance evaluation of single- versus dual-polarized MIMO systems operating over the mmWave channel in typical urban scenarios as well as address the impact of device- and network-centric parameters on the performance gains enabled by MIMO in dense to ultra-dense BS deployments. This study relies on our in-house ray-based modeler and takes into account the key mmWave system effects, such as multi-path propagation, utilization of dual-polarized antennas, and characteristic interference models. Our results show that the benefit of using mmWave- MIMO grows with increasing BS density, thus encouraging a further study of this technology especially for (ultra-)dense setups. We also demonstrate that non-coherent non-polarized diffuse scattering component may reduce the capacity gain of dual-polarized vs. single- polarized MIMO. AB - Dense deployments of millimeter-wave (mmWave) base stations (BSs) are being considered as the most feasible solution to meet the steadily growing data rate demands of mobile users. Accordingly, the achievable performance gains of mmWave-based dense networks in real deployments have to be studied carefully, since mmWave radio technology features specific transceiver, antenna, and propagation properties. In this paper, we contribute an accurate performance evaluation of single- versus dual-polarized MIMO systems operating over the mmWave channel in typical urban scenarios as well as address the impact of device- and network-centric parameters on the performance gains enabled by MIMO in dense to ultra-dense BS deployments. This study relies on our in-house ray-based modeler and takes into account the key mmWave system effects, such as multi-path propagation, utilization of dual-polarized antennas, and characteristic interference models. Our results show that the benefit of using mmWave- MIMO grows with increasing BS density, thus encouraging a further study of this technology especially for (ultra-)dense setups. We also demonstrate that non-coherent non-polarized diffuse scattering component may reduce the capacity gain of dual-polarized vs. single- polarized MIMO. U2 - 10.1109/VTCSpring.2018.8417788 DO - 10.1109/VTCSpring.2018.8417788 M3 - Conference contribution SP - 1 EP - 7 BT - 2018 IEEE 87th Vehicular Technology Conference, VTC Spring 2018 - Proceedings PB - IEEE ER - TY - GEN T1 - Real-time depth image-based rendering with layered dis-occlusion compensation and aliasing-free composition AU - Smirnov, Sergey AU - Gotchev, Atanas PY - 2015 Y1 - 2015 N2 - Depth Image-based Rendering (DIBR) is a popular view synthesis technique which utilizes the RGB+D image format, also referred to as view-plus-depth scene representation. Classical DIBR is prone to dis-occlusion artefacts, caused by the lack of information in areas behind foreground objects, which appear visible in the synthesized images. A number of recently proposed compensation techniques have addressed the problem of hole filling. However, their computational complexity does not allow for real-time view synthesis and may require additional user input. In this work, we propose a hole-compensation technique, which works fully automatically and in a perceptually-correct manner. The proposed technique applies a two-layer model of the given RGB+D imagery, which is specifically tailored for rendering with free viewpoint selection. The main two components of the proposed technique are an adaptive layering of depth into relative 'foreground' and 'background' layers to be rendered separately and an additional blending filtering aimed at creating a blending function for aliasing cancellation during the process of view composition. The proposed real-time implementation turns ordinary view-plus-depth images to true 3D scene representations, which allow visualization in the fly-around manner. AB - Depth Image-based Rendering (DIBR) is a popular view synthesis technique which utilizes the RGB+D image format, also referred to as view-plus-depth scene representation. Classical DIBR is prone to dis-occlusion artefacts, caused by the lack of information in areas behind foreground objects, which appear visible in the synthesized images. A number of recently proposed compensation techniques have addressed the problem of hole filling. However, their computational complexity does not allow for real-time view synthesis and may require additional user input. In this work, we propose a hole-compensation technique, which works fully automatically and in a perceptually-correct manner. The proposed technique applies a two-layer model of the given RGB+D imagery, which is specifically tailored for rendering with free viewpoint selection. The main two components of the proposed technique are an adaptive layering of depth into relative 'foreground' and 'background' layers to be rendered separately and an additional blending filtering aimed at creating a blending function for aliasing cancellation during the process of view composition. The proposed real-time implementation turns ordinary view-plus-depth images to true 3D scene representations, which allow visualization in the fly-around manner. U2 - 10.1117/12.2086895 DO - 10.1117/12.2086895 M3 - Conference contribution SN - 9781628414899 T3 - SPIE Conference Proceedings BT - Proceedings of SPIE - The International Society for Optical Engineering PB - SPIE ER - TY - GEN T1 - Robust Regulation of SISO Systems: The Fractional Ideal Approach AU - Laakkonen, Petteri AU - Quadrat, Alban PY - 2015 Y1 - 2015 N2 - We solve the robust regulation problem for single-input single-output plants by using the fractional ideal approach and without assuming the existence of coprime factorizations. In particular, we are able to formulate the famous internal model principle for stabilizable plants which do not necessarily admit coprime factorizations. We are able to give a necessary and suffcient solvability condition for the robust regulation problem, which leads to a design method for a robustly regulating controller. The theory is illustrated by examples. AB - We solve the robust regulation problem for single-input single-output plants by using the fractional ideal approach and without assuming the existence of coprime factorizations. In particular, we are able to formulate the famous internal model principle for stabilizable plants which do not necessarily admit coprime factorizations. We are able to give a necessary and suffcient solvability condition for the robust regulation problem, which leads to a design method for a robustly regulating controller. The theory is illustrated by examples. U2 - 10.1137/1.9781611974072.43 DO - 10.1137/1.9781611974072.43 M3 - Conference contribution SP - 311 EP - 318 BT - Proceedings of the SIAM Conference on Control and Its Applications (CT15) PB - SIAM, Society for Industrial and Applied Mathematics ER - TY - GEN T1 - Short-range supercontinuum based lidar for combustion diagnostics AU - Saleh, Abba AU - Ryczkowski, Piotr AU - Genty, Goery AU - Toivonen, Juha N1 - jufoid=71479 PY - 2019 Y1 - 2019 N2 - We developed a short range Lidar system using a supercontinuum source spectrally tailored to cover the ro-vibrational transition energies of desired components of a flue gas. The system enables simultaneous remote measurements of the gas parameters, like temperature and concentration which play a key role in the performance of combustion power plants. The technique requires only one inspection window and can thus be used in combustion units with limited access. It exploits differential absorption between specific wavelength bands of the gas absorption spectrum. The transmittance of individual wavelength band is derived from the detected backscattered temporal intensity of the supercontinuum pulses. We demonstrate preliminary industrial measurement of water vapor temperature and concentration in a full scale boiler. The technique also enables 3D mapping of temperature and concentration. AB - We developed a short range Lidar system using a supercontinuum source spectrally tailored to cover the ro-vibrational transition energies of desired components of a flue gas. The system enables simultaneous remote measurements of the gas parameters, like temperature and concentration which play a key role in the performance of combustion power plants. The technique requires only one inspection window and can thus be used in combustion units with limited access. It exploits differential absorption between specific wavelength bands of the gas absorption spectrum. The transmittance of individual wavelength band is derived from the detected backscattered temporal intensity of the supercontinuum pulses. We demonstrate preliminary industrial measurement of water vapor temperature and concentration in a full scale boiler. The technique also enables 3D mapping of temperature and concentration. KW - Combustion KW - Diagnostics KW - Lidar KW - Remote sensing KW - Supercontinuum U2 - 10.1117/12.2542720 DO - 10.1117/12.2542720 M3 - Conference contribution T3 - Proceedings of SPIE BT - SPIE Future Sensing Technologies A2 - Kimata, Masafumi A2 - Valenta, Christopher R. PB - SPIE, IEEE ER - TY - GEN T1 - Significance of graph theoretic measures in predicting neuronal network activity AU - Mäki-Marttunen, Tuomo Mikael AU - Acimovic, Jugoslava AU - Ruohonen, Keijo Pellervo AU - Linne, Marja-Leena PY - 2012/2/23 Y1 - 2012/2/23 N2 - One of the most prominent patterns of activity observed in developing cortical neuronal networks in vitro is network-wide spontaneous bursting (Wagenaar et al. 2005). In this work, we study computationally the spontaneous emergence of bursts and the effect of network structure on burst shape and frequency. Recent computational structure-function approaches show the effect of, e.g., second-order connections (Zhao et al. 2011) and degree distribution widths (Roxin 2011) on activity patterns. We aim to study a wider set of graph-theoretical measures using networks with identical in-degree distributions. We apply a biophysically plausible point-neuron model of a cortical cell (Golomb et al. 2006). The model network consists of a small (N=100) number of neurons, both excitatory pyramidal neurons and inhibitory interneurons. A model of short-term depression (Golomb and Amitai 1997) is used for glutamatergic synapses. The activity simulation is run over a wide set of classes of network structure. To quantify the structure of the network, we consider graph theoretical measures such as clustering coefficient, geodesic path length, node-betweenness and occurrence of different motifs. We restrict to unweighted bidirectional graph representation, hence the synaptic weights between the neurons are uniform. We study the significance of different graph theoretic measures using a prediction framework: How well can a bursting property, such as burst duration or frequency, be estimated using various measures of structure as attributes? We show that the prediction of bursting properties is improved by taking one or more of the aforementioned measures as prediction attributes. It is best improved when the prediction is based on the clustering coefficient or occurrence of the most highly connected motifs. We confirm the results using a noise-driven LIF model with short-term depression (Tsodyks et al. 2000). We conclude that the significance of measures of clustering is prominent compared to other measures of structure. AB - One of the most prominent patterns of activity observed in developing cortical neuronal networks in vitro is network-wide spontaneous bursting (Wagenaar et al. 2005). In this work, we study computationally the spontaneous emergence of bursts and the effect of network structure on burst shape and frequency. Recent computational structure-function approaches show the effect of, e.g., second-order connections (Zhao et al. 2011) and degree distribution widths (Roxin 2011) on activity patterns. We aim to study a wider set of graph-theoretical measures using networks with identical in-degree distributions. We apply a biophysically plausible point-neuron model of a cortical cell (Golomb et al. 2006). The model network consists of a small (N=100) number of neurons, both excitatory pyramidal neurons and inhibitory interneurons. A model of short-term depression (Golomb and Amitai 1997) is used for glutamatergic synapses. The activity simulation is run over a wide set of classes of network structure. To quantify the structure of the network, we consider graph theoretical measures such as clustering coefficient, geodesic path length, node-betweenness and occurrence of different motifs. We restrict to unweighted bidirectional graph representation, hence the synaptic weights between the neurons are uniform. We study the significance of different graph theoretic measures using a prediction framework: How well can a bursting property, such as burst duration or frequency, be estimated using various measures of structure as attributes? We show that the prediction of bursting properties is improved by taking one or more of the aforementioned measures as prediction attributes. It is best improved when the prediction is based on the clustering coefficient or occurrence of the most highly connected motifs. We confirm the results using a noise-driven LIF model with short-term depression (Tsodyks et al. 2000). We conclude that the significance of measures of clustering is prominent compared to other measures of structure. M3 - Conference contribution SP - 55 EP - 55 BT - Proceedings of The 9th annual Computational and Systems Neuroscience meeting (COSYNE 2012) CY - Salt Lake City ER - TY - GEN T1 - Simultenious binary hash and features learning for image retrieval AU - Frantc, V. A. AU - Makov, S. V. AU - Voronin, V. V. AU - Marchuk, V. I. AU - Semenishchev, E. A. AU - Egiazarian, K. O. AU - Agaian, S. PY - 2016 Y1 - 2016 N2 - Content-based image retrieval systems have plenty of applications in modern world. The most important one is the image search by query image or by semantic description. Approaches to this problem are employed in personal photo-collection management systems, web-scale image search engines, medical systems, etc. Automatic analysis of large unlabeled image datasets is virtually impossible without satisfactory image-retrieval technique. It's the main reason why this kind of automatic image processing has attracted so much attention during recent years. Despite rather huge progress in the field, semantically meaningful image retrieval still remains a challenging task. The main issue here is the demand to provide reliable results in short amount of time. This paper addresses the problem by novel technique for simultaneous learning of global image features and binary hash codes. Our approach provide mapping of pixel-based image representation to hash-value space simultaneously trying to save as much of semantic image content as possible. We use deep learning methodology to generate image description with properties of similarity preservation and statistical independence. The main advantage of our approach in contrast to existing is ability to fine-tune retrieval procedure for very specific application which allow us to provide better results in comparison to general techniques. Presented in the paper framework for data- dependent image hashing is based on use two different kinds of neural networks: convolutional neural networks for image description and autoencoder for feature to hash space mapping. Experimental results confirmed that our approach has shown promising results in compare to other state-of-the-art methods. AB - Content-based image retrieval systems have plenty of applications in modern world. The most important one is the image search by query image or by semantic description. Approaches to this problem are employed in personal photo-collection management systems, web-scale image search engines, medical systems, etc. Automatic analysis of large unlabeled image datasets is virtually impossible without satisfactory image-retrieval technique. It's the main reason why this kind of automatic image processing has attracted so much attention during recent years. Despite rather huge progress in the field, semantically meaningful image retrieval still remains a challenging task. The main issue here is the demand to provide reliable results in short amount of time. This paper addresses the problem by novel technique for simultaneous learning of global image features and binary hash codes. Our approach provide mapping of pixel-based image representation to hash-value space simultaneously trying to save as much of semantic image content as possible. We use deep learning methodology to generate image description with properties of similarity preservation and statistical independence. The main advantage of our approach in contrast to existing is ability to fine-tune retrieval procedure for very specific application which allow us to provide better results in comparison to general techniques. Presented in the paper framework for data- dependent image hashing is based on use two different kinds of neural networks: convolutional neural networks for image description and autoencoder for feature to hash space mapping. Experimental results confirmed that our approach has shown promising results in compare to other state-of-the-art methods. KW - autoencoder KW - content{based image retrieval KW - deep convolutional neural network KW - semantic hashing U2 - 10.1117/12.2223605 DO - 10.1117/12.2223605 M3 - Conference contribution T3 - SPIE Conference Proceedings BT - Mobile Multimedia/Image Processing, Security, and Applications 2016 PB - SPIE ER - TY - GEN T1 - Single exposure lensless subpixel phase imaging AU - Kocsis, Péter AU - Shevkunov, Igor AU - Katkovnik, Vladimir AU - Egiazarian, Karen PY - 2019 Y1 - 2019 N2 - Lensless phase-retrieval system with phase modulation of free propagation wavefront is proposed. Contrary to the traditional super-resolution phase-retrieval, the method in this paper requires a single observation only and uses advanced SR-SPAR iterative technique. Successful object imaging relies on modulation of the object wavefront with a random phase-mask, which generates enlarged intensity patterns, allowing us to extract more information than it is possible without such a mask. The achieved high-quality super-resolution phase-imaging is demonstrated by simulation-tests produced with the parameters corresponding to the physical prototype of the considered optical system. AB - Lensless phase-retrieval system with phase modulation of free propagation wavefront is proposed. Contrary to the traditional super-resolution phase-retrieval, the method in this paper requires a single observation only and uses advanced SR-SPAR iterative technique. Successful object imaging relies on modulation of the object wavefront with a random phase-mask, which generates enlarged intensity patterns, allowing us to extract more information than it is possible without such a mask. The achieved high-quality super-resolution phase-imaging is demonstrated by simulation-tests produced with the parameters corresponding to the physical prototype of the considered optical system. KW - Diffractive optical element KW - Lensless imaging KW - Lensless system design KW - Phase imaging KW - Phase measurement KW - Phase retrieval KW - Sparse representation KW - Sub-pixel resolution U2 - 10.1117/12.2525679 DO - 10.1117/12.2525679 M3 - Conference contribution T3 - Proceedings of SPIE - The International Society for Optical Engineering BT - Digital Optical Technologies 2019 A2 - Kress, Bernard C. A2 - Schelkens, Peter PB - SPIE, IEEE ER - TY - GEN T1 - Structural Similarity Index with Predictability of Image Blocks AU - Ponomarenko, Mykola AU - Egiazarian, Karen AU - Lukin, Vladimir AU - Abramova, Victoriya N1 - JUFOID=72887 EXT="Lukin, Vladimir" PY - 2018/9/10 Y1 - 2018/9/10 N2 - Structural similarity index (SSIM) is a widely used full-reference metric for assessment of visual quality of images and remote sensing data. It is calculated in a block-wise manner and is based on multiplication of three components: similarity of means of image blocks, similarity of contrasts and a correlation factor. In this paper, two modifications of SSIM are proposed. First, a fourth multiplicative component is introduced to SSIM (thus obtaining SSIM4) that describes a similarity of predictability of image blocks. A predictability for a given block is calculated as a minimal value of mean square error between the considered block and the neighboring blocks. Second, a simple scheme for calculating the metrics SSIM and SSIM4 for color images is proposed and optimized. Effectiveness of the proposed modifications is confirmed for the specialized image databases TID2013, LIVE, and FLT. In particular, the Spearman rank order correlation coefficient (SROCC) for the recently introduced FLT Database, calculated between the proposed metric color SSIM4 and mean opinion scores (MOS), has reached the value 0.85 (the best result for all compared metrics) whilst for SSIM it is equal to 0.58. AB - Structural similarity index (SSIM) is a widely used full-reference metric for assessment of visual quality of images and remote sensing data. It is calculated in a block-wise manner and is based on multiplication of three components: similarity of means of image blocks, similarity of contrasts and a correlation factor. In this paper, two modifications of SSIM are proposed. First, a fourth multiplicative component is introduced to SSIM (thus obtaining SSIM4) that describes a similarity of predictability of image blocks. A predictability for a given block is calculated as a minimal value of mean square error between the considered block and the neighboring blocks. Second, a simple scheme for calculating the metrics SSIM and SSIM4 for color images is proposed and optimized. Effectiveness of the proposed modifications is confirmed for the specialized image databases TID2013, LIVE, and FLT. In particular, the Spearman rank order correlation coefficient (SROCC) for the recently introduced FLT Database, calculated between the proposed metric color SSIM4 and mean opinion scores (MOS), has reached the value 0.85 (the best result for all compared metrics) whilst for SSIM it is equal to 0.58. KW - image visual quality assessment KW - masking of unpredictable energy U2 - 10.1109/MMET.2018.8460285 DO - 10.1109/MMET.2018.8460285 M3 - Conference contribution SN - 9781538654385 VL - 2018-July SP - 115 EP - 118 BT - 2018 IEEE 17th International Conference on Mathematical Methods in Electromagnetic Theory, MMET 2018 - Proceedings PB - IEEE COMPUTER SOCIETY PRESS ER - TY - GEN T1 - Switchable unidirectional second-harmonic emission through GaAs nanoantennas AU - Xu, Lei AU - Saerens, Grégoire AU - Timofeeva, Maria AU - Miroshnichenko, Andrey E. AU - Camacho-Morales, Rocio AU - Volkovskaya, Irina AU - Smirnova, Daria A. AU - Lysevych, Mykhaylo AU - Huang, Lujun AU - Cai, Marcus AU - Karouta, Fouad AU - Hoe Tan, H. AU - Kauranen, Martti AU - Jagadish, Chennupati AU - Grange, Rachel AU - Neshev, Dragomir N. AU - Rahmani, Mohsen N1 - jufoid=71479 PY - 2019 Y1 - 2019 N2 - Switching the scattering direction of high-index dielectric nanoantennas between forward and backward, via Mie resonances in the linear regime, has been widely studied, recently. However, switching the harmonic emission of nanoantennas without applying any physical change to the antennas, such as geometry, or environment, is a chal-lenging task that has not been demonstrated yet. Here, we investigate multipolar second-harmonic switch from GaAs nanoantennas. Based on the peculiar nonlinearities of zinc-blende semiconductors, we demonstrate both theoretically and experimentally unidirectional nonlinear emission routing and switching via pump polarization control. Our results offer exciting opportunities for nonlinear nanophotonics technologies, such as nanoscale light routing elements, nonlinear light sources, nonlinear imaging, multifunctional flat optical elements. AB - Switching the scattering direction of high-index dielectric nanoantennas between forward and backward, via Mie resonances in the linear regime, has been widely studied, recently. However, switching the harmonic emission of nanoantennas without applying any physical change to the antennas, such as geometry, or environment, is a chal-lenging task that has not been demonstrated yet. Here, we investigate multipolar second-harmonic switch from GaAs nanoantennas. Based on the peculiar nonlinearities of zinc-blende semiconductors, we demonstrate both theoretically and experimentally unidirectional nonlinear emission routing and switching via pump polarization control. Our results offer exciting opportunities for nonlinear nanophotonics technologies, such as nanoscale light routing elements, nonlinear light sources, nonlinear imaging, multifunctional flat optical elements. KW - Dielectric nanoresonators KW - Mie resonance KW - Second harmonic generation KW - Unidirectional emission U2 - 10.1117/12.2539887 DO - 10.1117/12.2539887 M3 - Conference contribution T3 - Proceedings of SPIE - The International Society for Optical Engineering BT - AOS Australian Conference on Optical Fibre Technology, ACOFT 2019 and Australian Conference on Optics, Lasers, and Spectroscopy, ACOLS 2019 A2 - Mitchell, Arnan A2 - Rubinsztein-Dunlop, Halina PB - SPIE ER - TY - GEN T1 - Tailoring directional scattering of second-harmonic generation from (111)-GaAs nanoantennas AU - Sautter, J. AU - Xu, L. AU - Miroshnichenko, A. AU - Lysevych, M. AU - Volkovskaya, I. AU - Smirnova, D. AU - Camacho Morales, M. AU - Zangeneh Kamali, K. AU - Karouta, F. AU - Vora, K. AU - Tan, H. H. AU - Kauranen, M. AU - Staude, I. AU - Jagadish, C. AU - Neshev, D. N. AU - Rahmani, M. N1 - jufoid=71479 PY - 2019 Y1 - 2019 N2 - The group of zincblende III-V compound semiconductors, especially (100)-grown AlGaAs and GaAs, have recently been presented as promising materials for second harmonic generation (SHG) at the nanoscale. However, major obstacles to push the technology towards practical applications are the limited control over directionality of the SH emission and especially zero forward/backward radiation. In this work we provide both theoretically and experimentally a solution to these problems by presenting the first SHG nanoantennas made from (111)-GaAs embedded in a low index material. These nanoantennas show superior forward directionality compared to their (100)-counterparts. Most importantly, it is possible to manipulate the SHG radiation pattern of the nanoantennas by changing the pump polarization without affecting the linear properties and the total nonlinear conversion efficiency. AB - The group of zincblende III-V compound semiconductors, especially (100)-grown AlGaAs and GaAs, have recently been presented as promising materials for second harmonic generation (SHG) at the nanoscale. However, major obstacles to push the technology towards practical applications are the limited control over directionality of the SH emission and especially zero forward/backward radiation. In this work we provide both theoretically and experimentally a solution to these problems by presenting the first SHG nanoantennas made from (111)-GaAs embedded in a low index material. These nanoantennas show superior forward directionality compared to their (100)-counterparts. Most importantly, it is possible to manipulate the SHG radiation pattern of the nanoantennas by changing the pump polarization without affecting the linear properties and the total nonlinear conversion efficiency. KW - Dielectric nanoantennas KW - Directional emission KW - Multipolar interference KW - Second harmonic generation U2 - 10.1117/12.2539086 DO - 10.1117/12.2539086 M3 - Conference contribution T3 - Proceedings of SPIE - The International Society for Optical Engineering BT - AOS Australian Conference on Optical Fibre Technology, ACOFT 2019 and Australian Conference on Optics, Lasers, and Spectroscopy, ACOLS 2019 A2 - Mitchell, Arnan A2 - Rubinsztein-Dunlop, Halina PB - SPIE ER - TY - GEN T1 - The different levels of magneto-mechanical coupling in energy conversion machines and devices AU - Belahcen, A. AU - Kouhia, R. AU - Fonteyn, K. PY - 2011 Y1 - 2011 N2 - This paper reviews the methods for coupling the magnetic and mechanical problems in magnetic materials and their application to electrical machines. The reviewed methods include both the material models and the computing methods as well as the methods for computing the magnetic forces. The paper shows that there are different levels of coupling the magnetic system with the mechanical one and that the use of a method or another depends on the application and the level of accuracy aimed at. The paper also clarifies some terms and concepts related to the coupling terminology such as strong, weak, local, global, direct and indirect coupling and put these terms in a coherent context. Most of the examples are related to the two dimensional analysis but some three dimensional ones are also shown. AB - This paper reviews the methods for coupling the magnetic and mechanical problems in magnetic materials and their application to electrical machines. The reviewed methods include both the material models and the computing methods as well as the methods for computing the magnetic forces. The paper shows that there are different levels of coupling the magnetic system with the mechanical one and that the use of a method or another depends on the application and the level of accuracy aimed at. The paper also clarifies some terms and concepts related to the coupling terminology such as strong, weak, local, global, direct and indirect coupling and put these terms in a coherent context. Most of the examples are related to the two dimensional analysis but some three dimensional ones are also shown. KW - Computing Methods KW - Coupled problems KW - Electrical machines KW - Magnetic forces KW - Magneto-mechanics KW - Magnetostriction UR - http://www.scopus.com/inward/record.url?scp=84857432902&partnerID=8YFLogxK M3 - Conference contribution SN - 9788489925786 SP - 472 EP - 483 BT - Proceedings of the 4th International Conference on Computational Methods for Coupled Problems in Science and Engineering, COUPLED PROBLEMS 2011 ER - TY - GEN T1 - The magical world of metamaterials AU - Caglayan, Humeyra AU - Ozbay, Ekmel N1 - EXT="Caglayan, Humeyra" PY - 2009 Y1 - 2009 N2 - We review experimental and theoretical studies performed on left-handed metamaterials (LHM). The metamaterials exhibit quiet unusual electromagnetic properties such as negative refraction, negative phase velocity, subwavelength focusing, subwavelength cavities and enhanced transmission. AB - We review experimental and theoretical studies performed on left-handed metamaterials (LHM). The metamaterials exhibit quiet unusual electromagnetic properties such as negative refraction, negative phase velocity, subwavelength focusing, subwavelength cavities and enhanced transmission. KW - Left-handed metamaterial KW - Metamaterials KW - Negative refractive index KW - Superlens UR - http://www.scopus.com/inward/record.url?scp=70349983117&partnerID=8YFLogxK U2 - 10.1117/12.821407 DO - 10.1117/12.821407 M3 - Conference contribution SN - 9780819476401 VL - 7366 T3 - Proceedings of SPIE BT - Photonic Materials, Devices, and Applications III ER - TY - GEN T1 - Thermal effects on a passive wireless antenna sensor for strain and crack sensing AU - Yi, Xiaohua AU - Vyas, Rushi AU - Cho, Chunhee AU - Fang, Chia Hung AU - Cooper, James AU - Wang, Yang AU - Leon, Roberto T. AU - Tentzeris, Manos M. PY - 2012 Y1 - 2012 N2 - For application in structural health monitoring, a folded patch antenna has been previously designed as a wireless sensor that monitors strain and crack in metallic structures. Resonance frequency of the RFID patch antenna is closely related with its dimension. To measure stress concentration in a base structure, the sensor is bonded to the structure like a traditional strain gage. When the antenna sensor is under strain/deformation together with the base structure, the antenna resonance frequency varies accordingly. The strain-related resonance frequency variation is wirelessly interrogated and recorded by a reader, and can be used to derive strain/deformation. Material properties of the antenna components can have significant effects on sensor performance. This paper investigates thermal effects through both numerical simulation and temperature chamber testing. When temperature fluctuates, previous sensor design (with a glass microfiber-reinforced PTFE substrate) shows relatively large variation in resonance frequency. To improve sensor performance, a new ceramic-filled PTFE substrate material is chosen for re-designing the antenna sensor. Temperature chamber experiments are also conducted to the sensor with new substrate material, and compared with previous design. AB - For application in structural health monitoring, a folded patch antenna has been previously designed as a wireless sensor that monitors strain and crack in metallic structures. Resonance frequency of the RFID patch antenna is closely related with its dimension. To measure stress concentration in a base structure, the sensor is bonded to the structure like a traditional strain gage. When the antenna sensor is under strain/deformation together with the base structure, the antenna resonance frequency varies accordingly. The strain-related resonance frequency variation is wirelessly interrogated and recorded by a reader, and can be used to derive strain/deformation. Material properties of the antenna components can have significant effects on sensor performance. This paper investigates thermal effects through both numerical simulation and temperature chamber testing. When temperature fluctuates, previous sensor design (with a glass microfiber-reinforced PTFE substrate) shows relatively large variation in resonance frequency. To improve sensor performance, a new ceramic-filled PTFE substrate material is chosen for re-designing the antenna sensor. Temperature chamber experiments are also conducted to the sensor with new substrate material, and compared with previous design. KW - Crack sensor KW - Folded patch antenna KW - Passive wireless sensor KW - RFID KW - Strain sensor KW - Thermal effect UR - http://www.scopus.com/inward/record.url?scp=84861112128&partnerID=8YFLogxK U2 - 10.1117/12.914833 DO - 10.1117/12.914833 M3 - Conference contribution SN - 9780819490025 VL - 8345 BT - Sensors and Smart Structures Technologies for Civil, Mechanical, and Aerospace Systems 2012 ER - TY - GEN T1 - Thickness variation study of RFID-based folded patch antennas for strain sensing AU - Yi, Xiaohua AU - Wu, Terence AU - Lantz, Gabriel AU - Wang, Yang AU - Leon, Roberto T. AU - Tentzeris, Manos M. PY - 2011 Y1 - 2011 N2 - This paper explores folded patch antennas for the development of low-cost and wireless smart-skin sensors that monitor the strain in metallic structures. When the patch antenna is under strain/deformation, its resonance frequency varies accordingly. The variation can be easily interrogated and recorded by a wireless reader that also provides power for the antenna operation. The patch antenna adopts a specially selected substrate material with low dielectric constant, as well as an inexpensive off-the-shelf radiofrequency identification (RFID) chip for signal modulation. A thicker substrate increases RFID signal-to-noise ratio, but reduces the strain transfer efficiency. To experimentally study the effect of substrate thickness, two prototype folded patch antennas with different substrate thicknesses have been designed and manufactured. For both prototypes, tensile testing results show strong linearity between the interrogated resonance frequency and the strain experienced by the antenna. Longer interrogation range is achieved with the larger substrate thickness. AB - This paper explores folded patch antennas for the development of low-cost and wireless smart-skin sensors that monitor the strain in metallic structures. When the patch antenna is under strain/deformation, its resonance frequency varies accordingly. The variation can be easily interrogated and recorded by a wireless reader that also provides power for the antenna operation. The patch antenna adopts a specially selected substrate material with low dielectric constant, as well as an inexpensive off-the-shelf radiofrequency identification (RFID) chip for signal modulation. A thicker substrate increases RFID signal-to-noise ratio, but reduces the strain transfer efficiency. To experimentally study the effect of substrate thickness, two prototype folded patch antennas with different substrate thicknesses have been designed and manufactured. For both prototypes, tensile testing results show strong linearity between the interrogated resonance frequency and the strain experienced by the antenna. Longer interrogation range is achieved with the larger substrate thickness. KW - folded patch antenna KW - passive wireless sensor KW - RFID KW - strain sensor KW - substrate thickness UR - http://www.scopus.com/inward/record.url?scp=79956325124&partnerID=8YFLogxK U2 - 10.1117/12.879868 DO - 10.1117/12.879868 M3 - Conference contribution SN - 9780819485434 VL - 7981 BT - Sensors and Smart Structures Technologies for Civil, Mechanical, and Aerospace Systems 2011 ER - TY - GEN T1 - Towards Algebraic Modeling of GPU Memory Access for Bank Conflict Mitigation AU - Ferranti, Luca AU - Boutellier, Jani PY - 2019/10/1 Y1 - 2019/10/1 N2 - Graphics Processing Units (GPU) have been widely used in various fields of scientific computing, such as in signal processing. GPUs have a hierarchical memory structure with memory layers that are shared between GPU processing elements. Partly due to the complex memory hierarchy, GPU programming is non-Trivial, and several aspects must be taken into account, one being memory access patterns. One of the fastest GPU memory layers, shared memory, is grouped into banks to enable fast, parallel access for processing elements. Unfortunately, it may happen that multiple threads of a GPU program may access the same shared memory bank simultaneously causing a bank conflict. If this happens, program execution slows down as memory accesses have to be rescheduled to determine which instruction to execute first. Bank conflicts are not taken into account automatically by the compiler, and hence the programmer must detect and deal with them prior to program execution. In this paper, we present an algebraic approach to detect bank conflicts and prove some theoretical results that can be used to predict when bank conflicts happen and how to avoid them. Also, our experimental results illustrate the savings in computation time. AB - Graphics Processing Units (GPU) have been widely used in various fields of scientific computing, such as in signal processing. GPUs have a hierarchical memory structure with memory layers that are shared between GPU processing elements. Partly due to the complex memory hierarchy, GPU programming is non-Trivial, and several aspects must be taken into account, one being memory access patterns. One of the fastest GPU memory layers, shared memory, is grouped into banks to enable fast, parallel access for processing elements. Unfortunately, it may happen that multiple threads of a GPU program may access the same shared memory bank simultaneously causing a bank conflict. If this happens, program execution slows down as memory accesses have to be rescheduled to determine which instruction to execute first. Bank conflicts are not taken into account automatically by the compiler, and hence the programmer must detect and deal with them prior to program execution. In this paper, we present an algebraic approach to detect bank conflicts and prove some theoretical results that can be used to predict when bank conflicts happen and how to avoid them. Also, our experimental results illustrate the savings in computation time. KW - block matching KW - Graphics processing units KW - memory hierarchy KW - OpenCL U2 - 10.1109/SiPS47522.2019.9020385 DO - 10.1109/SiPS47522.2019.9020385 M3 - Conference contribution T3 - IEEE Workshop on Signal Processing Systems, SiPS: Design and Implementation SP - 103 EP - 108 BT - 2019 IEEE International Workshop on Signal Processing Systems, SiPS 2019 PB - IEEE ER - TY - GEN T1 - Ultra-large mode area single frequency anisotropic MOPA with double clad Yb-doped tapered fiber AU - Noronen, Teppo AU - Fedotov, Andrei AU - Rissanen, Joona AU - Gumenyuk, Regina AU - Butov, Oleg AU - Chamorovskii, Yuri AU - Golant, Konstantin AU - Odnoblyudov, Maxim AU - Filippov, Valery N1 - EXT="Noronen, Teppo" EXT="Fedotov, Andrei" INT=fot, "Rissanen, Joona" EXT="Gumenyuk, Regina" EXT="Filippov, Valery" PY - 2018/1/1 Y1 - 2018/1/1 N2 - We demonstrates all-fiber master oscillator - power amplifier delivered 70W output power at 1033.33nm with 8 kHz FWHM linewidth without any problems with SBS. The anisotropic ytterbium doped tapered double clad amplifier with 50 μm MFD and polarization extinction ratio about 30 dB is developed as a burst stage. The output radiation demonstrated perfect beam quality (M2=1.03/1.08). AB - We demonstrates all-fiber master oscillator - power amplifier delivered 70W output power at 1033.33nm with 8 kHz FWHM linewidth without any problems with SBS. The anisotropic ytterbium doped tapered double clad amplifier with 50 μm MFD and polarization extinction ratio about 30 dB is developed as a burst stage. The output radiation demonstrated perfect beam quality (M2=1.03/1.08). KW - active fiber KW - fiber amplifier KW - Fiber laser U2 - 10.1117/12.2288942 DO - 10.1117/12.2288942 M3 - Conference contribution T3 - Proceedings of SPIE BT - Fiber Lasers XV PB - SPIE, IEEE ER - TY - GEN T1 - Wideband self-adaptive RF cancellation circuit for full-duplex radio T2 - Operating principle and measurements AU - Huusari, Timo AU - Choi, Yang Seok AU - Liikkanen, Petteri AU - Korpi, Dani AU - Talwar, Shilpa AU - Valkama, Mikko N1 - AUX=elt,"Huusari, Timo" AUX=elt,"Liikkanen, Petteri" PY - 2015/7/1 Y1 - 2015/7/1 N2 - This paper presents a novel RF circuit architecture for self-interference cancellation in inband full-duplex radio transceivers. The developed canceller is able to provide wideband cancellation with waveform bandwidths in the order of 100 MHz or beyond and contains also self-adaptive or self-healing features enabling automatic tracking of time-varying self-interference channel characteristics. In addition to architecture and operating principle descriptions, we also provide actual RF measurements at 2.4 GHz ISM band demonstrating the achievable cancellation levels with different bandwidths and when operating in different antenna configurations and under low-cost highly nonlinear power amplifier. In a very challenging example with a 100 MHz waveform bandwidth, around 41 dB total cancellation is obtained while the corresponding cancellation figure is close to 60 dB with the more conventional 20 MHz carrier bandwidth. Also, efficient tracking in time-varying reflection scenarios is demonstrated. AB - This paper presents a novel RF circuit architecture for self-interference cancellation in inband full-duplex radio transceivers. The developed canceller is able to provide wideband cancellation with waveform bandwidths in the order of 100 MHz or beyond and contains also self-adaptive or self-healing features enabling automatic tracking of time-varying self-interference channel characteristics. In addition to architecture and operating principle descriptions, we also provide actual RF measurements at 2.4 GHz ISM band demonstrating the achievable cancellation levels with different bandwidths and when operating in different antenna configurations and under low-cost highly nonlinear power amplifier. In a very challenging example with a 100 MHz waveform bandwidth, around 41 dB total cancellation is obtained while the corresponding cancellation figure is close to 60 dB with the more conventional 20 MHz carrier bandwidth. Also, efficient tracking in time-varying reflection scenarios is demonstrated. KW - Full-duplex KW - RF cancellation KW - Self adaptive KW - Self interference KW - Tracking U2 - 10.1109/VTCSpring.2015.7146163 DO - 10.1109/VTCSpring.2015.7146163 M3 - Conference contribution SN - 9781479980888 BT - 2015 IEEE 81st Vehicular Technology Conference (VTC Spring) PB - The Institute of Electrical and Electronics Engineers, Inc. ER - TY - CHAP T1 - Acoustic Modelling AU - Pohjolainen, Seppo AU - Suutala, Antti N1 - INT=mat,”Suutala, Antti" PY - 2016/6/30 Y1 - 2016/6/30 N2 - Let us examine the behaviour of sound in a gas or in a liquid medium. From a physical point of view, the sound we hear is created by the pressure change in the medium surrounding us that is sensed by our ears. The equations describing the behaviour of a liquid or a gas are based on well-known equations of fluid mechanics. Therefore in acoustics, they are often referred to as fluids. In the following sections we present a simple wave