Thresholding of semantic similarity networks using a spectral graph-based technique

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 8399 LNAI, Issue , 2014, Pages 201-213

  Guzzi, Pietro Hiram ^a   Veltri, Pierangelo ^a   Cannataro, Mario ^a  

^a UNIVERSITY MAGNA GRAECIA OF CATANZARO   (Italy)

Author keywords

Semantic similarity measures; Semantic similarity networks

Indexed keywords

ARTIFICIAL INTELLIGENCE; BIOINFORMATICS; CLUSTERING ALGORITHMS; COMPLEX NETWORKS; GRAPH THEORY; GRAPHIC METHODS; POPULATION DYNAMICS; PROTEINS; SIGNAL DETECTION;

COMMUNITY DETECTION ALGORITHMS; COMPUTATIONAL BIOLOGY; EDGE-WEIGHTED GRAPH; FUNCTIONAL SIMILARITY; GRAPH-BASED TECHNIQUES; SEMANTIC SIMILARITY; SEMANTIC SIMILARITY MEASURES; SPECTRAL GRAPH THEORY;

SANITARY SEWERS;

EID: 84905222032     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-319-08407-7_13     Document Type: Conference Paper

References (33)

1. Ala, U., Piro, R.M., Grassi, E., Damasco, C., Silengo, L., Oti, M., Provero, P., Cunto, F.D.: Prediction of human disease genes by human-mouse conserved coexpression analysis. PLoS Comput. Biol. 4(3), e1000043 (2008)
2. Bader, G.D., Hogue, C.W.V.: An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinform. 27, 1-27 (2003)
3. Bertolazzi, P., Bock, M.E., Guerra, C.: On the functional and structural characterization of hubs in protein-protein interaction networks. Biotechnol. Adv. 31(2), 274-286 (2013)
4. Domany, E., Blatt, M., Wiseman, S.: Superparamagnetic clustering of data. Phys. Rev. Lett. 76(18), 3251-3254 (1996)
5. Bolla, M., Tusnády, G.: Spectra and optimal partitions of weighted graphs. Discrete Math. 128(1), 1-20 (1994)
6. Brohée, S., van Helden, J.: Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinform. 7, 488 (2006)
7. Camon, E., Magrane, M., Barrell, D., Lee, V., Dimmer, E., Maslen, J., Binns, D., Harte, N., Lopez, R., Apweiler, R.: The gene ontology annotation (goa) database: sharing knowledge in uniprot with gene ontology. Nucl. Acids Res. 32(suppl-1), D262-D266 (2004)
8. Cannataro, M., Guzzi, P.H., Veltri, P.: Protein-to-protein interactions: technologies, databases, and algorithms. ACM Comput. Surv. 43, 1:1-1:36 (2010)
9. Cannataro, M., Guzzi, P.H., Sarica, A.: Data mining and life sciences applications on the grid. Wiley Interdisc. Rev.: Data Mining Knowl. Discov. 3(3), 216-238 (2013)
10. Chung, F.: Spectral Graph Theory. Regional Conference Series in Mathematics, vol. 92. American Mathematical Society, Providence (1994)
11. Cvetković, D., Simić, S.K.: Towards a spectral theory of graphs based on the signless laplacian, ii. Linear Algebra Appl. 432(9), 2257-2272 (2010)
12. Ding, C., He, X., Zha, H.: A spectral method to separate disconnected and nearlydisconnected web graph components. In: Proceedings of the Seventh ACM International Conference on Knowledge Discovery and Data Mining, San Francisco, 26-29 August 2001
13. Enright, S., Van Dongen, A.J., Ouzounis, C.A.: An efficient algorithm for largescale detection of protein families. Nucleic Acids Res. 30(7), 1575-1584 (2002)
14. Freeman, T.C., Goldovsky, L., Brosch, M., van Dongen, S., Maziere, P., Grocock, R.J., Freilich, S., Thornton, J., Enright, A.J.: Construction, visualization, and clustering of transcription networks from microarray expression data. PLoS Comput. Biol. 3(10), e206 (2007)
15. Guldener, U., Munsterkotter, M., Oesterheld, M., Pagel, P., Ruepp, A., Mewes, H.W., Stumpflen, V.: Mpact: the mips protein interaction resource on yeast. Nucleic Acids Res. 34, D436-D441 (2006)
16. Guzzi, P.H., Mina, M., Guerra, C., Cannataro, M.: Semantic similarity analysis of protein data: assessment with biological features and issues. Briefings Bioinform. 13(5), 569-585 (2012)
17. Harispe, S., Sanchez, D., Ranwez, S., Janaqi, S., Montmain, J.: A framework for unifying ontology-based semantic similarity measures: a study in the biomedical domain. J. Biomed. Inform. 48, 38-53 (2014)
18. Ji, J., Zhang, A., Liu, C., Quan, X., Liu, Z.: Survey: functional module detection from protein-protein interaction networks. IEEE Trans. Knowl. Data Eng. 99(PrePrints), 1 (2013)
19. King, A.D., Przulj, N., Jurisica, I.: Bioinformatics (Oxford, England)
20. Lee, H.K., Hsu, A.K., Sajdak, J., Qin, J., Pavlidis, P.: Coexpression analysis of human genes across many microarray data sets. Genome Res. 14, 1085-1094 (2004)
21. Lin, D.: An Information-Theoretic Definition of Similarity. Morgan Kaufmann, San Francisco (1998)
22. Ma, X., Gao, L.: Biological network analysis: insights into structure and functions. Briefings Funct. Genomics 11(6), 434-442 (2012)
23. Merris, R.: Laplacian matrices of graphs: a survey. Linear Algebra Appl. 197, 143-176 (1994)
24. Mina, M., Guzzi, P.H.: Alignmcl: comparative analysis of protein interaction networks through markov clustering. In: BIBM Workshops, pp. 174-181. IEEE (2012)
25. Mohar, B.: The laplacian spectrum of graphs. Graph Theor. Comb. Appl. 2, 871-898 (1991)
26. Ng, A.Y., Jordan, M.I., Weiss, Y., et al.: On spectral clustering: analysis and an algorithm. Adv. Neural Inf. Process. Syst. 2, 849-856 (2002)
27. Guzzi, P., Mina, M.: Investigating bias in semantic similarity measures for analysis of protein interactions. In: Proceedings of 1st International Workshop on Pattern Recognition in Proteomics, Structural Biology and Bioinformatics (PR PS BB 2011), pp. 71-80, 13 September 2011 (2012)
28. Pesquita, C., Faria, D., O Falcão, A., Lord, P., Couto, F.M.: Semantic similarity in biomedical ontologies. PLoS Comput. Biol. 5(7), e1000443 (2009)
29. Resnik, P.: Using information content to evaluate semantic similarity in a taxonomy. In: IJCAI, pp. 448-453 (1995)
30. Rito, T., Wang, Z., Deane, C.M., Reinert, G.: How threshold behaviour affects the use of subgraphs for network comparison. Bioinformatics 26(18), i611-i617 (2010)
31. Su, G., Kuchinsky, A., Morris, J.H., States, D.J., Meng, F.: Glay: community structure analysis of biological networks. Bioinformatics 26(24), 3135-3137 (2010)
32. Wang, H., Zheng, H., Azuaje, F.: Ontology- and graph-based similarity assessment in biological networks. Bioinformatics 26(20), 2643-2644 (2010)
33. Zhu, X., Gerstein, M., Snyder, M.: Getting connected: analysis and principles of biological networks. Genes Dev. 21(9), 1010-1024 (2007)