Publisher name: Oxford University Press PY - 2015/1/1 Y1 - 2015/1/1 N2 - Motivation: MS2-GFP-tagging of RNA is currently the only method to measure intervals between consecutive transcription events in live cells. For this, new transcripts must be accurately detected from intensity time traces. Results: We present a novel method for automatically estimating RNA numbers and production intervals from temporal data of cell fluorescence intensities that reduces uncertainty by exploiting temporal information. We also derive a robust variant, more resistant to outliers caused e.g. by RNAs moving out of focus. Using Monte Carlo simulations, we show that the quantification of RNA numbers and production intervals is generally improved compared with previous methods. Finally, we analyze data from live Escherichia coli and show statistically significant differences to previous methods. The new methods can be used to quantify numbers and production intervals of any fluorescent probes, which are present in low copy numbers, are brighter than the cell background and degrade slowly. Availability: Source code is available under Mozilla Public License at http://www.cs.tut.fi/%7ehakkin22/jumpdet/. Contact: AB - Motivation: MS2-GFP-tagging of RNA is currently the only method to measure intervals between consecutive transcription events in live cells. For this, new transcripts must be accurately detected from intensity time traces. Results: We present a novel method for automatically estimating RNA numbers and production intervals from temporal data of cell fluorescence intensities that reduces uncertainty by exploiting temporal information. We also derive a robust variant, more resistant to outliers caused e.g. by RNAs moving out of focus. Using Monte Carlo simulations, we show that the quantification of RNA numbers and production intervals is generally improved compared with previous methods. Finally, we analyze data from live Escherichia coli and show statistically significant differences to previous methods. The new methods can be used to quantify numbers and production intervals of any fluorescent probes, which are present in low copy numbers, are brighter than the cell background and degrade slowly. Availability: Source code is available under Mozilla Public License at http://www.cs.tut.fi/%7ehakkin22/jumpdet/. Contact: UR - http://www.scopus.com/inward/record.url?scp=84922352843&partnerID=8YFLogxK U2 - 10.1093/bioinformatics/btu592 DO - 10.1093/bioinformatics/btu592 M3 - Article VL - 31 SP - 69 EP - 75 JO - Bioinformatics JF - Bioinformatics SN - 1367-4803 IS - 1 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 - Gene set analysis for self-contained tests T2 - Complex null and specific alternative hypotheses AU - Rahmatallah, Y. AU - Emmert-Streib, F. AU - Glazko, G. PY - 2012/12 Y1 - 2012/12 N2 - Motivation: The analysis of differentially expressed gene sets became a routine in the analyses of gene expression data. There is a multitude of tests available, ranging from aggregation tests that summarize gene-level statistics for a gene set to true multivariate tests, accounting for intergene correlations. Most of them detect complex departures from the null hypothesis but when the null hypothesis is rejected the specific alternative leading to the rejection is not easily identifiable. Results: In this article we compare the power and Type I error rates of minimum-spanning tree (MST)-based non-parametric multivariate tests with several multivariate and aggregation tests, which are frequently used for pathway analyses. In our simulation study, we demonstrate that MST-based tests have power that is for many settings comparable with the power of conventional approaches, but outperform them in specific regions of the parameter space corresponding to biologically relevant configurations. Further, we find for simulated and for gene expression data that MST-based tests discriminate well against shift and scale alternatives. As a general result, we suggest a two-step practical analysis strategy that may increase the interpretability of experimental data: first, apply the most powerful multivariate test to find the subset of pathways for which the null hypothesis is rejected and second, apply MST-based tests to these pathways to select those that support specific alternative hypotheses. AB - Motivation: The analysis of differentially expressed gene sets became a routine in the analyses of gene expression data. There is a multitude of tests available, ranging from aggregation tests that summarize gene-level statistics for a gene set to true multivariate tests, accounting for intergene correlations. Most of them detect complex departures from the null hypothesis but when the null hypothesis is rejected the specific alternative leading to the rejection is not easily identifiable. Results: In this article we compare the power and Type I error rates of minimum-spanning tree (MST)-based non-parametric multivariate tests with several multivariate and aggregation tests, which are frequently used for pathway analyses. In our simulation study, we demonstrate that MST-based tests have power that is for many settings comparable with the power of conventional approaches, but outperform them in specific regions of the parameter space corresponding to biologically relevant configurations. Further, we find for simulated and for gene expression data that MST-based tests discriminate well against shift and scale alternatives. As a general result, we suggest a two-step practical analysis strategy that may increase the interpretability of experimental data: first, apply the most powerful multivariate test to find the subset of pathways for which the null hypothesis is rejected and second, apply MST-based tests to these pathways to select those that support specific alternative hypotheses. UR - http://www.scopus.com/inward/record.url?scp=84870441671&partnerID=8YFLogxK U2 - 10.1093/bioinformatics/bts579 DO - 10.1093/bioinformatics/bts579 M3 - Article VL - 28 SP - 3073 EP - 3080 JO - Bioinformatics JF - Bioinformatics SN - 1367-4803 IS - 23 ER - TY - JOUR T1 - Gene Sets Net Correlations Analysis (GSNCA) T2 - A multivariate differential coexpression test for gene sets AU - Rahmatallah, Yasir AU - Emmert-Streib, Frank AU - Glazko, Galina PY - 2014/2/1 Y1 - 2014/2/1 N2 - Motivation: To date, gene set analysis approaches primarily focus on identifying differentially expressed gene sets (pathways). Methods for identifying differentially coexpressed pathways also exist but are mostly based on aggregated pairwise correlations or other pairwise measures of coexpression. Instead, we propose Gene Sets Net Correlations Analysis (GSNCA), a multivariate differential coexpression test that accounts for the complete correlation structure between genes.Results: In GSNCA, weight factors are assigned to genes in proportion to the genes' cross-correlations (intergene correlations). The problem of finding the weight vectors is formulated as an eigenvector problem with a unique solution. GSNCA tests the null hypothesis that for a gene set there is no difference in the weight vectors of the genes between two conditions. In simulation studies and the analyses of experimental data, we demonstrate that GSNCA captures changes in the structure of genes' cross-correlations rather than differences in the averaged pairwise correlations. Thus, GSNCA infers differences in coexpression networks, however, bypassing method-dependent steps of network inference. As an additional result from GSNCA, we define hub genes as genes with the largest weights and show that these genes correspond frequently to major and specific pathway regulators, as well as to genes that are most affected by the biological difference between two conditions. In summary, GSNCA is a new approach for the analysis of differentially coexpressed pathways that also evaluates the importance of the genes in the pathways, thus providing unique information that may result in the generation of novel biological hypotheses. AB - Motivation: To date, gene set analysis approaches primarily focus on identifying differentially expressed gene sets (pathways). Methods for identifying differentially coexpressed pathways also exist but are mostly based on aggregated pairwise correlations or other pairwise measures of coexpression. Instead, we propose Gene Sets Net Correlations Analysis (GSNCA), a multivariate differential coexpression test that accounts for the complete correlation structure between genes.Results: In GSNCA, weight factors are assigned to genes in proportion to the genes' cross-correlations (intergene correlations). The problem of finding the weight vectors is formulated as an eigenvector problem with a unique solution. GSNCA tests the null hypothesis that for a gene set there is no difference in the weight vectors of the genes between two conditions. In simulation studies and the analyses of experimental data, we demonstrate that GSNCA captures changes in the structure of genes' cross-correlations rather than differences in the averaged pairwise correlations. Thus, GSNCA infers differences in coexpression networks, however, bypassing method-dependent steps of network inference. As an additional result from GSNCA, we define hub genes as genes with the largest weights and show that these genes correspond frequently to major and specific pathway regulators, as well as to genes that are most affected by the biological difference between two conditions. In summary, GSNCA is a new approach for the analysis of differentially coexpressed pathways that also evaluates the importance of the genes in the pathways, thus providing unique information that may result in the generation of novel biological hypotheses. UR - http://www.scopus.com/inward/record.url?scp=84893275855&partnerID=8YFLogxK U2 - 10.1093/bioinformatics/btt687 DO - 10.1093/bioinformatics/btt687 M3 - Article VL - 30 SP - 360 EP - 368 JO - Bioinformatics JF - Bioinformatics SN - 1367-4803 IS - 3 ER - TY - JOUR T1 - Graph distance measures based on topological indices revisited AU - Dehmer, Matthias AU - Emmert-Streib, Frank AU - Shi, Yongtang PY - 2015/6/18 Y1 - 2015/6/18 N2 - Graph distance measures based on topological indices have been already explored by Dehmer et al. Also, inequalities for those graph distance measures have been proved. In this paper, we continue studying such comparative graph measures based on the well-known Wiener index, graph energy and Randić index, respectively. We prove extremal properties of the graph distance measures for some special classes of graphs. To demonstrate useful properties of the measures, we also discuss numerical results. To conclude the paper we state some open problems. AB - Graph distance measures based on topological indices have been already explored by Dehmer et al. Also, inequalities for those graph distance measures have been proved. In this paper, we continue studying such comparative graph measures based on the well-known Wiener