equation, which is the simplest of (linear) equations used to model acoustical phenomena. Even though the wave equation is quite a simplified model, it has proven to be extremely useful for describing the behaviour of sound in the most common fluid we face every day, namely air. AB - Let us examine the behaviour of sound in a gas or in a liquid medium. From a physical point of view, the sound we hear is created by the pressure change in the medium surrounding us that is sensed by our ears. The equations describing the behaviour of a liquid or a gas are based on well-known equations of fluid mechanics. Therefore in acoustics, they are often referred to as fluids. In the following sections we present a simple wave equation, which is the simplest of (linear) equations used to model acoustical phenomena. Even though the wave equation is quite a simplified model, it has proven to be extremely useful for describing the behaviour of sound in the most common fluid we face every day, namely air. U2 - 10.1007/978-3-319-27836-0_11 DO - 10.1007/978-3-319-27836-0_11 M3 - Chapter SN - 978-3-319-27834-6 SP - 185 EP - 205 BT - Mathematical Modelling A2 - Pohjolainen, Seppo PB - Springer CY - Switzerland ER - TY - JOUR T1 - A simulation case study of production planning and control in printed wiring board manufacturing AU - Korhonen, H. M E AU - Heikkilä, Jussi AU - Törnwall, Jon M. PY - 2001/12/1 Y1 - 2001/12/1 N2 - Production planning and control in printed wiring board (PWB) manufacturing is becoming more difficult as PWB's technology is developing and the production routings become more complex. Simultaneously, the strategic importance of delivery accuracy, short delivery times, and production flexibility is increasing with the highly fluctuating demand and short product life cycles of end products. New principles, that minimize throughput time while guaranteering excellent customer service and adequate capacity utilization, are needed for production planning and control. Simulation is needed in order to develop the new principles and test their superiority. This paper presents an ongoing simulation product that aims at developing the production planning and control of a PWB manufacturer. In the project, a discrete event simulation model is built of a pilot case factory. The model is used for comparing the effect of scheduling, queuing rules, buffer policies, and lot sizes on customer service and cost efficiency. AB - Production planning and control in printed wiring board (PWB) manufacturing is becoming more difficult as PWB's technology is developing and the production routings become more complex. Simultaneously, the strategic importance of delivery accuracy, short delivery times, and production flexibility is increasing with the highly fluctuating demand and short product life cycles of end products. New principles, that minimize throughput time while guaranteering excellent customer service and adequate capacity utilization, are needed for production planning and control. Simulation is needed in order to develop the new principles and test their superiority. This paper presents an ongoing simulation product that aims at developing the production planning and control of a PWB manufacturer. In the project, a discrete event simulation model is built of a pilot case factory. The model is used for comparing the effect of scheduling, queuing rules, buffer policies, and lot sizes on customer service and cost efficiency. UR - http://www.scopus.com/inward/record.url?scp=0035708229&partnerID=8YFLogxK M3 - Conference article VL - 2 SP - 844 EP - 847 JO - Winter Simulation Conference Proceedings JF - Winter Simulation Conference Proceedings SN - 0275-0708 ER - TY - JOUR T1 - A comparative analysis of multidimensional features of objects resembling sets of graphs AU - Dehmer, Matthias AU - Emmert-Streib, Frank AU - Gesell, Tanja PY - 2008/2/15 Y1 - 2008/2/15 N2 - In the present paper, we introduce a notion of a style representing abstract, complex objects having characteristics that can be represented as structured objects. Furthermore, we provide some mathematical properties of such styles. As a main result, we present a novel approach to perform a meaningful comparative analysis of such styles by defining and using graph-theoretic measures. We compare two styles by comparing the underlying feature sets representing sets of graph structurally. To determine the structural similarity between the underlying graphs, we use graph similarity measures that are computationally efficient. More precisely, in order to compare styles, we map each feature set to a so-called median graph and compare the resulting median graphs. As an application, we perform an experimental study to compare special styles representing sets of undirected graphs and present numerical results thereof. AB - In the present paper, we introduce a notion of a style representing abstract, complex objects having characteristics that can be represented as structured objects. Furthermore, we provide some mathematical properties of such styles. As a main result, we present a novel approach to perform a meaningful comparative analysis of such styles by defining and using graph-theoretic measures. We compare two styles by comparing the underlying feature sets representing sets of graph structurally. To determine the structural similarity between the underlying graphs, we use graph similarity measures that are computationally efficient. More precisely, in order to compare styles, we map each feature set to a so-called median graph and compare the resulting median graphs. As an application, we perform an experimental study to compare special styles representing sets of undirected graphs and present numerical results thereof. KW - Classification KW - Object comparison KW - Similarity KW - Structural similarity KW - Structured objects U2 - 10.1016/j.amc.2007.05.058 DO - 10.1016/j.amc.2007.05.058 M3 - Article VL - 196 SP - 221 EP - 235 JO - Applied Mathematics and Computation JF - Applied Mathematics and Computation SN - 0096-3003 IS - 1 ER - TY - JOUR T1 - A comparison between joint regression analysis and the AMMI model T2 - A case study with barley AU - Pereira, Dulce G. AU - Rodrigues, Paulo C. AU - Mejza, Stanislaw AU - Mexia, João T. PY - 2012/2 Y1 - 2012/2 N2 - Joint regression analysis (JRA) and additive main effects and multiplicative interaction (AMMI) models are compared in order to (i) access the ability of describing a genotype by environment interaction effects and (ii) evaluate the agreement between the winners of mega-environments obtained from the AMMI analysis and the genotypes in the upper contour of the JRA. An iterative algorithm is used to obtain the environmental indexes for JRA, and standard multiple comparison procedures are adapted for genotype comparison and selection. This study includes three data sets from a spring barley (Hordeum vulgare L.) breeding programme carried out between 2004 and 2006 in Czech Republic. The results from both techniques are integrated in order to advise plant breeders, farmers and agronomists for better genotype selection and prediction for new years and/or new environments. AB - Joint regression analysis (JRA) and additive main effects and multiplicative interaction (AMMI) models are compared in order to (i) access the ability of describing a genotype by environment interaction effects and (ii) evaluate the agreement between the winners of mega-environments obtained from the AMMI analysis and the genotypes in the upper contour of the JRA. An iterative algorithm is used to obtain the environmental indexes for JRA, and standard multiple comparison procedures are adapted for genotype comparison and selection. This study includes three data sets from a spring barley (Hordeum vulgare L.) breeding programme carried out between 2004 and 2006 in Czech Republic. The results from both techniques are integrated in order to advise plant breeders, farmers and agronomists for better genotype selection and prediction for new years and/or new environments. KW - AMMI models KW - joint regression analysis KW - mega-environments KW - multiple comparisons KW - spring barley KW - zigzag algorithm UR - http://www.scopus.com/inward/record.url?scp=84856990001&partnerID=8YFLogxK U2 - 10.1080/00949655.2011.615839 DO - 10.1080/00949655.2011.615839 M3 - Article VL - 82 SP - 193 EP - 207 JO - JOURNAL OF STATISTICAL COMPUTATION AND SIMULATION JF - JOURNAL OF STATISTICAL COMPUTATION AND SIMULATION SN - 0094-9655 IS - 2 ER - TY - JOUR T1 - A Comprehensive Framework for Spectrum Sensing in Non-Linear and Generalized Fading Conditions AU - Sofotasios, Paschalis C. AU - Bagheri, Alireza AU - Tsiftsis, Theodoros A. AU - Freear, Steven AU - Shahzadi, Ali AU - Valkama, Mikko PY - 2017/10/1 Y1 - 2017/10/1 N2 - We derive a comprehensive analytical framework for the ED over generalized, extreme, and non-linear fading conditions which addresses the topic completely. This is carried out for both conventional and diversity receptions and it is based on the area under the ROC curve (AUC), which is an efficient performance measure that is widely used in physical sciences and engineering. This differentiates the considered methodology from the aforementioned routine approaches and additionally provides generic results on the arbitrary derivatives of the MGF of useful generalized processes. The asymptotic behavior of the derived expressions is also analyzed providing direct and concrete insights on the role and effect of the involved parameters on the ED performance. The offered analytic results are subsequently employed in quantifying the performance of ED over various types of fading conditions, which exhibits that ED performance is significantly degraded by even slight variations of the severity of fading. To this end, it is shown that the detrimental effects of fading can be effectively mitigated with the aid of square-law combining and switch-And-stay combining methods, as a low number of diversity branches can ensure sufficient and holistic performance improvement even in severe fading conditions. AB - We derive a comprehensive analytical framework for the ED over generalized, extreme, and non-linear fading conditions which addresses the topic completely. This is carried out for both conventional and diversity receptions and it is based on the area under the ROC curve (AUC), which is an efficient performance measure that is widely used in physical sciences and engineering. This differentiates the considered methodology from the aforementioned routine approaches and additionally provides generic results on the arbitrary derivatives of the MGF of useful generalized processes. The asymptotic behavior of the derived expressions is also analyzed providing direct and concrete insights on the role and effect of the involved parameters on the ED performance. The offered analytic results are subsequently employed in quantifying the performance of ED over various types of fading conditions, which exhibits that ED performance is significantly degraded by even slight variations of the severity of fading. To this end, it is shown that the detrimental effects of fading can be effectively mitigated with the aid of square-law combining and switch-And-stay combining methods, as a low number of diversity branches can ensure sufficient and holistic performance improvement even in severe fading conditions. KW - Area under ROC curve KW - Bell polynomials KW - cognitive radio KW - diversity KW - multipath fading KW - radar systems U2 - 10.1109/TVT.2017.2692278 DO - 10.1109/TVT.2017.2692278 M3 - Article VL - 66 SP - 8615 EP - 8631 JO - IEEE Transactions on Vehicular Technology JF - IEEE Transactions on Vehicular Technology SN - 0018-9545 IS - 10 ER - TY - JOUR T1 - Adaptive autoregressive model for reduction of noise in SPECT AU - Takalo, Reijo AU - Hytti, Heli AU - Ihalainen, Heimo AU - Sohlberg, Antti PY - 2015 Y1 - 2015 N2 - This paper presents improved autoregressive modelling (AR) to reduce noise in SPECT images. An AR filter was applied to prefilter projection images and postfilter ordered subset expectation maximisation (OSEM) reconstruction images (AR-OSEM-AR method). The performance of this method was compared with filtered back projection (FBP) preceded by Butterworth filtering (BW-FBP method) and the OSEM reconstruction method followed by Butterworth filtering (OSEM-BW method). A mathematical cylinder phantom was used for the study. It consisted of hot and cold objects. The tests were performed using three simulated SPECT datasets. Image quality was assessed by means of the percentage contrast resolution (CR%) and the full width at half maximum (FWHM) of the line spread functions of the cylinders. The BW-FBP method showed the highest CR% values and the AR-OSEM-AR method gave the lowest CR% values for cold stacks. In the analysis of hot stacks, the BW-FBP method had higher CR% values than the OSEM-BW method. The BW-FBP method exhibited the lowest FWHM values for cold stacks and the AR-OSEM-AR method for hot stacks. In conclusion, the AR-OSEM-AR method is a feasible way to remove noise from SPECT images. It has good spatial resolution for hot objects. AB - This paper presents improved autoregressive modelling (AR) to reduce noise in SPECT images. An AR filter was applied to prefilter projection images and postfilter ordered subset expectation maximisation (OSEM) reconstruction images (AR-OSEM-AR method). The performance of this method was compared with filtered back projection (FBP) preceded by Butterworth filtering (BW-FBP method) and the OSEM reconstruction method followed by Butterworth filtering (OSEM-BW method). A mathematical cylinder phantom was used for the study. It consisted of hot and cold objects. The tests were performed using three simulated SPECT datasets. Image quality was assessed by means of the percentage contrast resolution (CR%) and the full width at half maximum (FWHM) of the line spread functions of the cylinders. The BW-FBP method showed the highest CR% values and the AR-OSEM-AR method gave the lowest CR% values for cold stacks. In the analysis of hot stacks, the BW-FBP method had higher CR% values than the OSEM-BW method. The BW-FBP method exhibited the lowest FWHM values for cold stacks and the AR-OSEM-AR method for hot stacks. In conclusion, the AR-OSEM-AR method is a feasible way to remove noise from SPECT images. It has good spatial resolution for hot objects. UR - http://www.scopus.com/inward/record.url?scp=84930684783&partnerID=8YFLogxK U2 - 10.1155/2015/494691 DO - 10.1155/2015/494691 M3 - Article VL - 2015 JO - Computational and Mathematical Methods in Medicine JF - Computational and Mathematical Methods in Medicine SN - 1748-670X M1 - 494691 ER - TY - JOUR T1 - A general framework for island systems AU - Foldes, S. AU - Horváth, Eszter K. AU - Radeleczki, Sándor AU - Waldhauser, Tamás PY - 2015 Y1 - 2015 N2 - The notion of an island defined on a rectangular board is an elementary combinatorial concept that occurred first in [3]. Results of [3] were starting points for investigations exploring several variations and various aspects of this notion. In this paper we introduce a general framework for islands that subsumes all earlier studied concepts of islands on finite boards, moreover we show that the prime implicants of a Boolean function, the formal concepts of a formal context, convex subgraphs of a simple graph, and some particular subsets of a projective plane also fit into this framework. We axiomatize those cases where islands have the property of being pairwise comparable or disjoint, or they are distant, introducing the notion of a connective island domain and of a proximity domain, respectively. In the general case the maximal systems of islands are characterised by using the concept of an admissible system. We also characterise all possible island systems in the case of connective island domains and proximity domains. AB - The notion of an island defined on a rectangular board is an elementary combinatorial concept that occurred first in [3]. Results of [3] were starting points for investigations exploring several variations and various aspects of this notion. In this paper we introduce a general framework for islands that subsumes all earlier studied concepts of islands on finite boards, moreover we show that the prime implicants of a Boolean function, the formal concepts of a formal context, convex subgraphs of a simple graph, and some particular subsets of a projective plane also fit into this framework. We axiomatize those cases where islands have the property of being pairwise comparable or disjoint, or they are distant, introducing the notion of a connective island domain and of a proximity domain, respectively. In the general case the maximal systems of islands are characterised by using the concept of an admissible system. We also characterise all possible island systems in the case of connective island domains and proximity domains. KW - Admissible system KW - CD-independent and CDW-independent sets KW - Connected subgraph KW - Convex subgraph KW - Distant system KW - Formal concept KW - Height function KW - Island domain KW - Island system KW - Point-to-set proximity relation KW - Prime implicant KW - Projective plane KW - Proximity domain UR - http://www.scopus.com/inward/record.url?scp=84938827353&partnerID=8YFLogxK U2 - 10.14232/actasm-013-279-7 DO - 10.14232/actasm-013-279-7 M3 - Article VL - 81 SP - 3 EP - 24 JO - Acta Universitatis Szegediensis: Acta Scientiarum Mathematicarum JF - Acta Universitatis Szegediensis: Acta Scientiarum Mathematicarum SN - 0001-6969 IS - 1-2 ER - TY - JOUR T1 - A hybrid optimization grey model based on segmented gra and multi-strategy contest for short-term power load forecasting AU - Min, Jin AU - Xiang, Zhou AU - Zhiming, Zhang AU - Tentzeris, Manos M. PY - 2012 Y1 - 2012 N2 - In this paper, a hybrid grey model with both internal and external optimization is proposed to forecast the short-term power load which has the characteristics of nonlinear fluctuation and random growth. The internal optimization consists of modeling feasibility test and parameter a correction. The external optimization includes three aspects. First, the original series are selected from different viewpoints to construct different forecasting strategies. Second, the predicted day is divided into several smooth segments for separate forecasting. Finally, the different forecasting strategies are implemented respectively in the different segments through grey correlation contest. A practical application verifies that the proposed model has a higher forecasting accuracy and the independency on the choice of initial value. AB - In this paper, a hybrid grey model with both internal and external optimization is proposed to forecast the short-term power load which has the characteristics of nonlinear fluctuation and random growth. The internal optimization consists of modeling feasibility test and parameter a correction. The external optimization includes three aspects. First, the original series are selected from different viewpoints to construct different forecasting strategies. Second, the predicted day is divided into several smooth segments for separate forecasting. Finally, the different forecasting strategies are implemented respectively in the different segments through grey correlation contest. A practical application verifies that the proposed model has a higher forecasting accuracy and the independency on the choice of initial value. KW - External optimization KW - Hybrid grey model KW - Multi-strategy contest KW - Parameter a correction KW - Segmented grey correlation KW - Short-term power load forecasting UR - http://www.scopus.com/inward/record.url?scp=84858229525&partnerID=8YFLogxK M3 - Article VL - 24 SP - 15 EP - 28 JO - JOURNAL OF GREY SYSTEM JF - JOURNAL OF GREY SYSTEM SN - 0957-3720 IS - 1 ER - TY - JOUR T1 - Analysis of common rail pressure signal of dual-fuel large industrial engine for identification of injection duration of pilot diesel injectors AU - Krogerus, Tomi AU - Hyvönen, Mika AU - Huhtala, Kalevi PY - 2018/3 Y1 - 2018/3 N2 - In this paper, we address the problem of identification of injection duration of common rail (CR) diesel pilot injectors of dual-fuel engines. In these pilot injectors, the injected volume is small and the repeatability of injections and identification of drifts of injectors are important factors, which need to be taken into account in order to achieve good repeatability (shot-to-shot with every cylinder) and therefore a well-balanced engine and furthermore reduced overall wear. This information can then be used for calibration and diagnostics purposes to guarantee engine longevity facilitated by consistent operating conditions throughout the life of the unit. A diagnostics method based on analysis of CR pressure with experimental results is presented in this paper. Using the developed method, the relative duration of injection events can be identified for multiple injectors. We use the phenomenon of drop in rail pressure due to an injection event as a feature of the injection process. The method is based on filtered CR pressure data during and after the injection event. First, the pressure signal during injection is extracted after control of each injection event. After that, the signal is normalized and filtered. Then a derivative of the filtered signal is calculated. Change in the derivative of the filtered signal larger than a predefined threshold indicates an injection event that can be detected and its relative duration can be identified. We present the experimental results and demonstrate the efficacy of the proposed methods using two differenttypes of pressure sensors. We are able to properly identify a change of ≥10 μs (2%, 500 μs) in injection time. This shows that the developed method detects drifts in injection duration and the magnitude of drift. This information can be used for adaptive control of injection duration, so that finally the injected fuel volume is the same as the original. AB - In this paper, we address the problem of identification of injection duration of common rail (CR) diesel pilot injectors of dual-fuel engines. In these pilot injectors, the injected volume is small and the repeatability of injections and identification of drifts of injectors are important factors, which need to be taken into account in order to achieve good repeatability (shot-to-shot with every cylinder) and therefore a well-balanced engine and furthermore reduced overall wear. This information can then be used for calibration and diagnostics purposes to guarantee engine longevity facilitated by consistent operating conditions throughout the life of the unit. A diagnostics method based on analysis of CR pressure with experimental results is presented in this paper. Using the developed method, the relative duration of injection events can be identified for multiple injectors. We use the phenomenon of drop in rail pressure due to an injection event as a feature of the injection process. The method is based on filtered CR pressure data during and after the injection event. First, the pressure signal during injection is extracted after control of each injection event. After that, the signal is normalized and filtered. Then a derivative of the filtered signal is calculated. Change in the derivative of the filtered signal larger than a predefined threshold indicates an injection event that can be detected and its relative duration can be identified. We present the experimental results and demonstrate the efficacy of the proposed methods using two differenttypes of pressure sensors. We are able to properly identify a change of ≥10 μs (2%, 500 μs) in injection time. This shows that the developed method detects drifts in injection duration and the magnitude of drift. This information can be used for adaptive control of injection duration, so that finally the injected fuel volume is the same as the original. KW - Analysis KW - Dual-fuel engine KW - Diesel KW - Common rail KW - Injector KW - Rail pressure U2 - 10.1016/j.fuel.2017.11.152 DO - 10.1016/j.fuel.2017.11.152 M3 - Article VL - 216 SP - 1 EP - 9 JO - Fuel JF - Fuel SN - 0016-2361 ER - TY - JOUR T1 - Analysis of the damping characteristics of two power electronics-based devices using ‘individual channel analysis and design’ AU - Ugalde-Loo, Carlos E. AU - Acha, Enrique AU - Licéaga-Castro, Eduardo PY - 2018/7/1 Y1 - 2018/7/1 N2 - A comparison of the capabilities of two quite distinct power electronics-based ‘flexible AC transmission systems’ devices is presented. In particular, the damping of low frequency electromechanical oscillations is investigated aiming at improving the performance of power systems. The comparison is made using frequency domain methods under the ‘individual channel analysis and design’ framework. A synchronous generator feeding into a system with large inertia is used for such a purpose. Two system configurations including compensation are analysed: (a) in series in the form of a thyristor-controlled series compensator, and (b) in shunt through a static VAr compensator featuring a damping controller. Analyses are carried out to elucidate the dynamic behaviour of the synchronous generator in the presence of the power electronics-based controllers and for the case when no controller is present. Performance and robustness assessments are given particular emphasis. The crux of the matter is the comparison between the abilities of the static VAr compensator and the thyristor-controlled series compensator to eliminate the problematic switch-back characteristic intrinsic to synchronous generator operation by using the physical insight afforded by ‘individual channel analysis and design’. AB - A comparison of the capabilities of two quite distinct power electronics-based ‘flexible AC transmission systems’ devices is presented. In particular, the damping of low frequency electromechanical oscillations is investigated aiming at improving the performance of power systems. The comparison is made using frequency domain methods under the ‘individual channel analysis and design’ framework. A synchronous generator feeding into a system with large inertia is used for such a purpose. Two system configurations including compensation are analysed: (a) in series in the form of a thyristor-controlled series compensator, and (b) in shunt through a static VAr compensator featuring a damping controller. Analyses are carried out to elucidate the dynamic behaviour of the synchronous generator in the presence of the power electronics-based controllers and for the case when no controller is present. Performance and robustness assessments are given particular emphasis. The crux of the matter is the comparison between the abilities of the static VAr compensator and the thyristor-controlled series compensator to eliminate the problematic switch-back characteristic intrinsic to synchronous generator operation by using the physical insight afforded by ‘individual channel analysis and design’. KW - Flexible AC transmission systems KW - Frequency domain analysis KW - Individual channel analysis and design KW - Multivariable control KW - Static VAr compensator KW - Thyristor-controlled series compensator U2 - 10.1016/j.apm.2018.02.008 DO - 10.1016/j.apm.2018.02.008 M3 - Article VL - 59 SP - 527 EP - 545 JO - Applied Mathematical Modelling JF - Applied Mathematical Modelling SN - 0307-904X ER - TY - JOUR T1 - Analytical model for magnetic anisotropy of non-oriented steel sheets AU - Martin, Floran AU - Singh, Deepak AU - Belahcen, Anouar AU - Rasilo, Paavo AU - Haavisto, Ari AU - Arkkio, Antero PY - 2015/9/7 Y1 - 2015/9/7 N2 - Purpose - Recent investigations on magnetic properties of non-oriented (NO) steel sheets enhance the comprehension of the magnetic anisotropy behaviour of widely employed electrical sheets. The concept of energy/coenergy density can be employed to model these magnetic properties. However, it usually presents an implicit form which requires an iterative process. The purpose of this paper is to develop an analytical model to consider these magnetic properties with an explicit formulation in order to ease the computations. Design/methodology/approach - From rotational measurements, the anhysteretic curves are interpolated in order to extract the magnetic energy density for different directions and amplitudes of the magnetic flux density. Furthermore, the analytical representation of this energy is suggested based on statistical distribution which aims to minimize the intrinsic energy of the material. The model is finally validated by comparing measured and computed values of the magnetic field strength. Findings - The proposed model is based on an analytical formulation of the energy depending on the components of the magnetic flux density. This formulation is composed of three Gumbel distributions. Every functional parameters of energy density is formulated with only four parameters which are calculated by fitting the energy extracted from measurements. Finally, the proposed model is validated by comparing the computation and the measurements of 9 H loci for NO steel sheets at 10 Hz. The proposed analytical model shows good agreements with an average relative error of 27 per cent. Originality/value - The paper presents an original analytical method to model magnetic anisotropy for NO electrical sheets. With this analytical formulation, the determination of H does not require any iterative process as it is usually the case with this energy method coupled with implicit function. This method can be easily incorporated in finite element method since it does not require any extra iterative process. AB - Purpose - Recent investigations on magnetic properties of non-oriented (NO) steel sheets enhance the comprehension of the magnetic anisotropy behaviour of widely employed electrical sheets. The concept of energy/coenergy density can be employed to model these magnetic properties. However, it usually presents an implicit form which requires an iterative process. The purpose of this paper is to develop an analytical model to consider these magnetic properties with an explicit formulation in order to ease the computations. Design/methodology/approach - From rotational measurements, the anhysteretic curves are interpolated in order to extract the magnetic energy density for different directions and amplitudes of the magnetic flux density. Furthermore, the analytical representation of this energy is suggested based on statistical distribution which aims to minimize the intrinsic energy of the material. The model is finally validated by comparing measured and computed values of the magnetic field strength. Findings - The proposed model is based on an analytical formulation of the energy depending on the components of the magnetic flux density. This formulation is composed of three Gumbel distributions. Every functional parameters of energy density is formulated with only four parameters which are calculated by fitting the energy extracted from measurements. Finally, the proposed model is validated by comparing the computation and the measurements of 9 H loci for NO steel sheets at 10 Hz. The proposed analytical model shows good agreements with an average relative error of 27 per cent. Originality/value - The paper presents an original analytical method to model magnetic anisotropy for NO electrical sheets. With this analytical formulation, the determination of H does not require any iterative process as it is usually the case with this energy method coupled with implicit function. This method can be easily incorporated in finite element method since it does not require any extra iterative process. KW - FEM KW - Ferromagnetic materials KW - Magnetic anisotropy KW - Soft magnetic materials UR - http://www.scopus.com/inward/record.url?scp=84941117731&partnerID=8YFLogxK U2 - 10.1108/COMPEL-02-2015-0076 DO - 10.1108/COMPEL-02-2015-0076 M3 - Article VL - 34 SP - 1475 EP - 1488 JO - COMPEL: The International Journal for Computation and Mathematics in Electrical and Electronic Engineering JF - COMPEL: The International Journal for Computation and Mathematics in Electrical and Electronic Engineering SN - 0332-1649 IS - 5 ER - TY - JOUR T1 - An efficient heuristic approach to detecting graph isomorphism based on combinations of highly discriminating invariants AU - Dehmer, Matthias AU - Grabner, Martin AU - Mowshowitz, Abbe AU - Emmert-Streib, Frank PY - 2013/8 Y1 - 2013/8 N2 - The search for an easily computable, finite, complete set of graph invariants remains a challenging research topic. All measures characterizing the topology of a graph that have been developed thus far exhibit some degree of degeneracy, i.e., an inability to distinguish between non-isomorphic graphs. In this paper, we show that certain graph invariants can be useful in substantially reducing the computational complexity of isomorphism testing. Our findings are underpinned by numerical results based on a large scale statistical analysis. AB - The search for an easily computable, finite, complete set of graph invariants remains a challenging research topic. All measures characterizing the topology of a graph that have been developed thus far exhibit some degree of degeneracy, i.e., an inability to distinguish between non-isomorphic graphs. In this paper, we show that certain graph invariants can be useful in substantially reducing the computational complexity of isomorphism testing. Our findings are underpinned by numerical results based on a large scale statistical analysis. KW - Graph isomorphism KW - Graph measures KW - Graph topology KW - Graphs KW - Uniqueness UR - http://www.scopus.com/inward/record.url?scp=84884974800&partnerID=8YFLogxK U2 - 10.1007/s10444-012-9281-0 DO - 10.1007/s10444-012-9281-0 M3 - Article VL - 39 SP - 311 EP - 325 JO - Advances in Computational Mathematics JF - Advances in Computational Mathematics SN - 1019-7168 IS - 2 ER - TY - JOUR T1 - A New Approach to Sign-Bit-Based Parameter Estimation in OFDM Receivers AU - Diaz, Isael AU - Wilhelmsson, Leif R. AU - Sofotasios, Paschalis C. AU - Miao, Yun AU - Tan, Siyu AU - Edfors, Ove AU - Öwall, Viktor PY - 2015/11/23 Y1 - 2015/11/23 N2 - This article combines algorithm development, thorough analysis and implementation of sign-bit (SB) estimation techniques for symbol timing, carrier frequency offset (CFO) and signal-to-noise ratio (SNR) in orthogonal frequency division multiplexing receivers. The SB estimation is compared in terms of performance and hardware complexity to an equivalent implementation with higher quantization. The techniques are demonstrated by simulation of a SB time/frequency and SB-SNR estimator for 3rd Generation Partnership Project long-term evolution (LTE) cell search in 65-nm technology operating at nominal voltage of 1.2 V. According to post-layout power simulations with toggling information, the architecture estimates the corresponding CFO and SNR for as little as $$479\,\upmu \hbox {W}$$479μW average power for LTE-R8/10, while occupying a silicon area as small as $$0.03\,\hbox {mm}^2$$0.03mm2. Even though SB estimation experiences some relative performance penalty when compared to 8-bit quantization, this paper demonstrates various advantages and the potential of employing these techniques in low-complexity terminals. AB - This article combines algorithm development, thorough analysis and implementation of sign-bit (SB) estimation techniques for symbol timing, carrier frequency offset (CFO) and signal-to-noise ratio (SNR) in orthogonal frequency division multiplexing receivers. The SB estimation is compared in terms of performance and hardware complexity to an equivalent implementation with higher quantization. The techniques are demonstrated by simulation of a SB time/frequency and SB-SNR estimator for 3rd Generation Partnership Project long-term evolution (LTE) cell search in 65-nm technology operating at nominal voltage of 1.2 V. According to post-layout power simulations with toggling information, the architecture estimates the corresponding CFO and SNR for as little as $$479\,\upmu \hbox {W}$$479μW average power for LTE-R8/10, while occupying a silicon area as small as $$0.03\,\hbox {mm}^2$$0.03mm2. Even though SB estimation experiences some relative performance penalty when compared to 8-bit quantization, this paper demonstrates various advantages and the potential of employing these techniques in low-complexity terminals. KW - CFO KW - LTE KW - OFDM KW - Receiver design KW - SNR KW - Symbol timing KW - Time synchronization U2 - 10.1007/s00034-015-0025-5 DO - 10.1007/s00034-015-0025-5 M3 - Article VL - 34 SP - 3631 EP - 3660 JO - Circuits, Systems and Signal Processing JF - Circuits, Systems and Signal Processing SN - 0278-081X IS - 11 ER - TY - JOUR T1 - A similarity measure for graphs with low computational complexity AU - Dehmer, Matthias AU - Emmert-Streib, Frank AU - Kilian, Jürgen PY - 2006/11/1 Y1 - 2006/11/1 N2 - We present and analyze an algorithm to measure the structural similarity of generalized trees, a new graph class which includes rooted trees. For this, we represent structural properties of graphs as strings and define the similarity of two graphs as optimal alignments of the corresponding property stings. We prove that the obtained graph similarity measures are so called Backward similarity measures. From this we find that the time complexity of our algorithm is polynomial and, hence, significantly better than the time complexity of classical graph similarity methods based on isomorphic relations. AB - We present and analyze an algorithm to measure the structural similarity of generalized trees, a new graph class which includes rooted trees. For this, we represent structural properties of graphs as strings and define the similarity of two graphs as optimal alignments of the corresponding property stings. We prove that the obtained graph similarity measures are so called Backward similarity measures. From this we find that the time complexity of our algorithm is polynomial and, hence, significantly better than the time complexity of classical graph similarity methods based on isomorphic relations. KW - Computational complexity KW - Dynamic programming KW - Graph similarity KW - Graph theory UR - http://www.scopus.com/inward/record.url?scp=33750819438&partnerID=8YFLogxK U2 - 10.1016/j.amc.2006.04.006 DO - 10.1016/j.amc.2006.04.006 M3 - Article VL - 182 SP - 447 EP - 459 JO - Applied Mathematics and Computation JF - Applied Mathematics and Computation SN - 0096-3003 IS - 1 ER - TY - JOUR T1 - Asymptotic expansion of European options with mean-reverting stochastic volatility dynamics AU - Hu, Jun AU - Kanniainen, Juho PY - 2015/8 Y1 - 2015/8 N2 - We develop methods for pricing European options under general mean-reverting stochastic volatility dynamics, which can be used with both affine and non-affine volatility models. In our methods, the option price under stochastic volatility is expanded as a power series of parameters or variables by transferring the original partial differential equation to a set of solvable inhomogeneous Black–Scholes equations. The analytic approximation is more generally applicable than the fast Fourier transform, because it does not rely on the existence of a characteristic function. Finally, we numerically demonstrate our approach with the Heston, 3/2, and continuous-time GARCH models. AB - We develop methods for pricing European options under general mean-reverting stochastic volatility dynamics, which can be used with both affine and non-affine volatility models. In our methods, the option price under stochastic volatility is expanded as a power series of parameters or variables by transferring the original partial differential equation to a set of solvable inhomogeneous Black–Scholes equations. The analytic approximation is more generally applicable than the fast Fourier transform, because it does not rely on the existence of a characteristic function. Finally, we numerically demonstrate our approach with the Heston, 3/2, and continuous-time GARCH models. KW - Option pricing KW - Series expansion KW - Partial Differential Equations KW - Stochastic volatility KW - Non-affine models U2 - 10.1016/j.frl.2015.07.004 DO - 10.1016/j.frl.2015.07.004 M3 - Article VL - 14 SP - 1 EP - 10 JO - Finance Research Letters JF - Finance Research Letters SN - 1544-6123 ER - TY - JOUR T1 - Asymptotics for infinite systems of differential equations AU - Paunonen, Lassi AU - Seifert, David PY - 2017 Y1 - 2017 N2 - This paper investigates the asymptotic behavior of solutions to certain infinite systems of ordinary differential equations. In particular, we use results from ergodic theory and the asymptotic theory of C0-semigroups to obtain a characterization, in terms of convergence of certain Cesàro averages, of those initial values which lead to convergent solutions. Moreover, we obtain estimates on the rate of convergence for solutions whose initial values satisfy a stronger ergodic condition. These results rely on a detailed spectral analysis of the operator describing the system, which is made possible by certain structural assumptions on the operator. The resulting class of systems is sufficiently broad to cover a number of important applications including, in particular, both the so-called robot rendezvous problem and an important class of platoon systems arising in control theory. Our method leads to new results in both cases. AB - This paper investigates the asymptotic behavior of solutions to certain infinite systems of ordinary differential equations. In particular, we use results from ergodic theory and the asymptotic theory of C0-semigroups to obtain a characterization, in terms of convergence of certain Cesàro averages, of those initial values which lead to convergent solutions. Moreover, we obtain estimates on the rate of convergence for solutions whose initial values satisfy a stronger ergodic condition. These results rely on a detailed spectral analysis of the operator describing the system, which is made possible by certain structural assumptions on the operator. The resulting class of systems is sufficiently broad to cover a number of important applications including, in particular, both the so-called robot rendezvous problem and an important class of platoon systems arising in control theory. Our method leads to new results in both cases. KW - Asymptotic behavior KW - C0-semigroup KW - Ergodic theory KW - Ordinary differential equations KW - Rates of convergence KW - Spectrum KW - System U2 - 10.1137/15M1051993 DO - 10.1137/15M1051993 M3 - Article VL - 55 SP - 1153 EP - 1178 JO - SIAM Journal on Control and Optimization JF - SIAM Journal on Control and Optimization SN - 0363-0129 IS - 2 ER - TY - JOUR T1 - Asymptotics for periodic systems AU - Paunonen, Lassi AU - Seifert, David PY - 2019/5 Y1 - 2019/5 N2 - This paper investigates the asymptotic behaviour of solutions of periodic evolution equations. Starting with a general result concerning the quantified asymptotic behaviour of periodic evolution families we go on to consider a special class of dissipative systems arising naturally in applications. For this class of systems we analyse in detail the spectral properties of the associated monodromy operator, showing in particular that it is a so-called Ritt operator under a natural ‘resonance’ condition. This allows us to deduce from our general result a precise description of the asymptotic behaviour of the corresponding solutions. In particular, we present conditions for rational rates of convergence to periodic solutions in the case where the convergence fails to be uniformly exponential. We illustrate our general results by applying them to concrete problems including the one-dimensional wave equation with periodic damping. AB - This paper investigates the asymptotic behaviour of solutions of periodic evolution equations. Starting with a general result concerning the quantified asymptotic behaviour of periodic evolution families we go on to consider a special class of dissipative systems arising naturally in applications. For this class of systems we analyse in detail the spectral properties of the associated monodromy operator, showing in particular that it is a so-called Ritt operator under a natural ‘resonance’ condition. This allows us to deduce from our general result a precise description of the asymptotic behaviour of the corresponding solutions. In particular, we present conditions for rational rates of convergence to periodic solutions in the case where the convergence fails to be uniformly exponential. We illustrate our general results by applying them to concrete problems including the one-dimensional wave equation with periodic damping. KW - Damped wave equation KW - Evolution family KW - Non-autonomous system KW - Periodic KW - Rates of convergence KW - Ritt operator U2 - 10.1016/j.jde.2018.11.028 DO - 10.1016/j.jde.2018.11.028 M3 - Article VL - 266 SP - 7152 EP - 7172 JO - Journal of