Learning Graphs From Data: A Signal Representation Perspective

Publisher: IEEE

Abstract:
The construction of a meaningful graph topology plays a crucial role in the effective representation, processing, analysis, and visualization of structured data. When a natural choice of the graph is not readily available from the data sets, it is thus desirable to infer or learn a graph topology from the data. In this article, we survey solutions to the problem of graph learning, including classical viewpoints from statistics and physics, and more recent approaches that adopt a graph signal processing (GSP) perspective. We further emphasize the conceptual similarities and differences between classical and GSP-based graph-inference methods and highlight the potential advantage of the latter in a number of theoretical and practical scenarios. We conclude with several open issues and challenges that are keys to the design of future signal processing and machine-learning algorithms for learning graphs from data.
Published in: IEEE Signal Processing Magazine ( Volume: 36, Issue: 3, May 2019)
Page(s): 44 - 63
Date of Publication: 06 May 2019
ISSN Information:
INSPEC Accession Number: 18621116
Publisher: IEEE

The construction of a meaningful graph topology plays a crucial role in the effective representation, processing, analysis, and visualization of structured data. When a natural choice of the graph is not readily available from the data sets, it is thus desirable to infer or learn a graph topology from the data. In this article, we survey solutions to the problem of graph learning, including classical viewpoints from statistics and physics, and more recent approaches that adopt a graph signal processing (GSP) perspective. We further emphasize the conceptual similarities and differences between classical and GSP-based graph-inference methods and highlight the potential advantage of the latter in a number of theoretical and practical scenarios. We conclude with several open issues and challenges that are keys to the design of future signal processing and machine-learning algorithms for learning graphs from data.

References

1.X. Zhu, Semi-supervised learning with graphs, 2005.
2.S. Fortunato, "Community detection in graphs", Physics Rep., vol. 486, no. 3–5, pp. 75-174, 2010.
3.D. I. Shuman, S. K. Narang, P. Frossard, A. Ortega and P. Vandergheynst, "The emerging field of signal processing on graphs: Extending high-dimensional data analysis to networks and other irregular domains", IEEE Signal Process. Mag., vol. 30, no. 3, pp. 83-98, 2013.
4.J. Richiardi, S. Achard, H. Bunke and D. V. D. Ville, "Machine learning with brain graphs: Predictive modeling approaches for functional imaging in systems neuroscience", IEEE Signal Process. Mag., vol. 30, no. 3, pp. 58-70, 2013.
5.D. Koller and N. Friedman, Probabilistic Graphical Models: Principles and Techniques, Cambridge, MA:MIT Press, 2009.
6.O. Banerjee, L. E. Ghaoui and A. d’Aspremont, "Model selection through sparse maximum likelihood estimation for multivariate Gaussian or binary data", J. Mach. Learn. Res., vol. 9, pp. 485-516, 2008, [online] Available: https://dl.acm.org/citation.cfm?id=1390696.
7.M. Gomez-Rodriguez, J. Leskovec and A. Krause, "Inferring networks of diffusion and influence", Proc. ACM SIGKDD Int. Conf. Knowledge Discovery and Data Mining, pp. 1019-1028, 2010.
8.S. A. Myers and J. Leskovec, "On the convexity of latent social network inference", Proc. Neural Information Processing Systems (NIPS), pp. 1741-1749, 2010.
9.M. Gomez-Rodriguez, J. Leskovec, D. Balduzzi and B. Schölkopf, "Uncovering the structure and temporal dynamics of information propagation", Netw. Sci., vol. 2, no. 1, pp. 26-65, 2014.
10.N. Du, L. Song, A. J. Smola and M. Yuan, "Learning networks of heterogeneous influence", Proc. Neural Information Processing Systems (NIPS), pp. 2789-2797, 2012.
11.C. Groendyke, D. Welch and D. R. Hunter, "Bayesian inference for contact networks given epidemic data", Scandinavian J. Statist., vol. 38, no. 3, pp. 600-616, 2011.
