Topology Identification and Learning over Graphs: Accounting for Nonlinearities and Dynamics

Identifying graph topologies as well as processes evolving over graphs emerge in various applications involving gene-regulatory, brain, power, and social networks, to name a few. Key graph-aware learning tasks include regression, classification, subspace clustering, anomaly identification, interpolation, extrapolation, and dimensionality reduction. Scalable approaches to deal with such high-dimensional tasks experience a paradigm shift to address the unique modeling and computational challenges associated with data-driven sciences. Albeit simple and tractable, linear time-invariant models are limited since they are incapable of handling generally evolving topologies, as well as nonlinear and dynamic dependencies between nodal processes. To this end, the main goal of this paper is to outline overarching advances, and develop a principled framework to capture nonlinearities through kernels, which are judiciously chosen from a preselected dictionary to optimally fit the data. The framework encompasses and leverages (non) linear counterparts of partial correlation and partial Granger causality, as well as (non)linear structural equations and vector autoregressions, along with attributes such as low rank, sparsity, and smoothness to capture even directional dependencies with abrupt change points, as well as time-evolving processes over possibly time-evolving topologies. The overarching approach inherits the versatility and generality of kernel-based methods, and lends itself to batch and computationally affordable online learning algorithms, which include novel Kalman filters over graphs. Real data experiments highlight the impact of the nonlinear and dynamic models on consumer and financial networks, as well as gene-regulatory and functional connectivity brain networks, where connectivity patterns revealed exhibit discernible differences relative to existing approaches.

[1]  Alexander J. Smola,et al.  Kernels and Regularization on Graphs , 2003, COLT.

[2]  H. Bozdogan Model selection and Akaike's Information Criterion (AIC): The general theory and its analytical extensions , 1987 .

[3]  Michael I. Jordan,et al.  Nonparametric Bayesian Learning of Switching Linear Dynamical Systems , 2008, NIPS.

[4]  J. A. Hartigan,et al.  A k-means clustering algorithm , 1979 .

[5]  Alejandro Ribeiro,et al.  Consensus in Ad Hoc WSNs With Noisy Links—Part I: Distributed Estimation of Deterministic Signals , 2008, IEEE Transactions on Signal Processing.

[6]  Philip S. Yu,et al.  GraphScope: parameter-free mining of large time-evolving graphs , 2007, KDD '07.

[7]  James D. B. Nelson,et al.  High dimensional changepoint detection with a dynamic graphical lasso , 2014, 2014 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP).

[8]  Santiago Segarra,et al.  Network Topology Inference from Spectral Templates , 2016, IEEE Transactions on Signal and Information Processing over Networks.

[9]  Roberto Turrin,et al.  Performance of recommender algorithms on top-n recommendation tasks , 2010, RecSys '10.

[10]  Pascal Frossard,et al.  The emerging field of signal processing on graphs: Extending high-dimensional data analysis to networks and other irregular domains , 2012, IEEE Signal Processing Magazine.

[11]  Joseph K. Pickrell,et al.  Understanding mechanisms underlying human gene expression variation with RNA sequencing , 2010, Nature.

[12]  Georgios B. Giannakis,et al.  Topology inference of multilayer networks , 2017, 2017 IEEE Conference on Computer Communications Workshops (INFOCOM WKSHPS).

[13]  Leto Peel,et al.  Detecting Change Points in the Large-Scale Structure of Evolving Networks , 2014, AAAI.

[14]  Moriah E. Thomason,et al.  Vector autoregression, structural equation modeling, and their synthesis in neuroimaging data analysis , 2011, Comput. Biol. Medicine.

[15]  Georgios B. Giannakis,et al.  Nonparametric Basis Pursuit via Sparse Kernel-Based Learning: A Unifying View with Advances in Blind Methods , 2013, IEEE Signal Processing Magazine.

[16]  Yizhou Sun,et al.  Mining heterogeneous information networks: a structural analysis approach , 2013, SKDD.

[17]  E. David,et al.  Networks, Crowds, and Markets: Reasoning about a Highly Connected World , 2010 .

[18]  Tamara G. Kolda,et al.  Temporal Link Prediction Using Matrix and Tensor Factorizations , 2010, TKDD.

[19]  D. Donoho For most large underdetermined systems of linear equations the minimal 𝓁1‐norm solution is also the sparsest solution , 2006 .

[20]  Geert Leus,et al.  Autoregressive Moving Average Graph Filtering , 2016, IEEE Transactions on Signal Processing.

[21]  Sunil K. Narang,et al.  Signal processing techniques for interpolation in graph structured data , 2013, 2013 IEEE International Conference on Acoustics, Speech and Signal Processing.