index, graph energy and Randić index, respectively. We prove extremal properties of the graph distance measures for some special classes of graphs. To demonstrate useful properties of the measures, we also discuss numerical results. To conclude the paper we state some open problems. KW - Distance measure KW - Edit distance KW - Extremal graph KW - Topological index U2 - 10.1016/j.amc.2015.05.072 DO - 10.1016/j.amc.2015.05.072 M3 - Article VL - 266 SP - 623 EP - 633 JO - Applied Mathematics and Computation JF - Applied Mathematics and Computation SN - 0096-3003 ER - TY - JOUR T1 - Graph entropy based on the number of spanning forests of c-cyclic graphs AU - Wan, Pengfei AU - Tu, Jianhua AU - Dehmer, Matthias AU - Zhang, Shenggui AU - Emmert-Streib, Frank PY - 2019/12/15 Y1 - 2019/12/15 N2 - Graph entropies have been introduced to quantitatively measure the structural information content of graphs and networks; they have plenty of applications in various fields. Utilizing the number of subgraphs to establish measures for determining the complexity of molecular graphs are also prevalent in the study of mathematical chemistry. In this paper, we develop a new graph entropy measure that is based on the number of spanning forests. We prove explicit expressions for the entropy for trees, unicyclic and bicyclic graphs, and show that the cycle graph Cn attains the maximal value of the entropy for unicyclic graphs with order n and large cycle lengths. Based on generating numerical results, we conjecture extremal unicyclic graphs with respect to the entropy as well as we compare the values of our entropy for c-cyclic graphs, and generate graphs of bicyclic graphs and tricyclic graphs with 6 vertices for performing further research. AB - Graph entropies have been introduced to quantitatively measure the structural information content of graphs and networks; they have plenty of applications in various fields. Utilizing the number of subgraphs to establish measures for determining the complexity of molecular graphs are also prevalent in the study of mathematical chemistry. In this paper, we develop a new graph entropy measure that is based on the number of spanning forests. We prove explicit expressions for the entropy for trees, unicyclic and bicyclic graphs, and show that the cycle graph Cn attains the maximal value of the entropy for unicyclic graphs with order n and large cycle lengths. Based on generating numerical results, we conjecture extremal unicyclic graphs with respect to the entropy as well as we compare the values of our entropy for c-cyclic graphs, and generate graphs of bicyclic graphs and tricyclic graphs with 6 vertices for performing further research. KW - Graph entropy KW - Spanning forest KW - Subgraph U2 - 10.1016/j.amc.2019.124616 DO - 10.1016/j.amc.2019.124616 M3 - Article VL - 363 JO - Applied Mathematics and Computation JF - Applied Mathematics and Computation SN - 0096-3003 M1 - 124616 ER - TY - JOUR T1 - Growth behavior and magnetic properties of spherical uranium oxide nanoclusters AU - Ma, Li AU - Ray, Asok K. PY - 2013/2 Y1 - 2013/2 N2 - The growth behavior and magnetic properties of spherical uranium oxide nanoclusters have been investigated using the generalized gradient approximation (GGA) to density functional theory (DFT). The geometries of UnO m clusters remain the Oh symmetry after DFT relaxation. The largest binding energy corresponds to the cluster with the smallest deviation from the bulk (UO2) ratio. The electronic structures and magnetic properties of these nanoclusters are presented. We find the chemical bonding between the U and O atoms has a significant ionic character. The reduction of magnetism in the inner positions can be understood by the charge transfer and the hybridization between U atoms and the neighboring O atoms. AB - The growth behavior and magnetic properties of spherical uranium oxide nanoclusters have been investigated using the generalized gradient approximation (GGA) to density functional theory (DFT). The geometries of UnO m clusters remain the Oh symmetry after DFT relaxation. The largest binding energy corresponds to the cluster with the smallest deviation from the bulk (UO2) ratio. The electronic structures and magnetic properties of these nanoclusters are presented. We find the chemical bonding between the U and O atoms has a significant ionic character. The reduction of magnetism in the inner positions can be understood by the charge transfer and the hybridization between U atoms and the neighboring O atoms. KW - Growth behavior KW - Magnetism KW - Nanoclusters KW - Uranium oxide UR - http://www.scopus.com/inward/record.url?scp=84876525693&partnerID=8YFLogxK U2 - 10.1166/jctn.2013.2701 DO - 10.1166/jctn.2013.2701 M3 - Article VL - 10 SP - 334 EP - 340 JO - Journal of Computational and Theoretical Nanoscience JF - Journal of Computational and Theoretical Nanoscience SN - 1546-1955 IS - 2 ER - TY - JOUR T1 - Homogeneous (α,k)-Polynomial Solutions of the Fractional Riesz System in Hyperbolic Space AU - Orelma, H. AU - Vieira, N. PY - 2017 Y1 - 2017 N2 - In this paper we study the fractional analogous of the Laplace–Beltrami equation and the hyperbolic Riesz system studied previously by H. Leutwiler, in (Formula presented.). In both cases we replace the integer derivatives by Caputo fractional derivatives of order (Formula presented.). We characterize the space of solutions of the fractional Laplace–Beltrami equation, and we calculate its dimension. We establish relations between the solutions of the fractional Laplace–Beltrami equation and the solutions of the hyperbolic fractional Riesz system. Some examples of the polynomial solutions will be presented. Moreover, the behaviour of the obtained results when (Formula presented.) is presented, and a final remark about the consideration of Riemann–Liouville fractional derivatives instead of Caputo fractional derivatives is made. AB - In this paper we study the fractional analogous of the Laplace–Beltrami equation and the hyperbolic Riesz system studied previously by H. Leutwiler, in (Formula presented.). In both cases we replace the integer derivatives by Caputo fractional derivatives of order (Formula presented.). We characterize the space of solutions of the fractional Laplace–Beltrami equation, and we calculate its dimension. We establish relations between the solutions of the fractional Laplace–Beltrami equation and the solutions of the hyperbolic fractional Riesz system. Some examples of the polynomial solutions will be presented. Moreover, the behaviour of the obtained results when (Formula presented.) is presented, and a final remark about the consideration of Riemann–Liouville fractional derivatives instead of Caputo fractional derivatives is made. KW - Caputo fractional derivative KW - Hyperbolic KW - Hyperbolic fractional Riesz system KW - Hypermonogenic functions KW - Laplace–Beltrami fractional differential operator U2 - 10.1007/s11785-017-0666-4 DO - 10.1007/s11785-017-0666-4 M3 - Article VL - 11 SP - 1253 EP - 1267 JO - Complex Analysis and Operator Theory JF - Complex Analysis and Operator Theory SN - 1661-8254 IS - 5 ER - TY - JOUR T1 - Hypermonogenic Functions of Two Vector Variables AU - Eriksson, S. L. AU - Orelma, H. AU - Vieira, N. N1 - EXT="Eriksson, S. L." PY - 2018 Y1 - 2018 N2 - In this paper we introduce the modified Dirac operators (Formula presented.) and (Formula presented.), where (Formula presented.) is differentiable function, and (Formula presented.) is the Clifford algebra generated by the basis vectors of (Formula presented.). We look for solutions (Formula presented.) of the system (Formula presented.), where the first and third variables are invariant under rotations. These functions are called (Formula presented.)-hypermonogenic functions. We discuss about axially symmetric functions with respect to the symmetric group (Formula presented.). Some examples of axially symmetric (Formula presented.)-hypermonogenic functions generated by homogeneous functions and hypergeometric functions are presented. AB - In this paper we introduce the modified Dirac operators (Formula presented.) and (Formula presented.), where (Formula presented.) is differentiable function, and (Formula presented.) is the Clifford algebra generated by the basis vectors of (Formula presented.). We look for solutions (Formula presented.) of the system (Formula presented.), where the first and third variables are invariant under rotations. These functions are called (Formula presented.)-hypermonogenic functions. We discuss about axially symmetric functions with respect to the symmetric group (Formula presented.). Some examples of axially symmetric (Formula presented.)-hypermonogenic functions generated by homogeneous functions and hypergeometric functions are presented. KW - Axially symmetric functions KW - Hypermonogenic functions KW - Modified Dirac operator KW - Several vector variables U2 - 10.1007/s11785-017-0728-7 DO - 10.1007/s11785-017-0728-7 M3 - Article VL - 12 SP - 555 EP - 570 JO - Complex Analysis and Operator Theory JF - Complex Analysis and Operator Theory SN - 1661-8254 IS - 2 ER - TY - JOUR T1 - Hypermonogenic solutions and plane waves of the Dirac operator in Rp×Rq AU - Guzmán Adán, Alí AU - Orelma, Heikki AU - Sommen, Franciscus PY - 2019/4/1 Y1 - 2019/4/1 N2 - In this paper we first define hypermonogenic solutions of the Dirac operator in Rp×Rq and study some basic properties, e.g., obtaining a Cauchy integral formula in the unit hemisphere. Hypermonogenic solutions form a natural function class in classical Clifford analysis. After that, we define the corresponding hypermonogenic plane wave solutions and deduce explicit methods to compute these functions. AB - In this paper we first define hypermonogenic solutions of the Dirac operator in Rp×Rq and study some basic properties, e.g., obtaining a Cauchy integral formula in the unit hemisphere. Hypermonogenic solutions form a natural function class in classical Clifford analysis. After that, we define the corresponding hypermonogenic plane wave solutions and deduce explicit methods to compute these functions. KW - Cauchy's formula KW - Hypermonogenic solution KW - Plane wave U2 - 10.1016/j.amc.2018.09.058 DO - 10.1016/j.amc.2018.09.058 M3 - Article VL - 346 SP - 1 EP - 14 JO - Applied Mathematics and Computation JF - Applied Mathematics and Computation SN - 0096-3003 ER - TY - JOUR T1 - Information theoretic measures of UHG graphs with low computational complexity AU - Emmert-Streib, Frank AU - Dehmer, Matthias PY - 2007/7/15 Y1 - 2007/7/15 N2 - We introduce a novel graph class we call universal hierarchical graphs (UHG) whose topology can be found numerously in problems representing, e.g., temporal, spacial or general process structures of systems. For this graph class we show, that we can naturally assign two probability distributions, for nodes and for edges, which lead us directly to the definition of the entropy and joint entropy and, hence, mutual