Structural and Functional Discovery in Dynamic Networks with Non-negative Matrix Factorization

Time series of graphs are increasingly prevalent in modern data and pose unique challenges to visual exploration and pattern extraction. This paper describes the development and application of matrix factorizations for exploration and time-varying community detection in time-evolving graph sequences. The matrix factorization model allows the user to home in on and display interesting, underlying structure and its evolution over time. The methods are scalable to weighted networks with a large number of time points or nodes and can accommodate sudden changes to graph topology. Our techniques are demonstrated with several dynamic graph series from both synthetic and real-world data, including citation and trade networks. These examples illustrate how users can steer the techniques and combine them with existing methods to discover and display meaningful patterns in sizable graphs over many time points.

[1]  C. Ross Found , 1869, The Dental register.

[2]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[3]  E. B. Wilson PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES. , 1919, Science.

[4]  O. Bagasra,et al.  Proceedings of the National Academy of Sciences , 1914, Science.

[5]  O. William Journal Of The American Statistical Association V-28 , 1932 .

[6]  J. Meigs,et al.  WHO Technical Report , 1954, The Yale Journal of Biology and Medicine.

[7]  L. Goddard Information Theory , 1962, Nature.

[8]  J. Garloff Continuation of two previous bibliographies on interval mathematics , 1986 .

[9]  Michael I. Jordan,et al.  Advances in Neural Information Processing Systems 30 , 1995 .

[10]  Taylor Francis Online,et al.  Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America. , 1992 .

[11]  L. Serven,et al.  The World Bank research observer 11 (1) , 1992 .

[12]  P. Paatero,et al.  Positive matrix factorization: A non-negative factor model with optimal utilization of error estimates of data values† , 1994 .

[13]  Ioannis G. Tollis,et al.  Graph Drawing , 1994, Lecture Notes in Computer Science.

[14]  D. Signorini,et al.  Neural networks , 1995, The Lancet.

[15]  Bernie Mulgrew,et al.  IEEE Workshop on Neural Networks for Signal Processing , 1995 .

[16]  J. Herskowitz,et al.  Proceedings of the National Academy of Sciences, USA , 1996, Current Biology.

[17]  J. Stiglitz SOME LESSONS FROM THE EAST ASIAN MIRACLE , 1996 .

[18]  R. Nelson,et al.  Debt Sustainability Under Catastrophic Risk: The Case for Government Budget Insurance , 1997 .

[19]  A. Châtelain,et al.  The European Physical Journal D , 1999 .

[20]  H. Sebastian Seung,et al.  Learning the parts of objects by non-negative matrix factorization , 1999, Nature.

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

[22]  Jon Kleinberg,et al.  Authoritative sources in a hyperlinked environment , 1999, SODA '98.

[23]  Ling Guan,et al.  Proceedings of the 2000 IEEE Workshop on Neural Networks for Signal Processing , 2000 .

[24]  Carl D. Meyer,et al.  Matrix Analysis and Applied Linear Algebra , 2000 .

[25]  Andrew G. Glen,et al.  APPL , 2001 .

[26]  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.

[27]  Peter D. Hoff,et al.  Latent Space Approaches to Social Network Analysis , 2002 .

[28]  H. J. Mclaughlin,et al.  Learn , 2002 .

[29]  Roberto Scopigno,et al.  Computer Graphics forum , 2003, Computer Graphics Forum.

[30]  D. Ruppert The Elements of Statistical Learning: Data Mining, Inference, and Prediction , 2004 .

[31]  David B. Skillicorn,et al.  Proceedings of the Fourth SIAM International Conference on Data Mining, Lake Buena Vista, Florida, USA, April 22-24, 2004 , 2004, SDM.

[32]  Patrik O. Hoyer,et al.  Non-negative Matrix Factorization with Sparseness Constraints , 2004, J. Mach. Learn. Res..

[33]  Ericka Stricklin-Parker,et al.  Ann , 2005 .

[34]  Y. Koren,et al.  Drawing graphs by eigenvectors: theory and practice , 2005 .

[35]  Gerald L. Engel,et al.  VISUALIZATION AND COMPUTER GRAPHICS , 2005 .

[36]  J. Cavanaugh Biostatistics , 2005, Definitions.

[37]  T. Vicsek,et al.  Uncovering the overlapping community structure of complex networks in nature and society , 2005, Nature.

[38]  Robert L. Grossman,et al.  Proceedings of the eleventh ACM SIGKDD international conference on Knowledge discovery in data mining , 2005, KDD 2005.

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

[40]  Stephen P. Boyd,et al.  Convex Optimization , 2004, Algorithms and Theory of Computation Handbook.

[41]  Duncan J. Watts,et al.  The Structure and Dynamics of Networks: (Princeton Studies in Complexity) , 2006 .

[42]  Michael W. Berry,et al.  Algorithms and applications for approximate nonnegative matrix factorization , 2007, Comput. Stat. Data Anal..

[43]  E. A. Leicht,et al.  Large-scale structure of time evolving citation networks , 2007, 0706.0015.

[44]  Discriminant Subspace,et al.  PATTERN ANALYSIS AND MACHINE INTELLIGENCE A publication of the IEEE Computer Society , 2007 .

