Abstract
Persistent homology is a powerful tool in Topological Data Analysis (TDA) to capture topological properties of data succinctly at different spatial resolutions. For graphical data, shape and structure of the neighborhood of individual data items (nodes) is an essential means of characterizing their properties. We propose the use of persistent homology methods to capture structural and topological properties of graphs and use it to address the problem of link prediction. We achieve encouraging results on nine different real-world datasets that attest to the potential of persistent homology based methods for network analysis.
B. Chatterjee—Supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skodowska-Curie grant agreement No. 754411 (ISTPlus).
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Adamic, L.A., Adar, E.: Friends and neighbors on the web. Soc. Netw. 25(3), 211–230 (2003)
Backstrom, L., Leskovec, J.: Supervised random walks: predicting and recommending links in social networks. In: WSDM 2011 (2011)
Bauer, U.: Ripser (2018). https://github.com/Ripser/ripser
Bhatia, S., Caragea, C., Chen, H.H., Wu, J., Treeratpituk, P., Wu, Z., Khabsa, M., Mitra, P., Giles, C.L.: Specialized research datasets in the citeseer\(^x\) digital library. D-Lib Mag. 18(7/8) (2012)
Bhatia, S., Chatterjee, B., Nathani, D., Kaul, M.: Understanding and predicting links in graphs: a persistent homology perspective. arXiv preprint arXiv:1811.04049 (2018)
Bhatia, S., Vishwakarma, H.: Know thy neighbors, and more!: studying the role of context in entity recommendation. In: Hypertext (HT), pp. 87–95 (2018)
Carstens, C.J., Horadam, K.J.: Persistent homology of collaboration networks. Math. Probl. Eng. 2013, 7 (2013)
Chung, M.K., Bubenik, P., Kim, P.T.: Persistence diagrams of cortical surface data. In: International Conference on Information Processing in Medical Imaging, pp. 386–397 (2009)
Cohen, S., Zohar, A.: An axiomatic approach to link prediction. In: Twenty-Ninth AAAI Conference on Artificial Intelligence (2015)
Coulomb, S., Bauer, M., Bernard, D., Marsolier-Kergoat, M.C.: Gene essentiality and the topology of protein interaction networks. Proc. R. Soc. B: Biol. Sci. 272(1573), 1721–1725 (2005)
Edelsbrunner, H., Harer, J.: Persistent homology-a survey. Contemp. Math. 453, 257–282 (2008)
Edelsbrunner, H., Harer, J.: Computational Topology - An Introduction. American Mathematical Society, Providence (2010)
Eisinga, R., Breitling, R., Heskes, T.: The exact probability distribution of the rank product statistics for replicated experiments. FEBS Lett. 587(6), 677–682 (2013)
Ewing, R.M., Chu, P., Elisma, F., Li, H., Taylor, P., Climie, S., McBroom-Cerajewski, L., Robinson, M.D., O’Connor, L., Li, M., et al.: Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol. Syst. Biol. 3(1), 89 (2007)
Grover, A., Leskovec, J.: node2vec: scalable feature learning for networks. In: Proceedings of the 22nd ACM SIGKDD, pp. 855–864 (2016)
Hajij, M., Wang, B., Scheidegger, C., Rosen, P.: Visual detection of structural changes in time-varying graphs using persistent homology. In: PacificVis, pp. 125–134. IEEE (2018)
Hoff, P.D., Raftery, A.E., Handcock, M.S.: Latent space approaches to social network analysis. J. Am. Stat. Assoc. 97(460), 1090–1098 (2002)
Jeh, G., Widom, J.: SimRank: a measure of structural-context similarity, pp. 538–543. ACM (2002)
Johnson, D.B.: Efficient algorithms for shortest paths in sparse networks. J. ACM (JACM) 24(1), 1–13 (1977)
Kataria, S., Mitra, P., Bhatia, S.: Utilizing context in generative Bayesian models for linked corpus. In: AAAI, vol. 10, p. 1 (2010)
Katz, L.: A new status index derived from sociometric analysis. Psychometrika 18(1), 39–43 (1953)