Differential Equations JF - Journal of Differential Equations SN - 0022-0396 IS - 11 ER - TY - JOUR T1 - A topological algorithm for identification of structural domains of proteins AU - Emmert-Streib, Frank AU - Mushegian, Arcady PY - 2007/7/3 Y1 - 2007/7/3 N2 - Background: Identification of the structural domains of proteins is important for our understanding of the organizational principles and mechanisms of protein folding, and for insights into protein function and evolution. Algorithmic methods of dissecting protein of known structure into domains developed so far are based on an examination of multiple geometrical, physical and topological features. Successful as many of these approaches are, they employ a lot of heuristics, and it is not clear whether they illuminate any deep underlying principles of protein domain organization. Other well-performing domain dissection methods rely on comparative sequence analysis. These methods are applicable to sequences with known and unknown structure alike, and their success highlights a fundamental principle of protein modularity, but this does not directly improve our understanding of protein spatial structure. Results: We present a novel graph-theoretical algorithm for the identification of domains in proteins with known three-dimensional structure. We represent the protein structure as an undirected, unweighted and unlabeled graph whose nodes correspond to the secondary structure elements and edges represent physical proximity of at least one pair of alpha carbon atoms from two elements. Domains are identified as constrained partitions of the graph, corresponding to sets of vertices obtained by the maximization of the cycle distributions found in the graph. When a partition is found, the algorithm is iteratively applied to each of the resulting subgraphs. The decision to accept or reject a tentative cut position is based on a specific classifier. The algorithm is applied iteratively to each of the resulting subgraphs and terminates automatically if partitions are no longer accepted. The distribution of cycles is the only type of information on which the decision about protein dissection is based. Despite the barebone simplicity of the approach, our algorithm approaches the best heuristic algorithms in accuracy. Conclusion: Our graph-theoretical algorithm uses only topological information present in the protein structure itself to find the domains and does not rely on any geometrical or physical information about protein molecule. Perhaps unexpectedly, these drastic constraints on resources, which result in a seemingly approximate description of protein structures and leave only a handful of parameters available for analysis, do not lead to any significant deterioration of algorithm accuracy. It appears that protein structures can be rigorously treated as topological rather than geometrical objects and that the majority of information about protein domains can be inferred from the coarse-grained measure of pairwise proximity between elements of secondary structure elements. AB - Background: Identification of the structural domains of proteins is important for our understanding of the organizational principles and mechanisms of protein folding, and for insights into protein function and evolution. Algorithmic methods of dissecting protein of known structure into domains developed so far are based on an examination of multiple geometrical, physical and topological features. Successful as many of these approaches are, they employ a lot of heuristics, and it is not clear whether they illuminate any deep underlying principles of protein domain organization. Other well-performing domain dissection methods rely on comparative sequence analysis. These methods are applicable to sequences with known and unknown structure alike, and their success highlights a fundamental principle of protein modularity, but this does not directly improve our understanding of protein spatial structure. Results: We present a novel graph-theoretical algorithm for the identification of domains in proteins with known three-dimensional structure. We represent the protein structure as an undirected, unweighted and unlabeled graph whose nodes correspond to the secondary structure elements and edges represent physical proximity of at least one pair of alpha carbon atoms from two elements. Domains are identified as constrained partitions of the graph, corresponding to sets of vertices obtained by the maximization of the cycle distributions found in the graph. When a partition is found, the algorithm is iteratively applied to each of the resulting subgraphs. The decision to accept or reject a tentative cut position is based on a specific classifier. The algorithm is applied iteratively to each of the resulting subgraphs and terminates automatically if partitions are no longer accepted. The distribution of cycles is the only type of information on which the decision about protein dissection is based. Despite the barebone simplicity of the approach, our algorithm approaches the best heuristic algorithms in accuracy. Conclusion: Our graph-theoretical algorithm uses only topological information present in the protein structure itself to find the domains and does not rely on any geometrical or physical information about protein molecule. Perhaps unexpectedly, these drastic constraints on resources, which result in a seemingly approximate description of protein structures and leave only a handful of parameters available for analysis, do not lead to any significant deterioration of algorithm accuracy. It appears that protein structures can be rigorously treated as topological rather than geometrical objects and that the majority of information about protein domains can be inferred from the coarse-grained measure of pairwise proximity between elements of secondary structure elements. U2 - 10.1186/1471-2105-8-237 DO - 10.1186/1471-2105-8-237 M3 - Article VL - 8 JO - BMC Bioinformatics JF - BMC Bioinformatics SN - 1471-2105 M1 - 237 ER - TY - JOUR T1 - Bio-inspired service management framework T2 - Green data-centres case study AU - Carroll, Raymond AU - Balasubramaniam, Sasitharan AU - Suzuki, Junichi AU - Lee, Chonho AU - Donnelly, William AU - Botvich, Dmitri PY - 2013 Y1 - 2013 N2 - The internet is evolving into a full-scale distributed service platform, offering a plethora of services from communications to business, entertainment, social connectivity and much more. The range of services and applications offered is diversifying, with new applications constantly emerging. For example, utility-based computing (e.g. HPC and cloud computing) which relies heavily on data-centre resources. These services will be more dynamic and sophisticated, providing a range of complex capabilities, which puts further burden on datacentres, in terms of supporting and managing these services. At the same time, society is becoming acutely aware of the significant energy burden the communications industry, and in particular data-centres, are becoming. With these trends in mind we propose a biologically inspired service framework that supports services which can autonomously carry out management functions. We then apply this framework to address the emerging problem of a sustainable future internet by autonomously migrating services to greener locations. AB - The internet is evolving into a full-scale distributed service platform, offering a plethora of services from communications to business, entertainment, social connectivity and much more. The range of services and applications offered is diversifying, with new applications constantly emerging. For example, utility-based computing (e.g. HPC and cloud computing) which relies heavily on data-centre resources. These services will be more dynamic and sophisticated, providing a range of complex capabilities, which puts further burden on datacentres, in terms of supporting and managing these services. At the same time, society is becoming acutely aware of the significant energy burden the communications industry, and in particular data-centres, are becoming. With these trends in mind we propose a biologically inspired service framework that supports services which can autonomously carry out management functions. We then apply this framework to address the emerging problem of a sustainable future internet by autonomously migrating services to greener locations. KW - Bio-inspired services KW - Genetic algorithm KW - Green data-centres UR - http://www.scopus.com/inward/record.url?scp=84886912413&partnerID=8YFLogxK U2 - 10.1504/IJGUC.2013.057115 DO - 10.1504/IJGUC.2013.057115 M3 - Article VL - 4 SP - 278 EP - 292 JO - International Journal of Grid and Utility Computing JF - International Journal of Grid and Utility Computing SN - 1741-847X IS - 4 ER - TY - JOUR T1 - Capacity of Multiconnectivity mmWave Systems with Dynamic Blockage and Directional Antennas AU - Gerasimenko, Mikhail AU - Moltchanov, Dmitri AU - Gapeyenko, Margarita AU - Andreev, Sergey AU - Koucheryavy, Yevgeni PY - 2019/4/1 Y1 - 2019/4/1 N2 - The challenges of millimeter-wave (mmWave) radio propagation in dense crowded environments require dynamic re-associations between the available access points (APs) to reduce the chances of losing the line-of-sight path. However, the antenna beamsearching functionality in the mmWave systems may introduce significant delays in the course of AP re-association. In this paper, we analyze user performance in dense urban mmWave deployments that are susceptible to blockage by the dynamically moving crowd. Our approach relies on the ergodic capacity as the key parameter of interest. We conduct a detailed evaluation with respect to the impact of various system parameters on the ergodic capacity, such as AP density and height, blocker density and speed, number of antenna array elements, array switching time, degree of multiconnectivity, and employed connectivity strategies. Particularly, we demonstrate that dual connectivity delivers the desired performance out of all possible degrees of multiconnectivity, and there is an optimal density of mmWave APs that maximizes the capacity of cell-edge users. We also show that the use of low complexity 'reactive' multiconnectivity design, where the beamtracking is only performed when the currently active connection is lost, together with the utilization of iterative beamsearching algorithms, does not significantly deteriorate the ergodic capacity. AB - The challenges of millimeter-wave (mmWave) radio propagation in dense crowded environments require dynamic re-associations between the available access points (APs) to reduce the chances of losing the line-of-sight path. However, the antenna beamsearching functionality in the mmWave systems may introduce significant delays in the course of AP re-association. In this paper, we analyze user performance in dense urban mmWave deployments that are susceptible to blockage by the dynamically moving crowd. Our approach relies on the ergodic capacity as the key parameter of interest. We conduct a detailed evaluation with respect to the impact of various system parameters on the ergodic capacity, such as AP density and height, blocker density and speed, number of antenna array elements, array switching time, degree of multiconnectivity, and employed connectivity strategies. Particularly, we demonstrate that dual connectivity delivers the desired performance out of all possible degrees of multiconnectivity, and there is an optimal density of mmWave APs that maximizes the capacity of cell-edge users. We also show that the use of low complexity 'reactive' multiconnectivity design, where the beamtracking is only performed when the currently active connection is lost, together with the utilization of iterative beamsearching algorithms, does not significantly deteriorate the ergodic capacity. KW - Millimeter wave communication, 5G mobile communication, beam steering, multi-connectivity, dynamic blockage U2 - 10.1109/TVT.2019.2896565 DO - 10.1109/TVT.2019.2896565 M3 - Article VL - 68 SP - 3534 EP - 3549 JO - IEEE Transactions on Vehicular Technology JF - IEEE Transactions on Vehicular Technology SN - 0018-9545 IS - 4 ER - TY - JOUR T1 - Cauchy–Riemann Operators in Octonionic Analysis AU - Kauhanen, Janne AU - Orelma, Heikki PY - 2018 Y1 - 2018 N2 - In this paper we first recall the definition of the octonion algebra and its algebraic properties. We derive the so called e4-calculus and using it we obtain the list of generalized Cauchy–Riemann systems for octonionic monogenic functions. AB - In this paper we first recall the definition of the octonion algebra and its algebraic properties. We derive the so called e4-calculus and using it we obtain the list of generalized Cauchy–Riemann systems for octonionic monogenic functions. KW - Cauchy–Riemann operators KW - Dirac operators KW - Monogenic functions KW - Octonions U2 - 10.1007/s00006-018-0826-2 DO - 10.1007/s00006-018-0826-2 M3 - Article VL - 28 JO - Advances in Applied Clifford Algebras JF - Advances in Applied Clifford Algebras SN - 0188-7009 IS - 1 M1 - 1 ER - TY - JOUR T1 - Characterization and Performance Improvement of Cooperative Wireless Networks with Nonlinear Power Amplifier at Relay AU - Majidi, Mahdi AU - Mohammadi, Abbas AU - Abdipour, Abdolali AU - Valkama, Mikko PY - 2020/3/1 Y1 - 2020/3/1 N2 - In this paper, the performance of the cooperative cognitive radio network with the amplify-and-forward protocol is studied when the relay uses a nonlinear power amplifier (NLPA). Furthermore, taking the pulse shaping filter for the data signal into account, the power of the adjacent channel interference (ACI) to the primary users (PUs) caused by the spectral regrowth of the relay output signal is analytically calculated. Moreover, two compensation techniques are proposed which are implemented at the destination receiver to deal with the in-band nonlinear interference. The first technique is based on the calculation of the distorted signal constellation to enhance the performance of the demodulator. The second technique is feedforward compensation at the receiver. The bit error rate (BER) expressions for both techniques are presented. The ACI resulting from the spectral regrowth due to the relay NLPA is investigated by the simulation and numerical studies, and then, the BER performance degradation at the destination node and the performance improvement resulting from the proposed compensation methods are evaluated. Since the ACI confines the transmit power due to the interference power constraint of the PU, the achievable BER of the secondary user (SU) is studied. The simulation results show that the feedforward compensation technique has better BER performance than the modified constellation based approach. AB - In this paper, the performance of the cooperative cognitive radio network with the amplify-and-forward protocol is studied when the relay uses a nonlinear power amplifier (NLPA). Furthermore, taking the pulse shaping filter for the data signal into account, the power of the adjacent channel interference (ACI) to the primary users (PUs) caused by the spectral regrowth of the relay output signal is analytically calculated. Moreover, two compensation techniques are proposed which are implemented at the destination receiver to deal with the in-band nonlinear interference. The first technique is based on the calculation of the distorted signal constellation to enhance the performance of the demodulator. The second technique is feedforward compensation at the receiver. The bit error rate (BER) expressions for both techniques are presented. The ACI resulting from the spectral regrowth due to the relay NLPA is investigated by the simulation and numerical studies, and then, the BER performance degradation at the destination node and the performance improvement resulting from the proposed compensation methods are evaluated. Since the ACI confines the transmit power due to the interference power constraint of the PU, the achievable BER of the secondary user (SU) is studied. The simulation results show that the feedforward compensation technique has better BER performance than the modified constellation based approach. KW - Amplify and forward KW - cognitive radio KW - maximum ratio combining KW - nonlinearity compensation KW - power amplifier nonlinearity U2 - 10.1109/TVT.2020.2964628 DO - 10.1109/TVT.2020.2964628 M3 - Article VL - 69 SP - 3244 EP - 3255 JO - IEEE Transactions on Vehicular Technology JF - IEEE Transactions on Vehicular Technology SN - 0018-9545 IS - 3 M1 - 8951265 ER - TY - JOUR T1 - Characterization of Radio Links at 60 GHz Using Simple Geometrical and Highly Accurate 3-D Models AU - Semkin, Vasilii AU - Solomitckii, Dmitrii AU - Naderpour, Reza AU - Andreev, Sergey AU - Koucheryavy, Yevgeni AU - Räisänen, Antti V. PY - 2017/6/1 Y1 - 2017/6/1 N2 - In order to effectively deploy high data rate millimeter-wave communication systems in urban environments, accurate information about the radio-wave propagation channel is essential. Radio-wave propagation in urban scenarios strongly depends on the topography of the immediate surroundings. A measurement campaign has been carried out to evaluate the impact of propagation effects on the radio channel at the rooftop level of buildings. In the simulation part of the paper, we present two 3-D models produced with different techniques: first, a simple geometrical model and, second, a highly accurate close-range photogrammetry model; the latter replicates the detailed building geometry. To construct a highly accurate 3-D model, images obtained by an unmanned aerial vehicle were utilized together with the photogrammetry technique. In this paper, we provide a thorough comparison between the measured and the simulated power delay profiles by conducting shooting-and-bouncing ray-based simulations for the rooftop scenario using two 3-D models of different accuracy. The results show that the use of the close-range photogrammetry model can provide better propagation prediction at millimeter-wave frequencies. AB - In order to effectively deploy high data rate millimeter-wave communication systems in urban environments, accurate information about the radio-wave propagation channel is essential. Radio-wave propagation in urban scenarios strongly depends on the topography of the immediate surroundings. A measurement campaign has been carried out to evaluate the impact of propagation effects on the radio channel at the rooftop level of buildings. In the simulation part of the paper, we present two 3-D models produced with different techniques: first, a simple geometrical model and, second, a highly accurate close-range photogrammetry model; the latter replicates the detailed building geometry. To construct a highly accurate 3-D model, images obtained by an unmanned aerial vehicle were utilized together with the photogrammetry technique. In this paper, we provide a thorough comparison between the measured and the simulated power delay profiles by conducting shooting-and-bouncing ray-based simulations for the rooftop scenario using two 3-D models of different accuracy. The results show that the use of the close-range photogrammetry model can provide better propagation prediction at millimeter-wave frequencies. KW - Millimeter-wave KW - photogrammetry KW - radio-wave propagation KW - ray-based simulations KW - unmanned aerial vehicle (UAV) U2 - 10.1109/TVT.2016.2617919 DO - 10.1109/TVT.2016.2617919 M3 - Article VL - 66 SP - 4647 EP - 4656 JO - IEEE Transactions on Vehicular Technology JF - IEEE Transactions on Vehicular Technology SN - 0018-9545 IS - 6 ER - TY - JOUR T1 - Characterizing Radio Wave Propagation in Urban Street Canyon with Vehicular Blockage at 28 GHz AU - Solomitckii, Dmitrii AU - Koucheryavy, Yevgeni AU - Semkin, Vasilii AU - Karttunen, Aki AU - Petrov, Vitaly AU - Nguyen, Sinh Le Hong AU - Nikopour, Hosein AU - Haneda, Katsuyuki AU - Andreev, Sergey AU - Talwar, Shilpa PY - 2020/2/1 Y1 - 2020/2/1 N2 - The communications between two driving vehicles along a narrow street may be limited by the presence of a third vehicle blocking the transmission. In this work, we investigate radio wave propagation at 28 GHz in an urban street canyon scenario by conducting channel measurements, where the vehicle(s) occlude(s) the line-of-sight path. We quantify the impact of the car blockage and study the alternative propagation paths, which can be used for establishing a data link. Based on the obtained results, we report that besides the low-loss (3.4 dB) reflection from the wall, a radio link through the blocking car may potentially be established for data sharing. Specifically, the attenuation through clear windows is 2 dB, while the attenuation caused by sun protective film is 15 dB. Diffraction over the car and propagation in foliage reduce the multipath power drastically by 21-24 dB and 16-19 dB, respectively, and cannot be associated with reliable links. Finally, measurement results were compared with the ray-based simulation data, which demonstrate agreement to within ± 4.3 dB of measured losses. AB - The communications between two driving vehicles along a narrow street may be limited by the presence of a third vehicle blocking the transmission. In this work, we investigate radio wave propagation at 28 GHz in an urban street canyon scenario by conducting channel measurements, where the vehicle(s) occlude(s) the line-of-sight path. We quantify the impact of the car blockage and study the alternative propagation paths, which can be used for establishing a data link. Based on the obtained results, we report that besides the low-loss (3.4 dB) reflection from the wall, a radio link through the blocking car may potentially be established for data sharing. Specifically, the attenuation through clear windows is 2 dB, while the attenuation caused by sun protective film is 15 dB. Diffraction over the car and propagation in foliage reduce the multipath power drastically by 21-24 dB and 16-19 dB, respectively, and cannot be associated with reliable links. Finally, measurement results were compared with the ray-based simulation data, which demonstrate agreement to within ± 4.3 dB of measured losses. KW - 5G vehicular scenarios KW - blockage KW - Millimeter-wave KW - multipath KW - propagation losses KW - radio wave propagation U2 - 10.1109/TVT.2019.2959127 DO - 10.1109/TVT.2019.2959127 M3 - Article VL - 69 SP - 1227 EP - 1236 JO - IEEE Transactions on Vehicular Technology JF - IEEE Transactions on Vehicular Technology SN - 0018-9545 IS - 2 ER - TY - JOUR T1 - Comparative evaluation of gene set analysis approaches for RNA-Seq data AU - Rahmatallah, Yasir AU - Emmert-Streib, Frank AU - Glazko, Galina PY - 2014/12/5 Y1 - 2014/12/5 N2 - Background: Over the last few years transcriptome sequencing (RNA-Seq) has almost completely taken over microarrays for high-throughput studies of gene expression. Currently, the most popular use of RNA-Seq is to identify genes which are differentially expressed between two or more conditions. Despite the importance of Gene Set Analysis (GSA) in the interpretation of the results from RNA-Seq experiments, the limitations of GSA methods developed for microarrays in the context of RNA-Seq data are not well understood. Results: We provide a thorough evaluation of popular multivariate and gene-level self-contained GSA approaches on simulated and real RNA-Seq data. The multivariate approach employs multivariate non-parametric tests combined with popular normalizations for RNA-Seq data. The gene-level approach utilizes univariate tests designed for the analysis of RNA-Seq data to find gene-specific -values and combines them into a pathway -value using classical statistical techniques. Our results demonstrate that the Type I error rate and the power of multivariate tests depend only on the test statistics and are insensitive to the different normalizations. In general standard multivariate GSA tests detect pathways that do not have any bias in terms of pathways size, percentage of differentially expressed genes, or average gene length in a pathway. In contrast the Type I error rate and the power of gene-level GSA tests are heavily affected by the methods for combining -values, and all aforementioned biases are present in detected pathways. Conclusions: Our result emphasizes the importance of using self-contained non-parametric multivariate tests for detecting differentially expressed pathways for RNA-Seq data and warns against applying gene-level GSA tests, especially because of their high level of Type I error rates for both, simulated and real data. AB - Background: Over the last few years transcriptome sequencing (RNA-Seq) has almost completely taken over microarrays for high-throughput studies of gene expression. Currently, the most popular use of RNA-Seq is to identify genes which are differentially expressed between two or more conditions. Despite the importance of Gene Set Analysis (GSA) in the interpretation of the results from RNA-Seq experiments, the limitations of GSA methods developed for microarrays in the context of RNA-Seq data are not well understood. Results: We provide a thorough evaluation of popular multivariate and gene-level self-contained GSA approaches on simulated and real RNA-Seq data. The multivariate approach employs multivariate non-parametric tests combined with popular normalizations for RNA-Seq data. The gene-level approach utilizes univariate tests designed for the analysis of RNA-Seq data to find gene-specific -values and combines them into a pathway -value using classical statistical techniques. Our results demonstrate that the Type I error rate and the power of multivariate tests depend only on the test statistics and are insensitive to the different normalizations. In general standard multivariate GSA tests detect pathways that do not have any bias in terms of pathways size, percentage of differentially expressed genes, or average gene length in a pathway. In contrast the Type I error rate and the power of gene-level GSA tests are heavily affected by the methods for combining -values, and all aforementioned biases are present in detected pathways. Conclusions: Our result emphasizes the importance of using self-contained non-parametric multivariate tests for detecting differentially expressed pathways for RNA-Seq data and warns against applying gene-level GSA tests, especially because of their high level of Type I error rates for both, simulated and real data. UR - http://www.scopus.com/inward/record.url?scp=84923922737&partnerID=8YFLogxK U2 - 10.1186/s12859-014-0397-8 DO - 10.1186/s12859-014-0397-8 M3 - Article VL - 15 JO - BMC Bioinformatics JF - BMC Bioinformatics SN - 1471-2105 IS - 1 M1 - 397 ER - TY - JOUR T1 - Comparing large graphs efficiently by margins of feature vectors AU - Dehmer, Matthias AU - Emmert-Streib, Frank PY - 2007/5/15 Y1 - 2007/5/15 N2 - Measuring the structural similarity of graphs is a challenging and outstanding problem. Most of the classical approaches of the so-called exact graph matching methods are based on graph or subgraph isomorphic relations of the underlying graphs. In contrast to these methods in this paper we introduce a novel approach to measure the structural similarity of directed and undirected graphs that is mainly based on margins of feature vectors representing graphs. We introduce novel graph similarity and dissimilarity measures, provide some properties and analyze their algorithmic complexity. We find that the computational complexity of our measures is polynomial in the graph size and, hence, significantly better than classical methods from, e.g. exact graph matching which are NP-complete. Numerically, we provide some examples of our measure and compare the results with the well-known graph edit distance. AB - Measuring the structural similarity of graphs is a challenging and outstanding problem. Most of the classical approaches of the so-called exact graph matching methods are based on graph or subgraph isomorphic relations of the underlying graphs. In contrast to these methods in this paper we introduce a novel approach to measure the structural similarity of directed and undirected graphs that is mainly based on margins of feature vectors representing graphs. We introduce novel graph similarity and dissimilarity measures, provide some properties and analyze their algorithmic complexity. We find that the computational complexity of our measures is polynomial in the graph size and, hence, significantly better than classical methods from, e.g. exact graph matching which are NP-complete. Numerically, we provide some examples of our measure and compare the results with the well-known graph edit distance. KW - Degree vectors KW - Directed and undirected graphs KW - Graph similarity KW - Similarity measures UR - http://www.scopus.com/inward/record.url?scp=34248165422&partnerID=8YFLogxK U2 - 10.1016/j.amc.2006.11.185 DO - 10.1016/j.amc.2006.11.185 M3 - Article VL - 188 SP - 1699 EP - 1710 JO - Applied Mathematics and Computation JF - Applied Mathematics and Computation SN - 0096-3003 IS - 2 ER - TY - JOUR T1 - Continuum approach to high-cycle fatigue. The finite life-time case with stochastic stress history AU - Orelma, H. PY - 2019 Y1 - 2019 N2 - In this paper, we consider continuum approach for high-cycle fatigue in the case where life-time is finite. The method is based on differential equations and all basic concepts are explained. A stress history is assumed to be a stochastic process and this leads us to the theory of stochastic differential equations. The life-time is a quantity, which tells us when the breakdown of the material happens. In this method, it is naturally a random variable. The basic assumption is, that the distribution of the life-time is log-normal or Weibull. We give a numerical basic example to demonstrate the method. AB - In this paper, we consider continuum approach for high-cycle fatigue in the case where life-time is finite. The method is based on differential equations and all basic concepts are explained. A stress history is assumed to be a stochastic process and this leads us to the theory of stochastic differential equations. The life-time is a quantity, which tells us when the breakdown of the material happens. In this method, it is naturally a random variable. The basic assumption is, that the distribution of the life-time is log-normal or Weibull. We give a numerical basic example to demonstrate the method. KW - Evolution equation KW - High-cycle fatigue KW - Life-time U2 - 10.14498/vsgtu1705 DO - 10.14498/vsgtu1705 M3 - Article VL - 23 SP - 452 EP - 463 JO - Vestnik Samarskogo Gosudarstvennogo Tekhnicheskogo Universiteta, Seriya Fiziko-Matematicheskie Nauki JF - Vestnik Samarskogo Gosudarstvennogo Tekhnicheskogo Universiteta, Seriya Fiziko-Matematicheskie Nauki SN - 1991-8615 IS - 3 ER - TY - JOUR T1 - Customized dimensional analysis conceptual modelling framework for design optimization—a case study on the cross-flow micro turbine model AU - Woldemariam, Endashaw Tesfaye AU - Coatanéa, Eric AU - Wang, G. Gary AU - Lemu, Hirpa G. AU - Wu, Di PY - 2019 Y1 - 2019 N2 - Dimensional Analysis Conceptual Modelling (DACM) is a framework used for conceptual modelling and simulation in system and product designs. The framework is based on cause–effect analysis between variables and functions in a problem. This article presents an approach that mobilizes concepts from the DACM framework to assist solve high-dimensional expensive optimization problems with lower computational costs. The latter fundamentally utilizes theories and concepts from well-practised dimensional analysis, functional modelling and bond graphing. Statistical design-of-experiments theory is also utilized in the framework to measure impact levels of variables towards the objective. Simplifying as well as decomposing followed by optimization of expensive problems are the focuses of the article. To illustrate the approach, a case study on the performance optimization of a cross-flow micro hydro turbine is presented. The customized DACM framework assisted optimization approach converges faster and returns better results than the one without. A single-step simplification approach is employed in the case study and it returns a better average optimization result with about only one fifth of the function evaluations compared to optimization using the original model. AB - Dimensional Analysis Conceptual Modelling (DACM) is a framework used for conceptual modelling and simulation in system and product designs. The framework is based on cause–effect analysis between variables and functions in a problem. This article presents an approach that mobilizes concepts from the DACM framework to assist solve high-dimensional expensive optimization problems with lower computational costs. The latter fundamentally utilizes theories and concepts from well-practised dimensional analysis, functional modelling and bond graphing. Statistical design-of-experiments theory is also utilized in the framework to measure impact levels of variables towards the objective. Simplifying as well as decomposing followed by optimization of expensive problems are the focuses of the article. To illustrate the approach, a case study on the performance optimization of a cross-flow micro hydro turbine is presented. The customized DACM framework assisted optimization approach converges faster and returns better results than the one without. A single-step simplification approach is employed in the case study and it returns a better average optimization result with about only one fifth of the function evaluations compared to optimization using the original model. KW - Causality analysis KW - conceptual modelling KW - DACM assisted optimization KW - high-dimensional optimization KW - micro cross-flow turbine U2 - 10.1080/0305215X.2018.1519556 DO - 10.1080/0305215X.2018.1519556 M3 - Article VL - 51 SP - 1168 EP - 1184 JO - Engineering Optimization JF - Engineering Optimization SN - 0305-215X IS - 7 ER - TY - JOUR T1 - Damped Posterior Linearization Filter AU - Raitoharju, Matti AU - Svensson, Lennart AU - Garcia-Fernandez, Angel Froilan AU - Piche, Robert N1 - EXT="Raitoharju, Matti" PY - 2018 Y1 - 2018 N2 - In this letter, we propose an iterative Kalman type algorithm based on posterior linearization. The proposed algorithm uses a nested loop structure to optimize the mean of the estimate in the inner loop and update the covariance, which is a computationally more expensive operation, only in the outer loop. The optimization of the mean update is done using a damped algorithm to avoid divergence. Our simulations show that the proposed algorithm is more accurate than existing iterative Kalman filters. AB - In this letter, we propose an iterative Kalman type algorithm based on posterior linearization. The proposed algorithm uses a nested loop structure to optimize the mean of the estimate in the inner loop and update the covariance, which is a computationally more expensive operation, only in the outer loop. The optimization of the mean update is done using a damped algorithm to avoid divergence. Our simulations show that the proposed algorithm is more accurate than existing iterative Kalman filters. KW - Bayesian state estimation KW - Computational modeling KW - Convergence KW - Cost function KW - estimation KW - Kalman filters KW - Noise measurement KW - nonlinear KW - Signal processing algorithms U2 - 10.1109/LSP.2018.2806304 DO - 10.1109/LSP.2018.2806304 M3 - Article VL - 25 JO - IEEE Signal Processing Letters JF - IEEE Signal Processing Letters SN - 1070-9908 IS - 4 ER - TY - JOUR T1 - Data augmentation approaches for improving animal audio classification AU - Nanni, Loris AU - Maguolo, Gianluca AU - Paci, Michelangelo PY - 2020 Y1 - 2020 N2 - In this paper we present ensembles of classifiers for automated animal audio classification, exploiting different data augmentation techniques for training Convolutional Neural Networks (CNNs). The specific animal audio classification problems are i) birds and ii) cat sounds, whose datasets are freely available. We train five different CNNs on the original datasets and on their versions augmented by four augmentation protocols, working on the raw audio signals or their representations as spectrograms. We compared our best approaches with the state of the art, showing that we obtain the best recognition rate on the same datasets, without ad hoc parameter optimization. Our study shows that different CNNs can be trained for the purpose of animal audio classification and that their fusion works better than the stand-alone classifiers. To the best of our knowledge this is the largest study on data augmentation for CNNs in animal audio classification audio datasets using the same set of classifiers and parameters. Our MATLAB code is available at https://github.com/LorisNanni. AB - In this paper we present ensembles of classifiers for automated animal audio classification, exploiting different data augmentation techniques for training Convolutional Neural Networks (CNNs). The specific animal audio classification problems are i) birds and ii) cat sounds, whose datasets are freely available. We train five different CNNs on the original datasets and on their versions augmented by four augmentation protocols, working on the raw audio signals or their representations as spectrograms. We compared our best approaches with the state of the art, showing that we obtain the best recognition rate on the same datasets, without ad hoc parameter optimization. Our study shows that different CNNs can be trained for the purpose of animal audio classification and that their fusion works better than the stand-alone classifiers. To the best of our knowledge this is the largest study on data augmentation for CNNs in animal audio classification audio datasets using the same set of classifiers and parameters. Our MATLAB code is available at https://github.com/LorisNanni. KW - Acoustic features KW - Animal audio KW - Audio classification KW - Data augmentation KW - Ensemble of classifiers KW - Pattern recognition U2 - 10.1016/j.ecoinf.2020.101084 DO - 10.1016/j.ecoinf.2020.101084 M3 - Article VL - 57 JO - Ecological Informatics JF - Ecological Informatics SN - 1574-9541 M1 - 101084 ER - TY - JOUR T1 - Development of a constant dilution sampling system for particulate and gaseous pollutant measurements AU - Tzamkiozis, T. AU - Ntziachristos, L. AU - Amanatidis, S. AU - Niemelä, V. AU - Ukkonen, A. AU - Samaras, Z. PY - 2013/8 Y1 - 2013/8 N2 - This paper presents a new concept of a partial flow sampling system (PFSS), involving a two-stage diluter which operates on the principle of underpressure, while exhaust is sampled through a capillary. Due to the low flowrate through the capillary, the diluter may be sampling from a freely exhausting tailpipe and is not prone to pressure variations in the exhaust line. In addition, the PFSS operates at constant pressure conditions even upstream of diesel particle filters that increase the backpressure in the tailpipe. As a result, the PFSS offers a constant dilution ratio (DR) over any engine or vehicle operation condition. This study presents the diluter concept and a straightforward model developed to calculate the DR, depending on the dilution air flowrate and the diluter underpressure. The model is validated using CO2 as a trace gas, and very good agreement is demonstrated between the calculated and the measured DR values. Following validation, the PFSS is combined with aerosol measurement instruments to measure the exhaust particle concentration of a diesel engine operating at different steady-state modes. For demonstrating the stability of the DR and applicability of the PFSS, measurements are conducted with both heavy duty and light duty diesel exhaust gases. Future applications of this device include gas and particle exhaust measurements both in laboratory environments and on-board vehicles. AB - This paper presents a new concept of a partial flow sampling system (PFSS), involving a two-stage diluter which operates on the principle of underpressure, while exhaust is sampled through a capillary. Due to the low flowrate through the capillary, the diluter may be sampling from a freely exhausting tailpipe and is not prone to pressure variations in the exhaust line. In addition, the PFSS operates at constant pressure conditions even upstream of diesel particle filters that increase the backpressure in the tailpipe. As a result, the PFSS offers a constant dilution ratio (DR) over any engine or vehicle operation condition. This study presents the diluter concept and a straightforward model developed to calculate the DR, depending on the dilution air flowrate and the diluter underpressure. The model is validated using CO2 as a trace gas, and very good agreement is demonstrated between the calculated and the measured DR values. Following validation, the PFSS is combined with aerosol measurement instruments to measure the exhaust particle concentration of a diesel engine operating at different steady-state modes. For demonstrating the stability of the DR and applicability of the PFSS, measurements are conducted with both heavy duty and light duty diesel exhaust gases. Future applications of this device include gas and particle exhaust measurements both in laboratory environments and on-board vehicles. UR - http://www.scopus.com/inward/record.url?scp=84880789628&partnerID=8YFLogxK U2 - 10.1088/0957-0233/24/8/085801 DO - 10.1088/0957-0233/24/8/085801 M3 - Article VL - 24 JO - Measurement Science and Technology JF - Measurement Science and Technology SN - 0957-0233 IS - 8 M1 - 085801 ER - TY - JOUR T1 - Development of artificial neuronal networks for molecular communication AU - Balasubramaniam, Sasitharan AU - Boyle, Noreen T. AU - Della-Chiesa, Andrea AU - Walsh, Frank AU - Mardinoglu, Adil AU - Botvich, Dmitri AU - Prina-Mello, Adriele PY - 2011/6 Y1 - 2011/6 N2 - Communication at the nanoscale can enhance capabilities for nanodevices, and at the same time open new opportunities for numerous healthcare applications. One approach toward enabling communication between nanodevices is through molecular communications. While a number of solutions have been proposed for molecular communication (e.g. calcium signaling, molecular motors, bacteria communication), in this paper, we propose the use of neuronal networks for molecular communication network. In particular, we provide two design aspects of neuron networks, which includes, (i) the design of an interface between nanodevice and neurons that can initiate signaling, and (ii) the design of transmission scheduling to ensure that signals initiated by multiple devices will successfully reach the receiver with minimum interference. The solution for (i) is developed through wet lab experiments, while the solution for (ii) is developed through genetic algorithm optimization technique, and is validated through simulations. AB - Communication at the nanoscale can enhance capabilities for nanodevices, and at the same time open new opportunities for numerous healthcare applications. One approach toward enabling communication between nanodevices is through molecular communications. While a number of solutions have been proposed for molecular communication (e.g. calcium signaling, molecular motors, bacteria communication), in this paper, we propose the use of neuronal networks for molecular communication network. In particular, we provide two design aspects of neuron networks, which includes, (i) the design of an interface between nanodevice and neurons that can initiate signaling, and (ii) the design of transmission scheduling to ensure that signals initiated by multiple devices will successfully reach the receiver with minimum interference. The solution for (i) is developed through wet lab experiments, while the solution for (ii) is developed through genetic algorithm optimization technique, and is validated through simulations. KW - Molecular communications KW - Neuron networks KW - Scheduling UR - http://www.scopus.com/inward/record.url?scp=80052538220&partnerID=8YFLogxK U2 - 10.1016/j.nancom.2011.05.004 DO - 10.1016/j.nancom.2011.05.004 M3 - Article VL - 2 SP - 150 EP - 160 JO - Nano Communication Networks JF - Nano Communication Networks SN - 1878-7789 IS - 2-3 ER - TY - JOUR T1 - Diffusion and Fokker-Planck-Smoluchowski equations with generalized memory kernel AU - Sandev, Trifce AU - Chechkin, Aleksei AU - Kantz, Holger AU - Metzler, Ralf PY - 2015/8/1 Y1 - 2015/8/1 N2 - We consider anomalous stochastic processes based on the renewal continuous time random walk model with different forms for the probability density of waiting times between individual jumps. In the corresponding continuum limit we derive the generalized diffusion and Fokker-Planck- Smoluchowski equations with the corresponding memory kernels. We calculate the qth order moments in the unbiased and biased cases, and demonstrate that the generalized Einstein relation for the considered dynamics remains valid. The relaxation