[22]  S T Roweis,et al.  Nonlinear dimensionality reduction by locally linear embedding. , 2000, Science.

[23]  Georgios B. Giannakis,et al.  Identifiability of sparse structural equation models for directed and cyclic networks , 2013, 2013 IEEE Global Conference on Signal and Information Processing.

[24]  Jonathan D. Cryer,et al.  Time Series Analysis , 1986 .

[25]  Xiaohai Sun,et al.  Assessing Nonlinear Granger Causality from Multivariate Time Series , 2008, ECML/PKDD.

[26]  Mehryar Mohri,et al.  Learning Non-Linear Combinations of Kernels , 2009, NIPS.

[27]  George Karypis,et al.  SLIM: Sparse Linear Methods for Top-N Recommender Systems , 2011, 2011 IEEE 11th International Conference on Data Mining.

[28]  C. Granger Investigating causal relations by econometric models and cross-spectral methods , 1969 .

[29]  Georgios B. Giannakis,et al.  Multi-kernel change detection for dynamic functional connectivity graphs , 2017, 2017 51st Asilomar Conference on Signals, Systems, and Computers.

[30]  Georgios B. Giannakis,et al.  Nonlinear dimensionality reduction on graphs , 2017, 2017 IEEE 7th International Workshop on Computational Advances in Multi-Sensor Adaptive Processing (CAMSAP).

[31]  Michael P. H. Stumpf,et al.  Inference of temporally varying Bayesian Networks , 2012, Bioinform..

[32]  Mehryar Mohri,et al.  L2 Regularization for Learning Kernels , 2009, UAI.

[33]  A. Goldberger STRUCTURAL EQUATION METHODS IN THE SOCIAL SCIENCES , 1972 .

[34]  Holger Brandt,et al.  A Nonlinear Structural Equation Mixture Modeling Approach for Nonnormally Distributed Latent Predictor Variables , 2014 .

[35]  Mark W. Woolrich,et al.  Network modelling methods for FMRI , 2011, NeuroImage.

[36]  Xin-Yuan Song,et al.  Model comparison of nonlinear structural equation models with fixed covariates , 2003 .

[37]  David Liben-Nowell,et al.  The link-prediction problem for social networks , 2007 .

[38]  Qing Ling,et al.  Decentralized learning for wireless communications and networking , 2015, ArXiv.

[39]  V. Calhoun,et al.  The Chronnectome: Time-Varying Connectivity Networks as the Next Frontier in fMRI Data Discovery , 2014, Neuron.

[40]  Georgios B. Giannakis,et al.  Sketched Subspace Clustering , 2017, IEEE Transactions on Signal Processing.

[41]  Trevor Hastie,et al.  The Elements of Statistical Learning , 2001 .

[42]  Hongyuan Zha,et al.  Co-ranking Authors and Documents in a Heterogeneous Network , 2007, Seventh IEEE International Conference on Data Mining (ICDM 2007).

[43]  Stephen P. Boyd,et al.  Network Inference via the Time-Varying Graphical Lasso , 2017, KDD.

[44]  Rainer Goebel,et al.  Mapping directed influence over the brain using Granger causality and fMRI , 2005, NeuroImage.

[45]  S. Chen,et al.  Speaker, Environment and Channel Change Detection and Clustering via the Bayesian Information Criterion , 1998 .

[46]  B. Muthén A general structural equation model with dichotomous, ordered categorical, and continuous latent variable indicators , 1984 .

[47]  Georgios B. Giannakis,et al.  Prediction of Partially Observed Dynamical Processes Over Networks via Dictionary Learning , 2014, IEEE Transactions on Signal Processing.

[48]  Daniele Marinazzo,et al.  Kernel method for nonlinear granger causality. , 2007, Physical review letters.

[49]  Yun Chi,et al.  On evolutionary spectral clustering , 2009, TKDD.

[50]  Georgios B. Giannakis,et al.  Inference of Gene Regulatory Networks with Sparse Structural Equation Models Exploiting Genetic Perturbations , 2013, PLoS Comput. Biol..

[51]  Georgios B. Giannakis,et al.  Inference of spatiotemporal processes over graphs via kernel kriged Kalman filtering , 2017, 2017 25th European Signal Processing Conference (EUSIPCO).

[52]  Hui Li,et al.  A Deep Learning Approach to Link Prediction in Dynamic Networks , 2014, SDM.

[53]  Gonzalo Mateos,et al.  Proximal-Gradient Algorithms for Tracking Cascades Over Social Networks , 2014, IEEE Journal of Selected Topics in Signal Processing.