information establishing an information theory for this graph class. Furthermore, we provide some results under which conditions these constraint probability distributions maximize the corresponding entropy. Also, we demonstrate that these entropic measures can be computed efficiently which is a prerequisite for every large scale practical application and show some numerical examples. AB - We introduce a novel graph class we call universal hierarchical graphs (UHG) whose topology can be found numerously in problems representing, e.g., temporal, spacial or general process structures of systems. For this graph class we show, that we can naturally assign two probability distributions, for nodes and for edges, which lead us directly to the definition of the entropy and joint entropy and, hence, mutual information establishing an information theory for this graph class. Furthermore, we provide some results under which conditions these constraint probability distributions maximize the corresponding entropy. Also, we demonstrate that these entropic measures can be computed efficiently which is a prerequisite for every large scale practical application and show some numerical examples. KW - Entropy KW - Graph classes KW - Graph measures KW - Hierarchical graphs KW - Information theory UR - http://www.scopus.com/inward/record.url?scp=34250623666&partnerID=8YFLogxK U2 - 10.1016/j.amc.2007.02.095 DO - 10.1016/j.amc.2007.02.095 M3 - Article VL - 190 SP - 1783 EP - 1794 JO - Applied Mathematics and Computation JF - Applied Mathematics and Computation SN - 0096-3003 IS - 2 ER - TY - JOUR T1 - Integral kernels for k-hypermonogenic functions AU - Vuojamo, Vesa AU - Eriksson, Sirkka-Liisa N1 - EXT="Eriksson, Sirkka-Liisa" PY - 2017 Y1 - 2017 N2 - We consider the modified Cauchy–Riemann operator (Formula presented.) in the universal Clifford algebra (Formula presented.) with the basis (Formula presented.). The null-solutions of this operator are called k-hypermonogenic functions. We calculate the k-hyperbolic harmonic fundamental solutions, i.e. solutions to (Formula presented.), and use these solutions to find k-hypermonogenic kernels for a Cauchy-type integral formula in the upper half-space. AB - We consider the modified Cauchy–Riemann operator (Formula presented.) in the universal Clifford algebra (Formula presented.) with the basis (Formula presented.). The null-solutions of this operator are called k-hypermonogenic functions. We calculate the k-hyperbolic harmonic fundamental solutions, i.e. solutions to (Formula presented.), and use these solutions to find k-hypermonogenic kernels for a Cauchy-type integral formula in the upper half-space. KW - Cauchy integral formula KW - Clifford algebra KW - hyperbolic Laplace–Beltrami KW - k-hyperbolic harmonic KW - k-hypermonogenic U2 - 10.1080/17476933.2016.1250402 DO - 10.1080/17476933.2016.1250402 M3 - Article VL - 62 SP - 1 EP - 12 JO - Complex Variables and Elliptic Equations JF - Complex Variables and Elliptic Equations SN - 1747-6933 IS - 9 ER - TY - JOUR T1 - Introducing libeemd T2 - a program package for performing the ensemble empirical mode decomposition AU - Luukko, P. J. J. AU - Helske, J. AU - Räsänen, E. N1 - EXT="Luukko, P. J. J." PY - 2016/6/1 Y1 - 2016/6/1 N2 - The ensemble empirical mode decomposition (EEMD) and its complete variant (CEEMDAN) are adaptive, noise-assisted data analysis methods that improve on the ordinary empirical mode decomposition (EMD). All these methods decompose possibly nonlinear and/or nonstationary time series data into a finite amount of components separated by instantaneous frequencies. This decomposition provides a powerful method to look into the different processes behind a given time series data, and provides a way to separate short time-scale events from a general trend. We present a free software implementation of EMD, EEMD and CEEMDAN and give an overview of the EMD methodology and the algorithms used in the decomposition. We release our implementation, libeemd, with the aim of providing a user-friendly, fast, stable, well-documented and easily extensible EEMD library for anyone interested in using (E)EMD in the analysis of time series data. While written in C for numerical efficiency, our implementation includes interfaces to the Python and R languages, and interfaces to other languages are straightforward. AB - The ensemble empirical mode decomposition (EEMD) and its complete variant (CEEMDAN) are adaptive, noise-assisted data analysis methods that improve on the ordinary empirical mode decomposition (EMD). All these methods decompose possibly nonlinear and/or nonstationary time series data into a finite amount of components separated by instantaneous frequencies. This decomposition provides a powerful method to look into the different processes behind a given time series data, and provides a way to separate short time-scale events from a general trend. We present a free software implementation of EMD, EEMD and CEEMDAN and give an overview of the EMD methodology and the algorithms used in the decomposition. We release our implementation, libeemd, with the aim of providing a user-friendly, fast, stable, well-documented and easily extensible EEMD library for anyone interested in using (E)EMD in the analysis of time series data. While written in C for numerical efficiency, our implementation includes interfaces to the Python and R languages, and interfaces to other languages are straightforward. KW - Adaptive data analysis KW - Detrending KW - Hilbert–Huang transform KW - Intrinsic mode function KW - Noise-assisted data analysis KW - Time series analysis U2 - 10.1007/s00180-015-0603-9 DO - 10.1007/s00180-015-0603-9 M3 - Article VL - 31 SP - 545 EP - 557 JO - Computational Statistics JF - Computational Statistics SN - 0943-4062 IS - 2 ER - TY - GEN T1 - Introducing Multi-Convexity in Path Constrained Trajectory Optimization for Mobile Manipulators AU - Singh, Arun Kumar AU - Ahonen, Andrei AU - Ghabcheloo, Reza AU - Mueller, Andreas N1 - EXT="Singh, Arun Kumar" PY - 2020 Y1 - 2020 N2 - Mobile manipulators have a highly non-linear and non-convex mapping between the end-effector path and the manipulator's joints and position and orientation of the mobile base. As a result, trajectory optimization with end-effector path constraints takes the form of a difficult non-linear optimization problem. In this paper, we present the first multi-convex approximation to this difficult optimization problem that eventually reduces to solving a sequence of globally valid convex quadratic programs (QPs). The proposed optimizer rests on two novel building blocks. First, we introduce a set of auxiliary variables in which the non-linear constraints that arise out of manipulator kinematics and its coupling with the mobile base have a multi-affine form. Projecting the auxiliary variables to the space of actual configuration variables of the mobile manipulator involves a non-convex optimization. Thus, the second building block involves computing a convex surrogate for this non-convex projection. We show how large parts of the proposed optimizer can be solved in parallel providing the possibility of exploiting multi-core CPUs. We validate our trajectory optimization on different benchmark examples. Specifically, we highlight how it solves the cyclicity problem and provides a holistic approach where a diverse set of trajectories can be obtained by trading-off different aspects of manipulator and mobile base motion. AB - Mobile manipulators have a highly non-linear and non-convex mapping between the end-effector path and the manipulator's joints and position and orientation of the mobile base. As a result, trajectory optimization with end-effector path constraints takes the form of a difficult non-linear optimization problem. In this paper, we present the first multi-convex approximation to this difficult optimization problem that eventually reduces to solving a sequence of globally valid convex quadratic programs (QPs). The proposed optimizer rests on two novel building blocks. First, we introduce a set of auxiliary variables in which the non-linear constraints that arise out of manipulator kinematics and its coupling with the mobile base have a multi-affine form. Projecting the auxiliary variables to the space of actual configuration variables of the mobile manipulator involves a non-convex optimization. Thus, the second building block involves computing a convex surrogate for this non-convex projection. We show how large parts of the proposed optimizer can be solved in parallel providing the possibility of exploiting multi-core CPUs. We validate our trajectory optimization on different benchmark examples. Specifically, we highlight how it solves the cyclicity problem and provides a holistic approach where a diverse set of trajectories can be obtained by trading-off different aspects of manipulator and mobile base motion. M3 - Conference contribution SN - 978-1-7281-8813-3 SP - 1178 EP - 1185 BT - European Control Conference 2020, ECC 2020 PB - IEEE ER - TY - JOUR T1 - Machine learning T2 - How it can help nanocomputing AU - Uusitalo, Mikko A. AU - Peltonen, Jaakko AU - Ryhänen, Tapani PY - 2011/8 Y1 - 2011/8 N2 - We examine possibilities for making advances in nanocomputing by bringing in ideas from the field of machine learning. The potential from combining machine learning with nanocomputing seems to be underutilized. We review three complementary approaches. Firstly, machine learning can be used in the different phases of developing complicated nanocomputing devices: in modeling, designing, constructing, and programming the devices. Secondly, machine learning methods implemented by nanocomputing hardware can be a competitive solution especially for specialized application areas like sensory information processing; working towards such implementations advances nanocomputing by guiding development of the nanocomponents and architectures required for such applications. Thirdly, nanotechnology enabled quantum computing can significantly increase our capacity to solve NP-complete optimization problems; although this increase is not specific to machine learning, several such problems occur in machine learning and artificial intelligence, hence solving such problems is a useful goal that partly motivates development of quantum computing. The main value of this paper is to provide new ideas for researchers working on nanocomputing, nanoarchitectures, development and design of nanoprocessors and other nanocomponents, or nanomanufacturing. AB - We examine possibilities for making advances in nanocomputing by bringing in ideas from the field of machine learning. The potential from combining machine learning with nanocomputing seems to be underutilized. We review three complementary approaches. Firstly, machine learning can be used in the different phases of developing complicated nanocomputing devices: in modeling, designing, constructing, and programming the devices. Secondly, machine