Prediction of Links and Weights in Networks by Reliable Routes

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Zhao, Jing ^a   Miao, Lili ^b   Yang, Jian ^a   Fang, Haiyang ^a   Zhang, Qian Ming ^b   Nie, Min ^b   Holme, Petter ^c   Zhou, Tao ^b  

^a Logistical Engineering University of PLA   (China)

^b UNIVERSITY OF ELECTRONIC SCIENCE AND TECHNOLOGY OF CHINA   (China)

^c Sungkyunkwan University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; CLUSTER ANALYSIS; HUMAN; PROCEDURES; PROTEIN ANALYSIS;

ALGORITHMS; CLUSTER ANALYSIS; HUMANS; PROTEIN INTERACTION MAPPING;

EID: 84937874873     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep12261     Document Type: Article

References (54)

1. Lü, L. & Zhou, T. Link prediction in complex networks: A survey. Physica A: Statistical Mechanics and its Applications 390, 1150-1170 (2011).
2. Wang, W.-Q., Zhang, Q.-M. & Zhou, T. Evaluating network models: A likelihood analysis. EPL 98, 28004 (2012).
3. Zhang, Q.-M., Lü, L., Wang, W.-Q., Zhu, Y.-X. & Zhou, T. Potential Theory for Directed Networks. PLoS ONE 8, e55437 (2013).
4. Zhang, Q.-M., Xu, X.-K., Zhu, Y.-X. & Zhou, T. Measuring multiple evolution mechanisms of complex networks. arXiv: 1410.3519.
5. Popescul, A. & Ungar, L. in Proceedings of the IJCAI-2003 Workshop on Learning Statistical Models from Relational Data. 81-87 (ACM Press, 2003).
6. Barzel, B. & Barabási, A.-L. Network link prediction by global silencing of indirect correlations. Nature Biotechnology 31, 720-725 (2013).
7. Guo, F., Yang, Z. & Zhou, T. Predicting link directions via a recursive subgraph-based ranking. Physica A: Statistical Mechanics and its Applications 392, 3402-3408 (2013).
8. Liben-Nowell, D. & Kleinberg, J. The Link-Prediction Problem for Social Networks. J. Am. Soc. Inform. Sci. Technol. 58, 1019 (2007).
9. Zhou, T., Lü, L. & Zhang, Y.-C. Predicting missing links via local information. Eur. Phys. J. B. 71, 623-630 (2009).
10. Lü, L., Jin, C.-H. & Zhou, T. Similarity index based on local paths for link prediction of complex networks. Phys. Rev. E. 80, 046122 (2009).
11. Cannistraci, C. V., Alanis-Lobato, G. & Ravasi, T. From link-prediction in brain connectomes and protein interactomes to the local-community-paradigm in complex networks. Sci. Rep. 3, 1613 (2013).
12. Lei, C. & Ruan, J. A novel link prediction algorithm for reconstructing protein-protein interaction networks by topological similarity. Bioinformatics 29, 355-364. doi: 10.1093/bioinformatics/bts688 (2013).
13. Clauset, A., Moore, C. & Newman, M. E. J. Hierarchical structure and the prediction of missing links in networks. Nature 453, 98-101 (2008).
14. Guimera, R. & Sales-Pardo, M. Missing and spurious interactions and the reconstruction of complex networks. Proc. Natl. Acad. Sci. USA 106, 22073-22078 (2009).
15. Karrer, B. & Newman, M. E. J. Stochastic blockmodels and community structure in networks. Phys. Rev. E 83, 016107 (2011).
16. Celisse, A., Daudin, J. J. & Pierre, L. Consistency of maximum-likelihood and variational estimators in the stochastic block model. Electron. J. Stat. 6, 1847-1899 (2012).
17. Liu, Z., He, J.-L., Kapoor, K. & Srivastava, J. Correlations between Community Structure and Link Formation in Complex Networks. PLoS ONE 8, e72908 (2013).
18. Lü, L. & Zhou, T. Link prediction in weighted networks: The role of weak ties. Europhysics Letters 89, 18001 (2010).
19. Yang, Z. et al. in AsiaSim 2012, ser. Communications in Computer and Information Science. 119-126 (Springer 2012).
20. Sa, H. & Prudencio, R. in The 2011 International Joint Conference on Neural Networks (IJCNN). 2281-2288 (IEEE, 2011).
21. Kunegis, J. & Lommatzsch, A. in the 26 th International Conference on Machine Learning (ICML-09). 561-568 (ACM, 2009).
22. Murata, T. & Moriyasu, S. in IEEE/WIC/ACM International Conf Web Intelligence: 2007. 85-88 (IEEE, 2007).
23. Wind, D. & Mørup, M. in 2012 IEEE International Workshop on Machine Learning for Signal Processing (MLSP). 1-6 (IEEE, 2012).
24. Lin, Z., Xiong, Y. & Zhu, Y.-X. in 2012 IEEE/WIC/ACM International Conferences on Web Intelligence and Intelligent Agent Technology. 423-430 (IEEE, 2012).