[54]  Jorge Bacca,et al.  Sparse Subspace Clustering in Hyperspectral Images using Incomplete Pixels , 2019 .

[55]  Georgios B. Giannakis,et al.  Online Ensemble Multi-kernel Learning Adaptive to Non-stationary and Adversarial Environments , 2017, AISTATS.

[56]  Amr Ahmed,et al.  Recovering time-varying networks of dependencies in social and biological studies , 2009, Proceedings of the National Academy of Sciences.

[57]  Rainer Goebel,et al.  Investigating directed cortical interactions in time-resolved fMRI data using vector autoregressive modeling and Granger causality mapping. , 2003, Magnetic resonance imaging.

[58]  Alfred O. Hero,et al.  Dynamic Stochastic Blockmodels for Time-Evolving Social Networks , 2014, IEEE Journal of Selected Topics in Signal Processing.

[59]  Georgios B. Giannakis,et al.  Kernel-Based Reconstruction of Space-Time Functions on Dynamic Graphs , 2016, IEEE Journal of Selected Topics in Signal Processing.

[60]  Francesco Folino,et al.  An Evolutionary Multiobjective Approach for Community Discovery in Dynamic Networks , 2014, IEEE Transactions on Knowledge and Data Engineering.

[61]  Georgios B. Giannakis,et al.  Inferring directed network topologies via tensor factorization , 2016, 2016 50th Asilomar Conference on Signals, Systems and Computers.

[62]  Jane You,et al.  Low-rank matrix factorization with multiple Hypergraph regularizer , 2015, Pattern Recognit..

[63]  Nathanael Perraudin,et al.  Fast Robust PCA on Graphs , 2015, IEEE Journal of Selected Topics in Signal Processing.

[64]  Georgios B. Giannakis,et al.  Kernel-Based Reconstruction of Graph Signals , 2016, IEEE Transactions on Signal Processing.

[65]  Zan Huang,et al.  The Time-Series Link Prediction Problem with Applications in Communication Surveillance , 2009, INFORMS J. Comput..

[66]  Georgios B. Giannakis,et al.  Sparse graphical modeling of piecewise-stationary time series , 2011, 2011 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP).

[67]  Antonio Ortega,et al.  Graph Learning From Data Under Laplacian and Structural Constraints , 2016, IEEE Journal of Selected Topics in Signal Processing.

[68]  Charles A. Micchelli,et al.  Learning the Kernel Function via Regularization , 2005, J. Mach. Learn. Res..

[69]  Adeel Razi,et al.  Dynamic causal modelling revisited , 2017, NeuroImage.

[70]  Georgios B. Giannakis,et al.  Tracking Switched Dynamic Network Topologies From Information Cascades , 2016, IEEE Transactions on Signal Processing.

[71]  C. Granger Investigating Causal Relations by Econometric Models and Cross-Spectral Methods , 1969 .

[72]  F. Gonzalez-Lima,et al.  Structural equation modeling and its application to network analysis in functional brain imaging , 1994 .

[73]  Purnamrita Sarkar,et al.  Nonparametric Link Prediction in Dynamic Networks , 2012, ICML.

[74]  Fan Yang,et al.  Nonlinear structural equation models: The Kenny-Judd model with Interaction effects , 1996 .

[75]  Ali Ghodsi,et al.  Dimensionality Reduction A Short Tutorial , 2006 .

[76]  R. Tibshirani,et al.  Sparse inverse covariance estimation with the graphical lasso. , 2008, Biostatistics.

[77]  Sankaran Mahadevan,et al.  Bayesian nonlinear structural equation modeling for hierarchical validation of dynamical systems , 2010 .

[78]  Georgios B. Giannakis,et al.  Tensor Decompositions for Identifying Directed Graph Topologies and Tracking Dynamic Networks , 2016, IEEE Transactions on Signal Processing.

[79]  Georgios B. Giannakis,et al.  Dynamic Network Delay Cartography , 2012, IEEE Transactions on Information Theory.

[80]  Leandros Tassiulas,et al.  Backbone formation in military multi-layer ad hoc networks using complex network concepts , 2016, MILCOM 2016 - 2016 IEEE Military Communications Conference.

[81]  Mikhail Belkin,et al.  Laplacian Eigenmaps for Dimensionality Reduction and Data Representation , 2003, Neural Computation.

[82]  Pascal Frossard,et al.  Learning Laplacian Matrix in Smooth Graph Signal Representations , 2014, IEEE Transactions on Signal Processing.

[83]  Santo Fortunato,et al.  Community detection in graphs , 2009, ArXiv.