of modes in the case of an external harmonic potential and the convergence of the mean squared displacement to the thermal plateau are analyzed. AB - We consider anomalous stochastic processes based on the renewal continuous time random walk model with different forms for the probability density of waiting times between individual jumps. In the corresponding continuum limit we derive the generalized diffusion and Fokker-Planck- Smoluchowski equations with the corresponding memory kernels. We calculate the qth order moments in the unbiased and biased cases, and demonstrate that the generalized Einstein relation for the considered dynamics remains valid. The relaxation of modes in the case of an external harmonic potential and the convergence of the mean squared displacement to the thermal plateau are analyzed. KW - anomalous diffusion KW - continuous time random walk (CTRW) KW - Fokker- Planck-Smoluchowski equation KW - Mittag-Leffler functions KW - multi-scaling UR - http://www.scopus.com/inward/record.url?scp=84939133175&partnerID=8YFLogxK U2 - 10.1515/fca-2015-0059 DO - 10.1515/fca-2015-0059 M3 - Article VL - 18 SP - 1006 EP - 1038 JO - Fractional Calculus and Applied Analysis JF - Fractional Calculus and Applied Analysis SN - 1311-0454 IS - 4 ER - TY - JOUR T1 - Dimensionality reduction for data visualization AU - Kaski, Samuel AU - Peltonen, Jaakko PY - 2011/3 Y1 - 2011/3 N2 - Dimensionality reduction is one of the basic operations in the toolbox of data analysts and designers of machine learning and pattern recognition systems. Given a large set of measured variables but few observations, an obvious idea is to reduce the degrees of freedom in the measurements by representing them with a smaller set of more condensed variables. Another reason for reducing the dimensionality is to reduce computational load in further processing. A third reason is visualization. AB - Dimensionality reduction is one of the basic operations in the toolbox of data analysts and designers of machine learning and pattern recognition systems. Given a large set of measured variables but few observations, an obvious idea is to reduce the degrees of freedom in the measurements by representing them with a smaller set of more condensed variables. Another reason for reducing the dimensionality is to reduce computational load in further processing. A third reason is visualization. KW - Data models KW - Data visualization KW - Information retrieval KW - Machine learning KW - Manifolds KW - Probabilistic logic KW - Visualization UR - http://www.scopus.com/inward/record.url?scp=79951937674&partnerID=8YFLogxK U2 - 10.1109/MSP.2010.940003 DO - 10.1109/MSP.2010.940003 M3 - Article VL - 28 SP - 100 EP - 104 JO - IEEE Signal Processing Magazine JF - IEEE Signal Processing Magazine SN - 1053-5888 IS - 2 M1 - 5714379 ER - TY - JOUR T1 - Early analysis of resource consumption patterns in mobile applications AU - Berrocal, Javier AU - Garcia-Alonso, Jose AU - Vicente-Chicote, Cristina AU - Hernández, Juan AU - Mikkonen, Tommi AU - Canal, Carlos AU - Murillo, Juan M. PY - 2017 Y1 - 2017 N2 - Mobile device capabilities have increased tremendously in recent years, and the complexity of the applications executed in these devices has evolved accordingly. However, despite the efforts made by mobile manufactures, resource consumption, particularly battery and data traffic, are still limiting factors for mobile applications. The most important aspects determining the consumption of a mobile application is its software architecture and its behaviour. Hence, by comparing the resource consumption of different software architectures before an application is built, mobile developers can make decisions that are better informed. This work presents the consumption analysis of two applications, each of them built with two different architectures in order to identify under which situation each architecture is more efficient. In addition, by generalizing the analysis of the two applications, a conceptual framework is created with which to analyse the consumption pattern of applications in their early development phases. This conceptual framework will allow mobile developers to estimate the resource consumption of their applications under different conditions of software architecture and usage scenarios, providing them with information relevant for decision making. AB - Mobile device capabilities have increased tremendously in recent years, and the complexity of the applications executed in these devices has evolved accordingly. However, despite the efforts made by mobile manufactures, resource consumption, particularly battery and data traffic, are still limiting factors for mobile applications. The most important aspects determining the consumption of a mobile application is its software architecture and its behaviour. Hence, by comparing the resource consumption of different software architectures before an application is built, mobile developers can make decisions that are better informed. This work presents the consumption analysis of two applications, each of them built with two different architectures in order to identify under which situation each architecture is more efficient. In addition, by generalizing the analysis of the two applications, a conceptual framework is created with which to analyse the consumption pattern of applications in their early development phases. This conceptual framework will allow mobile developers to estimate the resource consumption of their applications under different conditions of software architecture and usage scenarios, providing them with information relevant for decision making. KW - Mobile software architecture KW - Mobile-centric KW - Resource consumption KW - Resource estimation U2 - 10.1016/j.pmcj.2016.06.011 DO - 10.1016/j.pmcj.2016.06.011 M3 - Article VL - 35 SP - 32 EP - 50 JO - Pervasive and Mobile Computing JF - Pervasive and Mobile Computing SN - 1574-1192 ER - TY - JOUR T1 - Efficient Noise Variance Estimation under Pilot Contamination for Large-Scale MIMO Systems AU - Iscar Vergara, Jorge AU - Guvenc, Ismail AU - Dikmese, Sener AU - Rupasinghe, Nadisanka PY - 2018 Y1 - 2018 N2 - Massive multiple-input multiple-output (MIMO) is expected to be one of the enabling technologies for fifth generation (5G) cellular networks. One of the major challenges in massive MIMO systems is the accurate joint estimation of the channel and noise variance, which significantly affects the performance of wireless communications in practical scenarios. In this paper, we first derive a novel maximum likelihood (ML) estimator for the noise variance at the receiver of massive MIMO systems considering practical impairments such as pilot contamination. Then, this estimate is used to compute the minimum mean square error (MMSE) estimate of the channel. In order to measure the performance of the proposed noise variance estimator, we derive the corresponding Cramer-Rao lower bound (CRLB). Simulation results show that the estimator is efficient in certain scenarios, outperforming existing approaches in the literature. Furthermore, we develop the estimator and CRLB for equal and different noise variance at the receive antennas. Although the proposed estimator is valid for all antenna array sizes, its use is particularly effective for massive MIMO systems. AB - Massive multiple-input multiple-output (MIMO) is expected to be one of the enabling technologies for fifth generation (5G) cellular networks. One of the major challenges in massive MIMO systems is the accurate joint estimation of the channel and noise variance, which significantly affects the performance of wireless communications in practical scenarios. In this paper, we first derive a novel maximum likelihood (ML) estimator for the noise variance at the receiver of massive MIMO systems considering practical impairments such as pilot contamination. Then, this estimate is used to compute the minimum mean square error (MMSE) estimate of the channel. In order to measure the performance of the proposed noise variance estimator, we derive the corresponding Cramer-Rao lower bound (CRLB). Simulation results show that the estimator is efficient in certain scenarios, outperforming existing approaches in the literature. Furthermore, we develop the estimator and CRLB for equal and different noise variance at the receive antennas. Although the proposed estimator is valid for all antenna array sizes, its use is particularly effective for massive MIMO systems. KW - 5G KW - Channel estimation KW - Contamination KW - Covariance matrices KW - CRLB KW - massive MIMO KW - maximum likelihood KW - Maximum likelihood estimation KW - method of moments KW - MIMO KW - MMSE channel estimation KW - noise variance estimation KW - Partial transmit sequences KW - pilot contamination U2 - 10.1109/TVT.2017.2766226 DO - 10.1109/TVT.2017.2766226 M3 - Article VL - 67 SP - 2982 EP - 2996 JO - IEEE Transactions on Vehicular Technology JF - IEEE Transactions on Vehicular Technology SN - 0018-9545 IS - 4 ER - TY - JOUR T1 - Energy Efficiency Maximization of Full-Duplex Two-Way Relay with Non-Ideal Power Amplifiers and Non-Negligible Circuit Power AU - Cui, Qimei AU - Zhang, Yuhao AU - Ni, Wei AU - Valkama, Mikko AU - Jantti, Riku PY - 2017/9/1 Y1 - 2017/9/1 N2 - In this paper, we maximize the energy efficiency (EE) of full-duplex (FD) two-way relay (TWR) systems under non-ideal power amplifiers (PAs) and non-negligible transmission-dependent circuit power. We start with the case where only the relay operates full duplex and two timeslots are required for TWR. Then, we extend to the advanced case, where the relay and the two nodes all operate full duplex, and accomplish TWR in a single timeslot. In both cases, we establish the intrinsic connections between the optimal transmit powers and durations, based on which the original non-convex EE maximization can be convexified and optimally solved. Simulations show the superiority of FD-TWR in terms of EE, especially when traffic demand is high. The simulations also reveal that the maximum EE of FD-TWR is more sensitive to the PA efficiency, than it is to self-cancellation. The full FD design of FD-TWR is susceptible to traffic imbalance, while the design with only the relay operating in the FD mode exhibits strong tolerance. AB - In this paper, we maximize the energy efficiency (EE) of full-duplex (FD) two-way relay (TWR) systems under non-ideal power amplifiers (PAs) and non-negligible transmission-dependent circuit power. We start with the case where only the relay operates full duplex and two timeslots are required for TWR. Then, we extend to the advanced case, where the relay and the two nodes all operate full duplex, and accomplish TWR in a single timeslot. In both cases, we establish the intrinsic connections between the optimal transmit powers and durations, based on which the original non-convex EE maximization can be convexified and optimally solved. Simulations show the superiority of FD-TWR in terms of EE, especially when traffic demand is high. The simulations also reveal that the maximum EE of FD-TWR is more sensitive to the PA efficiency, than it is to self-cancellation. The full FD design of FD-TWR is susceptible to traffic imbalance, while the design with only the relay operating in the FD mode exhibits strong tolerance. KW - Energy efficiency KW - full-duplex KW - non-ideal power amplifier KW - non-negligible circuit power KW - two-way relay U2 - 10.1109/TWC.2017.2721372 DO - 10.1109/TWC.2017.2721372 M3 - Article VL - 16 SP - 6264 EP - 6278 JO - IEEE Transactions on Wireless Communications JF - IEEE Transactions on Wireless Communications SN - 1536-1276 IS - 9 ER - TY - JOUR T1 - Energy-efficient and high-precision control of hydraulic robots AU - Koivumäki, Janne AU - Zhu, Wen Hong AU - Mattila, Jouni PY - 2019/4/1 Y1 - 2019/4/1 N2 - In addition to high-precision closed-loop control performance, energy efficiency is another vital characteristic in field-robotic hydraulic systems as energy source(s) must be carried on board in limited space. This study proposes an energy-efficient and high-precision closed-loop controller for the highly nonlinear hydraulic robotic manipulators. The proposed method is twofold: 1) A possibility for energy consumption reduction is realized by using a separate meter-in separate meter-out (SMISMO) control set-up, enabling an independent metering (pressure control) of each chamber in hydraulic actuators. 2) A novel subsystem-dynamics-based and modular controller is designed for the system actuators, and it is integrated to the previously designed state-of-the-art controller for multiple degrees-of-freedom (n-DOF) manipulators. Stability of the overall controller is rigorously proven. The comparative experiments with a three-DOF redundant hydraulic robotic manipulator (with a payload of 475 kg) demonstrate that: 1) It is possible to design the triple objective of high-precision piston position, piston force and chamber pressure trackings for the hydraulic actuators. 2) In relation to the previous SMISMO-control methods, unprecedented motion and chamber pressure tracking performances are reported. 3) In comparison to the state-of-the-art motion tracking controller with a conventional energy-inefficient servovalve control, the actuators’ energy consumption is reduced by 45% without noticeable motion control (position-tracking) deterioration. AB - In addition to high-precision closed-loop control performance, energy efficiency is another vital characteristic in field-robotic hydraulic systems as energy source(s) must be carried on board in limited space. This study proposes an energy-efficient and high-precision closed-loop controller for the highly nonlinear hydraulic robotic manipulators. The proposed method is twofold: 1) A possibility for energy consumption reduction is realized by using a separate meter-in separate meter-out (SMISMO) control set-up, enabling an independent metering (pressure control) of each chamber in hydraulic actuators. 2) A novel subsystem-dynamics-based and modular controller is designed for the system actuators, and it is integrated to the previously designed state-of-the-art controller for multiple degrees-of-freedom (n-DOF) manipulators. Stability of the overall controller is rigorously proven. The comparative experiments with a three-DOF redundant hydraulic robotic manipulator (with a payload of 475 kg) demonstrate that: 1) It is possible to design the triple objective of high-precision piston position, piston force and chamber pressure trackings for the hydraulic actuators. 2) In relation to the previous SMISMO-control methods, unprecedented motion and chamber pressure tracking performances are reported. 3) In comparison to the state-of-the-art motion tracking controller with a conventional energy-inefficient servovalve control, the actuators’ energy consumption is reduced by 45% without noticeable motion control (position-tracking) deterioration. KW - Energy efficiency KW - Hydraulic robots KW - Independent metering KW - Nonlinear control KW - SMISMO control KW - Stability analysis U2 - 10.1016/j.conengprac.2018.12.013 DO - 10.1016/j.conengprac.2018.12.013 M3 - Article VL - 85 SP - 176 EP - 193 JO - Control Engineering Practice JF - Control Engineering Practice SN - 0967-0661 ER - TY - JOUR T1 - Entropy analysis of word-length series of natural language texts T2 - Effects of text language and genre AU - Kalimeri, Maria AU - Constantoudis, Vassilios AU - Papadimitriou, Constantinos AU - Karamanos, Konstantinos AU - Diakonos, Fotis K. AU - Papageorgiou, Haris N1 - EXT="Kalimeri, Maria" PY - 2012/9 Y1 - 2012/9 N2 - We estimate the n-gram entropies of natural language texts in word-length representation and find that these are sensitive to text language and genre. We attribute this sensitivity to changes in the probability distribution of the lengths of single words and emphasize the crucial role of the uniformity of probabilities of having words with length between five and ten. Furthermore, comparison with the entropies of shuffled data reveals the impact of word length correlations on the estimated n-gram entropies. AB - We estimate the n-gram entropies of natural language texts in word-length representation and find that these are sensitive to text language and genre. We attribute this sensitivity to changes in the probability distribution of the lengths of single words and emphasize the crucial role of the uniformity of probabilities of having words with length between five and ten. Furthermore, comparison with the entropies of shuffled data reveals the impact of word length correlations on the estimated n-gram entropies. KW - N-gram entropies KW - Quantitative linguistics KW - Symbolic dynamics KW - Time series KW - Word-length representation UR - http://www.scopus.com/inward/record.url?scp=84867518276&partnerID=8YFLogxK U2 - 10.1142/S0218127412502239 DO - 10.1142/S0218127412502239 M3 - Article VL - 22 JO - INTERNATIONAL JOURNAL OF BIFURCATION AND CHAOS JF - INTERNATIONAL JOURNAL OF BIFURCATION AND CHAOS SN - 0218-1274 IS - 9 M1 - 1250223 ER - TY - JOUR T1 - Entropy and Channel Capacity under Optimum Power and Rate Adaptation over Generalized Fading Conditions AU - Sofotasios, Paschalis C. AU - Muhaidat, Sami AU - Valkama, Mikko AU - Ghogho, Mounir AU - Karagiannidis, George K. PY - 2015/11/1 Y1 - 2015/11/1 N2 - Accurate fading characterization and channel capacity determination are of paramount importance in both conventional and emerging communication systems. The present work addresses the non-linearity of the propagation medium and its effects on the channel capacity. Such fading conditions are first characterized using information theoretic measures, namely, Shannon entropy, cross entropy and relative entropy. The corresponding effects on the channel capacity with and without power adaptation are then analyzed. Closed-form expressions are derived and validated through computer simulations. It is shown that the effects of nonlinearities are significantly larger than those of fading parameters such as the scattered-wave power ratio, and the correlation coefficient between the in-phase and quadrature components in each cluster of multipath components. AB - Accurate fading characterization and channel capacity determination are of paramount importance in both conventional and emerging communication systems. The present work addresses the non-linearity of the propagation medium and its effects on the channel capacity. Such fading conditions are first characterized using information theoretic measures, namely, Shannon entropy, cross entropy and relative entropy. The corresponding effects on the channel capacity with and without power adaptation are then analyzed. Closed-form expressions are derived and validated through computer simulations. It is shown that the effects of nonlinearities are significantly larger than those of fading parameters such as the scattered-wave power ratio, and the correlation coefficient between the in-phase and quadrature components in each cluster of multipath components. KW - Adaptation policies KW - channel capacity KW - entropy U2 - 10.1109/LSP.2015.2464221 DO - 10.1109/LSP.2015.2464221 M3 - Article VL - 22 SP - 2162 EP - 2166 JO - IEEE Signal Processing Letters JF - IEEE Signal Processing Letters SN - 1070-9908 IS - 11 ER - TY - JOUR T1 - Entropy bounds for dendrimers AU - Chen, Zengqiang AU - Dehmer, Matthias AU - Emmert-Streib, Frank AU - Shi, Yongtang PY - 2014/9/1 Y1 - 2014/9/1 N2 - Many graph invariants have been used for the construction of entropy-based measures to characterize the structure of complex networks. When considering Shannon entropy-based graph measures, there has been very little work to find their extremal values. A reason for this might be the fact that Shannon's entropy represents a multivariate function and all probability values are not equal to zero when considering graph entropies. Dehmer and Kraus proved some extremal results for graph entropies which are based on information functionals and express some conjectures generated by numerical simulations to find extremal values of graph entropies. Dehmer and Kraus discussed the extremal values of entropies for dendrimers. In this paper, we continue to study the extremal values of graph entropy for dendrimers, which has most interesting applications in molecular structure networks, and also in the pharmaceutical and biomedical area. Among all dendrimers with n vertices, we obtain the extremal values of graph entropy based on different well-known information functionals. Numerical experiments verifies our results. AB - Many graph invariants have been used for the construction of entropy-based measures to characterize the structure of complex networks. When considering Shannon entropy-based graph measures, there has been very little work to find their extremal values. A reason for this might be the fact that Shannon's entropy represents a multivariate function and all probability values are not equal to zero when considering graph entropies. Dehmer and Kraus proved some extremal results for graph entropies which are based on information functionals and express some conjectures generated by numerical simulations to find extremal values of graph entropies. Dehmer and Kraus discussed the extremal values of entropies for dendrimers. In this paper, we continue to study the extremal values of graph entropy for dendrimers, which has most interesting applications in molecular structure networks, and also in the pharmaceutical and biomedical area. Among all dendrimers with n vertices, we obtain the extremal values of graph entropy based on different well-known information functionals. Numerical experiments verifies our results. KW - Dendrimers KW - Extremal values KW - Graph entropy KW - Information theory KW - Shannon's entropy UR - http://www.scopus.com/inward/record.url?scp=84903150191&partnerID=8YFLogxK U2 - 10.1016/j.amc.2014.05.105 DO - 10.1016/j.amc.2014.05.105 M3 - Article VL - 242 SP - 462 EP - 472 JO - Applied Mathematics and Computation JF - Applied Mathematics and Computation SN - 0096-3003 ER - TY - JOUR T1 - Enzyme-based circuit design for nano-scale computing AU - Ivanov, S. AU - Botvich, D. AU - Balasubramaniam, S. PY - 2012/9 Y1 - 2012/9 N2 - Enzyme-based logical gates have been proposed as an alternative to conventional semiconductor gates in order to support computing at the nano-scale for nano-devices. In particular, certain enzyme-based implementations of AND, OR and NOT gates were proposed for further composing enzyme-based circuits for various Boolean functions. However, inputs and outputs of these gates are presented by different chemical species, and this results in potential incompatibility between gates. Therefore, opposite to conventional semiconductor gates not just any pair of enzyme-based logical gates may be used consequently in a circuit. This significantly complicates circuit creation and raises the question of the existence of an enzyme-based circuit for a generic Boolean function. This paper addresses the issue while providing its formal mathematical description together with an algorithm for enzyme-based circuit design. AB - Enzyme-based logical gates have been proposed as an alternative to conventional semiconductor gates in order to support computing at the nano-scale for nano-devices. In particular, certain enzyme-based implementations of AND, OR and NOT gates were proposed for further composing enzyme-based circuits for various Boolean functions. However, inputs and outputs of these gates are presented by different chemical species, and this results in potential incompatibility between gates. Therefore, opposite to conventional semiconductor gates not just any pair of enzyme-based logical gates may be used consequently in a circuit. This significantly complicates circuit creation and raises the question of the existence of an enzyme-based circuit for a generic Boolean function. This paper addresses the issue while providing its formal mathematical description together with an algorithm for enzyme-based circuit design. KW - Circuit design KW - Enzyme logic KW - Nano-scale computing UR - http://www.scopus.com/inward/record.url?scp=84867739312&partnerID=8YFLogxK U2 - 10.1016/j.nancom.2012.09.002 DO - 10.1016/j.nancom.2012.09.002 M3 - Article VL - 3 SP - 168 EP - 174 JO - Nano Communication Networks JF - Nano Communication Networks SN - 1878-7789 IS - 3 ER - TY - JOUR T1 - Estimation of additional losses due to random contacts at the edges of stator of an electrical machine AU - Shah, Sahas Bikram AU - Rasilo, Paavo AU - Belahcen, Anouar AU - Arkkio, Antero PY - 2015/9/7 Y1 - 2015/9/7 N2 - Purpose - Punching of the electrical sheets impair the insulation and make random galvanic contacts between the edges of the sheets. The purpose of this paper is to model the random galvanic contacts at the stator edges of 37 kW induction machine and estimate the additional losses due to these contacts. Design/methodology/approach - The presence of the surface current at the edges of sheets causes the discontinuity in the tangential component of the magnetic field. The surface boundary layer model which is based on this concept is implemented to model the galvanic contacts at the edges of the sheets. Finite element analysis based on magnetic vector potential was done and theoretical statistical study of the random conductivity at the stator edge was performed using brute force method. Findings - Finite element analysis validates the interlaminar current when galvanic contacts are present at the edges of electrical sheets. The case studies show that the rotor and stator losses increases with the thickness of the contacts. Statistical studies show that the mean value of total electromagnetic loss was increased by 7.7 percent due to random contacts at the edges of sheets. Originality/value - The novel approach for modeling the galvanic contacts at the stator edges of induction machine is discussed in this paper. The hypothesis of interlaminar current due to galvanic contacts is also validated using finite element simulation. AB - Purpose - Punching of the electrical sheets impair the insulation and make random galvanic contacts between the edges of the sheets. The purpose of this paper is to model the random galvanic contacts at the stator edges of 37 kW induction machine and estimate the additional losses due to these contacts. Design/methodology/approach - The presence of the surface current at the edges of sheets causes the discontinuity in the tangential component of the magnetic field. The surface boundary layer model which is based on this concept is implemented to model the galvanic contacts at the edges of the sheets. Finite element analysis based on magnetic vector potential was done and theoretical statistical study of the random conductivity at the stator edge was performed using brute force method. Findings - Finite element analysis validates the interlaminar current when galvanic contacts are present at the edges of electrical sheets. The case studies show that the rotor and stator losses increases with the thickness of the contacts. Statistical studies show that the mean value of total electromagnetic loss was increased by 7.7 percent due to random contacts at the edges of sheets. Originality/value - The novel approach for modeling the galvanic contacts at the stator edges of induction machine is discussed in this paper. The hypothesis of interlaminar current due to galvanic contacts is also validated using finite element simulation. KW - Boundary conditions KW - Eddy current KW - Electrical conductivity KW - FEM KW - Magnetic vector potential UR - http://www.scopus.com/inward/record.url?scp=84941111680&partnerID=8YFLogxK U2 - 10.1108/COMPEL-02-2015-0083 DO - 10.1108/COMPEL-02-2015-0083 M3 - Article VL - 34 SP - 1501 EP - 1510 JO - COMPEL: The International Journal for Computation and Mathematics in Electrical and Electronic Engineering JF - COMPEL: The International Journal for Computation and Mathematics in Electrical and Electronic Engineering SN - 0332-1649 IS - 5 ER - TY - JOUR T1 - Evolutionary dynamics of the spatial Prisoner's Dilemma with self-inhibition AU - Emmert-Streib, Frank PY - 2012/2/5 Y1 - 2012/2/5 N2 - In this paper we study the influence of interventions on self-interactions in a spatial Prisoner's Dilemma on a two-dimensional grid with periodic boundary conditions and synchronous updating of the dynamics. We investigate two different types of self-interaction modifications. The first type (FSIP) is deterministic, effecting each self-interaction of a player by a constant factor, whereas the second type (PSIP) performs a probabilistic interventions. Both types of interventions lead to a reduction of the payoff of the players and, hence, represent inhibiting effects. We find that a constant but moderate reduction of self-interactions has a very beneficial effect on the evolution of cooperators in the population, whereas probabilistic interventions on self-interactions are in general counter productive for the coexistence of the two different strategies. AB - In this paper we study the influence of interventions on self-interactions in a spatial Prisoner's Dilemma on a two-dimensional grid with periodic boundary conditions and synchronous updating of the dynamics. We investigate two different types of self-interaction modifications. The first type (FSIP) is deterministic, effecting each self-interaction of a player by a constant factor, whereas the second type (PSIP) performs a probabilistic interventions. Both types of interventions lead to a reduction of the payoff of the players and, hence, represent inhibiting effects. We find that a constant but moderate reduction of self-interactions has a very beneficial effect on the evolution of cooperators in the population, whereas probabilistic interventions on self-interactions are in general counter productive for the coexistence of the two different strategies. KW - Evolutionary dynamics KW - Evolutionary game theory KW - Game theory KW - Prisoner's dilemma UR - http://www.scopus.com/inward/record.url?scp=84855904251&partnerID=8YFLogxK U2 - 10.1016/j.amc.2011.12.018 DO - 10.1016/j.amc.2011.12.018 M3 - Article VL - 218 SP - 6482 EP - 6488 JO - Applied Mathematics and Computation JF - Applied Mathematics and Computation SN - 0096-3003 IS - 11 ER - TY - JOUR T1 - Forward simulation and inverse dipole localization with the lowest order Raviart - Thomas elements for electroencephalography AU - Pursiainen, S. AU - Sorrentino, A. AU - Campi, C. AU - Piana, M. PY - 2011/4 Y1 - 2011/4 N2 - Electroencephalography is a non-invasive imaging modality in which a primary current density generated by the neural activity in the brain is to be reconstructed based on external electric potential measurements. This paper focuses on the finite element method (FEM) from both forward and inverse aspects. The goal is to establish a clear correspondence between the lowest order Raviart-Thomas basis functions and dipole sources as well as to show that the adopted FEM approach is computationally effective. Each basis function is associated with a dipole moment and a location. Four candidate locations are tested. Numerical experiments cover two different spherical multilayer head models, four mesh resolutions and two different forward simulation approaches, one based on FEM and another based on the boundary element method (BEM) with standard dipoles as sources. The forward simulation accuracy is examined through column- and matrix-wise relative errors as well as through performance in inverse dipole localization. A closed-form approximation of dipole potential was used as the reference forward simulation. The present approach is compared to the BEM and indirectly also to the recent FEM-based subtraction approach regarding both accuracy, computation time and accessibility of implementation. AB - Electroencephalography is a non-invasive imaging modality in which a primary current density generated by the neural activity in the brain is to be reconstructed based on external electric potential measurements. This paper focuses on the finite element method (FEM) from both forward and inverse aspects. The goal is to establish a clear correspondence between the lowest order Raviart-Thomas basis functions and dipole sources as well as to show that the adopted FEM approach is computationally effective. Each basis function is associated with a dipole moment and a location. Four candidate locations are tested. Numerical experiments cover two different spherical multilayer head models, four mesh resolutions and two different forward simulation approaches, one based on FEM and another based on the boundary element method (BEM) with standard dipoles as sources. The forward simulation accuracy is examined through column- and matrix-wise relative errors as well as through performance in inverse dipole localization. A closed-form approximation of dipole potential was used as the reference forward simulation. The present approach is compared to the BEM and indirectly also to the recent FEM-based subtraction approach regarding both accuracy, computation time and accessibility of implementation. UR - http://www.scopus.com/inward/record.url?scp=79953662770&partnerID=8YFLogxK U2 - 10.1088/0266-5611/27/4/045003 DO - 10.1088/0266-5611/27/4/045003 M3 - Article VL - 27 JO - Inverse Problems JF - Inverse Problems SN - 0266-5611 IS - 4 M1 - 045003 ER - TY - JOUR T1 - Frequency domain robust regulation of signals generated by an infinite-dimensional exosystem AU - Laakkonen, Petteri AU - Pohjolainen, Seppo PY - 2015 Y1 - 2015 N2 - This paper deals with frequency domain robust regulation of signals generated by an infinite-dimensional exosystem. The problem is formulated and the stability types are chosen so that one can generalize the existing finite-dimensional theory to more general classes of infinite-dimensional systems and signals. The main results of this article are extensions of the internal model principle, of a necessary and sufficient solvability condition for the robust regulation problem, and of Davison's simple servo compensator for stable plants in the chosen algebraic framework. AB - This paper deals with frequency domain robust regulation of signals generated by an infinite-dimensional exosystem. The problem is formulated and the stability types are chosen so that one can generalize the existing finite-dimensional theory to more general classes of infinite-dimensional systems and signals. The main results of this article are extensions of the internal model principle, of a necessary and sufficient solvability condition for the robust regulation problem, and of Davison's simple servo compensator for stable plants in the chosen algebraic framework. KW - Frequency domain KW - Infinite-dimensional exosystems KW - Infinite-dimensional systems KW - Internal model KW - Robust regulation UR - http://www.scopus.com/inward/record.url?scp=84923923144&partnerID=8YFLogxK U2 - 10.1137/130950057 DO - 10.1137/130950057 M3 - Article VL - 53 SP - 139 EP - 166 JO - SIAM Journal on Control and Optimization JF - SIAM Journal on Control and Optimization SN - 0363-0129 IS - 1 ER - TY - JOUR T1 - Frequency-selective PAPR reduction for OFDM AU - Gokceli, Selahattin AU - Levanen, Toni AU - Riihonen, Taneli AU - Renfors, Markku AU - Valkama, Mikko PY - 2019/6/1 Y1 - 2019/6/1 N2 - In this correspondence paper, we study the peak-To-Average power ratio (PAPR) problem in orthogonal frequency-division multiplexing systems. In conventional clipping and filtering based PAPR reduction techniques, clipping noise is allowed to spread over the whole active passband, thus degrading the transmit signal quality similarly at all active subcarriers. However, since modern radio networks support frequency multiplexing of users and services with highly different quality-of-service expectations, clipping noise from PAPR reduction should be distributed unequally over the corresponding physical resource blocks (PRBs). To facilitate this, we present an efficient PAPR reduction technique, where clipping noise can be flexibly controlled and filtered inside the transmitter passband, allowing to control the transmitted signal quality per PRB. Numerical results are provided in 5G new radio mobile network context, demonstrating the flexibility and efficiency of the proposed method. AB - In this correspondence paper, we study the peak-To-Average power ratio (PAPR) problem in orthogonal frequency-division multiplexing systems. In conventional clipping and filtering based PAPR reduction techniques, clipping noise is allowed to spread over the whole active passband, thus degrading the transmit signal quality similarly at all active subcarriers. However, since modern radio networks support frequency multiplexing of users and services with highly different quality-of-service expectations, clipping noise from PAPR reduction should be distributed unequally over the corresponding physical resource blocks (PRBs). To facilitate this, we present an efficient PAPR reduction technique, where clipping noise can be flexibly controlled and filtered inside the transmitter passband, allowing to control the transmitted signal quality per PRB. Numerical results are provided in 5G new radio mobile network context, demonstrating the flexibility and efficiency of the proposed method. KW - 5G New Radio (NR) KW - clipping KW - filtering KW - orthogonal frequency-division multiplexing (OFDM) KW - peak-To-Average-power ratio (PAPR) KW - waveform KW - wireless communications U2 - 10.1109/TVT.2019.2909643 DO - 10.1109/TVT.2019.2909643 M3 - Article VL - 68 SP - 6167 EP - 6171 JO - IEEE Transactions on Vehicular Technology JF - IEEE Transactions on Vehicular Technology SN - 0018-9545 IS - 6 ER - TY - JOUR T1 - Functional and genetic analysis of the colon cancer network. AU - Emmert-Streib, Frank AU - de Matos Simoes, Ricardo AU - Glazko, Galina AU - McDade, Simon AU - Haibe-Kains, Benjamin AU - Holzinger, Andreas AU - Dehmer, Matthias AU - Campbell, Frederick PY - 2014 Y1 - 2014 N2 - Cancer is a complex disease that has proven to be difficult to understand on the single-gene level. For this reason a functional elucidation needs to take interactions among genes on a systems-level into account. In this study, we infer a colon cancer network from a large-scale gene expression data set by using the method BC3Net. We provide a structural and a functional analysis of this network and also connect its molecular interaction structure with the chromosomal locations of the genes enabling the definition of cis- and trans-interactions. Furthermore, we investigate the interaction of genes that can be found in close neighborhoods on the chromosomes to gain insight into regulatory mechanisms. To our knowledge this is the first study analyzing the genome-scale colon cancer network. AB - Cancer is a complex disease that has proven to be difficult to understand on the single-gene level. For this reason a functional elucidation needs to take interactions among genes on a systems-level into account. In this study, we infer a colon cancer network from a large-scale gene expression data set by using the method BC3Net. We provide a structural and a functional analysis of this network and also connect its molecular interaction structure with the chromosomal locations of the genes enabling the definition of cis- and trans-interactions. Furthermore, we investigate the interaction of genes that can be found in close neighborhoods on the chromosomes to gain insight into regulatory mechanisms. To our knowledge this is the first study analyzing the genome-scale colon cancer network. UR - http://www.scopus.com/inward/record.url?scp=84907412397&partnerID=8YFLogxK M3 - Article VL - 15 JO - BMC Bioinformatics JF - BMC Bioinformatics SN - 1471-2105 IS - Suppl 6 M1 - S6 ER - TY - JOUR T1 - Further hardness results on rainbow and strong rainbow connectivity AU - Lauri, Juho PY - 2016 Y1 - 2016 N2 - A path in an edge-colored graph is rainbow if no two edges of it are colored the same. The graph is said to be rainbow connected if there is a rainbow path between every pair of vertices. If there is a rainbow shortest path between every pair of vertices, the graph is strong rainbow connected. We consider the complexity of the problem of deciding if a given edge-colored graph is rainbow or strong rainbow connected. These problems are called Rainbow connectivity and Strong rainbow connectivity, respectively. We prove both problems remain NP-complete on interval outerplanar graphs and k-regular graphs for k≥3. Previously, no graph class was known where the complexity of the two problems would differ. We show that for block graphs, which form a subclass of chordal graphs, Rainbow connectivity is NP-complete while Strong rainbow connectivity is in P. We conclude by considering some tractable special cases, and show for instance that both problems are in XP when parameterized by tree-depth. AB - A path in an edge-colored graph is rainbow if no two edges of it are colored the same. The graph is said to be rainbow connected if there is a rainbow path between every pair of vertices. If there is a rainbow shortest path between every pair of vertices, the graph is strong rainbow connected. We consider the complexity of the problem of deciding if a given edge-colored graph is rainbow or strong rainbow connected. These problems are called Rainbow connectivity and Strong rainbow connectivity, respectively. We prove both problems remain NP-complete on interval outerplanar graphs and k-regular graphs for k≥3. Previously, no graph class was known where the complexity of the two problems would differ. We show that for block graphs, which form a subclass of chordal graphs, Rainbow connectivity is NP-complete while Strong rainbow connectivity is in P. We conclude by considering some tractable special cases, and show for instance that both problems are in XP when parameterized by tree-depth. KW - Computational complexity KW - Rainbow connectivity U2 - 10.1016/j.dam.2015.07.041 DO - 10.1016/j.dam.2015.07.041 M3 - Article VL - 201 SP - 191 EP - 200 JO - Discrete Applied Mathematics JF - Discrete Applied Mathematics SN - 0166-218X ER - TY - JOUR T1 - Geometric solution strategy of Laplace problems with free boundary AU - Poutala, Arto AU - Tarhasaari, Timo AU - Kettunen, Lauri PY - 2016/3/9 Y1 - 2016/3/9 N2 - This paper introduces a geometric solution strategy for Laplace problems. Our main interest and emphasis is on efficient solution of the inverse problem with a boundary with Cauchy condition and with a free boundary. This type of problem is known to be sensitive to small errors. We start from the standard Laplace problem and establish the geometric solution strategy on the idea of deforming equipotential layers continuously along the field lines from one layer to another. This results in exploiting ordinary differential equations to solve any boundary value problem that belongs to the class of Laplace's problem. Interpretation in terms of a geometric flow will provide us with stability considerations. The approach is demonstrated with several examples. AB - This paper introduces a geometric solution strategy for Laplace problems. Our main interest and emphasis is on efficient solution of the inverse problem with a boundary with Cauchy condition and with a free boundary. This type of problem is known to be sensitive to small errors. We start from the standard Laplace problem and establish the geometric solution strategy on the idea of deforming equipotential layers continuously along the field lines from one layer to another. This results in exploiting ordinary differential equations to solve any boundary value problem that belongs to the class of Laplace's problem. Interpretation in terms of a geometric flow will provide us with stability considerations. The approach is demonstrated with several examples. KW - Bernoulli problem KW - Cauchy condition KW - Differential equations KW - Elliptic partial differential equations KW - Equipotential layers KW - Field lines KW - Inverse problem KW - Laplace problem KW - Mean curvature KW - Shape design U2 - 10.1002/nme.4988 DO - 10.1002/nme.4988 M3 - Article VL - 105 SP - 723 EP - 746 JO - International Journal for Numerical Methods in Engineering JF - International Journal for Numerical Methods in Engineering SN - 0029-5981 IS - 10 ER - TY - JOUR T1 - Graph distance measures based on topological indices revisited AU - Dehmer, Matthias AU - Emmert-Streib, Frank AU - Shi, Yongtang PY - 2015/6/18 Y1 - 2015/6/18 N2 - Graph distance measures based on topological indices have been already explored by Dehmer et al. Also, inequalities for those graph distance measures have been proved. In this paper, we continue studying such comparative graph measures based on the well-known Wiener index, graph energy and Randić index, respectively. We prove extremal properties of the graph distance measures for some special classes of graphs. To demonstrate useful properties