learning methods implemented by nanocomputing hardware can be a competitive solution especially for specialized application areas like sensory information processing; working towards such implementations advances nanocomputing by guiding development of the nanocomponents and architectures required for such applications. Thirdly, nanotechnology enabled quantum computing can significantly increase our capacity to solve NP-complete optimization problems; although this increase is not specific to machine learning, several such problems occur in machine learning and artificial intelligence, hence solving such problems is a useful goal that partly motivates development of quantum computing. The main value of this paper is to provide new ideas for researchers working on nanocomputing, nanoarchitectures, development and design of nanoprocessors and other nanocomponents, or nanomanufacturing. KW - Machine Learning KW - Nanoarchitectures KW - Nanocomputing KW - Nanotechnology KW - Neural Networks KW - Quantum Computing UR - http://www.scopus.com/inward/record.url?scp=84856844597&partnerID=8YFLogxK U2 - 10.1166/jctn.2011.1821 DO - 10.1166/jctn.2011.1821 M3 - Review Article VL - 8 SP - 1347 EP - 1363 JO - Journal of Computational and Theoretical Nanoscience JF - Journal of Computational and Theoretical Nanoscience SN - 1546-1955 IS - 8 ER - TY - JOUR T1 - Magnetic origin of the chemical balance in alloyed Fe-Cr stainless steels T2 - First-principles and Ising model study AU - Airiskallio, E. AU - Nurmi, E. AU - Väyrynen, I. J. AU - Kokko, K. AU - Ropo, M. AU - Punkkinen, M. P J AU - Johansson, B. AU - Vitos, L. PY - 2014 Y1 - 2014 N2 - Iron-chromium is the base material for most of the stainless steel grades. Recently, new insights into the origins of fundamental physical and chemical characteristics of Fe-Cr based alloys have been achieved. Some of the new results are quite unexpected and call for further investigations. The present study focuses on the magnetic contribution in the atomic driving forces related to the chemical composition in Fe-Cr when alloyed with Al, Ti, V, Mn, Co, Ni, and Mo. Using the ab initio exact muffin-tin orbitals method combined with an Ising-type spin model, we demonstrate that the magnetic moment of the solute atoms with the induced changes in the magnetic moments of the host atoms form the main factor in determining the mixing energy and chemical potentials of low-Cr Fe-Cr based alloys. The results obtained in the present work are related to the designing and tuning of the microstructure and corrosion protection of low-Cr steels. AB - Iron-chromium is the base material for most of the stainless steel grades. Recently, new insights into the origins of fundamental physical and chemical characteristics of Fe-Cr based alloys have been achieved. Some of the new results are quite unexpected and call for further investigations. The present study focuses on the magnetic contribution in the atomic driving forces related to the chemical composition in Fe-Cr when alloyed with Al, Ti, V, Mn, Co, Ni, and Mo. Using the ab initio exact muffin-tin orbitals method combined with an Ising-type spin model, we demonstrate that the magnetic moment of the solute atoms with the induced changes in the magnetic moments of the host atoms form the main factor in determining the mixing energy and chemical potentials of low-Cr Fe-Cr based alloys. The results obtained in the present work are related to the designing and tuning of the microstructure and corrosion protection of low-Cr steels. KW - Al KW - Chemical potential KW - Co KW - Corrosion protection KW - Cr KW - Fe KW - First principles calculation KW - Ising model KW - Magnetic moment KW - Mixing energy KW - Mn KW - Mo KW - Ni KW - Stainless steel KW - Ti KW - V UR - http://www.scopus.com/inward/record.url?scp=84902660256&partnerID=8YFLogxK U2 - 10.1016/j.commatsci.2014.05.036 DO - 10.1016/j.commatsci.2014.05.036 M3 - Article VL - 92 SP - 135 EP - 140 JO - Computational Materials Science JF - Computational Materials Science SN - 0927-0256 ER - TY - JOUR T1 - Melting of copper clusters AU - Valkealahti, S. AU - Manninen, M. PY - 1993/1/1 Y1 - 1993/1/1 N2 - Melting of icosahedral and Wulff polyhedral copper clusters are studied using molecular dynamics and effective medium theory. Icosahedral closed shell copper clusters are most stable up to a cluster size of ∼ 2500 atoms and their melting temperature is highest for small clusters, accordingly. Wulff polyhedra are most stable for larger clusters and, consequently, their melting temperature is highest for large clusters. The melting temperature decreases with decreasing cluster size and is proportional to the average coordination number of atoms. The whole icosahedral cluster melts simultaneously and can possibly be superheated. Icosahedral clusters with partially filled shells melt at lower temperatures than closed shell icosahedra, but no surface premelting is observed. (111) surface layers of large Wulff polyhedra are also solid up to the cluster melting temperatures, but (100) facets premelt at a lower temperature than the whole cluster. AB - Melting of icosahedral and Wulff polyhedral copper clusters are studied using molecular dynamics and effective medium theory. Icosahedral closed shell copper clusters are most stable up to a cluster size of ∼ 2500 atoms and their melting temperature is highest for small clusters, accordingly. Wulff polyhedra are most stable for larger clusters and, consequently, their melting temperature is highest for large clusters. The melting temperature decreases with decreasing cluster size and is proportional to the average coordination number of atoms. The whole icosahedral cluster melts simultaneously and can possibly be superheated. Icosahedral clusters with partially filled shells melt at lower temperatures than closed shell icosahedra, but no surface premelting is observed. (111) surface layers of large Wulff polyhedra are also solid up to the cluster melting temperatures, but (100) facets premelt at a lower temperature than the whole cluster. U2 - 10.1016/0927-0256(93)90003-6 DO - 10.1016/0927-0256(93)90003-6 M3 - Article VL - 1 SP - 123 EP - 134 JO - Computational Materials Science JF - Computational Materials Science SN - 0927-0256 IS - 2 ER - TY - JOUR T1 - Modeling mass transfer in fracture flows with the time domain-random walk method AU - Kuva, J. AU - Voutilainen, M. AU - Mattila, K. PY - 2019 Y1 - 2019 N2 - The time domain-random walk method was developed further for simulating mass transfer in fracture flows together with matrix diffusion in surrounding porous media. Specifically, a time domain-random walk scheme was developed for numerically approximating solutions of the advection-diffusion equation when the diffusion coefficient exhibits significant spatial variation or even discontinuities. The proposed scheme relies on second-order accurate, central-difference approximations of the advective and diffusive fluxes. The scheme was verified by comparing simulated results against analytical solutions in flow configurations involving a rectangular channel connected on one side with a porous matrix. Simulations with several flow rates, diffusion coefficients, and matrix porosities indicate good agreement between the numerical approximations and analytical solutions. AB - The time domain-random walk method was developed further for simulating mass transfer in fracture flows together with matrix diffusion in surrounding porous media. Specifically, a time domain-random walk scheme was developed for numerically approximating solutions of the advection-diffusion equation when the diffusion coefficient exhibits significant spatial variation or even discontinuities. The proposed scheme relies on second-order accurate, central-difference approximations of the advective and diffusive fluxes. The scheme was verified by comparing simulated results against analytical solutions in flow configurations involving a rectangular channel connected on one side with a porous matrix. Simulations with several flow rates, diffusion coefficients, and matrix porosities indicate good agreement between the numerical approximations and analytical solutions. KW - Advection KW - Breakthrough curve KW - Matrix diffusion KW - Porous media KW - Simulation KW - Solute transport U2 - 10.1007/s10596-019-09852-5 DO - 10.1007/s10596-019-09852-5 M3 - Article JO - COMPUTATIONAL GEOSCIENCES JF - COMPUTATIONAL GEOSCIENCES SN - 1420-0597 ER - TY - JOUR T1 - Modeling probability densities with sums of exponentials via polynomial approximation AU - Dumitrescu, Bogdan AU - Şicleru, Bogdan C. AU - Avram, Florin PY - 2016 Y1 - 2016 N2 - Abstract We propose a method for optimization with semi-infinite constraints that involve a linear combination of functions, focusing on shape-constrained optimization with exponential functions. Each function is lower and upper bounded on sub-intervals by low-degree polynomials. Thus, the constraints can be approximated with polynomial inequalities that can be implemented with linear matrix inequalities. Convexity is preserved, but the problem has now a finite number of constraints. We show how to take advantage of the properties of the exponential function in order to build quickly accurate approximations. The problem used for illustration is the least-squares fitting of a positive sum of exponentials to an empirical probability density function. When the exponents are given, the problem is convex, but we also give a procedure for optimizing the exponents. Several examples show that the method is flexible, accurate and gives better results than other methods for the investigated problems. AB - Abstract We propose a method for optimization with semi-infinite constraints that involve a linear combination of functions, focusing on shape-constrained optimization with exponential functions. Each function is lower and upper bounded on sub-intervals by low-degree polynomials. Thus, the constraints can be approximated with polynomial inequalities that can be implemented with linear matrix inequalities. Convexity is preserved, but the problem has now a finite number of constraints. We show how to take advantage of the properties of the exponential function in order to build quickly accurate approximations. The problem used for illustration is the least-squares fitting of a positive sum of exponentials to an empirical probability density function. When the exponents are given, the problem is convex, but we also give a procedure for optimizing the exponents. Several examples show that the method is flexible, accurate and gives better results than other methods for the investigated problems. KW - Density fitting KW - Optimization KW - Polynomial approximation KW - Semi-infinite programming KW - Sum of exponentials U2 - 10.1016/j.cam.2015.07.032 DO - 10.1016/j.cam.2015.07.032 M3 - Article VL - 292 SP - 513 EP - 525 JO - Journal of Computational and Applied Mathematics JF - Journal of Computational and Applied