Reconstructing Networks from Profit Sequences in Evolutionary Games via a Multiobjective Optimization Approach with Lasso Initialization

Evolutionary games (EG) model a common type of interactions in various complex, networked, natural and social systems. Given such a system with only profit sequences being available, reconstructing the interacting structure of EG networks is fundamental to understand and control its collective dynamics. Existing approaches used to handle this problem, such as the lasso, a convex optimization method, need a user-defined constant to control the tradeoff between the natural sparsity of networks and measurement error (the difference between observed data and simulated data). However, a shortcoming of these approaches is that it is not easy to determine these key parameters which can maximize the performance. In contrast to these approaches, we first model the EG network reconstruction problem as a multiobjective optimization problem (MOP), and then develop a framework which involves multiobjective evolutionary algorithm (MOEA), followed by solution selection based on knee regions, termed as MOEANet, to solve this MOP. We also design an effective initialization operator based on the lasso for MOEA. We apply the proposed method to reconstruct various types of synthetic and real-world networks, and the results show that our approach is effective to avoid the above parameter selecting problem and can reconstruct EG networks with high accuracy.

[1]  M. Newman,et al.  Finding community structure in networks using the eigenvectors of matrices. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

[2]  Diogo M. Camacho,et al.  Wisdom of crowds for robust gene network inference , 2012, Nature Methods.

[3]  Zhongke Gao,et al.  A directed weighted complex network for characterizing chaotic dynamics from time series , 2012 .

[4]  Duncan J. Watts,et al.  Collective dynamics of ‘small-world’ networks , 1998, Nature.

[5]  Kalyanmoy Deb,et al.  Finding Knees in Multi-objective Optimization , 2004, PPSN.

[6]  Xiao Han,et al.  Robust Reconstruction of Complex Networks from Sparse Data , 2015, Physical review letters.

[7]  Albert,et al.  Emergence of scaling in random networks , 1999, Science.

[8]  Arkady Pikovsky,et al.  Network reconstruction from random phase resetting. , 2010, Physical review letters.

[9]  Wen-Xu Wang,et al.  Predicting catastrophes in nonlinear dynamical systems by compressive sensing. , 2011, Physical review letters.

[10]  A. Barabasi,et al.  Network link prediction by global silencing of indirect correlations , 2013, Nature Biotechnology.

[11]  R. Tibshirani Regression Shrinkage and Selection via the Lasso , 1996 .

[12]  G. Caldarelli,et al.  Reconstructing a credit network , 2013, Nature Physics.

[13]  A. Ranga,et al.  3D niche microarrays for systems-level analyses of cell fate , 2014, Nature Communications.

[14]  M. Nowak Evolutionary Dynamics: Exploring the Equations of Life , 2006 .

[15]  Yong Wang,et al.  A Multiobjective Optimization-Based Evolutionary Algorithm for Constrained Optimization , 2006, IEEE Transactions on Evolutionary Computation.

[16]  A. Neubauer,et al.  A theoretical analysis of the non-uniform mutation operator for the modified genetic algorithm , 1997, Proceedings of 1997 IEEE International Conference on Evolutionary Computation (ICEC '97).

[17]  K. Deb,et al.  Understanding knee points in bicriteria problems and their implications as preferred solution principles , 2011 .

[18]  S. Strogatz Exploring complex networks , 2001, Nature.

[19]  J M Smith,et al.  Evolution and the theory of games , 1976 .

[20]  Xin Yao,et al.  An Evolutionary Multiobjective Approach to Sparse Reconstruction , 2014, IEEE Transactions on Evolutionary Computation.

[21]  Kalyanmoy Deb,et al.  A fast and elitist multiobjective genetic algorithm: NSGA-II , 2002, IEEE Trans. Evol. Comput..

[22]  M. Newman,et al.  Renormalization Group Analysis of the Small-World Network Model , 1999, cond-mat/9903357.

[23]  G. Szabó,et al.  Evolutionary prisoner's dilemma game on a square lattice , 1997, cond-mat/9710096.

[24]  Zhong-Ke Gao,et al.  Multi-frequency complex network from time series for uncovering oil-water flow structure , 2015, Scientific Reports.

[25]  Marc Timme,et al.  Revealing network connectivity from response dynamics. , 2006, Physical review letters.