12.A. Sandryhaila and J. M. F. Moura, "Discrete signal processing on graphs", IEEE Trans. Signal Process., vol. 61, no. 7, pp. 1644-1656, 2013.
13.A. Ortega, P. Frossard, J. Kovacˇevic´, J. M. F. Moura and P. Vandergheynst, "Graph signal processing: Overview challenges and applications", Proc. IEEE, vol. 106, no. 5, pp. 808-828, 2018.
14.N. Meinshausen and P. Bühlmann, "High-dimensional graphs and variable selection with the Lasso", Ann. Statist., vol. 34, no. 3, pp. 1436-1462, 2006.
15.J. Friedman, T. Hastie and R. Tibshirani, "Sparse inverse covariance estimation with the graphical Lasso", Biostatist., vol. 9, no. 3, pp. 432-441, 2008.
16.C.-J. Hsieh, I. S. Dhillon, P. K. Ravikumar and M. A. Sustik, "Sparse inverse covariance matrix estimation using quadratic approximation", Proc. Neural Information Processing Systems (NIPS), pp. 2330-2338, 2011.
17.D. Heckerman, A tutorial on learning with Bayesian networks, 1995.
18.A. P. Dempster, "Covariance selection", Biometrics, vol. 28, no. 1, pp. 157-175, 1972.
19.R. Tibshirani, "Regression shrinkage and selection via the Lasso", J. Roy. Statist. Soc. Series B, vol. 58, no. 1, pp. 267-288, 1995.
20.M. Yuan and Y. Lin, "Model selection and estimation in regression with grouped variables", J. Roy. Statist. Soc. Series B, vol. 68, no. 1, pp. 49-67, 2006.
21.B. A. Cipra, "An introduction to the Ising model", Amer. Math. Monthly, vol. 94, no. 10, pp. 937-959, 1987.
22.P. Ravikumar, M. J. Wainwright and J. Lafferty, "High-dimensional Ising model selection using l1-regularized logistic regression", Ann. Statist., vol. 38, no. 3, pp. 1287-1319, 2010.
23.M. Slawski and M. Hein, "Estimation of positive definite M-matrices and structure learning for attractive Gaussian Markov random fields", Linear Algebra Applicat., vol. 473, pp. 145-179, May 2015.
24.G. Poole and T. Boullion, "A survey on M-matrices", SIAM Rev., vol. 16, no. 4, pp. 419-427, 1974.
25.B. Lake and J. Tenenbaum, "Discovering structure by learning sparse graph", Proc. 32nd Annu. Meeting Cognitive Science Society (CogSci), pp. 778-784, 2010.
26.S. I. Daitch, J. A. Kelner and D. A. Spielman, "Fitting a graph to vector data", Proc. Int. Conf. Machine Learning, pp. 201-208, 2009.
27.C. Hu, L. Cheng, J. Sepulcre, K. A. Johnson, G. E. Fakhri, Y. M. Lu, et al., "A spectral graph regression model for learning brain connectivity of Alzheimer’s disease", PLoS ONE, vol. 10, no. 5, 2015.
28.S. T. Roweis and L. K. Saul, "Nonlinear dimensionality reduction by locally linear embedding", Amer. Math. Monthly, vol. 290, no. 5500, pp. 2323-2326, 2000.
29.R. Castro, M. Coates, G. Liang, R. Nowak and B. Yu, "Network tomography: Recent developments", Statistical Sci., vol. 19, no. 3, pp. 499-517, 2004.
30.S. Ratnasamy and S. McCanne, "Inference of multicast routing trees and bottleneck bandwidths using end-to-end measurements", Proc. IEEE Infocom, pp. 353-360, 1999.
31.M. Rabbat, M. Coates and R. Nowak, "Multiple-source internet tomography", IEEE J. Select. Areas Commun., vol. 24, no. 12, pp. 2221-2234, 2006.
32.P. Sattari, M. Kurant, A. Anandkumar, A. Markopoulou and M. Rabbat, "Active learning of multiple source multiple destination topologies", IEEE Trans. Signal Process., vol. 62, no. 8, pp. 1926-1937, 2014.
