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Py3plex: A Library for Scalable Multilayer Network Analysis and Visualization

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Complex Networks and Their Applications VII (COMPLEX NETWORKS 2018)

Part of the book series: Studies in Computational Intelligence ((SCI,volume 812))

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Abstract

Real-life systems are commonly represented as networks of interacting entities. While homogeneous networks consist of nodes of a single node type, multilayer networks are characterized by multiple types of nodes or edges, all present in the same system. Analysis and visualization of such networks represent a challenge for real-life complex network applications. The presented Py3plex Python-based library facilitates the exploration and visualization of multilayer networks. The library includes a diagonal projection-based network visualization, developed specifically for large networks with multiple node (and edge) types. The library also includes state-of-the-art methods for network decomposition and statistical analysis. The Py3plex functionality is showcased on real-world multilayer networks from the domains of biology and on synthetic networks.

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Notes

  1. 1.

    http://www.mkivela.com/pymnet/.

  2. 2.

    https://github.com/nkoub/multinetx.

  3. 3.

    http://muxviz.net/.

References

  1. Amato, R., Kouvaris, N.E., San Miguel, M., Díaz-Guilera, A.: Opinion competition dynamics on multiplex networks. New J. Phys. 19(12) (2017)

    Google Scholar 

  2. Bastian, M., Heymann, S., Jacomy, M., others: Gephi: an open source software for exploring and manipulating networks. In: International AAAI Conference on Web and Social Media Third International AAAI Conference on Weblogs and Social Media, vol. 8, pp. 361–362 (2009)

    Google Scholar 

  3. Blondel, V.D., Guillaume, J.L., Lambiotte, R., Lefebvre, E.: Fast unfolding of communities in large networks. J. Stat. Mech. Theor. Exp. 2008(10), P10,008 (2008)

    Google Scholar 

  4. Boccaletti, S., Bianconi, G., Criado, R., del Genio, C., Gómez-Gardeñes, J., Romance, M., Sendiña-Nadal, I., Wang, Z., Zanin, M.: The structure and dynamics of multilayer networks. Phys. Rep. 544(1), 1–122 (2014)

    Google Scholar 

  5. Cho, D.Y., Kim, Y.A., Przytycka, T.M.: Chapter 5: network biology approach to complex diseases. PLOS Comput. Biol. 8(12), 1–11 (2012)

    Google Scholar 

  6. De Domenico, M., Porter, M.A., Arenas, A.: MuxViz: a tool for multilayer analysis and visualization of networks. J. Complex Netw. 3(2), 159–176 (2015)

    Google Scholar 

  7. De Domenico, M., Solé-Ribalta, A., Cozzo, E., Kivelä, M., Moreno, Y., Porter, M.A., Gómez, S., Arenas, A.: Mathematical formulation of multilayer networks. Phys. Rev. X 3(4) (2013)

    Google Scholar 

  8. Eaton, J.W., Bateman, D., Hauberg, S.: GNU octave version 3.0. 1 manual: a high-level interactive language for numerical computations. SoHo Books (2007)

    Google Scholar 

  9. Grover, A., Leskovec, J.: Node2vec: scalable feature learning for networks. In: Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, KDD ’16, pp. 855–864. ACM, New York, NY, USA (2016)

    Google Scholar 

  10. Hagberg, A., Swart, P., S Chult, D.: Exploring network structure, dynamics, and function using Network X. In: Proceedings of the 7th Python in Science Conference (SciPy)(2008)

    Google Scholar 

  11. Jacomy, M., Venturini, T., Heymann, S., Bastian, M.: ForceAtlas2, a continuous graph algorithm for handy network visualization designed for the Gephi software. PloS One 9(6), e98,679 (2014)

    Google Scholar 

  12. Jones, E., Oliphant, T., Peterson, P., et al.: SciPy: open source scientific tools for Python (2001). http://www.scipy.org/

  13. Kivelä, M., Arenas, A., Barthelemy, M., Gleeson, J.P., Moreno, Y., Porter, M.A.: Multilayer networks. J. Complex. Netw. 2(3), 203–271 (2014)

    Google Scholar 

  14. Kralj, J., Robnik-Šikonja, M., Lavrač, N.: HINMINE: heterogeneous information network mining with information retrieval heuristics. J. Intell. Inf. Syst. 50(1), 29–61 (2018)

    Google Scholar 

  15. Leskovec, J., Sosič, R.: Snap: a general-purpose network analysis and graph-mining library. ACM Trans. Intell. Syst. Technol. 8(1), 1:1–1:20 (2016)

    Google Scholar 

  16. Milano, M., Guzzi, P.H., Cannataro, M.: HetNetAligner: a novel algorithm for local alignment of heterogeneous biological networks. In: Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB ’18, pp. 598–599. ACM, New York, NY, USA (2018)

    Google Scholar 

  17. Nepusz, G., Csárdi, G.: The igraph software package for complex network research. Complex Syst. 1695(5), 1–9 (2006)

    Google Scholar 

  18. Rosvall, M., Axelsson, D., Bergstrom, C.T.: The map equation. Eur. Phys. J. Spec. Top. 178(1), 13–23 (2009)

    Google Scholar 

  19. Shannon, P.: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13(11), 2498–2504 (2003)

    Google Scholar 

  20. Siek, J.G., Lee, L.Q., Lumsdaine, A.: Boost Graph Library: The User Guide and Reference Manual. Pearson Education (2001)

    Google Scholar 

  21. Škrlj, B., Kralj, J., Vavpetič, A., Lavrač, N.: Community-based semantic subgroup discovery. In: Appice, A., Loglisci, C., Manco, G., Masciari, E., Ras, Z.W. (eds.) Proceedings of New Frontiers in Mining Complex Patterns, pp. 182–196. Springer International Publishing (2018)

    Google Scholar 

  22. Walt, S.V.D., Colbert, S.C., Varoquaux, G.: The numpy array: a structure for efficient numerical computation. Comput. Sci. Eng. 13(2), 22–30 (2011)

    Google Scholar 

  23. Wang, Z., Wang, L., Szolnoki, A., Perc, M.: Evolutionary games on multilayer networks: a colloquium. Eur. Phys. J. B 88(5), 124 (2015)

    Google Scholar 

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Acknowledgements

This work was financially supported by the Slovenian Research Agency (ARRS) grants HinLife: Analysis of Heterogeneous Information Networks for Knowledge Discovery in Life Sciences (J7-7303) and Semantic Data Mining for Linked Open Data (financed under the ERC Complementary Scheme, N2-0078).

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Correspondence to Blaž Škrlj or Nada Lavrač .

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Škrlj, B., Kralj, J., Lavrač, N. (2019). Py3plex: A Library for Scalable Multilayer Network Analysis and Visualization. In: Aiello, L., Cherifi, C., Cherifi, H., Lambiotte, R., Lió, P., Rocha, L. (eds) Complex Networks and Their Applications VII. COMPLEX NETWORKS 2018. Studies in Computational Intelligence, vol 812. Springer, Cham. https://doi.org/10.1007/978-3-030-05411-3_60

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