of the measures, we also discuss numerical results. To conclude the paper we state some open problems. AB - Graph distance measures based on topological indices have been already explored by Dehmer et al. Also, inequalities for those graph distance measures have been proved. In this paper, we continue studying such comparative graph measures based on the well-known Wiener index, graph energy and Randić index, respectively. We prove extremal properties of the graph distance measures for some special classes of graphs. To demonstrate useful properties of the measures, we also discuss numerical results. To conclude the paper we state some open problems. KW - Distance measure KW - Edit distance KW - Extremal graph KW - Topological index U2 - 10.1016/j.amc.2015.05.072 DO - 10.1016/j.amc.2015.05.072 M3 - Article VL - 266 SP - 623 EP - 633 JO - Applied Mathematics and Computation JF - Applied Mathematics and Computation SN - 0096-3003 ER - TY - JOUR T1 - Graph entropy based on the number of spanning forests of c-cyclic graphs AU - Wan, Pengfei AU - Tu, Jianhua AU - Dehmer, Matthias AU - Zhang, Shenggui AU - Emmert-Streib, Frank PY - 2019/12/15 Y1 - 2019/12/15 N2 - Graph entropies have been introduced to quantitatively measure the structural information content of graphs and networks; they have plenty of applications in various fields. Utilizing the number of subgraphs to establish measures for determining the complexity of molecular graphs are also prevalent in the study of mathematical chemistry. In this paper, we develop a new graph entropy measure that is based on the number of spanning forests. We prove explicit expressions for the entropy for trees, unicyclic and bicyclic graphs, and show that the cycle graph Cn attains the maximal value of the entropy for unicyclic graphs with order n and large cycle lengths. Based on generating numerical results, we conjecture extremal unicyclic graphs with respect to the entropy as well as we compare the values of our entropy for c-cyclic graphs, and generate graphs of bicyclic graphs and tricyclic graphs with 6 vertices for performing further research. AB - Graph entropies have been introduced to quantitatively measure the structural information content of graphs and networks; they have plenty of applications in various fields. Utilizing the number of subgraphs to establish measures for determining the complexity of molecular graphs are also prevalent in the study of mathematical chemistry. In this paper, we develop a new graph entropy measure that is based on the number of spanning forests. We prove explicit expressions for the entropy for trees, unicyclic and bicyclic graphs, and show that the cycle graph Cn attains the maximal value of the entropy for unicyclic graphs with order n and large cycle lengths. Based on generating numerical results, we conjecture extremal unicyclic graphs with respect to the entropy as well as we compare the values of our entropy for c-cyclic graphs, and generate graphs of bicyclic graphs and tricyclic graphs with 6 vertices for performing further research. KW - Graph entropy KW - Spanning forest KW - Subgraph U2 - 10.1016/j.amc.2019.124616 DO - 10.1016/j.amc.2019.124616 M3 - Article VL - 363 JO - Applied Mathematics and Computation JF - Applied Mathematics and Computation SN - 0096-3003 M1 - 124616 ER - TY - JOUR T1 - GSAR T2 - Bioconductor package for Gene Set analysis in R AU - Rahmatallah, Yasir AU - Zybailov, Boris AU - Emmert-Streib, Frank AU - Glazko, Galina PY - 2017/1/24 Y1 - 2017/1/24 N2 - Background: Gene set analysis (in a form of functionally related genes or pathways) has become the method of choice for analyzing omics data in general and gene expression data in particular. There are many statistical methods that either summarize gene-level statistics for a gene set or apply a multivariate statistic that accounts for intergene correlations. Most available methods detect complex departures from the null hypothesis but lack the ability to identify the specific alternative hypothesis that rejects the null. Results: GSAR (Gene Set Analysis in R) is an open-source R/Bioconductor software package for gene set analysis (GSA). It implements self-contained multivariate non-parametric statistical methods testing a complex null hypothesis against specific alternatives, such as differences in mean (shift), variance (scale), or net correlation structure. The package also provides a graphical visualization tool, based on the union of two minimum spanning trees, for correlation networks to examine the change in the correlation structures of a gene set between two conditions and highlight influential genes (hubs). Conclusions: Package GSAR provides a set of multivariate non-parametric statistical methods that test a complex null hypothesis against specific alternatives. The methods in package GSAR are applicable to any type of omics data that can be represented in a matrix format. The package, with detailed instructions and examples, is freely available under the GPL (> = 2) license from the Bioconductor web site. AB - Background: Gene set analysis (in a form of functionally related genes or pathways) has become the method of choice for analyzing omics data in general and gene expression data in particular. There are many statistical methods that either summarize gene-level statistics for a gene set or apply a multivariate statistic that accounts for intergene correlations. Most available methods detect complex departures from the null hypothesis but lack the ability to identify the specific alternative hypothesis that rejects the null. Results: GSAR (Gene Set Analysis in R) is an open-source R/Bioconductor software package for gene set analysis (GSA). It implements self-contained multivariate non-parametric statistical methods testing a complex null hypothesis against specific alternatives, such as differences in mean (shift), variance (scale), or net correlation structure. The package also provides a graphical visualization tool, based on the union of two minimum spanning trees, for correlation networks to examine the change in the correlation structures of a gene set between two conditions and highlight influential genes (hubs). Conclusions: Package GSAR provides a set of multivariate non-parametric statistical methods that test a complex null hypothesis against specific alternatives. The methods in package GSAR are applicable to any type of omics data that can be represented in a matrix format. The package, with detailed instructions and examples, is freely available under the GPL (> = 2) license from the Bioconductor web site. KW - Gene set analysis KW - Kolmogorov-Smirnov KW - Minimum spanning tree KW - Non-parametric KW - Pathways KW - Wald Wolfowitz U2 - 10.1186/s12859-017-1482-6 DO - 10.1186/s12859-017-1482-6 M3 - Article VL - 18 JO - BMC Bioinformatics JF - BMC Bioinformatics SN - 1471-2105 IS - 1 M1 - 61 ER - TY - JOUR T1 - Harnessing the complexity of gene expression data from cancer T2 - From single gene to structural pathway methods AU - Emmert-Streib, Frank AU - Tripathi, Shailesh AU - Matos Simoes, Ricardo D. PY - 2012/12/10 Y1 - 2012/12/10 N2 - : High-dimensional gene expression data provide a rich source of information because they capture the expression level of genes in dynamic states that reflect the biological functioning of a cell. For this reason, such data are suitable to reveal systems related properties inside a cell, e.g., in order to elucidate molecular mechanisms of complex diseases like breast or prostate cancer. However, this is not only strongly dependent on the sample size and the correlation structure of a data set, but also on the statistical hypotheses tested. Many different approaches have been developed over the years to analyze gene expression data to (I) identify changes in single genes, (II) identify changes in gene sets or pathways, and (III) identify changes in the correlation structure in pathways. In this paper, we review statistical methods for all three types of approaches, including subtypes, in the context of cancer data and provide links to software implementations and tools and address also the general problem of multiple hypotheses testing. Further, we provide recommendations for the selection of such analysis methods.Reviewers: This article was reviewed by Arcady Mushegian, Byung-Soo Kim and Joel Bader. AB - : High-dimensional gene expression data provide a rich source of information because they capture the expression level of genes in dynamic states that reflect the biological functioning of a cell. For this reason, such data are suitable to reveal systems related properties inside a cell, e.g., in order to elucidate molecular mechanisms of complex diseases like breast or prostate cancer. However, this is not only strongly dependent on the sample size and the correlation structure of a data set, but also on the statistical hypotheses tested. Many different approaches have been developed over the years to analyze gene expression data to (I) identify changes in single genes, (II) identify changes in gene sets or pathways, and (III) identify changes in the correlation structure in pathways. In this paper, we review statistical methods for all three types of approaches, including subtypes, in the context of cancer data and provide links to software implementations and tools and address also the general problem of multiple hypotheses testing. Further, we provide recommendations for the selection of such analysis methods.Reviewers: This article was reviewed by Arcady Mushegian, Byung-Soo Kim and Joel Bader. KW - Cancer data KW - Cancer genomics KW - Correlation structure KW - Gene expression data KW - Pathway methods KW - Statistical analysis methods UR - http://www.scopus.com/inward/record.url?scp=84872650417&partnerID=8YFLogxK U2 - 10.1186/1745-6150-7-44 DO - 10.1186/1745-6150-7-44 M3 - Article VL - 7 JO - Biology Direct JF - Biology Direct SN - 1745-6150 M1 - 44 ER - TY - JOUR T1 - Hierarchical coordination of periodic genes in the cell cycle of Saccharomyces cerevisiae AU - Emmert-Streib, Frank AU - Dehmer, Matthias PY - 2009/7/20 Y1 - 2009/7/20 N2 - Background: Gene networks are a representation of molecular interactions among genes or products thereof and, hence, are forming causal networks. Despite intense studies during the last years most investigations focus so far on inferential methods to reconstruct gene networks from experimental data or on their structural properties, e.g., degree distributions. Their structural analysis to gain functional insights into organizational principles of, e.g., pathways remains so far under appreciated. Results: In the present paper we analyze cell cycle regulated genes in S. cerevisiae. Our analysis is based on the transcriptional regulatory network, representing causal interactions and not just associations or correlations between genes, and a list of known periodic genes. No further data are used. Partitioning the transcriptional regulatory network according to a graph theoretical property leads to a hierarchy in the network and, hence, in the information flow allowing to identify two groups of periodic genes. This reveals a novel conceptual interpretation of the working mechanism of the cell cycle and the genes regulated by this pathway. Conclusion: Aside from the obtained results for the cell cycle of yeast our approach could be exemplary for the analysis of general pathways by exploiting the rich causal structure of inferred and/or curated gene networks including protein or signaling networks. AB - Background: Gene networks are a representation of molecular interactions among genes or products thereof and, hence, are forming causal networks. Despite intense studies during the last years most investigations focus so far on inferential methods to reconstruct gene networks from experimental data or on their structural properties, e.g., degree distributions. Their structural analysis to gain functional insights into organizational principles of, e.g., pathways remains so far under appreciated. Results: In the present paper we analyze cell cycle regulated genes in S. cerevisiae. Our analysis is based on the transcriptional regulatory network, representing causal interactions and not just associations or correlations between genes, and a list of known periodic genes. No further data are used. Partitioning the transcriptional regulatory network according to a graph theoretical property leads to a hierarchy in the network and, hence, in the information flow allowing to identify two groups of periodic genes. This reveals a novel conceptual interpretation of the working mechanism of the cell cycle and the genes regulated by this pathway. Conclusion: Aside from the obtained results for the cell cycle of yeast our approach could be exemplary for the analysis of general pathways by exploiting the rich causal structure of inferred and/or curated gene networks including protein or signaling networks. UR - http://www.scopus.com/inward/record.url?scp=68949220295&partnerID=8YFLogxK U2 - 10.1186/1752-0509-3-76 DO - 10.1186/1752-0509-3-76 M3 - Article VL - 3 JO - BMC Systems Biology JF - BMC Systems Biology SN - 1752-0509 M1 - 76 ER - TY - JOUR T1 - Homogeneous (α,k)-Polynomial Solutions of the Fractional Riesz System in Hyperbolic Space AU - Orelma, H. AU - Vieira, N. PY - 2017 Y1 - 2017 N2 - In this paper we study the fractional analogous of the Laplace–Beltrami equation and the hyperbolic Riesz system studied previously by H. Leutwiler, in (Formula presented.). In both cases we replace the integer derivatives by Caputo fractional derivatives of order (Formula presented.). We characterize the space of solutions of the fractional Laplace–Beltrami equation, and we calculate its dimension. We establish relations between the solutions of the fractional Laplace–Beltrami equation and the solutions of the hyperbolic fractional Riesz system. Some examples of the polynomial solutions will be presented. Moreover, the behaviour of the obtained results when (Formula presented.) is presented, and a final remark about the consideration of Riemann–Liouville fractional derivatives instead of Caputo fractional derivatives is made. AB - In this paper we study the fractional analogous of the Laplace–Beltrami equation and the hyperbolic Riesz system studied previously by H. Leutwiler, in (Formula presented.). In both cases we replace the integer derivatives by Caputo fractional derivatives of order (Formula presented.). We characterize the space of solutions of the fractional Laplace–Beltrami equation, and we calculate its dimension. We establish relations between the solutions of the fractional Laplace–Beltrami equation and the solutions of the hyperbolic fractional Riesz system. Some examples of the polynomial solutions will be presented. Moreover, the behaviour of the obtained results when (Formula presented.) is presented, and a final remark about the consideration of Riemann–Liouville fractional derivatives instead of Caputo fractional derivatives is made. KW - Caputo fractional derivative KW - Hyperbolic KW - Hyperbolic fractional Riesz system KW - Hypermonogenic functions KW - Laplace–Beltrami fractional differential operator U2 - 10.1007/s11785-017-0666-4 DO - 10.1007/s11785-017-0666-4 M3 - Article VL - 11 SP - 1253 EP - 1267 JO - Complex Analysis and Operator Theory JF - Complex Analysis and Operator Theory SN - 1661-8254 IS - 5 ER - TY - JOUR T1 - Hyperbolic Function Theory in the Skew-Field of Quaternions AU - Eriksson, Sirkka-Liisa AU - Orelma, Heikki N1 - EXT="Eriksson, Sirkka-Liisa" PY - 2019/11/1 Y1 - 2019/11/1 N2 - We are studying hyperbolic function theory in the total skew-field of quaternions. Earlier the theory has been studied for quaternion valued functions depending only on three reduced variables. Our functions are depending on all four coordinates of quaternions. We consider functions, called α-hyperbolic harmonic, that are harmonic with respect to the Riemannian metric dsα2=dx02+dx12+dx22+dx32x3αin the upper half space R+4={(x0,x1,x2,x3)∈R4:x3>0}. If α= 2 , the metric is the hyperbolic metric of the Poincaré upper half-space. Hempfling and Leutwiler started to study this case and noticed that the quaternionic power function xm(m∈Z), is a conjugate gradient of a 2-hyperbolic harmonic function. They researched polynomial solutions. Using fundamental α-hyperbolic harmonic functions, depending only on the hyperbolic distance and x3, we verify a Cauchy type integral formula for conjugate gradient of α-hyperbolic harmonic functions. We also compare these results with the properties of paravector valued α-hypermonogenic in the Clifford algebra Cℓ0,3. AB - We are studying hyperbolic function theory in the total skew-field of quaternions. Earlier the theory has been studied for quaternion valued functions depending only on three reduced variables. Our functions are depending on all four coordinates of quaternions. We consider functions, called α-hyperbolic harmonic, that are harmonic with respect to the Riemannian metric dsα2=dx02+dx12+dx22+dx32x3αin the upper half space R+4={(x0,x1,x2,x3)∈R4:x3>0}. If α= 2 , the metric is the hyperbolic metric of the Poincaré upper half-space. Hempfling and Leutwiler started to study this case and noticed that the quaternionic power function xm(m∈Z), is a conjugate gradient of a 2-hyperbolic harmonic function. They researched polynomial solutions. Using fundamental α-hyperbolic harmonic functions, depending only on the hyperbolic distance and x3, we verify a Cauchy type integral formula for conjugate gradient of α-hyperbolic harmonic functions. We also compare these results with the properties of paravector valued α-hypermonogenic in the Clifford algebra Cℓ0,3. KW - Clifford algebra KW - Hyperbolic Laplace operator KW - Hyperbolic metric KW - Laplace–Beltrami operator KW - Monogenic function KW - Quaternions KW - α-hyperbolic harmonic KW - α-hypermonogenic U2 - 10.1007/s00006-019-1017-5 DO - 10.1007/s00006-019-1017-5 M3 - Article VL - 29 JO - Advances in Applied Clifford Algebras JF - Advances in Applied Clifford Algebras SN - 0188-7009 IS - 5 M1 - 97 ER - TY - JOUR T1 - Hypermonogenic Functions of Two Vector Variables AU - Eriksson, S. L. AU - Orelma, H. AU - Vieira, N. N1 - EXT="Eriksson, S. L." PY - 2018 Y1 - 2018 N2 - In this paper we introduce the modified Dirac operators (Formula presented.) and (Formula presented.), where (Formula presented.) is differentiable function, and (Formula presented.) is the Clifford algebra generated by the basis vectors of (Formula presented.). We look for solutions (Formula presented.) of the system (Formula presented.), where the first and third variables are invariant under rotations. These functions are called (Formula presented.)-hypermonogenic functions. We discuss about axially symmetric functions with respect to the symmetric group (Formula presented.). Some examples of axially symmetric (Formula presented.)-hypermonogenic functions generated by homogeneous functions and hypergeometric functions are presented. AB - In this paper we introduce the modified Dirac operators (Formula presented.) and (Formula presented.), where (Formula presented.) is differentiable function, and (Formula presented.) is the Clifford algebra generated by the basis vectors of (Formula presented.). We look for solutions (Formula presented.) of the system (Formula presented.), where the first and third variables are invariant under rotations. These functions are called (Formula presented.)-hypermonogenic functions. We discuss about axially symmetric functions with respect to the symmetric group (Formula presented.). Some examples of axially symmetric (Formula presented.)-hypermonogenic functions generated by homogeneous functions and hypergeometric functions are presented. KW - Axially symmetric functions KW - Hypermonogenic functions KW - Modified Dirac operator KW - Several vector variables U2 - 10.1007/s11785-017-0728-7 DO - 10.1007/s11785-017-0728-7 M3 - Article VL - 12 SP - 555 EP - 570 JO - Complex Analysis and Operator Theory JF - Complex Analysis and Operator Theory SN - 1661-8254 IS - 2 ER - TY - JOUR T1 - Hypermonogenic Plane Wave Solutions of the Dirac Equation in Superspace AU - Adán, Alí Guzmán AU - Orelma, Heikki AU - Sommen, Frank PY - 2019/9/1 Y1 - 2019/9/1 N2 - In this paper, we obtain Cauchy–Kovalevskaya theorems for hypermonogenic superfunctions depending only on purely bosonic and fermionic vector variables. In addition, we use these results to construct plane wave examples of such functions. AB - In this paper, we obtain Cauchy–Kovalevskaya theorems for hypermonogenic superfunctions depending only on purely bosonic and fermionic vector variables. In addition, we use these results to construct plane wave examples of such functions. KW - Cauchy–Kovalevskaya extension KW - Clifford analysis KW - Hypermonogenic functions KW - Plane waves KW - Superspace U2 - 10.1007/s00006-019-0981-0 DO - 10.1007/s00006-019-0981-0 M3 - Article VL - 29 JO - Advances in Applied Clifford Algebras JF - Advances in Applied Clifford Algebras SN - 0188-7009 IS - 4 M1 - 71 ER - TY - JOUR T1 - Hypermonogenic solutions and plane waves of the Dirac operator in Rp×Rq AU - Guzmán Adán, Alí AU - Orelma, Heikki AU - Sommen, Franciscus PY - 2019/4/1 Y1 - 2019/4/1 N2 - In this paper we first define hypermonogenic solutions of the Dirac operator in Rp×Rq and study some basic properties, e.g., obtaining a Cauchy integral formula in the unit hemisphere. Hypermonogenic solutions form a natural function class in classical Clifford analysis. After that, we define the corresponding hypermonogenic plane wave solutions and deduce explicit methods to compute these functions. AB - In this paper we first define hypermonogenic solutions of the Dirac operator in Rp×Rq and study some basic properties, e.g., obtaining a Cauchy integral formula in the unit hemisphere. Hypermonogenic solutions form a natural function class in classical Clifford analysis. After that, we define the corresponding hypermonogenic plane wave solutions and deduce explicit methods to compute these functions. KW - Cauchy's formula KW - Hypermonogenic solution KW - Plane wave U2 - 10.1016/j.amc.2018.09.058 DO - 10.1016/j.amc.2018.09.058 M3 - Article VL - 346 SP - 1 EP - 14 JO - Applied Mathematics and Computation JF - Applied Mathematics and Computation SN - 0096-3003 ER - TY - JOUR T1 - Improving reliability for classification of metallic objects using a WTMD portal AU - Makkonen, J. AU - Marsh, L. A. AU - Vihonen, J. AU - Järvi, A. AU - Armitage, D. W. AU - Visa, A. AU - Peyton, A. J. PY - 2015/8/26 Y1 - 2015/8/26 N2 - In this paper, a walk-through metal detection (WTMD) portal is used for classification of metallic objects. The classification is based on the inversion of the magnetic polarisability tensor (tensor) of the object. The nature of bias and noise components in the tensor are examined by using real walk-through data, and consequently, a novel classifier is introduced. Furthermore, a novel method for detecting poorly inverted tensors is presented, enabling self-diagnostics for the WTMD portal. Based on the results, the novel methods increase the accuracy of metal object classification and have the potential to improve the reliability of a WTMD system. AB - In this paper, a walk-through metal detection (WTMD) portal is used for classification of metallic objects. The classification is based on the inversion of the magnetic polarisability tensor (tensor) of the object. The nature of bias and noise components in the tensor are examined by using real walk-through data, and consequently, a novel classifier is introduced. Furthermore, a novel method for detecting poorly inverted tensors is presented, enabling self-diagnostics for the WTMD portal. Based on the results, the novel methods increase the accuracy of metal object classification and have the potential to improve the reliability of a WTMD system. KW - bias KW - classification KW - eigenvalues KW - electromagnetic polarisability KW - noise KW - tensor KW - WTMD U2 - 10.1088/0957-0233/26/10/105103 DO - 10.1088/0957-0233/26/10/105103 M3 - Article VL - 26 JO - Measurement Science and Technology JF - Measurement Science and Technology SN - 0957-0233 IS - 10 M1 - 105103 ER - TY - JOUR T1 - Indirect NOx emission monitoring in natural gas fired boilers AU - Korpela, Timo AU - Kumpulainen, Pekka AU - Majanne, Yrjö AU - Häyrinen, Anna AU - Lautala, Pentti PY - 2017/8/1 Y1 - 2017/8/1 N2 - New emission regulations will increase the need for inexpensive NOx emission monitoring solutions also in smaller power plants. The objective in this study is to find easily maintainable and transparent but still valid models to predict NOx emissions in natural gas fired hot water boilers utilizing existing process instrumentation. With a focus on long-term applicability in practical installations, the performance of linear regression is compared in two municipal 43 MW boilers with three widely used nonlinear methods: multilayer perceptron, support vector regression, and fuzzy inference system. The linear models were the most applicable providing the best estimation results (relative error of 1 applications in practise. However, each boiler model should be identified individually. AB - New emission regulations will increase the need for inexpensive NOx emission monitoring solutions also in smaller power plants. The objective in this study is to find easily maintainable and transparent but still valid models to predict NOx emissions in natural gas fired hot water boilers utilizing existing process instrumentation. With a focus on long-term applicability in practical installations, the performance of linear regression is compared in two municipal 43 MW boilers with three widely used nonlinear methods: multilayer perceptron, support vector regression, and fuzzy inference system. The linear models were the most applicable providing the best estimation results (relative error of 1 applications in practise. However, each boiler model should be identified individually. KW - Combustion KW - Estimation KW - Modelling KW - Monitoring KW - Natural gas KW - NO KW - Soft sensor U2 - 10.1016/j.conengprac.2017.04.013 DO - 10.1016/j.conengprac.2017.04.013 M3 - Article VL - 65 SP - 11 EP - 25 JO - Control Engineering Practice JF - Control Engineering Practice SN - 0967-0661 ER - TY - JOUR T1 - Inferring the conservative causal core of gene regulatory networks AU - Altay, Gökmen AU - Emmert-Streib, Frank PY - 2010/9/28 Y1 - 2010/9/28 N2 - Background: Inferring gene regulatory networks from large-scale expression data is an important problem that received much attention in recent years. These networks have the potential to gain insights into causal molecular interactions of biological processes. Hence, from a methodological point of view, reliable estimation methods based on observational data are needed to approach this problem practically.Results: In this paper, we introduce a novel gene regulatory network inference (GRNI) algorithm, called C3NET. We compare C3NET with four well known methods, ARACNE, CLR, MRNET and RN, conducting in-depth numerical ensemble simulations and demonstrate also for biological expression data from E. coli that C3NET performs consistently better than the best known GRNI methods in the literature. In addition, it has also a low computational complexity. Since C3NET is based on estimates of mutual information values in conjunction with a maximization step, our numerical investigations demonstrate that our inference algorithm exploits causal structural information in the data efficiently.Conclusions: For systems biology to succeed in the long run, it is of crucial importance to establish methods that extract large-scale gene networks from high-throughput data that reflect the underlying causal interactions among genes or gene products. Our method can contribute to this endeavor by demonstrating that an inference algorithm with a neat design permits not only a more intuitive and possibly biological interpretation of its working mechanism but can also result in superior results. AB - Background: Inferring gene regulatory networks from large-scale expression data is an important problem that received much attention in recent years. These networks have the potential to gain insights into causal molecular interactions of biological processes. Hence, from a methodological point of view, reliable estimation methods based on observational data are needed to approach this problem practically.Results: In this paper, we introduce a novel gene regulatory network inference (GRNI) algorithm, called C3NET. We compare C3NET with four well known methods, ARACNE, CLR, MRNET and RN, conducting in-depth numerical ensemble simulations and demonstrate also for biological expression data from E. coli that C3NET performs consistently better than the best known GRNI methods in the literature. In addition, it has also a low computational complexity. Since C3NET is based on estimates of mutual information values in conjunction with a maximization step, our numerical investigations demonstrate that our inference algorithm exploits causal structural information in the data efficiently.Conclusions: For systems biology to succeed in the long run, it is of crucial importance to establish methods that extract large-scale gene networks from high-throughput data that reflect the underlying causal interactions among genes or gene products. Our method can contribute to this endeavor by demonstrating that an inference algorithm with a neat design permits not only a more intuitive and possibly biological interpretation of its working mechanism but can also result in superior results. UR - http://www.scopus.com/inward/record.url?scp=77957141016&partnerID=8YFLogxK U2 - 10.1186/1752-0509-4-132 DO - 10.1186/1752-0509-4-132 M3 - Article VL - 4 JO - BMC Systems Biology JF - BMC Systems Biology SN - 1752-0509 M1 - 132 ER - TY - JOUR T1 - Information processing in the transcriptional regulatory network of yeast T2 - Functional robustness AU - Emmert-Streib, Frank AU - Dehmer, Matthias PY - 2009/3/19 Y1 - 2009/3/19 N2 - Background: Gene networks are considered to represent various aspects of molecular biological systems meaningfully because they naturally provide a systems perspective of molecular interactions. In this respect, the functional understanding of the transcriptional regulatory network is considered as key to elucidate the functional organization of an organism. Results: In this paper we study the functional robustness of the transcriptional regulatory network of S. cerevisiae. We model the information processing in the network as a first order Markov chain and study the influence of single gene perturbations on the global, asymptotic communication among genes. Modification in the communication is measured by an information theoretic measure allowing to predict genes that are 'fragile' with respect to single gene knockouts. Our results demonstrate that the predicted set of fragile genes contains a statistically significant enrichment of so called essential genes that are experimentally found to be necessary to ensure vital yeast. Further, a structural analysis of the transcriptional regulatory network reveals that there are significant differences between fragile genes, hub genes and genes with a high betweenness centrality value. Conclusion: Our study does not only demonstrate that a combination of graph theoretical, information theoretical and statistical methods leads to meaningful biological results but also that such methods allow to study information processing in gene networks instead of just their structural properties. AB - Background: Gene networks are considered to represent various aspects of molecular biological systems meaningfully because they naturally provide a systems perspective of molecular interactions. In this respect, the functional understanding of the transcriptional regulatory network is considered as key to elucidate the functional organization of an organism. Results: In this paper we study the functional robustness of the transcriptional regulatory network of S. cerevisiae. We model the information processing in the network as a first order Markov chain and study the influence of single gene perturbations on the global, asymptotic communication among genes. Modification in the communication is measured by an information theoretic measure allowing to predict genes that are 'fragile' with respect to single gene knockouts. Our results demonstrate that the predicted set of fragile genes contains a statistically significant enrichment of so called essential genes that are experimentally found to be necessary to ensure vital yeast. Further, a structural analysis of the transcriptional regulatory network reveals that there are significant differences between fragile genes, hub genes and genes with a high betweenness centrality value. Conclusion: Our study does not only demonstrate that a combination of graph theoretical, information theoretical and statistical methods leads to meaningful biological results but also that such methods allow to study information processing in gene networks instead of just their structural properties. UR - http://www.scopus.com/inward/record.url?scp=65649087188&partnerID=8YFLogxK U2 - 10.1186/1752-0509-3-35 DO - 10.1186/1752-0509-3-35 M3 - Article VL - 3 JO - BMC Systems Biology JF - BMC Systems Biology SN - 1752-0509 M1 - 35 ER - TY - JOUR T1 - Information theoretic measures of UHG graphs with low computational complexity AU - Emmert-Streib, Frank AU - Dehmer, Matthias PY - 2007/7/15 Y1 - 2007/7/15 N2 - We introduce a novel graph class we call universal hierarchical graphs (UHG) whose topology can be found numerously in problems representing, e.g., temporal, spacial or general process structures of systems. For this graph class we show, that we can naturally assign two probability distributions, for nodes and for edges, which lead us directly to the definition of the entropy and joint entropy and, hence, mutual information establishing an information theory for this graph class. Furthermore, we provide some results under which conditions these constraint probability distributions maximize the corresponding entropy. Also, we demonstrate that these entropic measures can be computed efficiently which is a prerequisite for every large scale practical application and show some numerical examples. AB - We introduce a novel graph class we call universal hierarchical graphs (UHG) whose topology can be found numerously in problems representing, e.g., temporal, spacial or general process structures of systems. For this graph class we show, that we can naturally assign two probability distributions, for nodes and for edges, which lead us directly to the definition of the entropy and joint entropy and, hence, mutual information establishing an information theory for this graph class. Furthermore, we provide some results under which conditions these constraint probability distributions maximize the corresponding entropy. Also, we demonstrate that these entropic measures can be computed efficiently which is a prerequisite for every large scale practical application and show some numerical examples. KW - Entropy KW - Graph classes KW - Graph measures KW - Hierarchical graphs KW - Information theory UR - http://www.scopus.com/inward/record.url?scp=34250623666&partnerID=8YFLogxK U2 - 10.1016/j.amc.2007.02.095 DO - 10.1016/j.amc.2007.02.095 M3 - Article VL - 190 SP - 1783 EP - 1794 JO - Applied Mathematics and Computation JF - Applied Mathematics and Computation SN - 0096-3003 IS - 2 ER - TY - JOUR T1 - Integral kernels for k-hypermonogenic functions AU - Vuojamo, Vesa AU - Eriksson, Sirkka-Liisa N1 - EXT="Eriksson, Sirkka-Liisa" PY - 2017 Y1 - 2017 N2 - We consider the modified Cauchy–Riemann operator (Formula presented.) in the universal Clifford algebra (Formula presented.) with the basis (Formula presented.). The null-solutions of this operator are called k-hypermonogenic functions. We calculate the k-hyperbolic harmonic fundamental solutions, i.e. solutions to (Formula presented.), and use these solutions to find k-hypermonogenic kernels for a Cauchy-type integral formula in the upper half-space. AB - We consider the modified Cauchy–Riemann operator (Formula presented.) in the universal Clifford algebra (Formula presented.) with the basis (Formula presented.). The null-solutions of this operator are called k-hypermonogenic functions. We calculate the k-hyperbolic harmonic fundamental solutions, i.e. solutions to (Formula presented.), and use these solutions to find k-hypermonogenic kernels for a Cauchy-type integral formula in the upper half-space. KW - Cauchy integral formula KW - Clifford algebra KW - hyperbolic Laplace–Beltrami KW - k-hyperbolic harmonic KW - k-hypermonogenic U2 - 10.1080/17476933.2016.1250402 DO - 10.1080/17476933.2016.1250402 M3 - Article VL - 62 SP - 1 EP - 12 JO - Complex Variables and Elliptic Equations JF - Complex Variables and Elliptic Equations SN - 1747-6933 IS - 9 ER - TY - JOUR T1 - Interference and SINR in Millimeter Wave and Terahertz Communication Systems With Blocking and Directional Antennas AU - Petrov, Vitaly AU - Komarov, Mikhail AU - Moltchanov, Dmitri AU - Jornet, Josep Miquel AU - Koucheryavy, Yevgeni PY - 2017/3/1 Y1 - 2017/3/1 N2 - The fifth generation wireless systems are expected to rely on a large number of small cells to massively offload traffic from the cellular and even from the wireless local area networks. To enable this functionality, mm-wave (EHF) and Terahertz (THF) bands are being actively explored. These bands are characterized by unique propagation properties compared with microwave systems. As a result, the interference structure in these systems could be principally different to what we observed so far at lower frequencies. In this paper, using the tools of stochastic geometry, we study the systems operating in the EHF/THF bands by explicitly capturing three phenomena inherent for these frequencies: 1) high directivity of the transmit and receive antennas; 2) molecular absorption; and 3) blocking of high-frequency radiation. We also define and compare two different antenna radiation pattern models. The metrics of interest are the mean interference and the signal-to-interference-plus-noise (SINR) ratio at the receiver. Our results reveal that: 1) for the same total emitted energy by a Poisson field of interferers, both the interference and SINR significantly increase when simultaneously both transmit and receive antennas are directive and 2) blocking has a profound impact on the interference and SINR creating much more favorable conditions for communications compared with no blocking case. AB - The fifth generation wireless systems are expected to rely on a large number of small cells to massively offload traffic from the cellular and even from the wireless local area networks. To enable this functionality, mm-wave (EHF) and Terahertz (THF) bands are being actively explored. These bands are characterized by unique propagation properties compared with microwave systems. As a result, the interference structure in these systems could be principally different to what we observed so far at lower frequencies. In this paper, using the tools of stochastic geometry, we study the systems operating in the EHF/THF bands by explicitly capturing three phenomena inherent for these frequencies: 1) high directivity of the transmit and receive antennas; 2) molecular absorption; and 3) blocking of high-frequency radiation. We also define and compare two different antenna radiation pattern models. The metrics of interest are the mean interference and the signal-to-interference-plus-noise (SINR) ratio at the receiver. Our results reveal that: 1) for the same total emitted energy by a Poisson field of interferers, both the interference and SINR significantly increase when simultaneously both transmit and receive antennas are directive and 2) blocking has a profound impact on the interference and SINR creating much more favorable conditions for communications compared with no blocking case. KW - 5G systems KW - blocking KW - directional antennas KW - Interference KW - millimeter waves KW - terahertz band U2 - 10.1109/TWC.2017.2654351 DO - 10.1109/TWC.2017.2654351 M3 - Article VL - 16 SP - 1791 EP - 1808 JO - IEEE Transactions on Wireless Communications JF - IEEE Transactions on Wireless Communications SN - 1536-1276 IS - 3 ER - TY - JOUR T1 - Iterative unsupervised domain adaptation for generalized cell detection from brightfield z-stacks AU - Liimatainen, Kaisa AU - Kananen, Lauri AU - Latonen, Leena AU - Ruusuvuori, Pekka N1 - DUPL=47150514 PY - 2019/2/15 Y1 - 2019/2/15 N2 - Background: Cell counting from cell cultures is required in multiple biological and biomedical research applications. Especially, accurate brightfield-based cell counting methods are needed for cell growth analysis. With deep learning, cells can be detected with high accuracy, but manually annotated training data is required. We propose a method for cell detection that requires annotated training data for one cell line only, and generalizes to other, unseen cell lines. Results: Training a deep learning model with one cell line only can provide accurate detections for similar unseen cell lines (domains). However, if the new domain is very dissimilar from training domain, high precision but lower recall is achieved. Generalization capabilities of the model can be improved with training data transformations, but only to a certain degree. To further improve the detection accuracy of unseen domains, we propose iterative unsupervised domain adaptation method. Predictions of unseen cell lines with high precision enable automatic generation of training data, which is used to train the model together with parts of the previously used annotated training data. We used U-Net-based model, and three consecutive focal planes from brightfield image z-stacks. We trained the model initially with PC-3 cell line, and used LNCaP, BT-474 and 22Rv1 cell lines as target domains for domain adaptation. Highest improvement in accuracy was achieved for 22Rv1 cells. F 1 -score after supervised training was only 0.65, but after unsupervised domain adaptation we achieved a score of 0.84. Mean accuracy for target domains was 0.87, with mean improvement of 16 percent. Conclusions: With our method for generalized cell detection, we can train a model that accurately detects different cell lines from brightfield images. A new cell line can be introduced to the model without a single manual annotation, and after iterative domain adaptation the model is ready to detect these cells with high accuracy. AB - Background: Cell counting from cell cultures is required in multiple biological and biomedical research applications. Especially, accurate brightfield-based cell counting methods are needed for cell growth analysis. With deep learning, cells can be detected with high accuracy, but manually annotated training data is required. We propose a method for cell detection that requires annotated training data for one cell line only, and generalizes to other, unseen cell lines. Results: Training a deep learning model with one cell line only can provide accurate detections for similar unseen cell lines (domains). However, if the new domain is very dissimilar from training domain, high precision but lower recall is achieved. Generalization capabilities of the model can be improved with training data transformations, but only to a certain degree. To further improve the detection accuracy of unseen domains, we propose iterative unsupervised domain adaptation method. Predictions of unseen cell lines with high precision enable automatic generation of training data, which is used to train the model together with parts of the previously used annotated training data. We used U-Net-based model, and three consecutive focal planes from brightfield image z-stacks. We trained the model initially with PC-3 cell line, and used LNCaP, BT-474 and 22Rv1 cell lines as target domains for domain adaptation. Highest improvement in accuracy was achieved for 22Rv1 cells. F 1 -score after supervised training was only 0.65, but after unsupervised domain adaptation we achieved a score of 0.84. Mean accuracy for target domains was 0.87, with mean improvement of 16 percent. Conclusions: With our method for generalized cell detection, we can train a model that accurately detects different cell lines from brightfield images. A new cell line can be introduced to the model without a single manual annotation, and after iterative domain adaptation the model is ready to detect these cells with high accuracy. KW - Brightfield KW - Cell detection KW - Deep learning KW - Semi-supervised learning KW - Unsupervised domain adaptation U2 - 10.1186/s12859-019-2605-z DO - 10.1186/s12859-019-2605-z M3 - Article VL - 20 JO - BMC Bioinformatics JF - BMC Bioinformatics SN - 1471-2105 IS - 1 M1 - 80 ER - TY - JOUR T1 - Magnetomechanical coupled FE simulations of rotating electrical machines AU - Belahcen, Anouar AU - Fonteyn, Katarzyna AU - Kouhia, Reijo AU - Rasilo, Paavo AU - Arkkio, Antero N1 - Contribution: organisation=ede,FACT1=1