[84]  Georgios B. Giannakis,et al.  Kernel-Based Structural Equation Models for Topology Identification of Directed Networks , 2016, IEEE Transactions on Signal Processing.

[85]  Martin A. Lindquist,et al.  Dynamic connectivity regression: Determining state-related changes in brain connectivity , 2012, NeuroImage.

[86]  Eric D. Kolaczyk,et al.  Statistical Analysis of Network Data: Methods and Models , 2009 .

[87]  Bernhard Schölkopf,et al.  Kernel Principal Component Analysis , 1997, ICANN.

[88]  Daniele Marinazzo,et al.  Kernel-Granger causality and the analysis of dynamical networks. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

[89]  Pascal Frossard,et al.  Clustering With Multi-Layer Graphs: A Spectral Perspective , 2011, IEEE Transactions on Signal Processing.

[90]  Yun Chi,et al.  Facetnet: a framework for analyzing communities and their evolutions in dynamic networks , 2008, WWW.

[91]  Johan A. K. Suykens,et al.  Least Squares Support Vector Machine Classifiers , 1999, Neural Processing Letters.

[92]  George Michailidis,et al.  Change point estimation in high dimensional Markov random‐field models , 2014, Journal of the Royal Statistical Society. Series B, Statistical methodology.

[93]  Nikos D. Sidiropoulos,et al.  Adaptive Algorithms to Track the PARAFAC Decomposition of a Third-Order Tensor , 2009, IEEE Transactions on Signal Processing.

[94]  Fei Wang,et al.  Graph dual regularization non-negative matrix factorization for co-clustering , 2012, Pattern Recognit..

[95]  Z. Wang,et al.  The structure and dynamics of multilayer networks , 2014, Physics Reports.

[96]  José M. F. Moura,et al.  Signal Processing on Graphs: Causal Modeling of Unstructured Data , 2015, IEEE Transactions on Signal Processing.

[97]  Brandi A. Weiss,et al.  A comparison of methods for estimating quadratic effects in nonlinear structural equation models. , 2012, Psychological methods.

[98]  Antonio Ortega,et al.  Generalized Laplacian precision matrix estimation for graph signal processing , 2016, 2016 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP).

[99]  Bo Zhao,et al.  Community evolution detection in dynamic heterogeneous information networks , 2010, MLG '10.

[100]  George Michailidis,et al.  Operator-valued kernel-based vector autoregressive models for network inference , 2014, Machine Learning.

[101]  Oren Etzioni,et al.  Grouper: A Dynamic Clustering Interface to Web Search Results , 1999, Comput. Networks.

[102]  Jin Tang,et al.  Graph-Laplacian PCA: Closed-Form Solution and Robustness , 2013, 2013 IEEE Conference on Computer Vision and Pattern Recognition.

[103]  Georgios B. Giannakis,et al.  Multi-kernel based nonlinear models for connectivity identification of brain networks , 2016, 2016 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP).

[104]  Sergio Barbarossa,et al.  Adaptive Least Mean Squares Estimation of Graph Signals , 2016, IEEE Transactions on Signal and Information Processing over Networks.

[105]  Georgios B. Giannakis,et al.  SEMI-BLIND INFERENCE OF TOPOLOGIES AND SIGNALS OVER GRAPHS , 2018, 2018 IEEE Data Science Workshop (DSW).

[106]  E. Rogers,et al.  Diffusion of innovations , 1964, Encyclopedia of Sport Management.

[107]  Alexander J. Hartemink,et al.  Learning Non-Stationary Dynamic Bayesian Networks , 2010, J. Mach. Learn. Res..

[108]  Georgios B. Giannakis,et al.  Kernel-based Inference of Functions over Graphs , 2017, ArXiv.

[109]  David A. Leopold,et al.  Dynamic functional connectivity: Promise, issues, and interpretations , 2013, NeuroImage.

[110]  Gang Wang,et al.  Going beyond linear dependencies to unveil connectivity of meshed grids , 2017, 2017 IEEE 7th International Workshop on Computational Advances in Multi-Sensor Adaptive Processing (CAMSAP).

[111]  Georgios B. Giannakis,et al.  Fast convergent algorithms for multi-kernel regression , 2016, 2016 IEEE Statistical Signal Processing Workshop (SSP).

[112]  Zhaohui S. Qin,et al.  A second generation human haplotype map of over 3.1 million SNPs , 2007, Nature.

[113]  Olaf Sporns,et al.  Complex network measures of brain connectivity: Uses and interpretations , 2010, NeuroImage.

[114]  G. Giannakis,et al.  Nonlinear Structural Vector Autoregressive Models for Inferring Effective Brain Network Connectivity , 2016, 1610.06551.