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A Persistent Homology Perspective to the Link Prediction Problem

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Part of the book series: Studies in Computational Intelligence ((SCI,volume 881))

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).

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Notes

  1. 1.

    https://topology.ima.umn.edu/node/53.

  2. 2.

    https://bitbucket.org/grey_narn/hera/src/master/.

  3. 3.

    https://github.com/sumit-research/persistent-homology-link-prediction.

References

  1. Adamic, L.A., Adar, E.: Friends and neighbors on the web. Soc. Netw. 25(3), 211–230 (2003)

    Article  Google Scholar 

  2. Backstrom, L., Leskovec, J.: Supervised random walks: predicting and recommending links in social networks. In: WSDM 2011 (2011)

    Google Scholar 

  3. Bauer, U.: Ripser (2018). https://github.com/Ripser/ripser

  4. 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)

    Google Scholar 

  5. Bhatia, S., Chatterjee, B., Nathani, D., Kaul, M.: Understanding and predicting links in graphs: a persistent homology perspective. arXiv preprint arXiv:1811.04049 (2018)

  6. Bhatia, S., Vishwakarma, H.: Know thy neighbors, and more!: studying the role of context in entity recommendation. In: Hypertext (HT), pp. 87–95 (2018)

    Google Scholar 

  7. Carstens, C.J., Horadam, K.J.: Persistent homology of collaboration networks. Math. Probl. Eng. 2013, 7 (2013)

    Article  MathSciNet  Google Scholar 

  8. 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)

    Google Scholar 

  9. Cohen, S., Zohar, A.: An axiomatic approach to link prediction. In: Twenty-Ninth AAAI Conference on Artificial Intelligence (2015)

    Google Scholar 

  10. 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)

    Article  Google Scholar 

  11. Edelsbrunner, H., Harer, J.: Persistent homology-a survey. Contemp. Math. 453, 257–282 (2008)

    Article  MathSciNet  Google Scholar 

  12. Edelsbrunner, H., Harer, J.: Computational Topology - An Introduction. American Mathematical Society, Providence (2010)

    MATH  Google Scholar 

  13. 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)

    Article  Google Scholar 

  14. 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)

    Article  Google Scholar 

  15. Grover, A., Leskovec, J.: node2vec: scalable feature learning for networks. In: Proceedings of the 22nd ACM SIGKDD, pp. 855–864 (2016)

    Google Scholar 

  16. 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)

    Google Scholar 

  17. 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)

    Article  MathSciNet  Google Scholar 

  18. Jeh, G., Widom, J.: SimRank: a measure of structural-context similarity, pp. 538–543. ACM (2002)

    Google Scholar 

  19. Johnson, D.B.: Efficient algorithms for shortest paths in sparse networks. J. ACM (JACM) 24(1), 1–13 (1977)

    Article  MathSciNet  Google Scholar 

  20. Kataria, S., Mitra, P., Bhatia, S.: Utilizing context in generative Bayesian models for linked corpus. In: AAAI, vol. 10, p. 1 (2010)

    Google Scholar 

  21. Katz, L.: A new status index derived from sociometric analysis. Psychometrika 18(1), 39–43 (1953)

    Article  Google Scholar 

  22. 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)

    Google Scholar 

  23. Leskovec, J., Backstrom, L., Kumar, R., Tomkins, A.: Microscopic evolution of social networks. In: KDD, pp. 462–470 (2008)

    Google Scholar 

  24. Leskovec, J., Kleinberg, J., Faloutsos, C.: Graph evolution: densification and shrinking diameters. ACM Trans. Knowl. Discov. Data 1(1) (2007)

    Article  Google Scholar 

  25. Liben-Nowell, D., Kleinberg, J.: The link-prediction problem for social networks. J. Am. Soc. Inf. Sci. Technol. 58(7), 1019–1031 (2007)

    Article  Google Scholar 

  26. 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

  27. McAuley, J., Leskovec, J.: Learning to discover social circles in ego networks. In: NIPS, pp. 548–556 (2012)

    Google Scholar 

  28. McPherson, M., Smith-Lovin, L., Cook, J.M.: Birds of a feather: homophily in social networks. Annu. Rev. Sociol. 27(1), 415–444 (2001)

    Article  Google Scholar 

  29. 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)

    Google Scholar 

  30. Misra, V., Bhatia, S.: Bernoulli embeddings for graphs. In: AAAI, pp. 3812–3819 (2018)

    Google Scholar 

  31. Nagarajan, M., et al.: Predicting future scientific discoveries based on a networked analysis of the past literature. In: KDD, pp. 2019–2028. ACM (2015)

    Google Scholar 

  32. Newman, M.E.J.: Finding community structure in networks using the eigenvectors of matrices. Phys. Rev. E 74(3), 036104 (2006)

    Article  MathSciNet  Google Scholar 

  33. 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)

    Google Scholar 

  34. Perozzi, B., Al-Rfou, R., Skiena, S.: Deepwalk: online learning of social representations. In: KDD, pp. 701–710 (2014)

    Google Scholar 

  35. Ribeiro, L.F., Saverese, P.H., Figueiredo, D.R.: struc2vec: learning node representations from structural identity. In: KDD, pp. 385–394 (2017)

    Google Scholar 

  36. Sarkar, P., Chakrabarti, D., Moore, A.W.: Theoretical justification of popular link prediction heuristics. In: IJCAI (2011)

    Google Scholar 

  37. Šubelj, L., Bajec, M.: Robust network community detection using balanced propagation. Eur. Phys. J. B 81(3), 353–362 (2011)

    Article  Google Scholar 

  38. Tang, J., Qu, M., Wang, M., Zhang, M., Yan, J., Mei, Q.: Line: Large-scale information network embedding. In: WWW, pp. 1067–1077 (2015)

    Google Scholar 

  39. Tang, L., Liu, H.: Relational learning via latent social dimensions. In: KDD, pp. 817–826 (2009)

    Google Scholar 

  40. Turner, K.: Generalizations of the rips filtration for quasi-metric spaces with persistent homology stability results. arXiv preprint arXiv:1608.00365 (2016)

  41. Watts, D.J., Strogatz, S.H.: Collective dynamics of ‘small-world’ networks. Nature 393(6684), 440 (1998)

    Article  Google Scholar 

  42. Zhu, X.: Persistent homology: an introduction and a new text representation for natural language processing. In: IJCAI (2013)

    Google Scholar 

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Correspondence to Sumit Bhatia .

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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

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