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 - 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 - 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 - 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 - 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 - GEN T1 - Design and simulation of a slotted patch antenna sensor for wireless strain sensing AU - Yi, Xiaohua AU - Cho, Chunhee AU - Cook, Benjamin AU - Wang, Yang AU - Tentzeris, Manos M. AU - Leon, Roberto T. PY - 2013 Y1 - 2013 N2 - In this work, a slotted patch antenna is employed as a wireless sensor for monitoring structural strain and fatigue crack. Using antenna miniaturization techniques to increase the current path length, the footprint of the slotted patch antenna can be reduced to one quarter of a previously presented folded patch antenna. Electromagnetic simulations show that the antenna resonance frequency varies when the antenna is under strain. The resonance frequency variation can be wirelessly interrogated and recorded by a radiofrequency identification (RFID) reader, and can be used to derive strain/deformation. The slotted patch antenna sensor is entirely passive (battery-free), by exploiting an inexpensive off-the-shelf RFID chip that receives power from the wireless interrogation by the reader. AB - In this work, a slotted patch antenna is employed as a wireless sensor for monitoring structural strain and fatigue crack. Using antenna miniaturization techniques to increase the current path length, the footprint of the slotted patch antenna can be reduced to one quarter of a previously presented folded patch antenna. Electromagnetic simulations show that the antenna resonance frequency varies when the antenna is under strain. The resonance frequency variation can be wirelessly interrogated and recorded by a radiofrequency identification (RFID) reader, and can be used to derive strain/deformation. The slotted patch antenna sensor is entirely passive (battery-free), by exploiting an inexpensive off-the-shelf RFID chip that receives power from the wireless interrogation by the reader. KW - RFID KW - Slotted patch antenna KW - Strain sensor KW - Wireless passive sensor UR - http://www.scopus.com/inward/record.url?scp=84878419679&partnerID=8YFLogxK U2 - 10.1117/12.2009233 DO - 10.1117/12.2009233 M3 - Conference contribution SN - 9780819494771 VL - 8694 BT - Nondestructive Characterization for Composite Materials, Aerospace Engineering, Civil Infrastructure, and Homeland Security 2013 ER - TY - GEN T1 - High-performance programs by source-level merging of RVC-CAL dataflow actors AU - Boutellier, J. AU - Ghazi, A. AU - Silvén, O. AU - Ersfolk, J. PY - 2013 Y1 - 2013 N2 - RVC-CAL is a dataflow language that has acquired an ecosystem of sophisticated design tools. Previous works have shown that RVC-CAL-based applications can automatically be deployed to multiprocessor platforms, as well as hardware descriptions with high efficiency. However, as RVC-CAL is a concurrent language, code generation for a single processor core requires careful application analysis and scheduling. Although much work has been done in this area, to this date no publication has reported that programs generated from RVC-CAL could rival handwritten programs on single-core processors. This paper proposes performance optimization of RVCCAL applications by actor merging at source code level. The proposed methodology is demonstrated with an IEEE 802.15.4 (ZigBee) transmitter case study. The transmitter baseband software, previously written in C, is rewritten in RVC-CAL and optimized with the proposed methodology. Experiments show that on a VLIW-flavored processor the RVC-CAL-based program achieves the performance of manually written software. AB - RVC-CAL is a dataflow language that has acquired an ecosystem of sophisticated design tools. Previous works have shown that RVC-CAL-based applications can automatically be deployed to multiprocessor platforms, as well as hardware descriptions with high efficiency. However, as RVC-CAL is a concurrent language, code generation for a single processor core requires careful application analysis and scheduling. Although much work has been done in this area, to this date no publication has reported that programs generated from RVC-CAL could rival handwritten programs on single-core processors. This paper proposes performance optimization of RVCCAL applications by actor merging at source code level. The proposed methodology is demonstrated with an IEEE 802.15.4 (ZigBee) transmitter case study. The transmitter baseband software, previously written in C, is rewritten in RVC-CAL and optimized with the proposed methodology. Experiments show that on a VLIW-flavored processor the RVC-CAL-based program achieves the performance of manually written software. KW - Dataflow computing KW - Design automation KW - Signal processing UR - http://www.scopus.com/inward/record.url?scp=84896457580&partnerID=8YFLogxK M3 - Conference contribution SN - 9781467362382 SP - 360 EP - 365 BT - 2013 IEEE Workshop on Signal Processing Systems, SiPS 2013 PB - Institute of Electrical and Electronics Engineers Inc. 