33.R. Pastor-Satorras, C. Castellano, P. V. Mieghem and A. Vespignani, "Epidemic processes in complex networks", Rev. Modern Physics, vol. 87, no. 3, pp. 925-979, 2015.
34.M. Gomez-Rodriguez, L. Song, H. Daneshmand and B. Schölkopf, "Estimating diffusion networks: Recovery conditions sample complexity and soft-thresholding algorithm", J. Mach. Learn. Res., no. 90, pp. 1-29, 2016, [online] Available: http://jmlr.org/papers/v17/14-430.html.
35.S. Shaghaghian and M. Coates, "Bayesian inference of diffusion networks with unknown infection times", Proc. 2016 IEEE Statistical Signal Processing Workshop (SSP), 2016.
36.D. K. Hammond, P. Vandergheynst and R. Gribonval, "Wavelets on graphs via spectral graph theory", Appl. Comput. Harmon. Anal., vol. 30, no. 2, pp. 129-150, 2011.
37.X. Zhang, X. Dong and P. Frossard, "Learning of structured graph dictionaries", Proc. IEEE Int. Conf. Acoustics Speech and Signal Processing, pp. 3373-3376, 2012.
38.D. Thanou, D. I. Shuman and P. Frossard, "Learning parametric dictionaries for signals on graphs", IEEE Trans. Signal Process., vol. 62, no. 15, pp. 3849-3862, 2014.
39.X. Dong, D. Thanou, P. Frossard and P. Vandergheynst, "Learning Laplacian matrix in smooth graph signal representations", IEEE Trans. Signal Process., vol. 64, no. 23, pp. 6160-6173, 2016.
40.V. Kalofolias, "How to learn a graph from smooth signals", Proc. Int. Conf. Artificial Intelligence and Statistics, pp. 920-929, 2016.
41.H. E. Egilmez, E. Pavez and A. Ortega, "Graph learning from data under structural and Laplacian constraints", IEEE J. Sel. Topics Signal Process., vol. 11, no. 6, pp. 825-841, 2017.
42.S. P. Chepuri, S. Liu, G. Leus and A. O. Hero, "Learning sparse graphs under smoothness prior", Proc. IEEE Int. Conf. Acoustics Speech and Signal Processing, pp. 6508-6512, 2017.
43.F. Chung, "The heat kernel as the pagerank of a graph", Proc. Nat. Academy Sci., vol. 104, no. 50, pp. 19,735-19,740, 2007.
44.H. Ma, H. Yang, M. R. Lyu and I. King, "Mining social networks using heat diffusion processes for marketing candidates selection", Proc. 17th ACM Conf. Information and Knowledge Management, pp. 233-242, 2008.
45.S. Segarra, A. G. Marques, G. Mateos and A. Ribeiro, "Network topology inference from spectral templates", IEEE Trans. Signal Inform. Process. Netw., vol. 3, no. 3, pp. 467-483, 2017.
46.B. Pasdeloup, V. Gripon, G. Mercier, D. Pastor and M. G. Rabbat, "Characterization and inference of graph diffusion processes from observations of stationary signals", IEEE Trans. Signal Inform. Process. Netw., vol. 4, no. 3, pp. 481-496, 2018.
47.D. Thanou, X. Dong, D. Kressner and P. Frossard, "Learning heat diffusion graphs", IEEE Trans. Signal Inform. Process. Netw., vol. 3, no. 3, pp. 484-499, 2017.
48.R. Shafipour, S. Segarra, A. G. Marques and G. Mateos, "Identifying the topology of undirected networks from diffused non-stationary graph signals", 2018, [online] Available: .
49.H. E. Egilmez, E. Pavez and A. Ortega, "Graph learning from filtered signals: Graph system and diffusion kernel identification", IEEE Trans. Signal Inform. Process. Netw..
50.H. P. Maretic, D. Thanou and P. Frossard, "Graph learning under sparsity priors", Proc. IEEE Int. Conf. Acoustics Speech and Signal Processing, pp. 6523-6527, 2017.