Mathematics SN - 0377-0427 ER - TY - JOUR T1 - Multichannel Blind Sound Source Separation using Spatial Covariance Model with Level and Time Differences and Non-Negative Matrix Factorization AU - Carabias Orti, Julio Jose AU - Nikunen, Joonas AU - Virtanen, Tuomas AU - Vera-Candeas, Pedro PY - 2018/9 Y1 - 2018/9 N2 - This paper presents an algorithm for multichannel sound source separation using explicit modeling of level and time differences in source spatial covariance matrices (SCM). We propose a novel SCM model in which the spatial properties are modeled by the weighted sum of direction of arrival (DOA) kernels. DOA kernels are obtained as the combination of phase and level difference covariance matrices representing both time and level differences between microphones for a grid of predefined source directions. The proposed SCM model is combined with the NMF model for the magnitude spectrograms. Opposite to other SCM models in the literature, in this work, source localization is implicitly defined in the model and estimated during the signal factorization. Therefore, no localization pre-processing is required. Parameters are estimated using complex-valued non-negative matrix factorization (CNMF) with both Euclidean distance and Itakura Saito divergence. Separation performance of the proposed system is evaluated using the two-channel SiSEC development dataset and four channels signals recorded in a regular room with moderate reverberation. Finally, a comparison to other state-of-the-art methods is performed, showing better achieved separation performance in terms of SIR and perceptual measures. AB - This paper presents an algorithm for multichannel sound source separation using explicit modeling of level and time differences in source spatial covariance matrices (SCM). We propose a novel SCM model in which the spatial properties are modeled by the weighted sum of direction of arrival (DOA) kernels. DOA kernels are obtained as the combination of phase and level difference covariance matrices representing both time and level differences between microphones for a grid of predefined source directions. The proposed SCM model is combined with the NMF model for the magnitude spectrograms. Opposite to other SCM models in the literature, in this work, source localization is implicitly defined in the model and estimated during the signal factorization. Therefore, no localization pre-processing is required. Parameters are estimated using complex-valued non-negative matrix factorization (CNMF) with both Euclidean distance and Itakura Saito divergence. Separation performance of the proposed system is evaluated using the two-channel SiSEC development dataset and four channels signals recorded in a regular room with moderate reverberation. Finally, a comparison to other state-of-the-art methods is performed, showing better achieved separation performance in terms of SIR and perceptual measures. KW - Covariance matrices KW - direction of arrival estimation KW - Direction-of-arrival estimation KW - interaural level difference KW - interaural time difference KW - Kernel KW - Microphones KW - multichannel source separation KW - non-negative matrix factorization KW - Source separation KW - spatial covariance model KW - Spectrogram KW - Time-frequency analysis U2 - 10.1109/TASLP.2018.2830105 DO - 10.1109/TASLP.2018.2830105 M3 - Article VL - 26 SP - 1512 EP - 1527 JO - Ieee-Acm transactions on audio speech and language processing JF - Ieee-Acm transactions on audio speech and language processing SN - 2329-9290 IS - 9 ER - TY - JOUR T1 - NetBioV T2 - An R package for visualizing large network data in biology and medicine AU - Tripathi, Shailesh AU - Dehmer, Matthias AU - Emmert-Streib, Frank PY - 2014/4/2 Y1 - 2014/4/2 N2 - NetBioV (Network Biology Visualization) is an R package that allows the visualization of large network data in biology and medicine. The purpose of NetBioV is to enable an organized and reproducible visualization of networks by emphasizing or highlighting specific structural properties that are of biological relevance. AB - NetBioV (Network Biology Visualization) is an R package that allows the visualization of large network data in biology and medicine. The purpose of NetBioV is to enable an organized and reproducible visualization of networks by emphasizing or highlighting specific structural properties that are of biological relevance. UR - http://www.scopus.com/inward/record.url?scp=84911403383&partnerID=8YFLogxK U2 - 10.1093/bioinformatics/btu384 DO - 10.1093/bioinformatics/btu384 M3 - Article VL - 30 SP - 2834 EP - 2836 JO - Bioinformatics JF - Bioinformatics SN - 1367-4803 IS - 19 ER - TY - JOUR T1 - On efficient network similarity measures AU - Dehmer, Matthias AU - Chen, Zengqiang AU - Shi, Yongtang AU - Zhang, Y. AU - Tripathi, Shailesh AU - Ghorbani, Modjtaba AU - Mowshowitz, Abbe AU - Emmert-Streib, F. PY - 2019/12/1 Y1 - 2019/12/1 N2 - This paper presents novel graph similarity measures which can be applied to simple directed and undirected networks. To define the graph similarity measures, we first map graphs to real numbers by utilizing structural graph measures. Then, we define measures of similarity between real numbers and prove that they can be used as proxies for graph similarity. Numerical results are derived to show the domain coverage of these measures as well as their clustering ability. The latter relates to the efficient grouping of graphs according to certain structural properties. Our numerical results are sensitive to these properties and offer insights useful for designing effective graph similarity measures. AB - This paper presents novel graph similarity measures which can be applied to simple directed and undirected networks. To define the graph similarity measures, we first map graphs to real numbers by utilizing structural graph measures. Then, we define measures of similarity between real numbers and prove that they can be used as proxies for graph similarity. Numerical results are derived to show the domain coverage of these measures as well as their clustering ability. The latter relates to the efficient grouping of graphs according to certain structural properties. Our numerical results are sensitive to these properties and offer insights useful for designing effective graph similarity measures. KW - Distance measures KW - Graphs KW - Inequalities KW - Networks KW - Similarity measures U2 - 10.1016/j.amc.2019.06.035 DO - 10.1016/j.amc.2019.06.035 M3 - Article VL - 362 JO - Applied Mathematics and Computation JF - Applied Mathematics and Computation SN - 0096-3003 M1 - 124521 ER - TY - JOUR T1 - On k-Hypermonogenic Functions and Their Mean Value Properties AU - Eriksson, Sirkka-Liisa AU - Orelma, Heikki PY - 2016 Y1 - 2016 N2 - We study a hyperbolic version of holomorphic functions to higher dimensions. In this frame work, a generalization of holomorphic functions are called (Formula presented.)-hypermonogenic functions. These functions are depending on several real variables and their values are in a Clifford algebra. They are defined in terms of hyperbolic Dirac operators. They are connected to harmonic functions with respect to the Riemannian metric (Formula presented.) in the same way as the usual harmonic function to holomorphic functions. We present the mean value property for (Formula presented.)-hypermonogenic functions and related results. Earlier the mean value properties has been proved for hypermonogenic functions. The key tools are the invariance properties of the hyperbolic metric. AB - We study a hyperbolic version of holomorphic functions to higher dimensions. In this frame work, a generalization of holomorphic functions are called (Formula presented.)-hypermonogenic functions. These functions are depending on several real variables and their values are in a Clifford algebra. They are defined in terms of hyperbolic Dirac operators. They are connected to harmonic functions with respect to the Riemannian metric (Formula presented.) in the same way as the usual harmonic function to holomorphic functions. We present the mean value property for (Formula presented.)-hypermonogenic functions and related results. Earlier the mean value properties has been proved for hypermonogenic functions. The key tools are the invariance properties of the hyperbolic metric. KW - Dirac operator KW - Hyperbolic metric KW - Hypermonogenic KW - Monogenic U2 - 10.1007/s11785-015-0445-z DO - 10.1007/s11785-015-0445-z M3 - Article VL - 10 SP - 311 EP - 325 JO - Complex Analysis and Operator Theory JF - Complex Analysis and Operator Theory SN - 1661-8254 IS - 2 ER - TY - JOUR T1 - Optimal energy decay for the wave-heat system on a rectangular domain AU - Batty, Charles AU - Paunonen, Lassi AU - Seifert, David PY - 2019 Y1 - 2019 N2 - We study the rate of energy decay for solutions of a coupled wave-heat system on a rectangular domain. Using techniques from the theory of C 0 -semigroups, and in particular a well-known result due to Borichev and Tomilov, we prove that the energy of classical solutions decays like t - 2/ 3 as t \rightarrow \infty . This rate is moreover shown to be sharp. Our result implies in particular that a general estimate in the literature, which predicts at least logarithmic decay and is known to be best possible in general, is suboptimal in the special case under consideration here. Our strategy of proof involves direct estimates based on separation of variables and a refined version of the technique developed in our earlier paper for a one-dimensional wave-heat system. AB - We study the rate of energy decay for solutions of a coupled wave-heat system on a rectangular domain. Using techniques from the theory of C 0 -semigroups, and in particular a well-known result due to Borichev and Tomilov, we prove that the energy of classical solutions decays like t - 2/ 3 as t \rightarrow \infty . This rate is moreover shown to be sharp. Our result implies in particular that a general estimate in the literature, which predicts at least logarithmic decay and is known to be best possible in general, is suboptimal in the special case under consideration here. Our strategy of proof involves direct estimates based on separation of variables and a refined version of the technique developed in our earlier paper for a one-dimensional wave-heat system. KW - C -semigroups KW - Coupled KW - Energy KW - Heat equation KW - Rates of decay KW - Rectangular domain KW - Resolvent estimates KW - Wave equation U2 - 10.1137/18M1195796 DO - 10.1137/18M1195796 M3 - Article VL - 51 SP - 808 EP - 819 JO - SIAM JOURNAL ON MATHEMATICAL ANALYSIS JF - SIAM JOURNAL ON MATHEMATICAL ANALYSIS SN - 0036-1410 IS - 2 ER - TY - JOUR T1 - Relations and bounds for the zeros of graph polynomials using vertex orbits AU - Dehmer, Matthias AU - Emmert-Streib, Frank AU - Mowshowitz, Abbe AU - Ilić, Aleksandar AU - Chen, Zengqiang AU - Yu, Guihai AU - Feng, Lihua AU - Ghorbani, Modjtaba AU - Varmuza, Kurt AU - Tao, Jin PY - 2020/9/1 