Portfolio EDEND: 2013-10-29

Publisher name: Emerald Group Publishing PY - 2013 Y1 - 2013 N2 - Purpose - The purpose is to implement and compare different approaches for modelling the magnetostriction phenomenon in iron sheet used in rotating electrical machines. Design/methodology/approach - In the force-based approach, the magnetostriction is modelled as a set of equivalent forces, which produce the same deformation of the material as the magnetostriction strains. These forces among other magnetic forces are computed from the solution of the finite element (FE) field computation and used as loads for the displacement-based mechanical FE analysis. In the strain-based approach, the equivalent magnetostrictive forces are not needed and an energy-based model is used to define magnetomechanically coupled constitutive equations of the material. These equations are then space-discretised and solved with the FE method for the magnetic field and the displacements. Findings - It is found that the equivalent forces method can reproduce the displacements and strains of the structure but it results in erroneous stress states. The energy-based method has the ability to reproduce both the stress and strains correctly; thus enabling the analysis of stress-dependent quantities such as the iron losses and the magnetostriction itself. Research limitations/implications - The investigated methods do not account for hysteresis and other dynamic effects. They also require long computation times. With the available computing resources, the computation time does not present any problem as far as they are not used in everyday design procedures but the modelling of dynamic effect needs to be elaborated. Originality/value - The developed and implemented methods are verified with measurements and simulation experiments and applied to as complex structure as an electrical machine. The problems related to the different approaches are investigated and explained through simulations. © Emerald Group Publishing Limited. AB - Purpose - The purpose is to implement and compare different approaches for modelling the magnetostriction phenomenon in iron sheet used in rotating electrical machines. Design/methodology/approach - In the force-based approach, the magnetostriction is modelled as a set of equivalent forces, which produce the same deformation of the material as the magnetostriction strains. These forces among other magnetic forces are computed from the solution of the finite element (FE) field computation and used as loads for the displacement-based mechanical FE analysis. In the strain-based approach, the equivalent magnetostrictive forces are not needed and an energy-based model is used to define magnetomechanically coupled constitutive equations of the material. These equations are then space-discretised and solved with the FE method for the magnetic field and the displacements. Findings - It is found that the equivalent forces method can reproduce the displacements and strains of the structure but it results in erroneous stress states. The energy-based method has the ability to reproduce both the stress and strains correctly; thus enabling the analysis of stress-dependent quantities such as the iron losses and the magnetostriction itself. Research limitations/implications - The investigated methods do not account for hysteresis and other dynamic effects. They also require long computation times. With the available computing resources, the computation time does not present any problem as far as they are not used in everyday design procedures but the modelling of dynamic effect needs to be elaborated. Originality/value - The developed and implemented methods are verified with measurements and simulation experiments and applied to as complex structure as an electrical machine. The problems related to the different approaches are investigated and explained through simulations. © Emerald Group Publishing Limited. KW - Coupled systems KW - Electrical equipment KW - Finite element simulation KW - Iron KW - Iron losses KW - Magnetoelasticity KW - Stress KW - Stress analysis UR - http://www.scopus.com/inward/record.url?scp=84884134763&partnerID=8YFLogxK U2 - 10.1108/COMPEL-04-2013-0109 DO - 10.1108/COMPEL-04-2013-0109 M3 - Article VL - 32 SP - 1484 EP - 1499 JO - COMPEL: The International Journal for Computation and Mathematics in Electrical and Electronic Engineering JF - COMPEL: The International Journal for Computation and Mathematics in Electrical and Electronic Engineering SN - 0332-1649 IS - 5 M1 - 17095978 ER - TY - JOUR T1 - Meeting a deadline T2 - shortest paths on stochastic directed acyclic graphs with information gathering AU - Lauri, Mikko AU - Ropponen, Aino AU - Ritala, Risto PY - 2017/4 Y1 - 2017/4 N2 - We consider the problem of an agent traversing a directed graph with the objective of maximizing the probability of reaching a goal node before a given deadline. Only the probability of the travel times of edges is known to the agent. The agent must balance between traversal actions towards the goal, and delays due to actions improving information about graph edge travel times. We describe the relationship of the problem to the more general partially observable Markov decision process. Further, we show that if edge travel times are independent and the underlying directed graph is acyclic, a closed loop solution can be computed. The solution specifies whether to execute a traversal or information-gathering action as a function of the current node, the time remaining until the deadline, and the information about edge travel times. We present results from two case studies, quantifying the usefulness of information-gathering as opposed to applying only traversal actions. AB - We consider the problem of an agent traversing a directed graph with the objective of maximizing the probability of reaching a goal node before a given deadline. Only the probability of the travel times of edges is known to the agent. The agent must balance between traversal actions towards the goal, and delays due to actions improving information about graph edge travel times. We describe the relationship of the problem to the more general partially observable Markov decision process. Further, we show that if edge travel times are independent and the underlying directed graph is acyclic, a closed loop solution can be computed. The solution specifies whether to execute a traversal or information-gathering action as a function of the current node, the time remaining until the deadline, and the information about edge travel times. We present results from two case studies, quantifying the usefulness of information-gathering as opposed to applying only traversal actions. KW - Applied probability KW - Decision processes KW - Dynamic programming KW - Markov processes KW - Transportation U2 - 10.1007/s10472-016-9527-5 DO - 10.1007/s10472-016-9527-5 M3 - Article VL - 79 SP - 337 EP - 370 JO - Annals of Mathematics and Artificial Intelligence JF - Annals of Mathematics and Artificial Intelligence SN - 1012-2443 IS - 4 ER - TY - JOUR T1 - Modeling carbon dioxide transport in PDMS-based microfluidic cell culture devices AU - Mäki, A. J. AU - Peltokangas, M. AU - Kreutzer, J. AU - Auvinen, S. AU - Kallio, P. N1 - ORG=ase,0.9 ORG=mol,0.1 PY - 2015/12/1 Y1 - 2015/12/1 N2 - Maintaining a proper pH level is crucial for successful cell culturing. Mammalian cells are commonly cultured in incubators, where the cell culture medium is saturated with a mixture of air and 5% carbon dioxide (CO2). Therefore, to keep cell culture medium pH in an acceptable level outside these incubators, a suitable CO2 concentration must be dissolved in the medium. However, it can be very difficult to control and measure precisely local concentration levels. Furthermore, possible undesired concentration gradients generated during long-term cell culturing are almost impossible to detect. Therefore, we have developed a computational model to estimate CO2 transport in silicone-based microfluidic devices. An extensive set of experiments was used to validate the finite element model. The model parameters were obtained using suitable measurement set-ups and the model was validated using a fully functional cell cultivation device. The predictions obtained by the simulations show very good responses to experiments. It is shown in this paper how the model helps to understand the dynamics of CO2 transport in silicone-based cell culturing devices possessing different geometries, thus providing cost-effective means for studying different device designs under a variety of experimental conditions without the need of actual testing. Finally, based on the results from the computational model, an alternative strategy for feeding CO2 is proposed to accelerate the system performance such that a faster and more uniform CO2 concentration response is achieved in the area of interest. AB - Maintaining a proper pH level is crucial for successful cell culturing. Mammalian cells are commonly cultured in incubators, where the cell culture medium is saturated with a mixture of air and 5% carbon dioxide (CO2). Therefore, to keep cell culture medium pH in an acceptable level outside these incubators, a suitable CO2 concentration must be dissolved in the medium. However, it can be very difficult to control and measure precisely local concentration levels. Furthermore, possible undesired concentration gradients generated during long-term cell culturing are almost impossible to detect. Therefore, we have developed a computational model to estimate CO2 transport in silicone-based microfluidic devices. An extensive set of experiments was used to validate the finite element model. The model parameters were obtained using suitable measurement set-ups and the model was validated using a fully functional cell cultivation device. The predictions obtained by the simulations show very good responses to experiments. It is shown in this paper how the model helps to understand the dynamics of CO2 transport in silicone-based cell culturing devices possessing different geometries, thus providing cost-effective means for studying different device designs under a variety of experimental conditions without the need of actual testing. Finally, based on the results from the computational model, an alternative strategy for feeding CO2 is proposed to accelerate the system performance such that a faster and more uniform CO2 concentration response is achieved in the area of interest. KW - Carbon dioxide KW - Finite element method KW - Mass transport KW - Microfluidics cell culturing KW - Numerical simulation KW - pH U2 - 10.1016/j.ces.2015.06.065 DO - 10.1016/j.ces.2015.06.065 M3 - Article VL - 137 SP - 515 EP - 524 JO - Chemical Engineering Science JF - Chemical Engineering Science SN - 0009-2509 ER - TY - JOUR T1 - Modeling probability densities with sums of exponentials via polynomial approximation AU - Dumitrescu, Bogdan AU - Şicleru, Bogdan C. AU - Avram, Florin PY - 2016 Y1 - 2016 N2 - Abstract We propose a method for optimization with semi-infinite constraints that involve a linear combination of functions, focusing on shape-constrained optimization with exponential functions. Each function is lower and upper bounded on sub-intervals by low-degree polynomials. Thus, the constraints can be approximated with polynomial inequalities that can be implemented with linear matrix inequalities. Convexity is preserved, but the problem has now a finite number of constraints. We show how to take advantage of the properties of the exponential function in order to build quickly accurate approximations. The problem used for illustration is the least-squares fitting of a positive sum of exponentials to an empirical probability density function. When the exponents are given, the problem is convex, but we also give a procedure for optimizing the exponents. Several examples show that the method is flexible, accurate and gives better results than other methods for the investigated problems. AB - Abstract We propose a method for optimization with semi-infinite constraints that involve a linear combination of functions, focusing on shape-constrained optimization with exponential functions. Each function is lower and upper bounded on sub-intervals by low-degree polynomials. Thus, the constraints can be approximated with polynomial inequalities that can be implemented with linear matrix inequalities. Convexity is preserved, but the problem has now a finite number of constraints. We show how to take advantage of the properties of the exponential function in order to build quickly accurate approximations. The problem used for illustration is the least-squares fitting of a positive sum of exponentials to an empirical probability density function. When the exponents are given, the problem is convex, but we also give a procedure for optimizing the exponents. Several examples show that the method is flexible, accurate and gives better results than other methods for the investigated problems. KW - Density fitting KW - Optimization KW - Polynomial approximation KW - Semi-infinite programming KW - Sum of exponentials U2 - 10.1016/j.cam.2015.07.032 DO - 10.1016/j.cam.2015.07.032 M3 - Article VL - 292 SP - 513 EP - 525 JO - Journal of Computational and Applied Mathematics JF - Journal of Computational and Applied Mathematics SN - 0377-0427 ER - TY - JOUR T1 - Modeling Transmit Power Reduction for a Typical Cell with Licensed Shared Access Capabilities AU - Mokrov, Evgeny AU - Ponomarenko-Timofeev, Aleksei AU - Gudkova, Irina AU - Masek, Pavel AU - Hosek, Jiri AU - Andreev, Sergey AU - Koucheryavy, Yevgeni AU - Gaidamaka, Yuliya PY - 2018/6 Y1 - 2018/6 N2 - Currently, there is a strong demand to augment capacity of mobile cellular deployments as dictated by advanced bandwidth-hungry applications and services. Network densification and the use of millimeter-wave frequencies develop as the mainstream solutions in fifth-generation (5G) systems, but both suffer from increased complexity and cost. A viable alternative is based on the Licensed Shared Access (LSA) framework that manages spectrum sharing between a limited number of participants. However, interference produced by the current user of the spectrum (the mobile operator) toward its owner (the incumbent) has to be carefully controlled and a number of LSA policies thus emerge. A feasible policy is to reduce the transmit power of the user equipment served by the mobile operator on the LSA bands whenever requested by the incumbent. This work contributes a novel mathematical analysis of the said LSA policy in a challenging scenario that features a highly-dynamic incumbent (the airport), as well as verifies the findings with more detailed system-level simulations. The proposed results constitute a tight estimate on the practical system operation. AB - Currently, there is a strong demand to augment capacity of mobile cellular deployments as dictated by advanced bandwidth-hungry applications and services. Network densification and the use of millimeter-wave frequencies develop as the mainstream solutions in fifth-generation (5G) systems, but both suffer from increased complexity and cost. A viable alternative is based on the Licensed Shared Access (LSA) framework that manages spectrum sharing between a limited number of participants. However, interference produced by the current user of the spectrum (the mobile operator) toward its owner (the incumbent) has to be carefully controlled and a number of LSA policies thus emerge. A feasible policy is to reduce the transmit power of the user equipment served by the mobile operator on the LSA bands whenever requested by the incumbent. This work contributes a novel mathematical analysis of the said LSA policy in a challenging scenario that features a highly-dynamic incumbent (the airport), as well as verifies the findings with more detailed system-level simulations. The proposed results constitute a tight estimate on the practical system operation. KW - Airplanes KW - Airports KW - Atmospheric modeling KW - Interference KW - Mobile communication KW - Telemetry U2 - 10.1109/TVT.2018.2799141 DO - 10.1109/TVT.2018.2799141 M3 - Article VL - 67 SP - 5505 EP - 5509 JO - IEEE Transactions on Vehicular Technology JF - IEEE Transactions on Vehicular Technology SN - 0018-9545 IS - 6 ER - TY - JOUR T1 - Multiresolution analysis for compactly supported interpolating tensor product wavelets AU - Höynälänmaa, Tommi PY - 2015/3/6 Y1 - 2015/3/6 N2 - We construct multidimensional interpolating tensor product multiresolution analyses (MRA's) of the function spaces C0(Rn,K), K = R or K = C, consisting of real or complex valued functions on Rn vanishing at infinity and the function spaces Cu(Rn,K) consisting of bounded and uniformly continuous functions on Rn. We also construct an interpolating dual MRA for both of these spaces. The theory of the tensor products of Banach spaces is used. We generalize the Besov space norm equivalence from the one-dimensional case to our n-dimensional construction. AB - We construct multidimensional interpolating tensor product multiresolution analyses (MRA's) of the function spaces C0(Rn,K), K = R or K = C, consisting of real or complex valued functions on Rn vanishing at infinity and the function spaces Cu(Rn,K) consisting of bounded and uniformly continuous functions on Rn. We also construct an interpolating dual MRA for both of these spaces. The theory of the tensor products of Banach spaces is used. We generalize the Besov space norm equivalence from the one-dimensional case to our n-dimensional construction. KW - Besov space KW - injective tensor norm KW - Interpolating wavelets KW - multiresolution analysis KW - multivariate wavelets KW - projective tensor norm KW - tensor Product UR - http://www.scopus.com/inward/record.url?scp=84928923864&partnerID=8YFLogxK U2 - 10.1142/S0219691315500101 DO - 10.1142/S0219691315500101 M3 - Article VL - 13 JO - International Journal of Wavelets Multiresolution and Information ProcessIng JF - International Journal of Wavelets Multiresolution and Information ProcessIng SN - 0219-6913 IS - 2 M1 - 1550010 ER - TY - JOUR T1 - Nonlocality-Reinforced Convolutional Neural Networks for Image Denoising AU - Cruz, Cristovao AU - Foi, Alessandro AU - Katkovnik, Vladimir AU - Egiazarian, Karen PY - 2018/8/1 Y1 - 2018/8/1 N2 - We introduce a paradigm for nonlocal sparsity reinforced deep convolutional neural network denoising. It is a combination of a local multiscale denoising by a convolutional neural network (CNN) based denoiser and a nonlocal denoising based on a nonlocal filter (NLF), exploiting the mutual similarities between groups of patches. CNN models are leveraged with noise levels that progressively decrease at every iteration of our framework, while their output is regularized by a nonlocal prior implicit within the NLF. Unlike complicated neural networks that embed the nonlocality prior within the layers of the network, our framework is modular, and it uses standard pretrained CNNs together with standard nonlocal filters. An instance of the proposed framework, called NN3D, is evaluated over large grayscale image datasets showing state-of-the-art performance. AB - We introduce a paradigm for nonlocal sparsity reinforced deep convolutional neural network denoising. It is a combination of a local multiscale denoising by a convolutional neural network (CNN) based denoiser and a nonlocal denoising based on a nonlocal filter (NLF), exploiting the mutual similarities between groups of patches. CNN models are leveraged with noise levels that progressively decrease at every iteration of our framework, while their output is regularized by a nonlocal prior implicit within the NLF. Unlike complicated neural networks that embed the nonlocality prior within the layers of the network, our framework is modular, and it uses standard pretrained CNNs together with standard nonlocal filters. An instance of the proposed framework, called NN3D, is evaluated over large grayscale image datasets showing state-of-the-art performance. KW - BM3D KW - convolutional neural network KW - image denoising KW - nonlocal filters U2 - 10.1109/LSP.2018.2850222 DO - 10.1109/LSP.2018.2850222 M3 - Article VL - 25 SP - 1216 EP - 1220 JO - IEEE Signal Processing Letters JF - IEEE Signal Processing Letters SN - 1070-9908 IS - 8 ER - TY - JOUR T1 - On derivatives of hypergeometric functions and classical polynomials with respect to parameters AU - Sofotasios, P. C. AU - Brychkov, Yu A. PY - 2018/11/2 Y1 - 2018/11/2 N2 - Closed expressions are obtained for derivatives of symbolic order with respect to parameters for the hypergeometric functions, Laguerre, Gegenbauer, Jacobi and some other polynomial. AB - Closed expressions are obtained for derivatives of symbolic order with respect to parameters for the hypergeometric functions, Laguerre, Gegenbauer, Jacobi and some other polynomial. KW - 33C20 KW - 33C45 KW - Bessel polynomial KW - C33 KW - Charlier polynomial KW - continuous Hahn polynomial KW - differentiation KW - Gegenbauer polynomial KW - Hahn polynomial KW - hypergeometric functions KW - Jacobi polynomial KW - Krawtchouk polynomial KW - Laguerre polynomial KW - Legendre function KW - Meixner polynomial KW - Special functions U2 - 10.1080/10652469.2018.1504042 DO - 10.1080/10652469.2018.1504042 M3 - Article VL - 29 SP - 852 EP - 865 JO - Integral Transforms and Special Functions JF - Integral Transforms and Special Functions SN - 1065-2469 IS - 11 ER - TY - JOUR T1 - On efficient network similarity measures AU - Dehmer, Matthias AU - Chen, Zengqiang AU - Shi, Yongtang AU - Zhang, Y. AU - Tripathi, Shailesh AU - Ghorbani, Modjtaba AU - Mowshowitz, Abbe AU - Emmert-Streib, F. PY - 2019/12/1 Y1 - 2019/12/1 N2 - This paper presents novel graph similarity measures which can be applied to simple directed and undirected networks. To define the graph similarity measures, we first map graphs to real numbers by utilizing structural graph measures. Then, we define measures of similarity between real numbers and prove that they can be used as proxies for graph similarity. Numerical results are derived to show the domain coverage of these measures as well as their clustering ability. The latter relates to the efficient grouping of graphs according to certain structural properties. Our numerical results are sensitive to these properties and offer insights useful for designing effective graph similarity measures. AB - This paper presents novel graph similarity measures which can be applied to simple directed and undirected networks. To define the graph similarity measures, we first map graphs to real numbers by utilizing structural graph measures. Then, we define measures of similarity between real numbers and prove that they can be used as proxies for graph similarity. Numerical results are derived to show the domain coverage of these measures as well as their clustering ability. The latter relates to the efficient grouping of graphs according to certain structural properties. Our numerical results are sensitive to these properties and offer insights useful for designing effective graph similarity measures. KW - Distance measures KW - Graphs KW - Inequalities KW - Networks KW - Similarity measures U2 - 10.1016/j.amc.2019.06.035 DO - 10.1016/j.amc.2019.06.035 M3 - Article VL - 362 JO - Applied Mathematics and Computation JF - Applied Mathematics and Computation SN - 0096-3003 M1 - 124521 ER - TY - JOUR T1 - On k-Hypermonogenic Functions and Their Mean Value Properties AU - Eriksson, Sirkka-Liisa AU - Orelma, Heikki PY - 2016 Y1 - 2016 N2 - We study a hyperbolic version of holomorphic functions to higher dimensions. In this frame work, a generalization of holomorphic functions are called (Formula presented.)-hypermonogenic functions. These functions are depending on several real variables and their values are in a Clifford algebra. They are defined in terms of hyperbolic Dirac operators. They are connected to harmonic functions with respect to the Riemannian metric (Formula presented.) in the same way as the usual harmonic function to holomorphic functions. We present the mean value property for (Formula presented.)-hypermonogenic functions and related results. Earlier the mean value properties has been proved for hypermonogenic functions. The key tools are the invariance properties of the hyperbolic metric. AB - We study a hyperbolic version of holomorphic functions to higher dimensions. In this frame work, a generalization of holomorphic functions are called (Formula presented.)-hypermonogenic functions. These functions are depending on several real variables and their values are in a Clifford algebra. They are defined in terms of hyperbolic Dirac operators. They are connected to harmonic functions with respect to the Riemannian metric (Formula presented.) in the same way as the usual harmonic function to holomorphic functions. We present the mean value property for (Formula presented.)-hypermonogenic functions and related results. Earlier the mean value properties has been proved for hypermonogenic functions. The key tools are the invariance properties of the hyperbolic metric. KW - Dirac operator KW - Hyperbolic metric KW - Hypermonogenic KW - Monogenic U2 - 10.1007/s11785-015-0445-z DO - 10.1007/s11785-015-0445-z M3 - Article VL - 10 SP - 311 EP - 325 JO - Complex Analysis and Operator Theory JF - Complex Analysis and Operator Theory SN - 1661-8254 IS - 2 ER - TY - JOUR T1 - Online Spectrogram Inversion for Low-Latency Audio Source Separation AU - Magron, Paul AU - Virtanen, Tuomas PY - 2020 Y1 - 2020 N2 - Audio source separation is usually achieved by estimating the short-time Fourier transform (STFT) magnitude of each source, and then applying a spectrogram inversion algorithm to retrieve time-domain signals. In particular, the multiple input spectrogram inversion (MISI) algorithm has been exploited successfully in several recent works. However, this algorithm suffers from two drawbacks, which we address in this letter. First, it has originally been introduced in a heuristic fashion: we propose here a rigorous optimization framework in which MISI is derived, thus proving the convergence of this algorithm. Besides, while MISI operates offline, we propose here an online version of MISI called oMISI, which is suitable for low-latency source separation, an important requirement for e.g., hearing aids applications. oMISI also allows one to use alternative phase initialization schemes exploiting the temporal structure of audio signals. Experiments conducted on a speech separation task show that oMISI performs as well as its offline counterpart, thus demonstrating its potential for real-time source separation. AB - Audio source separation is usually achieved by estimating the short-time Fourier transform (STFT) magnitude of each source, and then applying a spectrogram inversion algorithm to retrieve time-domain signals. In particular, the multiple input spectrogram inversion (MISI) algorithm has been exploited successfully in several recent works. However, this algorithm suffers from two drawbacks, which we address in this letter. First, it has originally been introduced in a heuristic fashion: we propose here a rigorous optimization framework in which MISI is derived, thus proving the convergence of this algorithm. Besides, while MISI operates offline, we propose here an online version of MISI called oMISI, which is suitable for low-latency source separation, an important requirement for e.g., hearing aids applications. oMISI also allows one to use alternative phase initialization schemes exploiting the temporal structure of audio signals. Experiments conducted on a speech separation task show that oMISI performs as well as its offline counterpart, thus demonstrating its potential for real-time source separation. KW - Audio source separation KW - low-latency KW - online spectrogram inversion KW - phase recovery KW - sinusoidal modeling U2 - 10.1109/LSP.2020.2970310 DO - 10.1109/LSP.2020.2970310 M3 - Article VL - 27 SP - 306 EP - 310 JO - IEEE Signal Processing Letters JF - IEEE Signal Processing Letters SN - 1070-9908 M1 - 8974192 ER - TY - JOUR T1 - On the complexity of restoring corrupted colorings AU - De Biasi, Marzio AU - Lauri, Juho PY - 2019/5 Y1 - 2019/5 N2 - In the r-Fix problem, we are given a graph G, a (non-proper) vertex-coloring c: V(G) → [r] , and a positive integer k. The goal is to decide whether a proper r-coloring c′ is obtainable from c by recoloring at most k vertices of G. Recently, Junosza-Szaniawski et al. (in: SOFSEM 2015: theory and practice of computer science, Springer, Berlin, 2015) asked whether the problem has a polynomial kernel parameterized by the number of recolorings k. In a full version of the manuscript, the authors together with Garnero and Montealegre, answered the question in the negative: for every r≥ 3 , the problem r-Fix does not admit a polynomial kernel unless [InlineEquation not available: see fulltext.]. Independently of their work, we give an alternative proof of the theorem. Furthermore, we study the complexity of r-Swap, where the only difference from r-Fix is that instead of k recolorings we have a budget of k color swaps. We show that for every r≥ 3 , the problem r-Swap is [InlineEquation not available: see fulltext.]-hard whereas r-Fix is known to be FPT. Moreover, when r is part of the input, we observe both Fix and Swap are [InlineEquation not available: see fulltext.]-hard parameterized by the treewidth of the input graph. We also study promise variants of the problems, where we are guaranteed that a proper r-coloring c′ is indeed obtainable from c by some finite number of swaps. For instance, we prove that for r= 3 , the problems r-Fix-Promise and r-Swap-Promise are [InlineEquation not available: see fulltext.]-hard for planar graphs. As a consequence of our reduction, the problems cannot be solved in 2o(n) time unless the Exponential Time Hypothesis fails. AB - In the r-Fix problem, we are given a graph G, a (non-proper) vertex-coloring c: V(G) → [r] , and a positive integer k. The goal is to decide whether a proper r-coloring c′ is obtainable from c by recoloring at most k vertices of G. Recently, Junosza-Szaniawski et al. (in: SOFSEM 2015: theory and practice of computer science, Springer, Berlin, 2015) asked whether the problem has a polynomial kernel parameterized by the number of recolorings k. In a full version of the manuscript, the authors together with Garnero and Montealegre, answered the question in the negative: for every r≥ 3 , the problem r-Fix does not admit a polynomial kernel unless [InlineEquation not available: see fulltext.]. Independently of their work, we give an alternative proof of the theorem. Furthermore, we study the complexity of r-Swap, where the only difference from r-Fix is that instead of k recolorings we have a budget of k color swaps. We show that for every r≥ 3 , the problem r-Swap is [InlineEquation not available: see fulltext.]-hard whereas r-Fix is known to be FPT. Moreover, when r is part of the input, we observe both Fix and Swap are [InlineEquation not available: see fulltext.]-hard parameterized by the treewidth of the input graph. We also study promise variants of the problems, where we are guaranteed that a proper r-coloring c′ is indeed obtainable from c by some finite number of swaps. For instance, we prove that for r= 3 , the problems r-Fix-Promise and r-Swap-Promise are [InlineEquation not available: see fulltext.]-hard for planar graphs. As a consequence of our reduction, the problems cannot be solved in 2o(n) time unless the Exponential Time Hypothesis fails. KW - Combinatorial reconfiguration KW - Computational complexity KW - Graph coloring KW - Local search KW - Parameterized complexity U2 - 10.1007/s10878-018-0342-2 DO - 10.1007/s10878-018-0342-2 M3 - Article VL - 37 SP - 1150 EP - 1169 JO - Journal of Combinatorial Optimization JF - Journal of Combinatorial Optimization SN - 1382-6905 IS - 4 ER - TY - JOUR T1 - On the Degree of Multi-Connectivity in 5G Millimeter-Wave Cellular Urban Deployments AU - Gapeyenko, Margarita AU - Petrov, Vitaly AU - Moltchanov, Dmitri AU - Akdeniz, Mustafa Riza AU - Andreev, Sergey AU - Himayat, Nageen AU - Koucheryavy, Yevgeni PY - 2019/2 Y1 - 2019/2 N2 - Outage event caused by dynamic link blockage at millimeter-wave (mmWave) frequencies is a challenging problem for cell-edge users. To address it, 3GPP is currently working on multi-connectivity mechanisms that allow a user to remain connected to several mmWave access points simultaneously as well as switch between them in case its active connection drops. However, the actual number of such simultaneous links -- named the degree of multi-connectivity -- to reach the desired trade-off between the system design simplicity and the outage probability levels remains an open research question. In this work, we characterize the outage probability and spectral efficiency associated with different degrees of multi-connectivity in a typical 5G urban scenario, where the line-of-sight propagation path can be blocked by buildings as well as humans. These results demonstrate that the degrees of multi-connectivity of up to 4 offer higher relative gains. At the same time, performance improvements brought by the multi-connectivity degrees of 5 and higher are much lower. Our analytical framework can be further employed for the performance analysis of multi-connectivity-capable mmWave systems across their different deployment configurations. AB - Outage event caused by dynamic link blockage at millimeter-wave (mmWave) frequencies is a challenging problem for cell-edge users. To address it, 3GPP is currently working on multi-connectivity mechanisms that allow a user to remain connected to several mmWave access points simultaneously as well as switch between them in case its active connection drops. However, the actual number of such simultaneous links -- named the degree of multi-connectivity -- to reach the desired trade-off between the system design simplicity and the outage probability levels remains an open research question. In this work, we characterize the outage probability and spectral efficiency associated with different degrees of multi-connectivity in a typical 5G urban scenario, where the line-of-sight propagation path can be blocked by buildings as well as humans. These results demonstrate that the degrees of multi-connectivity of up to 4 offer higher relative gains. At the same time, performance improvements brought by the multi-connectivity degrees of 5 and higher are much lower. Our analytical framework can be further employed for the performance analysis of multi-connectivity-capable mmWave systems across their different deployment configurations. KW - dynamic human body blockage KW - macro diversity KW - mmWave systems KW - multi-connectivity KW - outage probability U2 - 10.1109/TVT.2018.2887343 DO - 10.1109/TVT.2018.2887343 M3 - Article VL - 68 SP - 1973 EP - 1978 JO - IEEE Transactions on Vehicular Technology JF - IEEE Transactions on Vehicular Technology SN - 0018-9545 IS - 2 ER - TY - JOUR T1 - On the effect of deformation twinning and microstructure to strain hardening of high manganese austenitic steel 3D microstructure aggregates at large strains AU - Lindroos, Matti AU - Laukkanen, Anssi AU - Cailletaud, Georges AU - Kuokkala, Veli-Tapani N1 - EXT="Lindroos, Matti" PY - 2017 Y1 - 2017 N2 - The hardening and deformation characteristics of Hadfield microstructure are studied to investigate the effect of microstucture to the material behavior. A crystal plasticity model including dislocation slip and deformation twinning is employed. The role of deformation twinning to the overall strain hardening of the material is evaluated for two different grain structures. Large compressive strains are applied on 3D microstructural aggregates representing the uniform and non-uniform grain structures of Hadfield steels. The grain structure has an effect on the strain hardening rate as well as on the overall hardening capability of the microstructure. A major reason causing the difference in strain hardening arises from the different twin volume fraction evolution influenced by intra-grain and inter-grain interactions. A mixture of large and small grains was found to be more favorable for twinning and thus resulting in a greater hardening capability than uniform grain size. AB - The hardening and deformation characteristics of Hadfield microstructure are studied to investigate the effect of microstucture to the material behavior. A crystal plasticity model including dislocation slip and deformation twinning is employed. The role of deformation twinning to the overall strain hardening of the material is evaluated for two different grain structures. Large compressive strains are applied on 3D microstructural aggregates representing the uniform and non-uniform grain structures of Hadfield steels. The grain structure has an effect on the strain hardening rate as well as on the overall hardening capability of the microstructure. A major reason causing the difference in strain hardening arises from the different twin volume fraction evolution influenced by intra-grain and inter-grain interactions. A mixture of large and small grains was found to be more favorable for twinning and thus resulting in a greater hardening capability than uniform grain size. KW - Austenitic manganese steel KW - Crystal plasticity KW - Deformation twinning KW - Microstructure based modeling U2 - 10.1016/j.ijsolstr.2017.07.015 DO - 10.1016/j.ijsolstr.2017.07.015 M3 - Article VL - 125 SP - 68 EP - 76 JO - International Journal of Solids and Structures JF - International Journal of Solids and Structures SN - 0020-7683 ER - TY - JOUR T1 - On the Performance of Visible Light Communication Systems with Non-Orthogonal Multiple Access AU - Marshoud, Hanaa AU - Sofotasios, Paschalis C. AU - Muhaidat, Sami AU - Karagiannidis, George K. AU - Sharif, Bayan S. PY - 2017/10/1 Y1 - 2017/10/1 N2 - Visible light communication (VLC) has been proposed as a promising and efficient solution to indoor ubiquitous broadband connectivity. In this paper, non-orthogonal multiple access, which has been recently introduced as an effective scheme for fifth generation (5G) wireless networks, is considered in the context of VLC systems under different channel uncertainty models. To this end, we first derive a novel closed-form expression for the bit-error-rate (BER) under perfect channel state information (CSI). Capitalizing on this, we then quantify the effect of noisy and outdated CSI by deriving a simple and accurate approximation for the former and a tight upper bound for the latter. The offered results are corroborated by respective results from extensive Monte Carlo simulations and assist in developing useful insights on the effect of imperfect CSI knowledge on the overall system performance. Furthermore, it was shown that while noisy CSI leads to slight degradation in the BER performance, outdated CSI can cause considerable performance degradation, if the order of the users' channel gains change due to the involved mobility. AB - Visible light communication (VLC) has been proposed as a promising and efficient solution to indoor ubiquitous broadband connectivity. In this paper, non-orthogonal multiple access, which has been recently introduced as an effective scheme for fifth generation (5G) wireless networks, is considered in the context of VLC systems under different channel uncertainty models. To this end, we first derive a novel closed-form expression for the bit-error-rate (BER) under perfect channel state information (CSI). Capitalizing on this, we then quantify the effect of noisy and outdated CSI by deriving a simple and accurate approximation for the former and a tight upper bound for the latter. The offered results are corroborated by respective results from extensive Monte Carlo simulations and assist in developing useful insights on the effect of imperfect CSI knowledge on the overall system performance. Furthermore, it was shown that while noisy CSI leads to slight degradation in the BER performance, outdated CSI can cause considerable performance degradation, if the order of the users' channel gains change due to the involved mobility. KW - bit-error-rate KW - dimming control KW - imperfect channel state information KW - non-orthogonal multiple access KW - Visible light communications U2 - 10.1109/TWC.2017.2722441 DO - 10.1109/TWC.2017.2722441 M3 - Article VL - 16 SP - 6350 EP - 6364 JO - IEEE Transactions on Wireless Communications JF - IEEE Transactions on Wireless Communications SN - 1536-1276 IS - 10 ER - TY - JOUR T1 - On the Temporal Effects of Mobile Blockers in Urban Millimeter-Wave Cellular Scenarios AU - Gapeyenko, Margarita AU - Samuylov, Andrey AU - Gerasimenko, Mikhail AU - Moltchanov, Dmitri AU - Singh, Sarabjot AU - Akdeniz, Mustafa Riza AU - Aryafar, Ehsan AU - Himayat, Nageen AU - Andreev, Sergey AU - Koucheryavy, Yevgeni PY - 2017 Y1 - 2017 N2 - Millimeter-wave (mmWave) propagation is known to be severely affected by the blockage of the line-of-sight (LoS) path. In contrast to microwave systems, at shorter mmWave wavelengths such blockage can be caused by human bodies, where their mobility within environment makes wireless channel alternate between the blocked and non-blocked LoS states. Following the recent 3GPP requirements on modeling the dynamic blockage as well as the temporal consistency of the channel at mmWave frequencies, in this paper a new model for predicting the state of a user in the presence of mobile blockers for representative 3GPP scenarios is developed: urban micro cell (UMi) street canyon and park/stadium/square. It is demonstrated that the blockage effects produce an alternating renewal process with exponentially distributed non-blocked intervals, and blocked durations that follow the general distribution. The following metrics are derived (i) the mean and the fraction of time spent in blocked/non-blocked state, (ii) the residual blocked/non-blocked time, and (iii) the time-dependent conditional probability of having blockage/no blockage at time t1 given that there was blockage/no blockage at time t0. The latter is a function of the arrival rate (intensity), width, and height of moving blockers, distance to the mmWave access point (AP), as well as the heights of the AP and the user device. The proposed model can be used for system-level characterization of mmWave cellular communication systems. For example, the optimal height and the maximum coverage radius of the mmWave APs are derived, while satisfying the required mean data rate constraint. The system-level simulations corroborate that the use of the proposed method considerably reduces the modeling complexity. AB - Millimeter-wave (mmWave) propagation is known to be severely affected by the blockage of the line-of-sight (LoS) path. In contrast to microwave systems, at shorter mmWave wavelengths such blockage can be caused by human bodies, where their mobility within environment makes wireless channel alternate between the blocked and non-blocked LoS states. Following the recent 3GPP requirements on modeling the dynamic blockage as well as the temporal consistency of the channel at mmWave frequencies, in this paper a new model for predicting the state of a user in the presence of mobile blockers for representative 3GPP scenarios is developed: urban micro cell (UMi) street canyon and park/stadium/square. It is demonstrated that the blockage effects produce an alternating renewal process with exponentially distributed non-blocked intervals, and blocked durations that follow the general distribution. The following metrics are derived (i) the mean and the fraction of time spent in blocked/non-blocked state, (ii) the residual blocked/non-blocked time, and (iii) the time-dependent conditional probability of having blockage/no blockage at time t1 given that there was blockage/no blockage at time t0. The latter is a function of the arrival rate (intensity), width, and height of moving blockers, distance to the mmWave access point (AP), as well as the heights of the AP and the user device. The proposed model can be used for system-level characterization of mmWave cellular communication systems. For example, the optimal height and the maximum coverage radius of the mmWave APs are derived, while satisfying the required mean data rate constraint. The system-level simulations corroborate that the use of the proposed method considerably reduces the modeling complexity. KW - 3GPP KW - Analytical models KW - Biological system modeling KW - Cellular networks KW - Correlation KW - human body blockage KW - Mathematical model KW - mmWave KW - Mobile communication KW - mobility of blockers KW - temporal consistency KW - Vehicle dynamics U2 - 10.1109/TVT.2017.2754543 DO - 10.1109/TVT.2017.2754543 M3 - Article VL - 66 SP - 10124 