51.R. Rubinstein, A. M. Bruckstein and M. Elad, "Dictionaries for sparse representation modeling", Proc. IEEE, vol. 98, no. 6, pp. 1045-1057, 2010.
52.I. Tosic and P. Frossard, "Dictionary learning", IEEE Signal Process. Mag., vol. 28, no. 2, pp. 27-38, 2011.
53.K. J. Friston, "Functional and effective connectivity in neuroimaging: A synthesis", Human Brain Mapping, vol. 2, no. 1–2, pp. 56-78, 1994.
54.Y. Shen, B. Baingana and G. B. Giannakis, "Nonlinear structural vector autoregressive models for inferring effective brain network connectivity", 2016, [online] Available: .
55.J. Mei and J. M. F. Moura, "Signal processing on graphs: Causal modeling of unstructured data", IEEE Trans. Signal Process., vol. 65, no. 8, pp. 2077-2092, 2017.
56.J. Songsiri and L. Vandenberghe, "Topology selection in graphical models of autoregressive processes", J. Mach. Learn. Res., vol. 11, pp. 2671-2705, 2010, [online] Available: https://dl.acm.org/citation.cfm?id=1953020.
57.A. Bolstad, B. D. V. Veen and R. Nowak, "Causal network inference via group sparse regularization", IEEE Trans. Signal Process., vol. 59, no. 6, pp. 2628-2641, 2011.
58.A. Roebroeck, E. Formisano and R. Goebel, "Mapping directed influence over the brain using Granger causality and fMRI", NeuroImage, vol. 25, no. 1, pp. 230-242, 2005.
59.R. Goebel, A. Roebroeck, D.-S. Kim and E. Formisano, "Investigating directed cortical interactions in time-resolved fMRI data using vector autoregressive modeling and Granger causality mapping", Magn. Resonance Imag., vol. 21, no. 10, pp. 1251-1261, 2003.
60.D. W. Kaplan, Structural Equation Modeling: Foundations and Extensions, Newbury Park, CA:Sage, 2009.
61.A. McIntosh and F. Gonzalez-Lima, "Structural equation modeling and its application to network analysis in functional brain imaging", Hum. Brain Mapp., vol. 2, no. 1–2, pp. 2-22, 1994.
62.B. Baingana and G. B. Giannakis, "Tracking switched dynamic network topologies from information cascades", IEEE Trans. Signal Process., vol. 65, no. 4, pp. 985-997, 2017.
63.P. A. Traganitis, Y. Shen and G. B. Giannakis, "Network topology inference via elastic net structural equation models", Proc. European Signal Processing Conf., pp. 146-150, 2017.
64.G. Chen, D. R. Glen, Z. S. Saad, J. P. Hamilton, M. E. Thomason, I. H. Gotlib, et al., "Vector autoregression structural equation modeling and their synthesis in neuroimaging data analysis", Comput. Biol. Med., vol. 41, no. 12, pp. 1142-1155, 2011.
65.G. B. Giannakis, Y. Shen and G. V. Karanikolas, "Topology identification and learning over graphs: Accounting for nonlinearities and dynamics", Proc. IEEE, vol. 106, no. 5, pp. 787-807, 2018.
66.G. Cheung, E. Magli, Y. Tanaka and M. Ng, "Graph spectral image processing", Proc. IEEE, vol. 106, no. 5, pp. 907-930, 2018.
67.W. Hu, G. Cheung, A. Ortega and O. C. Au, "Multi-resolution graph Fourier transform for compression of piecewise smooth images", IEEE Trans. Image Process., vol. 24, no. 1, pp. 419-433, 2015.
68.I. Rotondo, G. Cheung, A. Ortega and H. E. Egilmez, "Designing sparse graphs via structure tensor for block transform coding of images", Proc. Asia-Pacific Signal and Information Processing Assoc. Annu. Summit and Conf., pp. 571-574, 2015.
69.G. Fracastoro, D. Thanou and P. Frossard, "Graph-based transform coding with application to image compression", 2017, [online] Available: .