Y1 - 2020/9/1 N2 - In this paper, we prove bounds for the unique, positive zero of OG ★(z):=1−OG(z), where OG(z) is the so-called orbit polynomial [1]. The orbit polynomial is based on the multiplicity and cardinalities of the vertex orbits of a graph. In [1], we have shown that the unique, positive zero δ ≤ 1 of OG ★(z) can serve as a meaningful measure of graph symmetry. In this paper, we study special graph classes with a specified number of orbits and obtain bounds on the value of δ. AB - In this paper, we prove bounds for the unique, positive zero of OG ★(z):=1−OG(z), where OG(z) is the so-called orbit polynomial [1]. The orbit polynomial is based on the multiplicity and cardinalities of the vertex orbits of a graph. In [1], we have shown that the unique, positive zero δ ≤ 1 of OG ★(z) can serve as a meaningful measure of graph symmetry. In this paper, we study special graph classes with a specified number of orbits and obtain bounds on the value of δ. KW - Data science KW - Graph measures KW - Graphs KW - Networks KW - Quantitative graph theory KW - Symmetry U2 - 10.1016/j.amc.2020.125239 DO - 10.1016/j.amc.2020.125239 M3 - Article VL - 380 JO - Applied Mathematics and Computation JF - Applied Mathematics and Computation SN - 0096-3003 M1 - 125239 ER - TY - GEN T1 - Resilient Cooperative Voltage Control for Distribution Network with High Penetration Distributed Energy Resources AU - Gusrialdi, Azwirman AU - Xu, Ying AU - Qu, Zhihua AU - Simaan, Marwan A. PY - 2020 Y1 - 2020 N2 - This paper considers the problem of designing a resilient distributed voltage control algorithm for distribution systems with high penetration of distributed energy resources in the presence of an unknown cyber-attack. The purpose of the attack is to force the system to violate the operating voltage limit by intercepting its communication channels and inserting exogenous signals to perturb and/or modify the information being exchanged. We first review the cooperative voltage control proposed in our previous work and provide a new stability analysis for it. Next, we present a resilient cooperative voltage control algorithm by introducing a virtual system interconnected with the original system such that the voltage can be maintained within the operational limit under unknown attacks. The resiliency of the proposed algorithm is demonstrated via simulations on the IEEE 8500-node system when subjected to an attack which consists of corrupting the data being exchanged in the communication network between two generation units. AB - This paper considers the problem of designing a resilient distributed voltage control algorithm for distribution systems with high penetration of distributed energy resources in the presence of an unknown cyber-attack. The purpose of the attack is to force the system to violate the operating voltage limit by intercepting its communication channels and inserting exogenous signals to perturb and/or modify the information being exchanged. We first review the cooperative voltage control proposed in our previous work and provide a new stability analysis for it. Next, we present a resilient cooperative voltage control algorithm by introducing a virtual system interconnected with the original system such that the voltage can be maintained within the operational limit under unknown attacks. The resiliency of the proposed algorithm is demonstrated via simulations on the IEEE 8500-node system when subjected to an attack which consists of corrupting the data being exchanged in the communication network between two generation units. KW - cooperative control KW - cyber attacks KW - distribution network KW - resilient control KW - Voltage control M3 - Conference contribution SN - 978-1-7281-8813-3 SP - 1533 EP - 1539 BT - European Control Conference 2020, ECC 2020 PB - IEEE ER - TY - JOUR T1 - Revealing differences in gene network inference algorithms on the network level by ensemble methods AU - Altay, Gökmen AU - Emmert-Streib, Frank PY - 2010/5/25 Y1 - 2010/5/25 N2 - Motivation: The inference of regulatory networks from large-scale expression data holds great promise because of the potentially causal interpretation of these networks. However, due to the difficulty to establish reliable methods based on observational data there is so far only incomplete knowledge about possibilities and limitations of such inference methods in this context. Results: In this article, we conduct a statistical analysis investigating differences and similarities of four network inference algorithms, ARACNE, CLR, MRNET and RN, with respect to local network-based measures. We employ ensemble methods allowing to assess the inferability down to the level of individual edges. Our analysis reveals the bias of these inference methods with respect to the inference of various network components and, hence, provides guidance in the interpretation of inferred regulatory networks from expression data. Further, as application we predict the total number of regulatory interactions in human B cells and hypothesize about the role of Myc and its targets regarding molecular information processing. AB - Motivation: The inference of regulatory networks from large-scale expression data holds great promise because of the potentially causal interpretation of these networks. However, due to the difficulty to establish reliable methods based on observational data there is so far only incomplete knowledge about possibilities and limitations of such inference methods in this context. Results: In this article, we conduct a statistical analysis investigating differences and similarities of four network inference algorithms, ARACNE, CLR, MRNET and RN, with respect to local network-based measures. We employ ensemble methods allowing to assess the inferability down to the level of individual edges. Our analysis reveals the bias of these inference methods with respect to the inference of various network components and, hence, provides guidance in the interpretation of inferred regulatory networks from expression data. Further, as application we predict the total number of regulatory interactions in human B cells and hypothesize about the role of Myc and its targets regarding molecular information processing. UR - http://www.scopus.com/inward/record.url?scp=77954484005&partnerID=8YFLogxK U2 - 10.1093/bioinformatics/btq259 DO - 10.1093/bioinformatics/btq259 M3 - Article VL - 26 SP - 1738 EP - 1744 JO - Bioinformatics JF - Bioinformatics SN - 1367-4803 IS - 14 M1 - btq259 ER - TY - JOUR T1 - SamExploreR T2 - Exploring reproducibility and robustness of RNA-seq results based on SAM files AU - Stupnikov, Alexey AU - Tripathi, Shailesh AU - De Matos Simoes, Ricardo AU - McArt, Darragh AU - Salto-Tellez, Manuel AU - Glazko, Galina AU - Dehmer, Matthias AU - Emmert-Streib, Frank PY - 2016/11/1 Y1 - 2016/11/1 N2 - Motivation: Data from RNA-seq experiments provide us with many new possibilities to gain insights into biological and disease mechanisms of cellular functioning. However, the reproducibility and robustness of RNA-seq data analysis results is often unclear. This is in part attributed to the two counter acting goals of (i) a cost efficient and (ii) an optimal experimental design leading to a compromise, e.g. in the sequencing depth of experiments. Results: We introduce an R package called samExploreR that allows the subsampling (m out of n bootstraping) of short-reads based on SAM files facilitating the investigation of sequencing depth related questions for the experimental design. Overall, this provides a systematic way for exploring the reproducibility and robustness of general RNA-seq studies. We exemplify the usage of samExploreR by studying the influence of the sequencing depth and the annotation on the identification of differentially expressed genes. AB - Motivation: Data from RNA-seq experiments provide us with many new possibilities to gain insights into biological and disease mechanisms of cellular functioning. However, the reproducibility and robustness of RNA-seq data analysis results is often unclear. This is in part attributed to the two counter acting goals of (i) a cost efficient and (ii) an optimal experimental design leading to a compromise, e.g. in the sequencing depth of experiments. Results: We introduce an R package called samExploreR that allows the subsampling (m out of n bootstraping) of short-reads based on SAM files facilitating the investigation of sequencing depth related questions for the experimental design. Overall, this provides a systematic way for exploring the reproducibility and robustness of general RNA-seq studies. We exemplify the usage of samExploreR by studying the influence of the sequencing depth and the annotation on the identification of differentially expressed genes. U2 - 10.1093/bioinformatics/btw475 DO - 10.1093/bioinformatics/btw475 M3 - Article VL - 32 SP - 3345 EP - 3347 JO - Bioinformatics JF - Bioinformatics SN - 1367-4803 IS - 21 ER - TY - JOUR T1 - Satisfiability of modal inclusion logic T2 - Lax and strict semantics AU - Hella, Lauri AU - Kuusisto, Antti AU - Meier, Arne AU - Vollmer, Heribert N1 - DUPL=50949587 PY - 2019/10/1 Y1 - 2019/10/1 N2 - We investigate the computational complexity of the satisfiability problem of modal inclusion logic. We distinguish two variants of the problem: one for the strict and another one for the lax semantics. Both problems turn out to be EXPTIME-complete on general structures. Finally,we showhowfor a specific class of structures NEXPTIME-completeness for these problems under strict semantics can be achieved. AB - We investigate the computational complexity of the satisfiability problem of modal inclusion logic. We distinguish two variants of the problem: one for the strict and another one for the lax semantics. Both problems turn out to be EXPTIME-complete on general structures. Finally,we showhowfor a specific class of structures NEXPTIME-completeness for these problems under strict semantics can be achieved. KW - Computational complexity KW - Modal inclusion logic KW - Satisfiability KW - Team semantics U2 - 10.1145/3356043 DO - 10.1145/3356043 M3 - Article VL - 21 JO - ACM TRANSACTIONS ON COMPUTATIONAL LOGIC JF - ACM TRANSACTIONS ON COMPUTATIONAL LOGIC SN - 1529-3785 IS - 1 M1 - 7 ER - TY - JOUR T1 - SCIP T2 - a single-cell image processor toolbox AU - Martins, Leonardo AU - Neeli-Venkata, Ramakanth AU - Oliveira, Samuel M.D. AU - Häkkinen, Antti AU - Ribeiro, Andre S. AU - Fonseca, José M. PY - 2018/12/15 Y1 - 2018/12/15 N2 - Summary: Each cell is a phenotypically unique individual that is influenced by internal and external processes, operating in parallel. To characterize the dynamics of cellular processes one needs to observe many individual cells from multiple points of view and over time, so as to identify commonalities and variability. With this aim, we engineered a software, 'SCIP', to analyze multi-modal, multi-process, time-lapse microscopy morphological and functional images. SCIP