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 - GEN T1 - Parameterized core functional dataflow graphs and their application to design and implementation of wireless communication systems AU - Wang, Lai Huei AU - Shen, Chung Ching AU - Bhattacharyya, Shuvra S. PY - 2013 Y1 - 2013 N2 - Due to the increased complexity of dynamics in modern DSP applications, dataflow-based design methodologies require significant enhancements in modeling and scheduling techniques to provide for efficient and flexible handling of dynamic behavior. In this paper, we address this problem through a new framework that is based on integrating two complementary modeling techniques, core functional dataflow (CFDF) and parameterized synchronous dataflow (PSDF). We apply, in a systematically integrated way, the structured mode-based dynamic dataflow modeling capability of CFDF together with the features of PSDF for dynamic parameter reconfiguration and quasi-static scheduling. We refer to this integrated methodology for mode - and dynamic-parameter - based modeling and scheduling as core functional parameterized synchronous dataflow (CF-PSDF). Through a wireless communication case study involving MIMO detection, we demonstrate the utility of design and implementation using CF-PSDF graphs. Experimental results on this case study demonstrate the efficiency and flexibility of our proposed new CF-PSDF based design methodology. AB - Due to the increased complexity of dynamics in modern DSP applications, dataflow-based design methodologies require significant enhancements in modeling and scheduling techniques to provide for efficient and flexible handling of dynamic behavior. In this paper, we address this problem through a new framework that is based on integrating two complementary modeling techniques, core functional dataflow (CFDF) and parameterized synchronous dataflow (PSDF). We apply, in a systematically integrated way, the structured mode-based dynamic dataflow modeling capability of CFDF together with the features of PSDF for dynamic parameter reconfiguration and quasi-static scheduling. We refer to this integrated methodology for mode - and dynamic-parameter - based modeling and scheduling as core functional parameterized synchronous dataflow (CF-PSDF). Through a wireless communication case study involving MIMO detection, we demonstrate the utility of design and implementation using CF-PSDF graphs. Experimental results on this case study demonstrate the efficiency and flexibility of our proposed new CF-PSDF based design methodology. KW - Dataflow graph KW - Dynamic scheduling KW - MIMO detector KW - Parameterized modeling UR - http://www.scopus.com/inward/record.url?scp=84896476923&partnerID=8YFLogxK M3 - Conference contribution SN - 9781467362382 SP - 1 EP - 6 BT - 2013 IEEE Workshop on Signal Processing Systems, SiPS 2013 PB - Institute of Electrical and Electronics Engineers Inc. ER - TY - GEN T1 - Programmable implementation of zero-crossing demodulator on an application specific processor AU - Ghazi, Amanullah AU - Boutellier, Jani AU - Hannuksela, Jari AU - Shahabuddin, Shahriar AU - Silvén, Olli PY - 2013 Y1 - 2013 N2 - The zero-intermediate frequency zero-crossing demodulator (ZIFZCD) is extensively used for demodulating continuous phase frequency shift keying (CPFSK) signals in low power and low cost devices. ZIFZCD has previously been implemented as hardwired circuits. Many variations have been suggested to the ZIFZCD algorithm for different modulation methods and channel conditions. To support all these variants, a programmable processor based implementation of the ZIFZCD is needed. This paper describes a programmable software implementation of ZIFZCD on an application specific processor (ASP). The ASP is based on transport triggered architecture (TTA) and provides an ideal low power platform for ZIFZCD implementation due to its simplicity. The designed processor operates at a maximum clock frequency of 250 MHz and has gate count of 134 kGE for a 32-bit TTA processor and 76 kGE for a 16-bit processor. The demodulator has been developed as a part of an open source radio implementation for wireless sensor nodes. AB - The zero-intermediate frequency zero-crossing demodulator (ZIFZCD) is extensively used for demodulating continuous phase frequency shift keying (CPFSK) signals in low power and low cost devices. ZIFZCD has previously been implemented as hardwired circuits. Many variations have been suggested to the ZIFZCD algorithm for different modulation methods and channel conditions. To support all these variants, a programmable processor based implementation of the ZIFZCD is needed. This paper describes a programmable software implementation of ZIFZCD on an application specific processor (ASP). The ASP is based on transport triggered architecture (TTA) and provides an ideal low power platform for ZIFZCD implementation due to its simplicity. The designed processor operates at a maximum clock frequency of 250 MHz and has gate count of 134 kGE for a 32-bit TTA processor and 76 kGE for a 16-bit processor. The demodulator has been developed as a part of an open source radio implementation for wireless sensor nodes. KW - Demodulation KW - Signal Processing KW - Software radio UR - http://www.scopus.com/inward/record.url?scp=84896460964&partnerID=8YFLogxK M3 - Conference contribution SN - 9781467362382 SP - 231 EP - 236 BT - 2013 IEEE Workshop on Signal Processing Systems, SiPS 2013 PB - Institute of Electrical and Electronics Engineers Inc. 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 - 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 - GEN T1 - In silico study on structure and dynamics in bursting neuronal networks AU - Mäki-Marttunen, Tuomo Mikael AU - Acimovic, Jugoslava AU - Ruohonen, Keijo Pellervo AU - Linne, Marja-Leena PY - 2012/10/13 Y1 - 2012/10/13 N2 - In vitro cell cultures have been widely used as a model system for studying neuronal development and electroresponsiveness in the absence of in vivo regulation. These networks are characterized by population bursts that vary largely in both frequency and shape (Wagenaar et al., BMC Neurosci. 2000). In this work we study the interplay of structure and activity in simulated spontaneously bursting networks. The computational approach is useful due to the difficulty of gaining enough control on the structure in in vitro experiments, although promising attempts are being made in cultured neuronal networks (Wheeler, Proc. IEEE 2010). Recently, the effect of network structure on activity has been analyzed through, e.g., the degree distribution width (Roxin, Front. Comp. Neurosci. 2011) and occurrence of second-order connections (Zhao et al. 2011, Front. Comp. Neurosci. 2011). In the present work we apply a set of graph measures to a wide set of different networks in order to determine which of the structural measures are relevant in the prediction of the bursting network activity. The network activity is quantified using standard measures such as number of bursts and burst duration.We use two neuron models that are applicable to small (N=100) spontaneously bursting networks, namely, an integrate-and-fire model with short-term plasticity (Tsodyks et al., J. Neurosci. 2000) and a more detailed point-neuron model with four ionic and three synaptic currents (Golomb et al., J. Neurophysiol. 2006). We show that when the in-degree is sharp (binomial), the network activity is best predicted by using the clustering coefficient of the underlying graph. By contrast, when a broad in-degree is used (power-law), the maximum eigenvalue of the connectivity matrix becomes dominant in predicting the network activity. The results are consistent across the two neuron models. In our work the neurons are identical by their features, and no input is applied to the network, and hence all statistical difference between the compared networks is caused by the network structure and the network structure only.The obtained results shed light on the relevance of different aspects of structure. In in vivo applications the full connectome is rarely accessible, but estimates of certain structural measures may be assessed indirectly (Vlachos et al., PLoS Comp. Biol. 2012). Extracting the structure-function relationship in neuronal networks may have implication on both the way experiments are conducted and on how biologically inspired artificial intelligence will be designed in the future. AB - In vitro cell cultures have been widely used as a model system for studying neuronal development and electroresponsiveness in the absence of in vivo regulation. These networks are characterized by population bursts that vary largely in both frequency and shape (Wagenaar et al., BMC Neurosci. 2000). In this work we study the interplay of structure and activity in simulated spontaneously bursting networks. The computational approach is useful due to the difficulty of gaining enough control on the structure in in vitro experiments, although promising attempts are being made in cultured neuronal networks (Wheeler, Proc. IEEE 2010). Recently, the effect of network structure on activity has been analyzed through, e.g., the degree distribution width (Roxin, Front. Comp. Neurosci. 