70.V. Kalofolias, A. Loukas, D. Thanou and P. Frossard, "Learning time varying graphs", Proc. IEEE Int. Conf. Acoustics Speech and Signal Processing, pp. 2826-2830, 2017.
71.K.-S. Lu and A. Ortega, "A graph Laplacian matrix learning method for fast implementation of graph Fourier transform", Proc. IEEE Int. Conf. Image Processing, pp. 1677-1681, 2017.
72.W. Huang, T. A. W. Bolton, J. D. Medaglia, D. S. Bassett, A. Ribeiro and D. V. D. Ville, "A graph signal processing perspective on functional brain imaging", 2018, [online] Available: .
73.R. Liu, H. Nejati and N.-M. Cheung, "Joint estimation of low-rank components and connectivity graph in high-dimensional graph signals: Application to brain imaging", 2018, [online] Available: .
74.I. Jablonski, "Graph signal processing in applications to sensor networks smart grids and smart cities", IEEE Sensors J., vol. 17, no. 23, pp. 7659-7666, 2017.
75.A. Gadde, A. Anis and A. Ortega, "Active semi-supervised learning using sampling theory for graph signals", Proc. ACM SIGKDD Int. Conf. Knowledge Discovery and Data Mining, pp. 492-501, 2014.
76.S. Vlaski, H. Maretic, R. Nassif, P. Frossard and A. H. Sayed, "Online graph learning from sequential data", Proc. IEEE Data Science Workshop, pp. 190-194, 2018.
77.H. N. Mhaskar, "A unified framework for harmonic analysis of functions on directed graphs and changing data", Appl. Comput. Harmon. Anal., vol. 44, no. 3, pp. 611-644, 2018.
78.B. Girault, A. Ortega and S. Narayanan, "Irregularity-aware graph Fourier transforms", IEEE Trans. Signal Process., vol. 66, no. 21, pp. 5746-5761, 2018.
79.S. Sardellitti, S. Barbarossa and P. D. Lorenzo, "On the graph Fourier transform for directed graphs", IEEE J. Sel. Topics Signal Process., vol. 11, no. 6, pp. 796-811, 2017.
80.R. Shafipour, A. Khodabakhsh, G. Mateos and E. Nikolova, "A directed graph Fourier transform with spread frequency components", 2018, [online] Available: .
81.A. D. Col, P. Valdivia, F. Petronetto, F. Dias, C. T. Silva and L. G. Nonato, "Wavelet-based visual analysis of dynamic networks", IEEE Trans. Vis. Comput. Graph., vol. 24, no. 8, pp. 2456-2469, 2018.
82.E. Pavez, H. E. Egilmez and A. Ortega, "Learning graphs with monotone topology properties and multiple connected components", IEEE Trans. Signal Process., vol. 66, no. 9, pp. 2399-2413, 2018.
83.M. Sundin, A. Venkitaraman, M. Jansson and S. Chatterjee, "A connectedness constraint for learning sparse graphs", Proc. European Signal Processing Conf., pp. 151-155, 2017.
84.X. Dong, P. Frossard, P. Vandergheynst and N. Nefedov, "Clustering on multi-layer graphs via subspace analysis on Grassmann manifolds", IEEE Trans. Signal Process., vol. 62, no. 4, pp. 905-918, 2014.
85.S. Segarra, G. Mateos, A. G. Marques and A. Ribeiro, "Blind identification of graph filters", IEEE Trans. Signal Process., vol. 65, no. 5, pp. 1146-1159, 2017.
86.S. Sardellitti, S. Barbarossa and P. Di Lorenzo, "Graph topology inference based on transform learning", Proc. IEEE Global Conf. Signal and Information Processing, pp. 356-360, 2016.
87.Y. Yankelevsky and M. Elad, "Dual graph regularized dictionary learning", IEEE Trans. Signal Inform. Process. Netw., vol. 2, no. 4, pp. 611-624, 2016.
88.D. Hallac, Y. Park, S. Boyd and J. Leskovec, "Network inference via the time-varying graphical Lasso", Proc. ACM SIGKDD Int. Conf. Knowledge Discovery and Data Mining, pp. 205-213, 2017.