[45]  S. Fortunato,et al.  Resolution limit in community detection , 2006, Proceedings of the National Academy of Sciences.

[46]  Rich Caruana,et al.  Proceedings of the 13th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, San Jose, California, USA, August 12-15, 2007 , 2007, KDD.

[47]  Chih-Jen Lin,et al.  On the Convergence of Multiplicative Update Algorithms for Nonnegative Matrix Factorization , 2007, IEEE Transactions on Neural Networks.

[48]  Yunhao Liu,et al.  Proceedings of the 17th international conference on World Wide Web , 2008, WWW 2008.

[49]  Ayellet Tal,et al.  Online Dynamic Graph Drawing , 2008, IEEE Transactions on Visualization and Computer Graphics.

[50]  Karthik Devarajan,et al.  Nonnegative Matrix Factorization: An Analytical and Interpretive Tool in Computational Biology , 2008, PLoS Comput. Biol..

[51]  Chris H. Q. Ding,et al.  On the equivalence between Non-negative Matrix Factorization and Probabilistic Latent Semantic Indexing , 2008, Comput. Stat. Data Anal..

[52]  Le Song,et al.  Estimating time-varying networks , 2008, ISMB 2008.

[53]  Srinivasan Parthasarathy,et al.  An event-based framework for characterizing the evolutionary behavior of interaction graphs , 2009, ACM Trans. Knowl. Discov. Data.

[54]  Patrick O. Perry,et al.  Bi-cross-validation of the SVD and the nonnegative matrix factorization , 2009, 0908.2062.

[55]  R. Rosenfeld Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[56]  R. Tibshirani,et al.  A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis. , 2009, Biostatistics.

[57]  R. Maitra,et al.  Supplement to “ A k-mean-directions Algorithm for Fast Clustering of Data on the Sphere ” published in the Journal of Computational and Graphical Statistics , 2009 .

[58]  Mark E. J. Newman,et al.  Power-Law Distributions in Empirical Data , 2007, SIAM Rev..

[59]  M. D. Martínez-Miranda,et al.  Computational Statistics and Data Analysis , 2009 .

[60]  Silvia Miksch,et al.  Proceedings of the ACM SIGKDD Workshop on Visual Analytics and Knowledge Discovery: Integrating Automated Analysis with Interactive Exploration, Paris, France, June 28, 2009 , 2009, KDD Workshop on Visual Analytics and Knowledge Discovery.

[61]  Daniel Weiskopf,et al.  Computer Graphics Forum (Proceedings Eurographics/IEEE Symposium on Visualization) , 2010 .

[62]  Niklas Elmqvist,et al.  TimeMatrix: Analyzing Temporal Social Networks Using Interactive Matrix-Based Visualizations , 2010, Int. J. Hum. Comput. Interact..

[63]  Fei Wang,et al.  Community discovery using nonnegative matrix factorization , 2011, Data Mining and Knowledge Discovery.

[64]  Thomas S. Huang,et al.  Graph Regularized Nonnegative Matrix Factorization for Data Representation. , 2011, IEEE transactions on pattern analysis and machine intelligence.

[65]  Stephen Roberts,et al.  Overlapping community detection using Bayesian non-negative matrix factorization. , 2011, Physical review. E, Statistical, nonlinear, and soft matter physics.

[66]  Mark E. J. Newman,et al.  An efficient and principled method for detecting communities in networks , 2011, Physical review. E, Statistical, nonlinear, and soft matter physics.

[67]  Bin Yu,et al.  Spectral clustering and the high-dimensional stochastic blockmodel , 2010, 1007.1684.

[68]  Daniel W. Archambault,et al.  Animation, Small Multiples, and the Effect of Mental Map Preservation in Dynamic Graphs , 2011, IEEE Transactions on Visualization and Computer Graphics.

[69]  Arjan Kuijper,et al.  Visual Analysis of Large Graphs: State‐of‐the‐Art and Future Research Challenges , 2011, Eurographics.

[70]  Stephen E. Fienberg,et al.  A Brief History of Statistical Models for Network Analysis and Open Challenges , 2012 .

[71]  W. Marsden I and J , 2012 .

[72]  Roummel F. Marcia,et al.  Sequential Anomaly Detection in the Presence of Noise and Limited Feedback , 2009, IEEE Transactions on Information Theory.

[73]  O. de Weck,et al.  Overview of metrics and their correlation patterns for multiple-metric topology analysis on heterogeneous graph ensembles. , 2012, Physical review. E, Statistical, nonlinear, and soft matter physics.

[74]  Niklas Elmqvist,et al.  Perception of Animated Node‐Link Diagrams for Dynamic Graphs , 2012, Comput. Graph. Forum.

[75]  Shuliang Wang,et al.  Data Mining and Knowledge Discovery , 2005, Mathematical Principles of the Internet.

[76]  35th Annual Conference of the European Association for Computer Graphics, Eurographics 2014 - State of the Art Reports, Strasbourg, France, April 7-11, 2014 , 2014, Eurographics.

[77]  Aaas News,et al.  Book Reviews , 1893, Buffalo Medical and Surgical Journal.

[78]  U. Feige,et al.  Spectral Graph Theory , 2015 .