is capable of automatic and/or manually corrected segmentation of cells and lineages, automatic alignment of different microscopy channels, as well as detect, count and characterize fluorescent spots (such as RNA tagged by MS2-GFP), nucleoids, Z rings, Min system, inclusion bodies, undefined structures, etc. The results can be exported into *mat files and all results can be jointly analyzed, to allow studying not only each feature and process individually, but also find potential relationships. While we exemplify its use on Escherichia coli, many of its functionalities are expected to be of use in analyzing other prokaryotes and eukaryotic cells as well. We expect SCIP to facilitate the finding of relationships between cellular processes, from small-scale (e.g. gene expression) to large-scale (e.g. cell division), in single cells and cell lineages. Availability and implementation: http://www.ca3-uninova.org/project_scip. Supplementary information: Supplementary data are available at Bioinformatics online. AB - Summary: Each cell is a phenotypically unique individual that is influenced by internal and external processes, operating in parallel. To characterize the dynamics of cellular processes one needs to observe many individual cells from multiple points of view and over time, so as to identify commonalities and variability. With this aim, we engineered a software, 'SCIP', to analyze multi-modal, multi-process, time-lapse microscopy morphological and functional images. SCIP is capable of automatic and/or manually corrected segmentation of cells and lineages, automatic alignment of different microscopy channels, as well as detect, count and characterize fluorescent spots (such as RNA tagged by MS2-GFP), nucleoids, Z rings, Min system, inclusion bodies, undefined structures, etc. The results can be exported into *mat files and all results can be jointly analyzed, to allow studying not only each feature and process individually, but also find potential relationships. While we exemplify its use on Escherichia coli, many of its functionalities are expected to be of use in analyzing other prokaryotes and eukaryotic cells as well. We expect SCIP to facilitate the finding of relationships between cellular processes, from small-scale (e.g. gene expression) to large-scale (e.g. cell division), in single cells and cell lineages. Availability and implementation: http://www.ca3-uninova.org/project_scip. Supplementary information: Supplementary data are available at Bioinformatics online. U2 - 10.1093/bioinformatics/bty505 DO - 10.1093/bioinformatics/bty505 M3 - Article VL - 34 SP - 4318 EP - 4320 JO - Bioinformatics JF - Bioinformatics SN - 1367-4803 IS - 24 ER - TY - JOUR T1 - Sound Event Detection in the DCASE 2017 Challenge AU - Mesaros, Annamaria AU - Diment, Aleksandr AU - Elizalde, Benjamin AU - Heittola, Toni AU - Vincent, Emmanuel AU - Raj, Bhiksha AU - Virtanen, Tuomas PY - 2019/6/1 Y1 - 2019/6/1 N2 - Each edition of the challenge on Detection and Classification of Acoustic Scenes and Events (DCASE) contained several tasks involving sound event detection in different setups. DCASE 2017 presented participants with three such tasks, each having specific datasets and detection requirements: Task 2, in which target sound events were very rare in both training and testing data, Task 3 having overlapping events annotated in real-life audio, and Task 4, in which only weakly labeled data were available for training. In this paper, we present three tasks, including the datasets and baseline systems, and analyze the challenge entries for each task. We observe the popularity of methods using deep neural networks, and the still widely used mel frequency-based representations, with only few approaches standing out as radically different. Analysis of the systems behavior reveals that task-specific optimization has a big role in producing good performance; however, often this optimization closely follows the ranking metric, and its maximization/minimization does not result in universally good performance. We also introduce the calculation of confidence intervals based on a jackknife resampling procedure to perform statistical analysis of the challenge results. The analysis indicates that while the 95% confidence intervals for many systems overlap, there are significant differences in performance between the top systems and the baseline for all tasks. AB - Each edition of the challenge on Detection and Classification of Acoustic Scenes and Events (DCASE) contained several tasks involving sound event detection in different setups. DCASE 2017 presented participants with three such tasks, each having specific datasets and detection requirements: Task 2, in which target sound events were very rare in both training and testing data, Task 3 having overlapping events annotated in real-life audio, and Task 4, in which only weakly labeled data were available for training. In this paper, we present three tasks, including the datasets and baseline systems, and analyze the challenge entries for each task. We observe the popularity of methods using deep neural networks, and the still widely used mel frequency-based representations, with only few approaches standing out as radically different. Analysis of the systems behavior reveals that task-specific optimization has a big role in producing good performance; however, often this optimization closely follows the ranking metric, and its maximization/minimization does not result in universally good performance. We also introduce the calculation of confidence intervals based on a jackknife resampling procedure to perform statistical analysis of the challenge results. The analysis indicates that while the 95% confidence intervals for many systems overlap, there are significant differences in performance between the top systems and the baseline for all tasks. KW - confidence intervals KW - jackknife estimates KW - pattern recognition KW - Sound event detection KW - weak labels U2 - 10.1109/TASLP.2019.2907016 DO - 10.1109/TASLP.2019.2907016 M3 - Article VL - 27 SP - 992 EP - 1006 JO - Ieee-Acm transactions on audio speech and language processing JF - Ieee-Acm transactions on audio speech and language processing SN - 2329-9290 IS - 6 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 - 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 - JOUR T1 - The watching system as a generalization of identifying code AU - Ghorbani, Modjtaba AU - Dehmer, Matthias AU - Maimani, Hamidreza AU - Maddah, Sheyda AU - Roozbayani, Maryam AU - Emmert-Streib, Frank PY - 2020 Y1 - 2020 N2 - The watching system, as a generalization of identifying code, has been defined by Auger in 2010. The identifying code has been used to wireless networks and it has been also applied to locate objects in the sensor networks. On the other hand, the graph product is employed in most of the mathematic branches such as network design to study the structure of network elements. In this paper, we give some upper bounds for the watching number of well-know product graphs. AB - The watching system, as a generalization of identifying code, has been defined by Auger in 2010. The identifying code has been used to wireless networks and it has been also applied to locate objects in the sensor networks. On the other hand, the graph product is employed in most of the mathematic branches such as network design to study the structure of network elements. In this paper, we give some upper bounds for the watching number of well-know product graphs. KW - Domination number KW - Graph products KW - Identifying code KW - Watching system U2 - 10.1016/j.amc.2020.125302 DO - 10.1016/j.amc.2020.125302 M3 - Article VL - 380 JO - Applied Mathematics and Computation JF - Applied Mathematics and Computation SN - 0096-3003 M1 - 125302 ER - TY - JOUR T1 - Topological mappings between graphs, trees and generalized trees AU - Emmert-Streib, Frank AU - Dehmer, Matthias PY - 2007/3/15 Y1 - 2007/3/15 N2 - We present novel topological mappings between graphs, trees and generalized trees that means between structured objects with different properties. The two major contributions of this paper are, first, to clarify the relation between graphs, trees and generalized trees, a graph class recently introduced. Second, these transformations provide a unique opportunity to transform structured objects into a representation that might be beneficial for a processing, e.g., by machine learning techniques for graph classification. AB - We present novel topological mappings between graphs, trees and generalized trees that means between structured objects with different properties. The two major contributions of this paper are, first, to clarify the relation between graphs, trees and generalized trees, a graph class recently introduced. Second, these transformations provide a unique opportunity to transform structured objects into a representation that might be beneficial for a processing, e.g., by machine learning techniques for graph classification. KW - Applied graph theory KW - Graph transformation KW - Hierarchical graphs UR - http://www.scopus.com/inward/record.url?scp=33947616843&partnerID=8YFLogxK U2 - 10.1016/j.amc.2006.07.162 DO - 10.1016/j.amc.2006.07.162 M3 - Article VL - 186 SP - 1326 EP - 1333 JO - Applied Mathematics and Computation JF - Applied Mathematics and Computation SN - 0096-3003 IS - 2 ER - TY - CHAP T1 - Two models for hydraulic cylinders in flexible multibody simulations AU - Ylinen, Antti AU - Mäkinen, Jari AU - Kouhia, Reijo N1 - JUFOID=79940 EXT="Ylinen, Antti" PY - 2016 Y1 - 2016 N2 - In modelling hydraulic cylinders interaction between the structural response and the hydraulic system needs to be taken into account. In this chapter two approaches for modelling flexible multibody systems coupled with hydraulic actuators i.e. cylinders are presented and compared. These models are the truss-elementlike cylinder and bending flexible cylinder models. The bending flexible cylinder element is a super-element combining the geometrically exact Reissner-beam element, the C1-continuous slide-spring element needed for the telescopc movement and the hydraulic fluid field. Both models are embeded with a friction model based on a bristle approach. The models are implemented in a finite element enviroment. In time the coupled stiff differential equation system is integrated using the L-stable Rosenbrock method. AB - In modelling hydraulic cylinders interaction between the structural response and the hydraulic system needs to be taken into account. In this chapter two approaches for modelling flexible multibody systems coupled with hydraulic actuators i.e. cylinders are presented and compared. These models are the truss-elementlike cylinder and bending flexible cylinder models. The bending flexible cylinder element is a super-element combining the geometrically exact Reissner-beam element, the C1-continuous slide-spring element needed for the telescopc movement and the hydraulic