2011) and occurrence of second-order connections (Zhao et al. 2011, Front. Comp. Neurosci. 2011). In the present work we apply a set of graph measures to a wide set of different networks in order to determine which of the structural measures are relevant in the prediction of the bursting network activity. The network activity is quantified using standard measures such as number of bursts and burst duration.We use two neuron models that are applicable to small (N=100) spontaneously bursting networks, namely, an integrate-and-fire model with short-term plasticity (Tsodyks et al., J. Neurosci. 2000) and a more detailed point-neuron model with four ionic and three synaptic currents (Golomb et al., J. Neurophysiol. 2006). We show that when the in-degree is sharp (binomial), the network activity is best predicted by using the clustering coefficient of the underlying graph. By contrast, when a broad in-degree is used (power-law), the maximum eigenvalue of the connectivity matrix becomes dominant in predicting the network activity. The results are consistent across the two neuron models. In our work the neurons are identical by their features, and no input is applied to the network, and hence all statistical difference between the compared networks is caused by the network structure and the network structure only.The obtained results shed light on the relevance of different aspects of structure. In in vivo applications the full connectome is rarely accessible, but estimates of certain structural measures may be assessed indirectly (Vlachos et al., PLoS Comp. Biol. 2012). Extracting the structure-function relationship in neuronal networks may have implication on both the way experiments are conducted and on how biologically inspired artificial intelligence will be designed in the future. M3 - Conference contribution BT - Neuroscience 2012; 42nd Annual Meeting, New Orleans, USA, October 14-18, 2012 PB - Society for Neuroscience (SfN) 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 - 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 - 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 - 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 - 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 - 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 - 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 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 - GEN T1 - Multidimensional dataflow graph modeling and mapping for efficient GPU implementation AU - Wang, Lai Huei AU - Shen, Chung Ching AU - Seetharaman, Gunasekaran AU - Palaniappan, Kannappan AU - Bhattacharyya, Shuvra S. PY - 2012 Y1 - 2012 N2 - Multidimensional synchronous dataflow (MDSDF) provides an effective model of computation for a variety of multidimensional DSP systems that have static dataflow structures. In this paper, we develop new methods for optimized implementation of MDSDF graphs on embedded platforms that employ multiple levels of parallelism to enhance performance at different levels of granularity. Our approach allows designers to systematically represent and transform multi-level parallelism specifications from a common, MDSDF-based application level model. We demonstrate our methods with a case study of image histogram implementation on a graphics processing unit (GPU). Experimental results from this study show that our approach can be used to derive fast GPU implementations, and enhance trade-off analysis during design space exploration. AB - Multidimensional synchronous dataflow (MDSDF) provides an effective model of computation for a variety of multidimensional DSP systems that have static dataflow structures. In this paper, we develop new methods for optimized implementation of MDSDF graphs on embedded platforms that employ multiple levels of parallelism to enhance performance at different levels of granularity. Our approach allows designers to systematically represent and transform multi-level parallelism specifications from a common, MDSDF-based application level model. We demonstrate our methods with a case study of image histogram implementation on a graphics processing unit (GPU). Experimental results from this study show that our approach can be used to derive fast GPU implementations, and enhance trade-off analysis during design space exploration. KW - Dataflow graph KW - Graphics processing unit KW - Integral histogram KW - Multidimensional synchronous dataflow UR - http://www.scopus.com/inward/record.url?scp=84875330462&partnerID=8YFLogxK U2 - 10.1109/SiPS.2012.10 DO - 10.1109/SiPS.2012.10 M3 - Conference contribution SN - 9780769548562 SP - 300 EP - 305 BT - Proceedings - 2012 IEEE Workshop on Signal Processing Systems, SiPS 2012 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 - 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 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 - 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 - GEN T1 - Effects of structure on spontaneous activity in simulated neuronal networks AU - Mäki-Marttunen, Tuomo AU - Acimovic, Jugoslava AU - Ruohonen, Keijo AU - Linne, Marja-Leena PY - 2011/4/11 Y1 - 2011/4/11 M3 - Conference contribution BT - Proceedings of Mathematical Neuroscience (ICMS 2011), April 11-13, 2011, Edinburgh, Scotland 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 - 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 - GEN T1 - Multicolor nonlinear pulse compression by consecutive optical parametric amplification in quasi-phase matched structures AU - Sapaev, U. K. AU - Yusupov, D. B. AU - Assanto, G. PY - 2011 Y1 - 2011 N2 - Simultaneous generation of the 2nd and 3rd harmonic, excited by linearly frequency-chirped fundamental pulse in quasiphase matched grating with linearly varying inverse domain sizes has been studied numerically with taking into account effects of the group velocity mismatches and dispersions. Mechanisms of efficient nonlinear pulse compressions and conversion efficiencies of the generated harmonics have been analyzed. AB - Simultaneous generation of the 2nd and 3rd harmonic, excited by linearly frequency-chirped fundamental pulse in quasiphase matched grating with linearly varying inverse domain sizes has been studied numerically with taking into account effects of the group velocity mismatches and dispersions. Mechanisms of efficient nonlinear pulse compressions and conversion efficiencies of the generated harmonics have been analyzed. KW - Cascading KW - Lithium niobate KW - Nonlinear pulse compression KW - Parametric effects KW - Quasi-phase matching KW - Simultaneous frequency doubling and tripling UR - http://www.scopus.com/inward/record.url?scp=79951653950&partnerID=8YFLogxK U2 - 10.1117/12.882887 DO - 10.1117/12.882887 M3 - Conference contribution SN - 9780819485663 VL - 7993 BT - ICONO 2010: International Conference on Coherent and Nonlinear Optics 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - GEN T1 - Labyrinth based left-handed metamaterials and sub-wavelength focusing of electromagnetic waves AU - Ozbay, Ekmel AU - Bulu, Irfan AU - Caglayan, Humeyra N1 - EXT="Caglayan, Humeyra" PY - 2006 Y1 - 2006 N2 - We propose and demonstrate a resonant structure that solves two major problems related to the split-ring resonator structure. These major problems may be stated as the bianisotropy and electric coupling to the magnetic resonance. These two problems introduce difficulties in obtaining isotropic left-handed metamaterial mediums. The resonant structure that we propose here solves both of these problems. We further show that in addition to the magnetic resonance, when combined with a suitable wire medium, the structure that we propose exhibits left-handed transmission band. We further demonstrate the sub-wavelength focusing of electromagnetic waves by use of a two dimensional labyrinth based metamaterial. Our experimental results showed that it is possible to focus the source field with half widths as small as λ/4 by using the labyrinth based metamaterial. AB - We propose and demonstrate a resonant structure that solves two major problems related to the split-ring resonator structure. These major problems may be stated as the bianisotropy and electric coupling to the magnetic resonance. These two problems introduce difficulties in obtaining isotropic left-handed metamaterial mediums. The resonant structure that we propose here solves both of these problems. We further show that in addition to the magnetic resonance, when combined with a suitable wire medium, the structure that we propose exhibits left-handed transmission band. We further demonstrate the sub-wavelength focusing of electromagnetic waves by use of a two dimensional labyrinth based metamaterial. Our experimental results showed that it is possible to focus the source field with half widths as small as λ/4 by using the labyrinth based metamaterial. KW - Left-handed medium KW - Magnetic Resonance KW - Metamaterial KW - Split-ring Resonator KW - Sub-wavelength Focusing UR - http://www.scopus.com/inward/record.url?scp=33745626124&partnerID=8YFLogxK U2 - 10.1117/12.649548 DO - 10.1117/12.649548 M3 - Conference contribution SN - 0819461709 SN - 9780819461704 VL - 6128 T3 - Proceedings of SPIE BT - Photonic Crystal Materials and Devices IV 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 -