EP - 10138 JO - IEEE Transactions on Vehicular Technology JF - IEEE Transactions on Vehicular Technology SN - 0018-9545 IS - 11 ER - TY - JOUR T1 - Opportunistic routing through conjugation in bacteria communication nanonetwork AU - Lio', Pietro AU - Balasubramaniam, Sasitharan PY - 2012/3 Y1 - 2012/3 N2 - As the field of molecular communication continues to grow, numerous solutions have been proposed to enable communication between nanomachines. Amongst these solutions, bacteria communication nanonetworks has been proposed as a promising approach for molecular communication. This is driven by a number of attractive properties found in bacteria, which includes biased motility toward the destination through chemotaxis process, as well as the ability of bacteria to transfer genetic information between each other using conjugation. Bacterial conjugation is a major mechanism for Lateral Gene Transfer (LGT) that enables information transfer among bacteria. In this paper, we propose an opportunistic routing process in bacteria communication network using these two properties. The paper presents the simulation work to analyze the performance of message delivery for three different topology shapes, which includes grid, hexagon, and T-shape topologies. The aim of simulating on different shape topologies is to determine the impact that conjugation will have to improve message delivery. In all topologies, the use of conjugation helped improve the reliability of message delivery to the destination point. The paper will analyze various commonly used metrics used in communication networks, such as the average delay, the number of messages, as well as the distribution of messages and their originating node. The conjugation process is most beneficial in complexed shaped topologies, where the directionality from the source to the destination is a number of hops apart, as represented in the T-shape topology. AB - As the field of molecular communication continues to grow, numerous solutions have been proposed to enable communication between nanomachines. Amongst these solutions, bacteria communication nanonetworks has been proposed as a promising approach for molecular communication. This is driven by a number of attractive properties found in bacteria, which includes biased motility toward the destination through chemotaxis process, as well as the ability of bacteria to transfer genetic information between each other using conjugation. Bacterial conjugation is a major mechanism for Lateral Gene Transfer (LGT) that enables information transfer among bacteria. In this paper, we propose an opportunistic routing process in bacteria communication network using these two properties. The paper presents the simulation work to analyze the performance of message delivery for three different topology shapes, which includes grid, hexagon, and T-shape topologies. The aim of simulating on different shape topologies is to determine the impact that conjugation will have to improve message delivery. In all topologies, the use of conjugation helped improve the reliability of message delivery to the destination point. The paper will analyze various commonly used metrics used in communication networks, such as the average delay, the number of messages, as well as the distribution of messages and their originating node. The conjugation process is most beneficial in complexed shaped topologies, where the directionality from the source to the destination is a number of hops apart, as represented in the T-shape topology. KW - Bacteria communication nanonetworks KW - Opportunistic routing UR - http://www.scopus.com/inward/record.url?scp=84858002058&partnerID=8YFLogxK U2 - 10.1016/j.nancom.2011.10.003 DO - 10.1016/j.nancom.2011.10.003 M3 - Article VL - 3 SP - 36 EP - 45 JO - Nano Communication Networks JF - Nano Communication Networks SN - 1878-7789 IS - 1 ER - TY - JOUR T1 - Optimal energy decay for the wave-heat system on a rectangular domain AU - Batty, Charles AU - Paunonen, Lassi AU - Seifert, David PY - 2019 Y1 - 2019 N2 - We study the rate of energy decay for solutions of a coupled wave-heat system on a rectangular domain. Using techniques from the theory of C 0 -semigroups, and in particular a well-known result due to Borichev and Tomilov, we prove that the energy of classical solutions decays like t - 2/ 3 as t \rightarrow \infty . This rate is moreover shown to be sharp. Our result implies in particular that a general estimate in the literature, which predicts at least logarithmic decay and is known to be best possible in general, is suboptimal in the special case under consideration here. Our strategy of proof involves direct estimates based on separation of variables and a refined version of the technique developed in our earlier paper for a one-dimensional wave-heat system. AB - We study the rate of energy decay for solutions of a coupled wave-heat system on a rectangular domain. Using techniques from the theory of C 0 -semigroups, and in particular a well-known result due to Borichev and Tomilov, we prove that the energy of classical solutions decays like t - 2/ 3 as t \rightarrow \infty . This rate is moreover shown to be sharp. Our result implies in particular that a general estimate in the literature, which predicts at least logarithmic decay and is known to be best possible in general, is suboptimal in the special case under consideration here. Our strategy of proof involves direct estimates based on separation of variables and a refined version of the technique developed in our earlier paper for a one-dimensional wave-heat system. KW - C -semigroups KW - Coupled KW - Energy KW - Heat equation KW - Rates of decay KW - Rectangular domain KW - Resolvent estimates KW - Wave equation U2 - 10.1137/18M1195796 DO - 10.1137/18M1195796 M3 - Article VL - 51 SP - 808 EP - 819 JO - SIAM JOURNAL ON MATHEMATICAL ANALYSIS JF - SIAM JOURNAL ON MATHEMATICAL ANALYSIS SN - 0036-1410 IS - 2 ER - TY - JOUR T1 - Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma. AU - de Matos Simoes, Ricardo AU - Tripathi, Shailesh AU - Emmert-Streib, Frank PY - 2012/5/14 Y1 - 2012/5/14 N2 - The physical periphery of a biological cell is mainly described by signaling pathways which are triggered by transmembrane proteins and receptors that are sentinels to control the whole gene regulatory network of a cell. However, our current knowledge about the gene regulatory mechanisms that are governed by extracellular signals is severely limited. The purpose of this paper is three fold. First, we infer a gene regulatory network from a large-scale B-cell lymphoma expression data set using the C3NET algorithm. Second, we provide a functional and structural analysis of the largest connected component of this network, revealing that this network component corresponds to the peripheral region of a cell. Third, we analyze the hierarchical organization of network components of the whole inferred B-cell gene regulatory network by introducing a new approach which exploits the variability within the data as well as the inferential characteristics of C3NET. As a result, we find a functional bisection of the network corresponding to different cellular components. Overall, our study allows to highlight the peripheral gene regulatory network of B-cells and shows that it is centered around hub transmembrane proteins located at the physical periphery of the cell. In addition, we identify a variety of novel pathological transmembrane proteins such as ion channel complexes and signaling receptors in B-cell lymphoma. AB - The physical periphery of a biological cell is mainly described by signaling pathways which are triggered by transmembrane proteins and receptors that are sentinels to control the whole gene regulatory network of a cell. However, our current knowledge about the gene regulatory mechanisms that are governed by extracellular signals is severely limited. The purpose of this paper is three fold. First, we infer a gene regulatory network from a large-scale B-cell lymphoma expression data set using the C3NET algorithm. Second, we provide a functional and structural analysis of the largest connected component of this network, revealing that this network component corresponds to the peripheral region of a cell. Third, we analyze the hierarchical organization of network components of the whole inferred B-cell gene regulatory network by introducing a new approach which exploits the variability within the data as well as the inferential characteristics of C3NET. As a result, we find a functional bisection of the network corresponding to different cellular components. Overall, our study allows to highlight the peripheral gene regulatory network of B-cells and shows that it is centered around hub transmembrane proteins located at the physical periphery of the cell. In addition, we identify a variety of novel pathological transmembrane proteins such as ion channel complexes and signaling receptors in B-cell lymphoma. KW - B-cell lymphoma KW - Gene expression data KW - Gene regulatory network KW - Statistical network inference UR - http://www.scopus.com/inward/record.url?scp=84865119369&partnerID=8YFLogxK U2 - 10.1186/1752-0509-6-38 DO - 10.1186/1752-0509-6-38 M3 - Article VL - 6 JO - BMC Systems Biology JF - BMC Systems Biology SN - 1752-0509 M1 - 38 ER - TY - JOUR T1 - Performance analysis of simultaneous communications in bacterial nanonetworks AU - Komarov, Mikhail AU - Deng, Boya AU - Petrov, Vitaly AU - Moltchanov, Dmitri PY - 2016 Y1 - 2016 N2 - Utilizing biological components for data transfer is considered as a promising technique for communications at nanoscales. The ability to store data in its DNA strands as well as natural mobility make flagellated bacteria a good candidate for such systems. The use of advanced mechanisms such as replication-based encoding and conjugation to improve the performance of bacterial nanonetworks as well as stochastic bacteria movement pattern make their performance assessment a non-trivial task. Universal analytical frameworks taking into account these mechanisms are still missing. The situation is complicated by the possibility of having more than a single transmitter-receiver (Tx-Rx) pair communicating in the environment of interest. In this paper, we develop a framework to characterize performance of the bacterial networks taking all the abovementioned mechanisms into account and capable to address the case of simultaneous communications between a number of Tx-Rx pairs. The framework is based on the absorbing Markov chains theory and allows to reveal inherent trade-offs related to delay performance of bacterial nanonetworks. AB - Utilizing biological components for data transfer is considered as a promising technique for communications at nanoscales. The ability to store data in its DNA strands as well as natural mobility make flagellated bacteria a good candidate for such systems. The use of advanced mechanisms such as replication-based encoding and conjugation to improve the performance of bacterial nanonetworks as well as stochastic bacteria movement pattern make their performance assessment a non-trivial task. Universal analytical frameworks taking into account these mechanisms are still missing. The situation is complicated by the possibility of having more than a single transmitter-receiver (Tx-Rx) pair communicating in the environment of interest. In this paper, we develop a framework to characterize performance of the bacterial networks taking all the abovementioned mechanisms into account and capable to address the case of simultaneous communications between a number of Tx-Rx pairs. The framework is based on the absorbing Markov chains theory and allows to reveal inherent trade-offs related to delay performance of bacterial nanonetworks. KW - Analytical model KW - Bacterial nanonetworks KW - Multiple Tx-Rx communicating pairs KW - Performance analysis U2 - 10.1016/j.nancom.2016.02.002 DO - 10.1016/j.nancom.2016.02.002 M3 - Article VL - 8 SP - 55 EP - 67 JO - Nano Communication Networks JF - Nano Communication Networks SN - 1878-7789 ER - TY - JOUR T1 - Properties of graph distance measures by means of discrete inequalities AU - Dehmer, Matthias AU - Chen, Zengqiang AU - Emmert-Streib, Frank AU - Shi, Yongtang AU - Tripathi, Shailesh AU - Musa, Aliyu AU - Mowshowitz, Abbe N1 - EXT="Tripathi, Shailesh" PY - 2018/7/1 Y1 - 2018/7/1 N2 - In this paper, we investigate graph distance measures based on topological graph measures. Those measures can be used to measure the structural distance between graphs. When studying the scientific literature, one is aware that measuring distance/similarity between graphs meaningfully has been intricate. We demonstrate that our measures are well-defined and prove bounds for investigating their value domain. Also, we generate numerical results and demonstrate that the measures have useful properties. AB - In this paper, we investigate graph distance measures based on topological graph measures. Those measures can be used to measure the structural distance between graphs. When studying the scientific literature, one is aware that measuring distance/similarity between graphs meaningfully has been intricate. We demonstrate that our measures are well-defined and prove bounds for investigating their value domain. Also, we generate numerical results and demonstrate that the measures have useful properties. KW - Distance measures KW - Graphs KW - Inequalities KW - Networks KW - Similarity measures U2 - 10.1016/j.apm.2018.01.027 DO - 10.1016/j.apm.2018.01.027 M3 - Article VL - 59 SP - 739 EP - 749 JO - Applied Mathematical Modelling JF - Applied Mathematical Modelling SN - 0307-904X ER - TY - JOUR T1 - Real-time observation of bacterial gene expression noise AU - Anufrieva, Olga AU - Sala, Adrien AU - Yli-Harja, Olli AU - Kandhavelu, Meenakshisundaram PY - 2016/6 Y1 - 2016/6 N2 - The mRNA variability in the single cells attributes to random periods of transcription bursts. The cell cycle possesses a global role in affecting transcriptional output. By expressing this process as a communication system at the nanoscale, this transcription output often accounts for the gene expression noise, and this quantifies the promoter activity. However, current stochastic models ignore the fact that gene expression noise is affected not only by the cell cycle and promoter activity, but, also, by the time during which new mRNAs are produced. Here we show that noise from the lac promoter in E.coli is dominated by intrinsic and extrinsic noises in slow and fast dividing cells, respectively. Such domination of the noise components in phases with different generation times is achieved through distinct and combinatorial interactions between the upstream/downstream regulatory elements. These mechanisms serve as an adaptive strategy for increasing population homogeneity under changing environments. AB - The mRNA variability in the single cells attributes to random periods of transcription bursts. The cell cycle possesses a global role in affecting transcriptional output. By expressing this process as a communication system at the nanoscale, this transcription output often accounts for the gene expression noise, and this quantifies the promoter activity. However, current stochastic models ignore the fact that gene expression noise is affected not only by the cell cycle and promoter activity, but, also, by the time during which new mRNAs are produced. Here we show that noise from the lac promoter in E.coli is dominated by intrinsic and extrinsic noises in slow and fast dividing cells, respectively. Such domination of the noise components in phases with different generation times is achieved through distinct and combinatorial interactions between the upstream/downstream regulatory elements. These mechanisms serve as an adaptive strategy for increasing population homogeneity under changing environments. KW - Bursty mRNA production KW - Cell cycle KW - Gene expression KW - lac promoter KW - Noise components U2 - 10.1016/j.nancom.2016.03.001 DO - 10.1016/j.nancom.2016.03.001 M3 - Article VL - 8 SP - 68 EP - 75 JO - Nano Communication Networks JF - Nano Communication Networks SN - 1878-7789 ER - TY - JOUR T1 - Restoration of low-dose digital breast tomosynthesis AU - Borges, Lucas R. AU - Azzari, Lucio AU - Bakic, Predrag R. AU - Maidment, Andrew D.A. AU - Vieira, Marcelo A.C. AU - Foi, Alessandro PY - 2018/4/19 Y1 - 2018/4/19 N2 - In breast cancer screening, the radiation dose must be kept to the minimum necessary to achieve the desired diagnostic objective, thus minimizing risks associated with cancer induction. However, decreasing the radiation dose also degrades the image quality. In this work we restore digital breast tomosynthesis (DBT) projections acquired at low radiation doses with the goal of achieving a quality comparable to that obtained from current standard full-dose imaging protocols. A multiframe denoising algorithm was applied to low-dose projections, which are filtered jointly. Furthermore, a weighted average was used to inject a varying portion of the noisy signal back into the denoised one, in order to attain a signal-to-noise ratio comparable to that of standard full-dose projections. The entire restoration framework leverages a signal-dependent noise model with quantum gain which varies both upon the projection angle and on the pixel position. A clinical DBT system and a 3D anthropomorphic breast phantom were used to validate the proposed method, both on DBT projections and slices from the 3D reconstructed volume. The framework is shown to attain the standard full-dose image quality from data acquired at 50% lower radiation dose, whereas progressive loss of relevant details compromises the image quality if the dosage is further decreased. AB - In breast cancer screening, the radiation dose must be kept to the minimum necessary to achieve the desired diagnostic objective, thus minimizing risks associated with cancer induction. However, decreasing the radiation dose also degrades the image quality. In this work we restore digital breast tomosynthesis (DBT) projections acquired at low radiation doses with the goal of achieving a quality comparable to that obtained from current standard full-dose imaging protocols. A multiframe denoising algorithm was applied to low-dose projections, which are filtered jointly. Furthermore, a weighted average was used to inject a varying portion of the noisy signal back into the denoised one, in order to attain a signal-to-noise ratio comparable to that of standard full-dose projections. The entire restoration framework leverages a signal-dependent noise model with quantum gain which varies both upon the projection angle and on the pixel position. A clinical DBT system and a 3D anthropomorphic breast phantom were used to validate the proposed method, both on DBT projections and slices from the 3D reconstructed volume. The framework is shown to attain the standard full-dose image quality from data acquired at 50% lower radiation dose, whereas progressive loss of relevant details compromises the image quality if the dosage is further decreased. KW - denoising KW - digital breast tomosynthesis KW - dose reduction KW - variance stabilization U2 - 10.1088/1361-6501/aab2f6 DO - 10.1088/1361-6501/aab2f6 M3 - Article VL - 29 JO - Measurement Science and Technology JF - Measurement Science and Technology SN - 0957-0233 IS - 6 M1 - 064003 ER - TY - JOUR T1 - Robust controllers for regular linear systems with infinite-dimensional exosystems AU - Paunonen, Lassi PY - 2017 Y1 - 2017 N2 - We construct two error feedback controllers for robust output tracking and disturbance rejection of a regular linear system with nonsmooth reference and disturbance signals. We show that for sufficiently smooth signals the output converges to the reference at a rate that depends on the behavior of the transfer function of the plant on the imaginary axis. In addition, we construct a controller that can be designed to achieve robustness with respect to a given class of uncertainties in the system, and we present a novel controller structure for output tracking and disturbance rejection without the robustness requirement. We also generalize the internal model principle for regular linear systems with boundary disturbance and for controllers with unbounded input and output operators. The construction of controllers is illustrated with an example where we consider output tracking of a nonsmooth periodic reference signal for a two-dimensional heat equation with boundary control and observation, and with periodic disturbances on the boundary. AB - We construct two error feedback controllers for robust output tracking and disturbance rejection of a regular linear system with nonsmooth reference and disturbance signals. We show that for sufficiently smooth signals the output converges to the reference at a rate that depends on the behavior of the transfer function of the plant on the imaginary axis. In addition, we construct a controller that can be designed to achieve robustness with respect to a given class of uncertainties in the system, and we present a novel controller structure for output tracking and disturbance rejection without the robustness requirement. We also generalize the internal model principle for regular linear systems with boundary disturbance and for controllers with unbounded input and output operators. The construction of controllers is illustrated with an example where we consider output tracking of a nonsmooth periodic reference signal for a two-dimensional heat equation with boundary control and observation, and with periodic disturbances on the boundary. KW - Controller Design KW - Feedback KW - Regular Linear Systems KW - Robust Output Regulation KW - Stability U2 - 10.1137/16M107181X DO - 10.1137/16M107181X M3 - Article VL - 55 SP - 1567 EP - 1597 JO - SIAM Journal on Control and Optimization JF - SIAM Journal on Control and Optimization SN - 0363-0129 IS - 3 ER - TY - JOUR T1 - Robust data reconciliation of combustion variables in multi-fuel fired industrial boilers AU - Korpela, Timo AU - Suominen, Olli AU - Majanne, Yrjö AU - Laukkanen, Ville AU - Lautala, Pentti PY - 2016/7/21 Y1 - 2016/7/21 N2 - This paper introduces an application of simultaneous nonlinear data reconciliation and gross error detection for power plants utilizing a complex but computationally light first principle combustion model. Element and energy balances and robust techniques introduce nonlinearity and the consequent optimization problem is solved using nonlinear optimization. Data reconciliation improves estimation of process variables and enables improved sensor quality control and identification of process anomalies. The approach was applied to an industrial 200 MWth fluidized bed boiler combusting wood, peat, bark, and slurry. The results indicate that the approach is valid and is able to perform in various process conditions. As the combustion model is generic, the method is applicable in any boiler environment. AB - This paper introduces an application of simultaneous nonlinear data reconciliation and gross error detection for power plants utilizing a complex but computationally light first principle combustion model. Element and energy balances and robust techniques introduce nonlinearity and the consequent optimization problem is solved using nonlinear optimization. Data reconciliation improves estimation of process variables and enables improved sensor quality control and identification of process anomalies. The approach was applied to an industrial 200 MWth fluidized bed boiler combusting wood, peat, bark, and slurry. The results indicate that the approach is valid and is able to perform in various process conditions. As the combustion model is generic, the method is applicable in any boiler environment. KW - Data reconciliation KW - Diagnostics KW - Estimation KW - Gross error detection KW - Monitoring KW - Power plant U2 - 10.1016/j.conengprac.2016.07.002 DO - 10.1016/j.conengprac.2016.07.002 M3 - Article VL - 55 SP - 101 EP - 115 JO - Control Engineering Practice JF - Control Engineering Practice SN - 0967-0661 ER - TY - JOUR T1 - Robust Inference for State-Space Models with Skewed Measurement Noise AU - Nurminen, Henri AU - Ardeshiri, Tohid AU - Piché, Robert AU - Gustafsson, Fredrik PY - 2015/11/1 Y1 - 2015/11/1 N2 - Filtering and smoothing algorithms for linear discrete-time state-space models with skewed and heavy-tailed measurement noise are presented. The algorithms use a variational Bayes approximation of the posterior distribution of models that have normal prior and skew-t-distributed measurement noise. The proposed filter and smoother are compared with conventional low-complexity alternatives in a simulated pseudorange positioning scenario. In the simulations the proposed methods achieve better accuracy than the alternative methods, the computational complexity of the filter being roughly 5 to 10 times that of the Kalman filter. AB - Filtering and smoothing algorithms for linear discrete-time state-space models with skewed and heavy-tailed measurement noise are presented. The algorithms use a variational Bayes approximation of the posterior distribution of models that have normal prior and skew-t-distributed measurement noise. The proposed filter and smoother are compared with conventional low-complexity alternatives in a simulated pseudorange positioning scenario. In the simulations the proposed methods achieve better accuracy than the alternative methods, the computational complexity of the filter being roughly 5 to 10 times that of the Kalman filter. KW - Kalman filter KW - robust filtering KW - RTS smoother KW - skew t KW - skewness KW - t-distribution KW - variational Bayes U2 - 10.1109/LSP.2015.2437456 DO - 10.1109/LSP.2015.2437456 M3 - Article VL - 22 SP - 1898 EP - 1902 JO - IEEE Signal Processing Letters JF - IEEE Signal Processing Letters SN - 1070-9908 IS - 11 ER - TY - JOUR T1 - Rotation Invariant Texture Description Using Symmetric Dense Microblock Difference AU - Mehta, Rakesh AU - Egiazarian, Karen PY - 2016/6/1 Y1 - 2016/6/1 N2 - This letter is devoted to the problem of rotation invariant texture classification. Novel rotation invariant feature, symmetric dense microblock difference (SDMD), is proposed which captures the information at different orientations and scales. N-fold symmetry is introduced in the feature design configuration, while retaining the random structure that provides discriminative power. The symmetry is utilized to achieve a rotation invariance. The SDMD is extracted using an image pyramid and encoded by the Fisher vector approach resulting in a descriptor which captures variations at different resolutions without increasing the dimensionality. The proposed image representation is combined with the linear SVM classifier. Extensive experiments are conducted on four texture data sets [Brodatz, UMD, UIUC, and Flickr material data set (FMD)] using standard protocols. The results demonstrate that our approach outperforms the state of the art in texture classification. The MATLAB code is made available.1 1Matlab Code: http://www.cs.tut.fi/~mehta/symdmd. AB - This letter is devoted to the problem of rotation invariant texture classification. Novel rotation invariant feature, symmetric dense microblock difference (SDMD), is proposed which captures the information at different orientations and scales. N-fold symmetry is introduced in the feature design configuration, while retaining the random structure that provides discriminative power. The symmetry is utilized to achieve a rotation invariance. The SDMD is extracted using an image pyramid and encoded by the Fisher vector approach resulting in a descriptor which captures variations at different resolutions without increasing the dimensionality. The proposed image representation is combined with the linear SVM classifier. Extensive experiments are conducted on four texture data sets [Brodatz, UMD, UIUC, and Flickr material data set (FMD)] using standard protocols. The results demonstrate that our approach outperforms the state of the art in texture classification. The MATLAB code is made available.1 1Matlab Code: http://www.cs.tut.fi/~mehta/symdmd. KW - image representation KW - local features KW - Rotation invariant features KW - texture classification U2 - 10.1109/LSP.2016.2561311 DO - 10.1109/LSP.2016.2561311 M3 - Article VL - 23 SP - 833 EP - 837 JO - IEEE Signal Processing Letters JF - IEEE Signal Processing Letters SN - 1070-9908 IS - 6 ER - TY - JOUR T1 - sgnesR T2 - An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters AU - Tripathi, Shailesh AU - Lloyd-Price, Jason AU - Ribeiro, Andre AU - Yli-Harja, Olli AU - Dehmer, Matthias AU - Emmert-Streib, Frank PY - 2017/7/4 Y1 - 2017/7/4 N2 - Background: sgnesR (Stochastic Gene Network Expression Simulator in R) is an R package that provides an interface to simulate gene expression data from a given gene network using the stochastic simulation algorithm (SSA). The package allows various options for delay parameters and can easily included in reactions for promoter delay, RNA delay and Protein delay. A user can tune these parameters to model various types of reactions within a cell. As examples, we present two network models to generate expression profiles. We also demonstrated the inference of networks and the evaluation of association measure of edge and non-edge components from the generated expression profiles. Results: The purpose of sgnesR is to enable an easy to use and a quick implementation for generating realistic gene expression data from biologically relevant networks that can be user selected. Conclusions: sgnesR is freely available for academic use. The R package has been tested for R 3.2.0 under Linux, Windows and Mac OS X. AB - Background: sgnesR (Stochastic Gene Network Expression Simulator in R) is an R package that provides an interface to simulate gene expression data from a given gene network using the stochastic simulation algorithm (SSA). The package allows various options for delay parameters and can easily included in reactions for promoter delay, RNA delay and Protein delay. A user can tune these parameters to model various types of reactions within a cell. As examples, we present two network models to generate expression profiles. We also demonstrated the inference of networks and the evaluation of association measure of edge and non-edge components from the generated expression profiles. Results: The purpose of sgnesR is to enable an easy to use and a quick implementation for generating realistic gene expression data from biologically relevant networks that can be user selected. Conclusions: sgnesR is freely available for academic use. The R package has been tested for R 3.2.0 under Linux, Windows and Mac OS X. KW - Gene expression data KW - Gene network KW - Simulation U2 - 10.1186/s12859-017-1731-8 DO - 10.1186/s12859-017-1731-8 M3 - Article VL - 18 JO - BMC Bioinformatics JF - BMC Bioinformatics SN - 1471-2105 IS - 1 M1 - 325 ER - TY - JOUR T1 - Solutions to integrals involving the marcum Q-function and applications AU - Sofotasios, Paschalis C. AU - Muhaidat, Sami AU - Karagiannidis, George K. AU - Sharif, Bayan S. PY - 2015/10/1 Y1 - 2015/10/1 N2 - Novel analytic solutions are derived for integrals that involve the generalized Marcum Q -function, exponential functions and arbitrary powers. Simple closed-form expressions are also derived for specific cases of the generic integrals. The offered expressions are both convenient and versatile, which is particularly useful in applications relating to natural sciences and engineering, including wireless communications and signal processing. To this end, they are employed in the derivation of the average probability of detection in energy detection of unknown signals over multipath fading channels as well as of the channel capacity with fixed rate and channel inversion in the case of correlated multipath fading and switched diversity. AB - Novel analytic solutions are derived for integrals that involve the generalized Marcum Q -function, exponential functions and arbitrary powers. Simple closed-form expressions are also derived for specific cases of the generic integrals. The offered expressions are both convenient and versatile, which is particularly useful in applications relating to natural sciences and engineering, including wireless communications and signal processing. To this end, they are employed in the derivation of the average probability of detection in energy detection of unknown signals over multipath fading channels as well as of the channel capacity with fixed rate and channel inversion in the case of correlated multipath fading and switched diversity. U2 - 10.1109/LSP.2015.2432064 DO - 10.1109/LSP.2015.2432064 M3 - Article VL - 22 SP - 1752 EP - 1756 JO - IEEE Signal Processing Letters JF - IEEE Signal Processing Letters SN - 1070-9908 IS - 10 ER - TY - JOUR T1 - Sparse Overcomplete Denoising T2 - Aggregation Versus Global Optimization AU - Carrera, Diego AU - Boracchi, Giacomo AU - Foi, Alessandro AU - Wohlberg, Brendt N1 - EXT="Carrera, Diego" EXT="Boracchi, Giacomo" PY - 2017/10/1 Y1 - 2017/10/1 N2 - Denoising is often addressed via sparse coding with respect to an overcomplete dictionary. There are two main approaches when the dictionary is composed of translates of an orthonormal basis. The first, traditionally employed by techniques such as wavelet cycle spinning, separately seeks sparsity w.r.t. each translate of the orthonormal basis, solving multiple partial optimizations and obtaining a collection of sparse approximations of the noise-free image, which are aggregated together to obtain a final estimate. The second approach, recently employed by convolutional sparse representations, instead seeks sparsity over the entire dictionary via a global optimization. It is tempting to view the former approach as providing a suboptimal solution of the latter. In this letter, we analyze whether global sparsity is a desirable property, and under what conditions the global optimization provides a better solution to the denoising problem. In particular, our experimental analysis shows that the two approaches attain comparable performance in case of natural images and global optimization outperforms the simpler aggregation of partial estimates only when the image admits an extremely sparse representation. We explain this phenomenon by separately studying the bias and variance of these solutions, and by noting that the variance of the global solution increases very rapidly as the original signal becomes less and less sparse. AB - Denoising is often addressed via sparse coding with respect to an overcomplete dictionary. There are two main approaches when the dictionary is composed of translates of an orthonormal basis. The first, traditionally employed by techniques such as wavelet cycle spinning, separately seeks sparsity w.r.t. each translate of the orthonormal basis, solving multiple partial optimizations and obtaining a collection of sparse approximations of the noise-free image, which are aggregated together to obtain a final estimate. The second approach, recently employed by convolutional sparse representations, instead seeks sparsity over the entire dictionary via a global optimization. It is tempting to view the former approach as providing a suboptimal solution of the latter. In this letter, we analyze whether global sparsity is a desirable property, and under what conditions the global optimization provides a better solution to the denoising problem. In particular, our experimental analysis shows that the two approaches attain comparable performance in case of natural images and global optimization outperforms the simpler aggregation of partial estimates only when the image admits an extremely sparse representation. We explain this phenomenon by separately studying the bias and variance of these solutions, and by noting that the variance of the global solution increases very rapidly as the original signal becomes less and less sparse. KW - Convolutional sparse coding KW - denoising KW - overcomplete representations KW - sparse representations U2 - 10.1109/LSP.2017.2734119 DO - 10.1109/LSP.2017.2734119 M3 - Article VL - 24 SP - 1468 EP - 1472 JO - IEEE Signal Processing Letters JF - IEEE Signal Processing Letters SN - 1070-9908 IS - 10 ER - TY - JOUR T1 - Spatial Interpolation of Cyclostationary Test Statistics in Cognitive Radio Networks T2 - Methods and Field Measurements AU - Chaudhari, Sachin AU - Kosunen, Marko AU - Mäkinen, Semu AU - Chandrasekaran, Ramanathan AU - Oksanen, Jan AU - Laatta, Markus AU - Ryynänen, Jussi AU - Koivunen, Visa AU - Valkama, Mikko PY - 2018 Y1 - 2018 N2 - The focus of this paper is on evaluating different spatial interpolation methods for the construction of radio environment map (REM) using field measurements obtained by cyclostationary based mobile sensors. Mobile sensing devices employing cyclostationary detectors provide lot of advantages compared to widely used energy detectors such as robustness to noise uncertainty and ability to distinguish among different primary user signals. However, mobile sensing results are not available at locations between the sensors making it difficult for a secondary user (possibly without a spectrum sensor) to decide whether or not to use primary user resources at that location. To overcome this, spatial interpolation of test statistics measured at limited number of locations can be carried out to create a channel occupancy map at unmeasured locations between the sensors. For this purpose, different spatial interpolation techniques for the cyclostationary test statistic have been employed in this paper such as inverse distance weighting (IDW), ordinary Kriging (OK), and universal Kriging (UK). The effectiveness of these methods is demonstrated by applying them on extensive real-world field measurement data obtained by mobile-phone-compliant spectrum sensors. The field measurements were carried out using four mobile spectrum sensors measuring eight DVB-T channels at more than hundred locations encompassing roughly one-third of the area of the city of Espoo in Finland. The accuracy of the spatial interpolation results based on the field measurements is determined using the cross validation approach with the widely used root mean square error (RMSE) as the metric. Field measurement results indicate that reliable results with spatial coverage can be achieved using Kriging for cyclostationary based test statistics. Comparison of spatial interpolation results of cyclostationary test statistics is also carried out with those of energy values obtained during the measurement campaign in the form of received signal strength indicator (RSSI). Comparison results clearly show the performance improvement and robustness obtained by the use of cyclostationary based detectors instead of energy detectors. AB - The focus of this paper is on evaluating different spatial interpolation methods for the construction of radio environment map (REM) using field measurements obtained by cyclostationary based mobile sensors. Mobile sensing devices employing cyclostationary detectors provide lot of advantages compared to widely used energy detectors such as robustness to noise uncertainty and ability to distinguish among different primary user signals. However, mobile sensing results are not available at locations between the sensors making it difficult for a secondary user (possibly without a spectrum sensor) to decide whether or not to use primary user resources at that location. To overcome this, spatial interpolation of test statistics measured at limited number of locations can be carried out to create a channel occupancy map at unmeasured locations between the sensors. For this purpose, different spatial interpolation techniques for the cyclostationary test statistic have been employed in this paper such as inverse distance weighting (IDW), ordinary Kriging (OK), and universal Kriging (UK). The effectiveness of these methods is demonstrated by applying them on extensive real-world field measurement data obtained by mobile-phone-compliant spectrum sensors. The field measurements were carried out using four mobile spectrum sensors measuring eight DVB-T channels at more than hundred locations encompassing roughly one-third of the area of the city of Espoo in Finland. The accuracy of the spatial interpolation results based on the field measurements is determined using the cross validation approach with the widely used root mean square error (RMSE) as the metric. Field measurement results indicate that reliable results with spatial coverage can be achieved using Kriging for cyclostationary based test statistics. Comparison of spatial interpolation results of cyclostationary test statistics is also carried out with those of energy values obtained during the measurement campaign in the form of received signal strength indicator (RSSI). Comparison results clearly show the performance improvement and robustness obtained by the use of cyclostationary based detectors instead of energy detectors. KW - Cognitive radio KW - cyclostationary detection KW - Databases KW - Detectors KW - energy detection KW - Hardware KW - Interference KW - Interpolation KW - Kriging KW - Mobile communication KW - radio environment map KW - spatial estimation KW - spectrum sensing U2 - 10.1109/TVT.2017.2717379 DO - 10.1109/TVT.2017.2717379 M3 - Article VL - 67 SP - 1113 EP - 1129 JO - IEEE Transactions on Vehicular Technology JF - IEEE Transactions on Vehicular Technology SN - 0018-9545 IS - 2 ER - TY - JOUR T1 - Spectral modeling of time series with missing data AU - Rodrigues, Paulo C. AU - de Carvalho, Miguel PY - 2013/4/1 Y1 - 2013/4/1 N2 - Singular spectrum analysis is a natural generalization of principal component methods for time series data. In this paper we propose an imputation method to be used with singular spectrum-based techniques which is based on a weighted combination of the forecasts and hindcasts yield by the recurrent forecast method. Despite its ease of implementation, the obtained results suggest an overall good fit of our method, being able to yield a similar adjustment ability in comparison with the alternative method, according to some measures of predictive performance. AB - Singular spectrum analysis is a natural generalization of principal component methods for time series data. In this paper we propose an imputation method to be used with singular spectrum-based techniques which is based on a weighted combination of the forecasts and hindcasts yield by the recurrent forecast method. Despite its ease of implementation, the obtained results suggest an overall good fit of our method, being able to yield a similar adjustment ability in comparison with the alternative method, according to some measures of predictive performance. KW - Karhunen-Loève decomposition KW - Missing data KW - Singular spectrum analysis KW - Time series analysis UR - http://www.scopus.com/inward/record.url?scp=84872620531&partnerID=8YFLogxK U2 - 10.1016/j.apm.2012.09.040 DO - 10.1016/j.apm.2012.09.040 M3 - Article VL - 37 SP - 4676 EP - 4684 JO - Applied Mathematical Modelling JF - Applied Mathematical Modelling SN - 0307-904X IS - 7 ER - TY - JOUR T1 - Stabilization to trajectories for parabolic equations AU - Phan, Duy AU - Rodrigues, Sérgio S. PY - 2018/6/1 Y1 - 2018/6/1 N2 - Both internal and boundary feedback exponential stabilization to trajectories for semilinear parabolic equations in a given bounded domain are addressed. The values of the controls are linear combinations of a finite number of actuators which are supported in a small region. A condition on the family of actuators is given which guarantees the local stabilizability of the control system. It is shown that a linearization-based Riccati feedback stabilizing controller can be constructed. The results of numerical simulations are presented and discussed. AB - Both internal and boundary feedback exponential stabilization to trajectories for semilinear parabolic equations in a given bounded domain are addressed. The values of the controls are linear combinations of a finite number of actuators which are supported in a small region. A condition on the family of actuators is given which guarantees the local stabilizability of the control system. It is shown that a linearization-based Riccati feedback stabilizing controller can be constructed. The results of numerical simulations are presented and discussed. KW - Feedback stabilization to trajectories KW - Semilinear parabolic equations U2 - 10.1007/s00498-018-0218-0 DO - 10.1007/s00498-018-0218-0 M3 - Article VL - 30 JO - Mathematics of Control Signals and Systems JF - Mathematics of Control Signals and Systems SN - 0932-4194 IS - 2 M1 - 11 ER - TY - JOUR T1 - State Estimation for a Class of Piecewise Affine State-Space Models AU - Rui, Rafael AU - Ardeshiri, Tohid AU - Nurminen, Henri AU - Bazanella, Alexandre AU - Gustafsson, Fredrik PY - 