25. Tabourier, L., Libert, A.-S. & Lambiotte, R. in 2nd International Workshop on Dynamic Networks and Knowledge Discovery (PKDD 2014 workshop). LIP611313 (CEUR-WS.org, 2014).
26. Weng, Z., Taylor, J. A., Turner, C. E., Brugge, J. S. & Seidel-Dugan, C. Detection of Src homology 3-binding proteins, including paxillin, in normal and v-Src-transformed Balb/c 3T3 cells. Journal of Biological Chemistry 268, 14956-14963 (1993).
27. Bonifacino, J. S., Dell'Angelica, E. C. & Springer, T. A. in Current Protocols in Molecular Biology (John Wiley & Sons, Inc., 2001). doi: 10.1002/0471142727.mb1016s48
28. Kishimoto, A., Ogura, T. & Esumi, H. A pull-down assay for 5' AMP-activated protein kinase activity using the GST-fused protein. Molecular Biotechnology 32, 17-21 (2006).
29. Uetz, P. et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627 (2000).
30. Havugimana, P. C. et al. A Census of Human Soluble Protein Complexes. Cell 150, 1068-1081 (2012).
31. von Mering, C. et al. STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucl. Acids Res. 33, D433-437. doi: 10.1093/nar/gki005 (2005).
32. Aicher, C., Jacobs, A. Z. & Clauset, A. Learning latent block structure in weighted networks. Journal of Complex Networks. doi: 10.1093/comnet/cnu1026, (2014).
33. Taha, H. A. Operations Research. An Introduction. Eighth Edition. (Pearson Education Inc., 2007).
34. Newman, M. E. J. The structure of scientific collaboration networks. Proc. Natl. Acad.Sci. USA 98, 404-409 (2001).
35. Newman, M. E. J. Scientific collaboration networks. II. Shortest paths, weighted networks, and centrality. Phys. Rev. E 64, 016132 (2001).
36. Li, M. et al. Evolving model of weighted networks inspired by scientific collaboration networks. Physica A: Statistical Mechanics and its Applications 375, 355-364 (2007).
37. Chua, H. N., Sung, W.-K. & Wong, L. Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. Bioinformatics 22 1623-1630 (2006).
38. Zhou, T., Ren, J., Medo, M. & Zhang, Y. C. Bipartite network projection and personal recommendation. Phys. Rev. E. 76, 046115 (2007).
39. Marbach, D. et al. Wisdom of crowds for robust gene network inference. Nature Methods 9, 796-804 (2012).
40. Szumilas, M. Explaining Odds Ratios. J Can Acad Child Adolesc Psychiatry 19, 227-229 (2010).
41. Golub, G. H. & Van Loan, C. F. Matrix Computations. 3rd edn (Baltimore MD: Johns Hopkins University Press, 1996).
42. Kossinets, G. & Watts, D. J. Empirical analysis of an evolving social network. Science 311, 88-90 (2006).
43. Adamic, L. A. & Adar, E. Friends and neighbors on the Web. Social Networks 25, 211-230 (2003).
44. Ou, Q., Jin, Y. D., Zhou, T., Wang, B. H. & Yin, B. Q. Power-law strength-degree correlation from resource-allocation dynamics on weighted networks. Physical Review E 75, 021102 (2007).
45. Varshney, L. R., Chen, B. L., Paniagua, E., Hall, D. H. & Chklovskii, D. B. Structural Properties of the Caenorhabditis elegans Neuronal Network. PLoS Comput Biol 7, e1001066 (2011).
46. Knuth, D. E. The Stanford GraphBase: A Platform for Combinatorial Computing. (Boston MA: Addison-Wesley, 1993).
47. Jensen, L. J. et al. STRING 8-a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Research 37, D412-D416, doi: 10.1093/nar/gkn760 (2009).
48. Ruepp, A. et al. CORUM: the comprehensive resource of mammalian protein complexes-2009. Nucleic Acids Research 38, D497-D501. doi: 10.1093/nar/gkp914 (2010).
49. Watts, D. J. & Strogatz, S. H. Collective dynamics of 'small-world' networks. Nature 393, 440-442 (1998).
50. Holme, P., Park, S. M., Kim, B. J. & Edling, C. R. Korean university life in a network perspective: Dynamics of a large affiliation network. Physica A: Statistical Mechanics and its Applications 373, 821-830 (2007).
51. Reguly, T. et al. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. Journal of Biology 5, 11 (2006).
52. Amaral, L. A. N. A truer measure of our ignorance. Proceedings of the National Academy of Sciences 105, 6795-6796. doi: 10.1073/pnas.0802459105 (2008).
53. Zhang, Q. C. et al. Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature 490, 556-560 (2012).
54. Shoemaker, B. A. & Panchenko, A. R. Deciphering Protein-protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners. PLoS Comput Biol 3, e43 (2007).