fluid field. Both models are embeded with a friction model based on a bristle approach. The models are implemented in a finite element enviroment. In time the coupled stiff differential equation system is integrated using the L-stable Rosenbrock method. U2 - 10.1007/978-3-319-27996-1_17 DO - 10.1007/978-3-319-27996-1_17 M3 - Chapter SN - 978-3-319-27994-7 T3 - Computational Methods in Applied Sciences SP - 463 EP - 493 BT - Computational Methods for Solids and Fluids PB - Springer ER - TY - JOUR T1 - Unite and conquer T2 - Univariate and multivariate approaches for finding differentially expressed gene sets AU - Glazko, Galina V. AU - Emmert-Streib, Frank PY - 2009/9 Y1 - 2009/9 N2 - Motivation: Recently, many univariate and several multivariate approaches have been suggested for testing differential expression of gene sets between different phenotypes. However, despite a wealth of literature studying their performance on simulated and real biological data, still there is a need to quantify their relative performance when they are testing different null hypotheses. Results: In this article, we compare the performance of univariate and multivariate tests on both simulated and biological data. In the simulation study we demonstrate that high correlations equally affect the power of both, univariate as well as multivariate tests. In addition, for most of them the power is similarly affected by the dimensionality of the gene set and by the percentage of genes in the set, for which expression is changing between two phenotypes. The application of different test statistics to biological data reveals that three statistics (sum of squared t-tests, Hotelling's T2, N-statistic), testing different null hypotheses, find some common but also some complementing differentially expressed gene sets under specific settings. This demonstrates that due to complementing null hypotheses each test projects on different aspects of the data and for the analysis of biological data it is beneficial to use all three tests simultaneously instead of focusing exclusively on just one. AB - Motivation: Recently, many univariate and several multivariate approaches have been suggested for testing differential expression of gene sets between different phenotypes. However, despite a wealth of literature studying their performance on simulated and real biological data, still there is a need to quantify their relative performance when they are testing different null hypotheses. Results: In this article, we compare the performance of univariate and multivariate tests on both simulated and biological data. In the simulation study we demonstrate that high correlations equally affect the power of both, univariate as well as multivariate tests. In addition, for most of them the power is similarly affected by the dimensionality of the gene set and by the percentage of genes in the set, for which expression is changing between two phenotypes. The application of different test statistics to biological data reveals that three statistics (sum of squared t-tests, Hotelling's T2, N-statistic), testing different null hypotheses, find some common but also some complementing differentially expressed gene sets under specific settings. This demonstrates that due to complementing null hypotheses each test projects on different aspects of the data and for the analysis of biological data it is beneficial to use all three tests simultaneously instead of focusing exclusively on just one. U2 - 10.1093/bioinformatics/btp406 DO - 10.1093/bioinformatics/btp406 M3 - Article VL - 25 SP - 2348 EP - 2354 JO - Bioinformatics JF - Bioinformatics SN - 1367-4803 IS - 18 ER - TY - JOUR T1 - Universal construction mechanism for networks from one-dimensional symbol sequences AU - Emmert-Streib, Frank PY - 2012/10/15 Y1 - 2012/10/15 N2 - In this paper we introduce construction mechanisms to generate directed networks from one-dimensional symbol sequences. We prove that any of these construction mechanism leads to the same undirected network. Further, we prove that the introduced construction mechanisms are universal in the sense that any undirected network can be generated by such a mechanism. In addition, we provide various numerical examples to demonstrate the applicability of the introduced mechanism. AB - In this paper we introduce construction mechanisms to generate directed networks from one-dimensional symbol sequences. We prove that any of these construction mechanism leads to the same undirected network. Further, we prove that the introduced construction mechanisms are universal in the sense that any undirected network can be generated by such a mechanism. In addition, we provide various numerical examples to demonstrate the applicability of the introduced mechanism. KW - Complex networks KW - Network construction KW - Random networks KW - Symbol sequences KW - Universal network construction UR - http://www.scopus.com/inward/record.url?scp=84867336661&partnerID=8YFLogxK U2 - 10.1016/j.amc.2012.07.006 DO - 10.1016/j.amc.2012.07.006 M3 - Article VL - 219 SP - 1020 EP - 1030 JO - Applied Mathematics and Computation JF - Applied Mathematics and Computation SN - 0096-3003 IS - 3 ER - TY - JOUR T1 - Van der Waals interactions are critical in Car-Parrinello molecular dynamics simulations of porphyrin-fullerene dyads AU - Karilainen, Topi AU - Cramariuc, Oana AU - Kuisma, Mikael AU - Tappura, Kirsi AU - Hukka, Terttu I. N1 - ORG=fys,0.5 ORG=keb,0.5 PY - 2015 Y1 - 2015 N2 - The interplay between electrostatic and van der Waals (vdW) interactions in porphyrin-C60 dyads is still under debate despite its importance in influencing the structural characteristics of such complexes considered for various applications in molecular photovoltaics. In this article, we sample the conformational space of a porphyrin-C60 dyad using Car-Parrinello molecular dynamics simulations with and without empirical vdW corrections. Long-range vdW interactions, which are poorly described by the commonly used density functional theory functionals, prove to be essential for a proper dynamics of the dyad moieties. Inclusion of vdW corrections brings porphyrin and C60 close together in an orientation that is in agreement with experimental observations. The structural differences arising from the vdW corrections are shown to be significant for several properties and potentially less important for others. Additionally, our Mulliken population analysis reveals that contrary to the common belief, porphyrin is not the primary electron donating moiety for C60. In the considered dyad, fullerene's affinity for electrons is primarily satisfied by charge transfer from the amide group of the linker. However, we show that in the absence of another suitable bound donor, C60 can withdraw electrons from porphyrin if it is sufficiently close. AB - The interplay between electrostatic and van der Waals (vdW) interactions in porphyrin-C60 dyads is still under debate despite its importance in influencing the structural characteristics of such complexes considered for various applications in molecular photovoltaics. In this article, we sample the conformational space of a porphyrin-C60 dyad using Car-Parrinello molecular dynamics simulations with and without empirical vdW corrections. Long-range vdW interactions, which are poorly described by the commonly used density functional theory functionals, prove to be essential for a proper dynamics of the dyad moieties. Inclusion of vdW corrections brings porphyrin and C60 close together in an orientation that is in agreement with experimental observations. The structural differences arising from the vdW corrections are shown to be significant for several properties and potentially less important for others. Additionally, our Mulliken population analysis reveals that contrary to the common belief, porphyrin is not the primary electron donating moiety for C60. In the considered dyad, fullerene's affinity for electrons is primarily satisfied by charge transfer from the amide group of the linker. However, we show that in the absence of another suitable bound donor, C60 can withdraw electrons from porphyrin if it is sufficiently close. KW - Car-Parrinello molecular dynamics KW - Fullerene KW - Porphyrin KW - Time-dependent-density functional theory UR - http://www.scopus.com/inward/record.url?scp=84923259668&partnerID=8YFLogxK U2 - 10.1002/jcc.23834 DO - 10.1002/jcc.23834 M3 - Article VL - 36 SP - 612 EP - 621 JO - Journal of Computational Chemistry JF - Journal of Computational Chemistry SN - 0192-8651 IS - 9 ER - TY - GEN T1 - Visibility-Aware Part Coding for Vehicle Viewing Angle Estimation AU - Yang, Dan AU - Qian, Yanlin AU - Cai, Dingding AU - Yan, Song AU - Kämäräinen, Joni-Kristian AU - Chen, Ke N1 - EXT="Chen, Ke" jufoid=79229 PY - 2019/8/1 Y1 - 2019/8/1 N2 - A number of spatially-localised semantic parts of vehicles sensitive to pose changes are encoded their visible probabilities into a mid-level feature vector. Car pose estimation is then formulated into a regression on concatenated low-and mid-level features to continuously changing viewing angles. Each dimension of our visibility-Aware part codes separates all the training samples into two groups according to its visual existence in images, which provides additional part-specific range constraint of viewing angles. Moreover, the proposed codes can alleviate the suffering from sparse and imbalanced data distribution in the light of modelling latent dependency across angle targets. Experimental evaluation for car pose estimation on the EPFL Multi-View Car benchmark demonstrates significant improvement of our method over the state-of-The-Art regression methods, especially when only sparse and imbalanced data is available. AB - A number of spatially-localised semantic parts of vehicles sensitive to pose changes are encoded their visible probabilities into a mid-level feature vector. Car pose estimation is then formulated into a regression on concatenated low-and mid-level features to continuously changing viewing angles. Each dimension of our visibility-Aware part codes separates all the training samples into two groups according to its visual existence in images, which provides additional part-specific range constraint of viewing angles. Moreover, the proposed codes can alleviate the suffering from sparse and imbalanced data distribution in the light of modelling latent dependency across angle targets. Experimental evaluation for car pose estimation on the EPFL Multi-View Car benchmark demonstrates significant improvement of our method over the state-of-The-Art regression methods, especially when only sparse and imbalanced data is available. KW - Car pose estimation KW - Coding KW - Pose-sensitive parts KW - Regression forests KW - Visibility-Aware U2 - 10.1109/ICIST.2019.8836907 DO - 10.1109/ICIST.2019.8836907 M3 - Conference contribution SP - 65 EP - 70 BT - 9th International Conference on Information Science and Technology, ICIST 2019 PB - IEEE ER -