Kerber, M., Morozov, D., Nigmetov, A.: Geometry helps to compare persistence diagrams. In: 2016 Proceedings of the Eighteenth Workshop on Algorithm Engineering and Experiments (ALENEX), pp. 103–112. SIAM (2016)
Leskovec, J., Backstrom, L., Kumar, R., Tomkins, A.: Microscopic evolution of social networks. In: KDD, pp. 462–470 (2008)
Leskovec, J., Kleinberg, J., Faloutsos, C.: Graph evolution: densification and shrinking diameters. ACM Trans. Knowl. Discov. Data 1(1) (2007)
Liben-Nowell, D., Kleinberg, J.: The link-prediction problem for social networks. J. Am. Soc. Inf. Sci. Technol. 58(7), 1019–1031 (2007)
Lu, Q., Getoor, L.: Link-based classification. In: Fawcett, T., Mishra, N. (eds.) ICML, pp. 496–503. AAAI Press (2003). http://www.aaai.org/Library/ICML/2003/icml03-066.php
McAuley, J., Leskovec, J.: Learning to discover social circles in ego networks. In: NIPS, pp. 548–556 (2012)
McPherson, M., Smith-Lovin, L., Cook, J.M.: Birds of a feather: homophily in social networks. Annu. Rev. Sociol. 27(1), 415–444 (2001)
Milne, D., Witten, I.: An effective, low-cost measure of semantic relatedness obtained from Wikipedia links. In: AAAI Workshop on Wikipedia and Artificial Intelligence: An Evolving Synergy, pp. 25–30 (2008)
Misra, V., Bhatia, S.: Bernoulli embeddings for graphs. In: AAAI, pp. 3812–3819 (2018)
Nagarajan, M., et al.: Predicting future scientific discoveries based on a networked analysis of the past literature. In: KDD, pp. 2019–2028. ACM (2015)
Newman, M.E.J.: Finding community structure in networks using the eigenvectors of matrices. Phys. Rev. E 74(3), 036104 (2006)
Pal, S., Moore, T.J., Ramanathan, R., Swami, A.: Comparative topological signatures of growing collaboration networks. In: Workshop on Complex Networks CompleNet, pp. 201–209. Springer (2017)
Perozzi, B., Al-Rfou, R., Skiena, S.: Deepwalk: online learning of social representations. In: KDD, pp. 701–710 (2014)
Ribeiro, L.F., Saverese, P.H., Figueiredo, D.R.: struc2vec: learning node representations from structural identity. In: KDD, pp. 385–394 (2017)
Sarkar, P., Chakrabarti, D., Moore, A.W.: Theoretical justification of popular link prediction heuristics. In: IJCAI (2011)
Šubelj, L., Bajec, M.: Robust network community detection using balanced propagation. Eur. Phys. J. B 81(3), 353–362 (2011)
Tang, J., Qu, M., Wang, M., Zhang, M., Yan, J., Mei, Q.: Line: Large-scale information network embedding. In: WWW, pp. 1067–1077 (2015)
Tang, L., Liu, H.: Relational learning via latent social dimensions. In: KDD, pp. 817–826 (2009)
Turner, K.: Generalizations of the rips filtration for quasi-metric spaces with persistent homology stability results. arXiv preprint arXiv:1608.00365 (2016)
Watts, D.J., Strogatz, S.H.: Collective dynamics of ‘small-world’ networks. Nature 393(6684), 440 (1998)
Zhu, X.: Persistent homology: an introduction and a new text representation for natural language processing. In: IJCAI (2013)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Nature Switzerland AG
About this paper
Cite this paper
Bhatia, S., Chatterjee, B., Nathani, D., Kaul, M. (2020). A Persistent Homology Perspective to the Link Prediction Problem. In: Cherifi, H., Gaito, S., Mendes, J., Moro, E., Rocha, L. (eds) Complex Networks and Their Applications VIII. COMPLEX NETWORKS 2019. Studies in Computational Intelligence, vol 881. Springer, Cham. https://doi.org/10.1007/978-3-030-36687-2_3
Download citation
DOI: https://doi.org/10.1007/978-3-030-36687-2_3
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-36686-5
Online ISBN: 978-3-030-36687-2
eBook Packages: Intelligent Technologies and RoboticsIntelligent Technologies and Robotics (R0)