[26]  Donald E. Knuth,et al.  The Stanford GraphBase - a platform for combinatorial computing , 1993 .

[27]  Claire J. Tomlin,et al.  Exact reconstruction of gene regulatory networks using compressive sensing , 2014, BMC Bioinformatics.

[28]  M. Newman,et al.  Hierarchical structure and the prediction of missing links in networks , 2008, Nature.

[29]  Yong Wang,et al.  Combining Multiobjective Optimization With Differential Evolution to Solve Constrained Optimization Problems , 2012, IEEE Transactions on Evolutionary Computation.

[30]  M. Nowak,et al.  Evolutionary games and spatial chaos , 1992, Nature.

[31]  C. Coello TREATING CONSTRAINTS AS OBJECTIVES FOR SINGLE-OBJECTIVE EVOLUTIONARY OPTIMIZATION , 2000 .

[32]  Jens Keilwagen,et al.  PRROC: computing and visualizing precision-recall and receiver operating characteristic curves in R , 2015, Bioinform..

[33]  Muriel Médard,et al.  Network deconvolution as a general method to distinguish direct dependencies in networks , 2013, Nature Biotechnology.

[34]  J Kurths,et al.  Inner composition alignment for inferring directed networks from short time series. , 2011, Physical review letters.

[35]  Lily Rachmawati,et al.  Multiobjective Evolutionary Algorithm With Controllable Focus on the Knees of the Pareto Front , 2009, IEEE Transactions on Evolutionary Computation.

[36]  D. Lusseau,et al.  The bottlenose dolphin community of Doubtful Sound features a large proportion of long-lasting associations , 2003, Behavioral Ecology and Sociobiology.

[37]  G. Szabó,et al.  Evolutionary games on graphs , 2006, cond-mat/0607344.

[38]  Ying-Cheng Lai,et al.  Motif distributions in phase-space networks for characterizing experimental two-phase flow patterns with chaotic features. , 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.

[39]  Wen-Xu Wang,et al.  Reconstructing propagation networks with natural diversity and identifying hidden sources , 2014, Nature Communications.

[40]  Jörgen W. Weibull,et al.  Evolutionary Game Theory , 1996 .

[41]  Jieping Ye,et al.  Network Reconstruction Based on Evolutionary-Game Data via Compressive Sensing , 2011, Physical Review X.

[42]  Zhong-Ke Gao,et al.  Multivariate weighted complex network analysis for characterizing nonlinear dynamic behavior in two-phase flow , 2015 .

[43]  Zhongke Gao,et al.  Flow-pattern identification and nonlinear dynamics of gas-liquid two-phase flow in complex networks. , 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.

[44]  Ying-Cheng Lai,et al.  Reconstructing direct and indirect interactions in networked public goods game , 2016, Scientific Reports.

[45]  Qingfu Zhang,et al.  MOEA/D: A Multiobjective Evolutionary Algorithm Based on Decomposition , 2007, IEEE Transactions on Evolutionary Computation.

[46]  Hod Lipson,et al.  Automated reverse engineering of nonlinear dynamical systems , 2007, Proceedings of the National Academy of Sciences.

[47]  Josef Hofbauer,et al.  Evolutionary Games and Population Dynamics , 1998 .

[48]  Wen-Xu Wang,et al.  Noise bridges dynamical correlation and topology in coupled oscillator networks. , 2010, Physical review letters.

[49]  J. Collins,et al.  Inferring Genetic Networks and Identifying Compound Mode of Action via Expression Profiling , 2003, Science.

[50]  Maoguo Gong,et al.  ADAPTIVE RANKS CLONE AND k‐NEAREST NEIGHBOR LIST–BASED IMMUNE MULTI‐OBJECTIVE OPTIMIZATION , 2010, Comput. Intell..

[51]  Jürgen Kurths,et al.  Multivariate recurrence network analysis for characterizing horizontal oil-water two-phase flow. , 2013, Physical review. E, Statistical, nonlinear, and soft matter physics.

[52]  Zhong-Ke Gao,et al.  Multiscale complex network for analyzing experimental multivariate time series , 2015 .

[53]  M E J Newman,et al.  Community structure in social and biological networks , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[54]  W. Zachary,et al.  An Information Flow Model for Conflict and Fission in Small Groups , 1977, Journal of Anthropological Research.