2017/1 Y1 - 2017/1 N2 - We propose a filter for piecewise affine state-space models. In each filtering recursion, the true filtering posterior distribution is a mixture of truncated normal distributions. The proposed filter approximates the mixture with a single normal distribution via moment matching. The proposed algorithm is compared with the extended Kalman filter (EKF) in a numerical simulation, where the proposed method obtains, on average, better root mean square error than the EKF. AB - We propose a filter for piecewise affine state-space models. In each filtering recursion, the true filtering posterior distribution is a mixture of truncated normal distributions. The proposed filter approximates the mixture with a single normal distribution via moment matching. The proposed algorithm is compared with the extended Kalman filter (EKF) in a numerical simulation, where the proposed method obtains, on average, better root mean square error than the EKF. KW - piecewise affine KW - state-space models KW - nonlinear filtering KW - Kalman filtering U2 - 10.1109/LSP.2016.2633624 DO - 10.1109/LSP.2016.2633624 M3 - Article VL - 24 SP - 61 EP - 65 JO - IEEE Signal Processing Letters JF - IEEE Signal Processing Letters SN - 1070-9908 IS - 1 ER - TY - JOUR T1 - Still image/video frame lossy compression providing a desired visual quality AU - Zemliachenko, Alexander AU - Lukin, Vladimir AU - Ponomarenko, Nikolay AU - Egiazarian, Karen AU - Astola, Jaakko PY - 2016 Y1 - 2016 N2 - The problem of how to automatically provide a desired (required) visual quality in lossy compression of still images and video frames is considered in this paper. The quality can be measured based on different conventional and visual quality metrics. In this paper, we mainly employ human visual system (HVS) based metrics PSNR-HVS-M and MSSIM since both of them take into account several important peculiarities of HVS. To provide a desired visual quality with high accuracy, iterative image compression procedures are proposed and analyzed. An experimental study is performed for a large number of grayscale test images. We demonstrate that there exist several coders for which the number of iterations can be essentially decreased using a reasonable selection of the starting value and the variation interval for the parameter controlling compression (PCC). PCC values attained at the end of the iterative procedure may heavily depend upon the coder used and the complexity of the image. Similarly, the compression ratio also considerably depends on the above factors. We show that for some modern coders that take HVS into consideration it is possible to give practical recommendations on setting a fixed PCC to provide a desired visual quality in a non-iterative manner. The case when original images are corrupted by visible noise is also briefly studied. AB - The problem of how to automatically provide a desired (required) visual quality in lossy compression of still images and video frames is considered in this paper. The quality can be measured based on different conventional and visual quality metrics. In this paper, we mainly employ human visual system (HVS) based metrics PSNR-HVS-M and MSSIM since both of them take into account several important peculiarities of HVS. To provide a desired visual quality with high accuracy, iterative image compression procedures are proposed and analyzed. An experimental study is performed for a large number of grayscale test images. We demonstrate that there exist several coders for which the number of iterations can be essentially decreased using a reasonable selection of the starting value and the variation interval for the parameter controlling compression (PCC). PCC values attained at the end of the iterative procedure may heavily depend upon the coder used and the complexity of the image. Similarly, the compression ratio also considerably depends on the above factors. We show that for some modern coders that take HVS into consideration it is possible to give practical recommendations on setting a fixed PCC to provide a desired visual quality in a non-iterative manner. The case when original images are corrupted by visible noise is also briefly studied. KW - Compression ratio KW - Lossy compression KW - Required quality KW - Visual quality metrics UR - http://www.scopus.com/inward/record.url?scp=84930357751&partnerID=8YFLogxK U2 - 10.1007/s11045-015-0333-8 DO - 10.1007/s11045-015-0333-8 M3 - Article VL - 27 SP - 697 EP - 718 JO - Multidimensional Systems and Signal Processing JF - Multidimensional Systems and Signal Processing SN - 0923-6082 IS - 3 ER - TY - JOUR T1 - Structural influence of gene networks on their inference T2 - Analysis of C3NET AU - Altay, Gökmen AU - Emmert-Streib, Frank PY - 2011/6/22 Y1 - 2011/6/22 N2 - Background: The availability of large-scale high-throughput data possesses considerable challenges toward their functional analysis. For this reason gene network inference methods gained considerable interest. However, our current knowledge, especially about the influence of the structure of a gene network on its inference, is limited.Results: In this paper we present a comprehensive investigation of the structural influence of gene networks on the inferential characteristics of C3NET - a recently introduced gene network inference algorithm. We employ local as well as global performance metrics in combination with an ensemble approach. The results from our numerical study for various biological and synthetic network structures and simulation conditions, also comparing C3NET with other inference algorithms, lead a multitude of theoretical and practical insights into the working behavior of C3NET. In addition, in order to facilitate the practical usage of C3NET we provide an user-friendly R package, called c3net, and describe its functionality. It is available from https://r-forge.r-project.org/projects/c3net and from the CRAN package repository.Conclusions: The availability of gene network inference algorithms with known inferential properties opens a new era of large-scale screening experiments that could be equally beneficial for basic biological and biomedical research with auspicious prospects. The availability of our easy to use software package c3net may contribute to the popularization of such methods.Reviewers: This article was reviewed by Lev Klebanov, Joel Bader and Yuriy Gusev. AB - Background: The availability of large-scale high-throughput data possesses considerable challenges toward their functional analysis. For this reason gene network inference methods gained considerable interest. However, our current knowledge, especially about the influence of the structure of a gene network on its inference, is limited.Results: In this paper we present a comprehensive investigation of the structural influence of gene networks on the inferential characteristics of C3NET - a recently introduced gene network inference algorithm. We employ local as well as global performance metrics in combination with an ensemble approach. The results from our numerical study for various biological and synthetic network structures and simulation conditions, also comparing C3NET with other inference algorithms, lead a multitude of theoretical and practical insights into the working behavior of C3NET. In addition, in order to facilitate the practical usage of C3NET we provide an user-friendly R package, called c3net, and describe its functionality. It is available from https://r-forge.r-project.org/projects/c3net and from the CRAN package repository.Conclusions: The availability of gene network inference algorithms with known inferential properties opens a new era of large-scale screening experiments that could be equally beneficial for basic biological and biomedical research with auspicious prospects. The availability of our easy to use software package c3net may contribute to the popularization of such methods.Reviewers: This article was reviewed by Lev Klebanov, Joel Bader and Yuriy Gusev. UR - http://www.scopus.com/inward/record.url?scp=79959327654&partnerID=8YFLogxK U2 - 10.1186/1745-6150-6-31 DO - 10.1186/1745-6150-6-31 M3 - Article VL - 6 JO - Biology Direct JF - Biology Direct SN - 1745-6150 M1 - 31 ER - TY - JOUR T1 - Structural Measures for Network Biology Using QuACN AU - Mueller, Laurin A. J. AU - Kugler, Karl G. AU - Graber, Armin AU - Emmert-Streib, Frank AU - Dehmer, Matthias PY - 2011/12/24 Y1 - 2011/12/24 N2 - Background: Structural measures for networks have been extensively developed, but many of them have not yet demonstrated their sustainably. That means, it remains often unclear whether a particular measure is useful and feasible to solve a particular problem in network biology. Exemplarily, the classification of complex biological networks can be named, for which structural measures are used leading to a minimal classification error. Hence, there is a strong need to provide freely available software packages to calculate and demonstrate the appropriate usage of structural graph measures in network biology.Results: Here, we discuss topological network descriptors that are implemented in the R-package QuACN and demonstrate their behavior and characteristics by applying them to a set of example graphs. Moreover, we show a representative application to illustrate their capabilities for classifying biological networks. In particular, we infer gene regulatory networks from microarray data and classify them by methods provided by QuACN. Note that QuACN is the first freely available software written in R containing a large number of structural graph measures.Conclusion: The R package QuACN is under ongoing development and we add promising groups of topological network descriptors continuously. The package can be used to answer intriguing research questions in network biology, e.g., classifying biological data or identifying meaningful biological features, by analyzing the topology of biological networks. AB - Background: Structural measures for networks have been extensively developed, but many of them have not yet demonstrated their sustainably. That means, it remains often unclear whether a particular measure is useful and feasible to solve a particular problem in network biology. Exemplarily, the classification of complex biological networks can be named, for which structural measures are used leading to a minimal classification error. Hence, there is a strong need to provide freely available software packages to calculate and demonstrate the appropriate usage of structural graph measures in network biology.Results: Here, we discuss topological network descriptors that are implemented in the R-package QuACN and demonstrate their behavior and characteristics by applying them to a set of example graphs. Moreover, we show a representative application to illustrate their capabilities for classifying biological networks. In particular, we infer gene regulatory networks from microarray data and classify them by methods provided by QuACN. Note that QuACN is the first freely available software written in R containing a large number of structural graph measures.Conclusion: The R package QuACN is under ongoing development and we add promising groups of topological network descriptors continuously. The package can be used to answer intriguing research questions in network biology, e.g., classifying biological data or identifying meaningful biological features, by analyzing the topology of biological networks. UR - http://www.scopus.com/inward/record.url?scp=84155173344&partnerID=8YFLogxK U2 - 10.1186/1471-2105-12-492 DO - 10.1186/1471-2105-12-492 M3 - Article VL - 12 JO - BMC Bioinformatics JF - BMC Bioinformatics SN - 1471-2105 IS - 1 M1 - 492 ER - TY - JOUR T1 - Structural Results for Quaternionic Gabor Frames AU - Cerejeiras, Paula AU - Hartmann, Stefan AU - Orelma, Heikki PY - 2018/11/1 Y1 - 2018/11/1 N2 - We study quaternionic Gabor frames based on the two-sided quaternionic windowed Fourier transform. Since classical Hilbert space based methods do not work in this case we introduce appropriated versions of translation and modulation operators. We prove Janssen’s and Walnut’s representations, as well as modified versions of the Wexler–Raz biorthogonality and Ron–Shen duality based on the concept of correlation function. We end up with a characterization of tight quaternionic Gabor frames. AB - We study quaternionic Gabor frames based on the two-sided quaternionic windowed Fourier transform. Since classical Hilbert space based methods do not work in this case we introduce appropriated versions of translation and modulation operators. We prove Janssen’s and Walnut’s representations, as well as modified versions of the Wexler–Raz biorthogonality and Ron–Shen duality based on the concept of correlation function. We end up with a characterization of tight quaternionic Gabor frames. KW - Frame bounds KW - Janssen’s representation KW - Quaternionic frame operator KW - Quaternionic Gabor frames KW - Two-sided QWFT KW - Wexler–Raz biorthogonality U2 - 10.1007/s00006-018-0901-8 DO - 10.1007/s00006-018-0901-8 M3 - Article VL - 28 JO - Advances in Applied Clifford Algebras JF - Advances in Applied Clifford Algebras SN - 0188-7009 IS - 5 M1 - 86 ER - TY - JOUR T1 - Structural similarity of directed universal hierarchical graphs T2 - A low computational complexity approach AU - Dehmer, Matthias AU - Emmert-Streib, Frank PY - 2007/12/1 Y1 - 2007/12/1 N2 - In the present paper we mainly introduce an efficient approach to measure the structural similarity of so called directed universal hierarchical graphs. We want to underline that directed universal hierarchical graphs can be obtained from generalized trees which are already introduced. In order to classify these graphs, we state our novel graph similarity method. As a main result we notice that our novel algorithm has low computational complexity. AB - In the present paper we mainly introduce an efficient approach to measure the structural similarity of so called directed universal hierarchical graphs. We want to underline that directed universal hierarchical graphs can be obtained from generalized trees which are already introduced. In order to classify these graphs, we state our novel graph similarity method. As a main result we notice that our novel algorithm has low computational complexity. KW - Complexity analysis KW - Graph classes KW - Graph classification KW - Graph similarity KW - Hierarchical models KW - Structured objects UR - http://www.scopus.com/inward/record.url?scp=35648968162&partnerID=8YFLogxK U2 - 10.1016/j.amc.2007.04.006 DO - 10.1016/j.amc.2007.04.006 M3 - Article VL - 194 SP - 7 EP - 20 JO - Applied Mathematics and Computation JF - Applied Mathematics and Computation SN - 0096-3003 IS - 1 ER - TY - JOUR T1 - Target tracking via combination of particle filter and optimisation techniques AU - Hosseini, Seyyed Soheil Sadat AU - Jamali, Mohsin M. AU - Astola, Jaakko AU - Gorsevski, Peter V. PY - 2016 Y1 - 2016 N2 - Particle filters (PFs) have been used for the nonlinear estimation for a number of years. However, they suffer from the impoverishment phenomenon. It is brought by resampling which intends to prevent particle degradation, and therefore becomes the inherent weakness of this technique. To solve the problem of sample impoverishment and to improve the performance of the standard particle filter we propose a modification to this method by adding a sampling mechanism inspired by optimisation techniques, namely, the pattern search, particle swarm optimisation, differential evolution and Nelder-Mead algorithms. In the proposed methods, the true state of the target can be better expressed by the optimised particle set and the number of meaningful particles can be grown significantly. The efficiency of the proposed particle filters is supported by a truck-trailer problem. Simulations show that the hybridised particle filter with Nelder-Mead search is better than other optimisation approaches in terms of particle diversity. AB - Particle filters (PFs) have been used for the nonlinear estimation for a number of years. However, they suffer from the impoverishment phenomenon. It is brought by resampling which intends to prevent particle degradation, and therefore becomes the inherent weakness of this technique. To solve the problem of sample impoverishment and to improve the performance of the standard particle filter we propose a modification to this method by adding a sampling mechanism inspired by optimisation techniques, namely, the pattern search, particle swarm optimisation, differential evolution and Nelder-Mead algorithms. In the proposed methods, the true state of the target can be better expressed by the optimised particle set and the number of meaningful particles can be grown significantly. The efficiency of the proposed particle filters is supported by a truck-trailer problem. Simulations show that the hybridised particle filter with Nelder-Mead search is better than other optimisation approaches in terms of particle diversity. KW - Differential evolution KW - Nelder-Mead KW - Particle filter KW - Particle swarm optimisation KW - Pattern search KW - PSO KW - Target tracking U2 - 10.1504/IJMMNO.2016.077068 DO - 10.1504/IJMMNO.2016.077068 M3 - Article VL - 7 SP - 212 EP - 229 JO - International Journal of Mathematical Modelling and Numerical Optimization JF - International Journal of Mathematical Modelling and Numerical Optimization SN - 2040-3607 IS - 2 ER - TY - JOUR T1 - The Impact of Interference from the Side Lanes on mmWave/THz Band V2V Communication Systems with Directional Antennas AU - Petrov, Vitaly AU - Kokkoniemi, Joonas AU - Moltchanov, Dmitri AU - Lehtomaki, Janne AU - Juntti, Markku AU - Koucheryavy, Yevgeni PY - 2018/6 Y1 - 2018/6 N2 - Communications systems operating in the millimeter and terahertz band have been recently suggested to enable high data-rate vehicle-to-vehicle communications in future networks. However, massive deployment of such systems may lead to significant interference, affecting the performance of information transmission. While the multipath interference caused by the signal reflections from the road has been extensively discussed in literature, the interference caused by the vehicles on the side lanes has been insufficiently studied so far. In this paper, using a combination of measurement, simulation, and analytical methods we comprehensively characterize the interference from the side lanes in two typical deployments including highway and urban road environments for millimeter and low terahertz bands. Both the multipath interference and direct interference from the transmitting vehicles on the side lanes are taken into account. As a result of the presented study, we reveal that: i) the interference from the side lanes can be well approximated using two-dimensional stochastic models without any notable loss of accuracy; and ii) even when highly directional antennas are used there are special spatial configurations, where the interference may greatly affect the communication systems performance. We lately apply the developed models to estimate the signal-to-interference ratio and link capacity of mmWave/THz band V2V communications with directional antennas. AB - Communications systems operating in the millimeter and terahertz band have been recently suggested to enable high data-rate vehicle-to-vehicle communications in future networks. However, massive deployment of such systems may lead to significant interference, affecting the performance of information transmission. While the multipath interference caused by the signal reflections from the road has been extensively discussed in literature, the interference caused by the vehicles on the side lanes has been insufficiently studied so far. In this paper, using a combination of measurement, simulation, and analytical methods we comprehensively characterize the interference from the side lanes in two typical deployments including highway and urban road environments for millimeter and low terahertz bands. Both the multipath interference and direct interference from the transmitting vehicles on the side lanes are taken into account. As a result of the presented study, we reveal that: i) the interference from the side lanes can be well approximated using two-dimensional stochastic models without any notable loss of accuracy; and ii) even when highly directional antennas are used there are special spatial configurations, where the interference may greatly affect the communication systems performance. We lately apply the developed models to estimate the signal-to-interference ratio and link capacity of mmWave/THz band V2V communications with directional antennas. KW - Analytical models KW - Antenna measurements KW - Communication systems KW - Directional antennas KW - Interference KW - Millimeter waves KW - Propagation losses KW - Road transportation KW - SIR KW - THz band KW - Vehicle-to-Vehicle communications U2 - 10.1109/TVT.2018.2799564 DO - 10.1109/TVT.2018.2799564 M3 - Article VL - 67 SP - 5028 EP - 5041 JO - IEEE Transactions on Vehicular Technology JF - IEEE Transactions on Vehicular Technology SN - 0018-9545 IS - 6 ER - TY - JOUR T1 - The watching system as a generalization of identifying code AU - Ghorbani, Modjtaba AU - Dehmer, Matthias AU - Maimani, Hamidreza AU - Maddah, Sheyda AU - Roozbayani, Maryam AU - Emmert-Streib, Frank PY - 2020/9/1 Y1 - 2020/9/1 N2 - The watching system, as a generalization of identifying code, has been defined by Auger in 2010. The identifying code has been used to wireless networks and it has been also applied to locate objects in the sensor networks. On the other hand, the graph product is employed in most of the mathematic branches such as network design to study the structure of network elements. In this paper, we give some upper bounds for the watching number of well-know product graphs. AB - The watching system, as a generalization of identifying code, has been defined by Auger in 2010. The identifying code has been used to wireless networks and it has been also applied to locate objects in the sensor networks. On the other hand, the graph product is employed in most of the mathematic branches such as network design to study the structure of network elements. In this paper, we give some upper bounds for the watching number of well-know product graphs. KW - Domination number KW - Graph products KW - Identifying code KW - Watching system U2 - 10.1016/j.amc.2020.125302 DO - 10.1016/j.amc.2020.125302 M3 - Article VL - 380 JO - Applied Mathematics and Computation JF - Applied Mathematics and Computation SN - 0096-3003 M1 - 125302 ER - TY - JOUR T1 - Topological mappings between graphs, trees and generalized trees AU - Emmert-Streib, Frank AU - Dehmer, Matthias PY - 2007/3/15 Y1 - 2007/3/15 N2 - We present novel topological mappings between graphs, trees and generalized trees that means between structured objects with different properties. The two major contributions of this paper are, first, to clarify the relation between graphs, trees and generalized trees, a graph class recently introduced. Second, these transformations provide a unique opportunity to transform structured objects into a representation that might be beneficial for a processing, e.g., by machine learning techniques for graph classification. AB - We present novel topological mappings between graphs, trees and generalized trees that means between structured objects with different properties. The two major contributions of this paper are, first, to clarify the relation between graphs, trees and generalized trees, a graph class recently introduced. Second, these transformations provide a unique opportunity to transform structured objects into a representation that might be beneficial for a processing, e.g., by machine learning techniques for graph classification. KW - Applied graph theory KW - Graph transformation KW - Hierarchical graphs UR - http://www.scopus.com/inward/record.url?scp=33947616843&partnerID=8YFLogxK U2 - 10.1016/j.amc.2006.07.162 DO - 10.1016/j.amc.2006.07.162 M3 - Article VL - 186 SP - 1326 EP - 1333 JO - Applied Mathematics and Computation JF - Applied Mathematics and Computation SN - 0096-3003 IS - 2 ER - TY - JOUR T1 - Transmit Power Optimization and Feasibility Analysis of Self-backhauling Full-Duplex Radio Access Systems AU - Korpi, Dani AU - Riihonen, Taneli AU - Sabharwal, Ashutosh AU - Valkama, Mikko PY - 2018 Y1 - 2018 N2 - We analyze an inband full-duplex access node that is serving mobile users while simultaneously connecting to a core network over a wireless backhaul link, utilizing the same frequency band for all communication tasks. Such wireless self-backhauling is an intriguing option for the next generation wireless systems since a wired backhaul connection might not be economically viable if the access nodes are deployed densely. In particular, we derive the optimal transmit power allocation for such a system in closed form under Quality-of-Service (QoS) requirements, which are defined in terms of the minimum data rates for each mobile user. For comparison, the optimal transmit power allocation is solved also for two reference scenarios: a purely half-duplex access node, and a relay-type full-duplex access node. Based on the obtained expressions for the optimal transmit powers, we then show that the systems utilizing a full-duplex capable access node have a fundamental feasibility boundary, meaning that there are circumstances under which the QoS requirements cannot be fulfilled using finite transmit powers. This fundamental feasibility boundary is also derived in closed form. The feasibility boundaries and optimal transmit powers are then numerically evaluated in order to compare the different communication schemes. In general, utilizing the purely full-duplex access node results in the lowest transmit powers for all the communicating parties, although there are some network geometries under which such a system is not capable of reaching the required minimum data rates. In addition, the numerical results indicate that a full-duplex capable access node is best suited for relatively small cells. AB - We analyze an inband full-duplex access node that is serving mobile users while simultaneously connecting to a core network over a wireless backhaul link, utilizing the same frequency band for all communication tasks. Such wireless self-backhauling is an intriguing option for the next generation wireless systems since a wired backhaul connection might not be economically viable if the access nodes are deployed densely. In particular, we derive the optimal transmit power allocation for such a system in closed form under Quality-of-Service (QoS) requirements, which are defined in terms of the minimum data rates for each mobile user. For comparison, the optimal transmit power allocation is solved also for two reference scenarios: a purely half-duplex access node, and a relay-type full-duplex access node. Based on the obtained expressions for the optimal transmit powers, we then show that the systems utilizing a full-duplex capable access node have a fundamental feasibility boundary, meaning that there are circumstances under which the QoS requirements cannot be fulfilled using finite transmit powers. This fundamental feasibility boundary is also derived in closed form. The feasibility boundaries and optimal transmit powers are then numerically evaluated in order to compare the different communication schemes. In general, utilizing the purely full-duplex access node results in the lowest transmit powers for all the communicating parties, although there are some network geometries under which such a system is not capable of reaching the required minimum data rates. In addition, the numerical results indicate that a full-duplex capable access node is best suited for relatively small cells. KW - full-duplex wireless KW - massive MIMO KW - Self-backhauling KW - transmit power optimization U2 - 10.1109/TWC.2018.2821682 DO - 10.1109/TWC.2018.2821682 M3 - Article VL - 17 SP - 4219 EP - 4236 JO - IEEE Transactions on Wireless Communications JF - IEEE Transactions on Wireless Communications SN - 1536-1276 IS - 6 ER - TY - JOUR T1 - Two-Sided Hypergenic Functions AU - Eriksson, Sirkka-Liisa AU - Orelma, Heikki AU - Vieira, Nelson PY - 2017 Y1 - 2017 N2 - In this paper we present an analogous of the class of two-sided axial monogenic functions to the case of axial κ-hypermonogenic functions. In order to do that we will solve a Vekua-type system in terms of Bessel functions. AB - In this paper we present an analogous of the class of two-sided axial monogenic functions to the case of axial κ-hypermonogenic functions. In order to do that we will solve a Vekua-type system in terms of Bessel functions. KW - $${\kappa}$$κ-Hypergenic functions KW - Clifford algebras KW - Hypergenic functions KW - Two-side hypergenic functions UR - http://www.scopus.com/inward/record.url?scp=84941331725&partnerID=8YFLogxK U2 - 10.1007/s00006-015-0605-2 DO - 10.1007/s00006-015-0605-2 M3 - Article VL - 27 SP - 111 EP - 123 JO - Advances in Applied Clifford Algebras JF - Advances in Applied Clifford Algebras SN - 0188-7009 IS - 1 ER - TY - JOUR T1 - Unbiased Injection of Signal-Dependent Noise in Variance-Stabilized Range AU - Borges, Lucas AU - Vieira, Marcelo AU - Foi, Alessandro PY - 2016 Y1 - 2016 N2 - The design, optimization, and validation of many image processing or image-based analysis systems often requires testing of the system performance over a dataset of images corrupted by noise at different signal-to-noise ratio regimes. A noise-free ground-truth image may not be available, and different SNRs are simulated by injecting extra noise into an already noisy image. However, noise in real-world systems is typically signal-dependent, with variance determined by the noise-free image. Thus, also the noise to be injected shall depend on the unknown ground-truth image. To circumvent this issue, we consider the additive injection of noise in variance-stabilized range, where no previous knowledge of the ground-truth signal is necessary. Specifically, we design a special noise-injection operator that prevents the errors on expectation and variance that would otherwise arise when standard variance-stabilizing transformations are used for this task. Thus, the proposed operator is suitable for accurately injecting signal-dependent noise even to images acquired at very low counts. AB - The design, optimization, and validation of many image processing or image-based analysis systems often requires testing of the system performance over a dataset of images corrupted by noise at different signal-to-noise ratio regimes. A noise-free ground-truth image may not be available, and different SNRs are simulated by injecting extra noise into an already noisy image. However, noise in real-world systems is typically signal-dependent, with variance determined by the noise-free image. Thus, also the noise to be injected shall depend on the unknown ground-truth image. To circumvent this issue, we consider the additive injection of noise in variance-stabilized range, where no previous knowledge of the ground-truth signal is necessary. Specifically, we design a special noise-injection operator that prevents the errors on expectation and variance that would otherwise arise when standard variance-stabilizing transformations are used for this task. Thus, the proposed operator is suitable for accurately injecting signal-dependent noise even to images acquired at very low counts. KW - Anscombe transformation KW - Noise injection KW - optimization KW - Poisson noise KW - variance stabilization U2 - 10.1109/LSP.2016.2601689 DO - 10.1109/LSP.2016.2601689 M3 - Article VL - 23 SP - 1494 EP - 1498 JO - IEEE Signal Processing Letters JF - IEEE Signal Processing Letters SN - 1070-9908 IS - 10 ER - TY - JOUR T1 - Uncertainty propagation of iron loss from characterization measurements to computation of electrical machines AU - Belahcen, Anouar AU - Rasilo, Paavo AU - Nguyen, Thu Trang AU - Clénet, Stephane PY - 2015 Y1 - 2015 N2 - Purpose - The purpose of this paper is to find out how uncertainties in the characterization of magnetic materials propagate through identification and numerical simulation to the computation of iron losses in electrical machines. Design/methodology/approach - The probabilistic uncertainties in the iron losses are modelled with the spectral approach using chaos polynomials. The Sobol indices are used for the global sensitivity analysis. The machine is modelled with a 2D finite element method and the iron losses are computed with a previously developed accurate method. Findings - The uncertainties propagate in different ways to the different components of losses, i.e. eddy current, hysteresis, and excess losses. The propagation is also different depending on the investigated region of the machine, i.e. Stator or rotor teeth, yokes, tooth tips. Research limitations/implications - The method does not account for uncertainties related to the manufacturing process, which might result in even larger variability. Practical implications - A major implication of the findings is that the identification of iron loss parameters at low frequencies does not affect the loss variability. The identification with high-frequency measurement is very important for the rotor tooth tips. The variability in the excess loss parameters is of low impact. Originality/value - The presented results are of importance for the magnetic material manufacturers and the electrical machine designers. The manufacturers can plan the measurement and identification procedures as to minimize the output variability of the parameters. The designers of the machine can use the result and the presented procedures to estimate the variability of their design. AB - Purpose - The purpose of this paper is to find out how uncertainties in the characterization of magnetic materials propagate through identification and numerical simulation to the computation of iron losses in electrical machines. Design/methodology/approach - The probabilistic uncertainties in the iron losses are modelled with the spectral approach using chaos polynomials. The Sobol indices are used for the global sensitivity analysis. The machine is modelled with a 2D finite element method and the iron losses are computed with a previously developed accurate method. Findings - The uncertainties propagate in different ways to the different components of losses, i.e. eddy current, hysteresis, and excess losses. The propagation is also different depending on the investigated region of the machine, i.e. Stator or rotor teeth, yokes, tooth tips. Research limitations/implications - The method does not account for uncertainties related to the manufacturing process, which might result in even larger variability. Practical implications - A major implication of the findings is that the identification of iron loss parameters at low frequencies does not affect the loss variability. The identification with high-frequency measurement is very important for the rotor tooth tips. The variability in the excess loss parameters is of low impact. Originality/value - The presented results are of importance for the magnetic material manufacturers and the electrical machine designers. The manufacturers can plan the measurement and identification procedures as to minimize the output variability of the parameters. The designers of the machine can use the result and the presented procedures to estimate the variability of their design. KW - Electrical machine KW - Finite element methods KW - Iron losses KW - Uncertainty estimation U2 - 10.1108/COMPEL-10-2014-0271 DO - 10.1108/COMPEL-10-2014-0271 M3 - Article VL - 34 SP - 624 EP - 636 JO - COMPEL: The International Journal for Computation and Mathematics in Electrical and Electronic Engineering JF - COMPEL: The International Journal for Computation and Mathematics in Electrical and Electronic Engineering SN - 0332-1649 IS - 3 ER - TY - JOUR T1 - Universal construction mechanism for networks from one-dimensional symbol sequences AU - Emmert-Streib, Frank PY - 2012/10/15 Y1 - 2012/10/15 N2 - In this paper we introduce construction mechanisms to generate directed networks from one-dimensional symbol sequences. We prove that any of these construction mechanism leads to the same undirected network. Further, we prove that the introduced construction mechanisms are universal in the sense that any undirected network can be generated by such a mechanism. In addition, we provide various numerical examples to demonstrate the applicability of the introduced mechanism. AB - In this paper we introduce construction mechanisms to generate directed networks from one-dimensional symbol sequences. We prove that any of these construction mechanism leads to the same undirected network. Further, we prove that the introduced construction mechanisms are universal in the sense that any undirected network can be generated by such a mechanism. In addition, we provide various numerical examples to demonstrate the applicability of the introduced mechanism. KW - Complex networks KW - Network construction KW - Random networks KW - Symbol sequences KW - Universal network construction UR - http://www.scopus.com/inward/record.url?scp=84867336661&partnerID=8YFLogxK U2 - 10.1016/j.amc.2012.07.006 DO - 10.1016/j.amc.2012.07.006 M3 - Article VL - 219 SP - 1020 EP - 1030 JO - Applied Mathematics and Computation JF - Applied Mathematics and Computation SN - 0096-3003 IS - 3 ER - TY - JOUR T1 - Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data AU - Matos Simoes, Ricardo de AU - Dalleau, Sabine AU - Williamson, Kate E. AU - Emmert-Streib, Frank PY - 2015/5/14 Y1 - 2015/5/14 N2 - Background: Urothelial pathogenesis is a complex process driven by an underlying network of interconnected genes. The identification of novel genomic target regions and gene targets that drive urothelial carcinogenesis is crucial in order to improve our current limited understanding of urothelial cancer (UC) on the molecular level. The inference of genome-wide gene regulatory networks (GRN) from large-scale gene expression data provides a promising approach for a detailed investigation of the underlying network structure associated to urothelial carcinogenesis. Methods: In our study we inferred and compared three GRNs by the application of the BC3Net inference algorithm to large-scale transitional cell carcinoma gene expression data sets from Illumina RNAseq (179 samples), Illumina Bead arrays (165 samples) and Affymetrix Oligo microarrays (188 samples). We investigated the structural and functional properties of GRNs for the identification of molecular targets associated to urothelial cancer. Results: We found that the urothelial cancer (UC) GRNs show a significant enrichment of subnetworks that are associated with known cancer hallmarks including cell cycle, immune response, signaling, differentiation and translation. Interestingly, the most prominent subnetworks of co-located genes were found on chromosome regions 5q31.3 (RNAseq), 8q24.3 (Oligo) and 1q23.3 (Bead), which all represent known genomic regions frequently deregulated or aberated in urothelial cancer and other cancer types. Furthermore, the identified hub genes of the individual GRNs, e.g., HID1/DMC1 (tumor development), RNF17/TDRD4 (cancer antigen) and CYP4A11 (angiogenesis/ metastasis) are known cancer associated markers. The GRNs were highly dataset specific on the interaction level between individual genes, but showed large similarities on the biological function level represented by subnetworks. Remarkably, the RNAseq UC GRN showed twice the proportion of significant functional subnetworks. Based on our analysis of inferential and experimental networks the Bead UC GRN showed the lowest performance compared to the RNAseq and Oligo UC GRNs. Conclusion: To our knowledge, this is the first study investigating genome-scale UC GRNs. RNAseq based gene expression data is the data platform of choice for a GRN inference. Our study offers new avenues for the identification of novel putative diagnostic targets for subsequent studies in bladder tumors. AB - Background: Urothelial pathogenesis is a complex process driven by an underlying network of interconnected genes. The identification of novel genomic target regions and gene targets that drive urothelial carcinogenesis is crucial in order to improve our current limited understanding of urothelial cancer (UC) on the molecular level. The inference of genome-wide gene regulatory networks (GRN) from large-scale gene expression data provides a promising approach for a detailed investigation of the underlying network structure associated to urothelial carcinogenesis. Methods: In our study we inferred and compared three GRNs by the application of the BC3Net inference algorithm to large-scale transitional cell carcinoma gene expression data sets from Illumina RNAseq (179 samples), Illumina Bead arrays (165 samples) and Affymetrix Oligo microarrays (188 samples). We investigated the structural and functional properties of GRNs for the identification of molecular targets associated to urothelial cancer. Results: We found that the urothelial cancer (UC) GRNs show a significant enrichment of subnetworks that are associated with known cancer hallmarks including cell cycle, immune response, signaling, differentiation and translation. Interestingly, the most prominent subnetworks of co-located genes were found on chromosome regions 5q31.3 (RNAseq), 8q24.3 (Oligo) and 1q23.3 (Bead), which all represent known genomic regions frequently deregulated or aberated in urothelial cancer and other cancer types. Furthermore, the identified hub genes of the individual GRNs, e.g., HID1/DMC1 (tumor development), RNF17/TDRD4 (cancer antigen) and CYP4A11 (angiogenesis/ metastasis) are known cancer associated markers. The GRNs were highly dataset specific on the interaction level between individual genes, but showed large similarities on the biological function level represented by subnetworks. Remarkably, the RNAseq UC GRN showed twice the proportion of significant functional subnetworks. Based on our analysis of inferential and experimental networks the Bead UC GRN showed the lowest performance compared to the RNAseq and Oligo UC GRNs. Conclusion: To our knowledge, this is the first study investigating genome-scale UC GRNs. RNAseq based gene expression data is the data platform of choice for a GRN inference. Our study offers new avenues for the identification of novel putative diagnostic targets for subsequent studies in bladder tumors. KW - BC3Net KW - Computational genomics KW - Gene regulatory network KW - Urothelial cancer U2 - 10.1186/s12918-015-0165-z DO - 10.1186/s12918-015-0165-z M3 - Article VL - 9 JO - BMC Systems Biology JF - BMC Systems Biology SN - 1752-0509 M1 - 21 ER - TY - JOUR T1 - Variance Stabilization for Noisy+Estimate Combination in Iterative Poisson Denoising AU - Azzari, Lucio AU - Foi, Alessandro PY - 2016/8/1 Y1 - 2016/8/1 N2 - We denoise Poisson images with an iterative algorithm that progressively improves the effectiveness of variance-stabilizing transformations (VST) for Gaussian denoising filters. At each iteration, a combination of the Poisson observations with the denoised estimate from the previous iteration is treated as scaled Poisson data and filtered through a VST scheme. Due to the slight mismatch between a true scaled Poisson distribution and this combination, a special exact unbiased inverse is designed. We present an implementation of this approach based on the BM3D Gaussian denoising filter. With a computational cost at worst twice that of the noniterative scheme, the proposed algorithm provides significantly better quality, particularly at low signal-to-noise ratio, outperforming much costlier state-of-the-art alternatives. AB - We denoise Poisson images with an iterative algorithm that progressively improves the effectiveness of variance-stabilizing transformations (VST) for Gaussian denoising filters. At each iteration, a combination of the Poisson observations with the denoised estimate from the previous iteration is treated as scaled Poisson data and filtered through a VST scheme. Due to the slight mismatch between a true scaled Poisson distribution and this combination, a special exact unbiased inverse is designed. We present an implementation of this approach based on the BM3D Gaussian denoising filter. With a computational cost at worst twice that of the noniterative scheme, the proposed algorithm provides significantly better quality, particularly at low signal-to-noise ratio, outperforming much costlier state-of-the-art alternatives. KW - Anscombe transformation KW - image denoising KW - iterative filtering KW - photon-limited imaging KW - Poisson noise U2 - 10.1109/LSP.2016.2580600 DO - 10.1109/LSP.2016.2580600 M3 - Article VL - 23 SP - 1086 EP - 1090 JO - IEEE Signal Processing Letters JF - IEEE Signal Processing Letters SN - 1070-9908 IS - 8 ER -