메뉴 건너뛰기




Volumn 4, Issue 2, 2010, Pages 615-644

Ranking relations using analogies in biological and information networks

Author keywords

Bayesian inference; Data integration; Information retrieval; Network analysis; Ranking; Saccharomyces cerevisiae; Variational approximation

Indexed keywords


EID: 84255211601     PISSN: 19326157     EISSN: 19417330     Source Type: Journal    
DOI: 10.1214/09-AOAS321     Document Type: Article
Times cited : (6)

References (76)
  • 1
    • 37849051695 scopus 로고    scopus 로고
    • Getting started in probabilistic graphical models
    • Airoldi, E. M. (2007). Getting started in probabilistic graphical models. PLoS Computational Biology 3 e252.
    • (2007) PLoS Computational Biology , vol.3
    • Airoldi, E.M.1
  • 6
    • 54349104506 scopus 로고    scopus 로고
    • NetGrep: Fast network schema searches in interactomes
    • Banks, E., Nabieva, E., Peterson, R. and Singh, M. (2008). NetGrep: Fast network schema searches in interactomes. Genome Biology 24 1473-1480.
    • (2008) Genome Biology , vol.24 , pp. 1473-1480
    • Banks, E.1    Nabieva, E.2    Peterson, R.3    Singh, M.4
  • 7
    • 34547473549 scopus 로고    scopus 로고
    • Reconstructing the topology of protein complexes
    • In, (T. Speed and H. Huang, eds.). Lecture Notes in Bioinformatics, Springer, Berlin
    • Bernard, A., Vaughn, D. S. and Hartemink, A. J. (2007). Reconstructing the topology of protein complexes. In Research in Computational Molecular Biology 2007 (RECOMB07) (T. Speed and H. Huang, eds.). Lecture Notes in Bioinformatics 4453 32-46. Springer, Berlin.
    • (2007) Research in Computational Molecular Biology 2007 (RECOMB07) , vol.4453 , pp. 32-46
    • Bernard, A.1    Vaughn, D.S.2    Hartemink, A.J.3
  • 8
    • 70349610382 scopus 로고    scopus 로고
    • Ph.D. thesis, Ludwig-Maximilians-Univ. Munich
    • Borgwardt, K. (2007). Graph kernels. Ph.D. thesis, Ludwig-Maximilians-Univ. Munich.
    • (2007) Graph kernels
    • Borgwardt, K.1
  • 10
    • 0037264524 scopus 로고    scopus 로고
    • The GRID: The General Repository for Interaction Datasets
    • Breitkreutz, B. J., Stark, C. and Tyers, M. (2003). The GRID: The General Repository for Interaction Datasets. Genome Biology 4 R23.
    • (2003) Genome Biology , vol.4
    • Breitkreutz, B.J.1    Stark, C.2    Tyers, M.3
  • 11
    • 23644434284 scopus 로고    scopus 로고
    • Genetic interactions between polymorphisms that affect gene expression in yeast
    • Brem, R. B., Storey, J. D., Whittle, J. and Kruglyak, L. (2005). Genetic interactions between polymorphisms that affect gene expression in yeast. Nature 436 701-703.
    • (2005) Nature , vol.436 , pp. 701-703
    • Brem, R.B.1    Storey, J.D.2    Whittle, J.3    Kruglyak, L.4
  • 12
    • 33750739920 scopus 로고    scopus 로고
    • Technical report 2006-04-02, Univ. Washington, Dept. Computer Science and Engineering
    • Cafarella, M., Banko, M. and Etzioni, O. (2006). Relational web search. Technical report 2006-04-02, Univ. Washington, Dept. Computer Science and Engineering.
    • (2006) Relational web search
    • Cafarella, M.1    Banko, M.2    Etzioni, O.3
  • 16
    • 0024406857 scopus 로고
    • A novel genetic system to detect protein-protein interactions
    • Fields, S. and Song, O. (1989). A novel genetic system to detect protein-protein interactions. Nature 340 245-246.
    • (1989) Nature , vol.340 , pp. 245-246
    • Fields, S.1    Song, O.2
  • 18
    • 0036570378 scopus 로고    scopus 로고
    • The computational modeling of analogy-making
    • French, R. (2002). The computational modeling of analogy-making. Trends in Cognitive Sciences 6 200-205.
    • (2002) Trends in Cognitive Sciences , vol.6 , pp. 200-205
    • French, R.1
  • 23
    • 48749148075 scopus 로고
    • Structure-mapping: A theoretical framework for analogy
    • Gentner, D. (1983). Structure-mapping: A theoretical framework for analogy. Cognitive Science 7 155-170.
    • (1983) Cognitive Science , vol.7 , pp. 155-170
    • Gentner, D.1
  • 24
    • 0031616946 scopus 로고    scopus 로고
    • Similarity and the development of rules
    • Gentner, D. and Medina, J. (1998). Similarity and the development of rules. Cognition 65 263-297.
    • (1998) Cognition , vol.65 , pp. 263-297
    • Gentner, D.1    Medina, J.2
  • 30
    • 85162055675 scopus 로고    scopus 로고
    • Modeling homophily and stochastic equivalence in symmetric relational data
    • Hoff, P. D. (2008). Modeling homophily and stochastic equivalence in symmetric relational data. Advances in Neural Information Procesing Systems 20 657-664.
    • (2008) Advances in Neural Information Procesing Systems , vol.20 , pp. 657-664
    • Hoff, P.D.1
  • 31
    • 0010826363 scopus 로고
    • Local structure in social networks
    • In, (D. Heise, ed.) Jossey-Bass, New York
    • Holland, P. W. and Leinhardt, S. (1975). Local structure in social networks. In Sociological Methodology (D. Heise, ed.) 1-45. Jossey-Bass, New York.
    • (1975) Sociological Methodology , pp. 1-45
    • Holland, P.W.1    Leinhardt, S.2
  • 33
    • 0033974688 scopus 로고    scopus 로고
    • Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins
    • Itô, T., Tashiro, K., Muta, S., Ozawa, R., Chiba, T., Nishizawa, M., Yamamoto, K., Kuhara, S. and Sakaki, Y. (2000). Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc. Natl. Acad. Sci. 97 1143-1147.
    • (2000) Proc. Natl. Acad. Sci , vol.97 , pp. 1143-1147
    • Itô, T.1    Tashiro, K.2    Muta, S.3    Ozawa, R.4    Chiba, T.5    Nishizawa, M.6    Yamamoto, K.7    Kuhara, S.8    Sakaki, Y.9
  • 34
    • 0042685161 scopus 로고    scopus 로고
    • Bayesian parameter estimation via variational methods
    • Jaakkola, T. and Jordan, M. (2000). Bayesian parameter estimation via variational methods. Stat. Comput. 10 25-37.
    • (2000) Stat. Comput , vol.10 , pp. 25-37
    • Jaakkola, T.1    Jordan, M.2
  • 35
    • 1942450651 scopus 로고    scopus 로고
    • Linkage and autocorrelation cause feature selection bias in relational learning
    • In, Morgan Kaufmann, San Francisco
    • Jensen, D. and Neville, J. (2002). Linkage and autocorrelation cause feature selection bias in relational learning. In Proc. 19th International Conference on Machine Learning. Morgan Kaufmann, San Francisco.
    • (2002) Proc. 19th International Conference on Machine Learning
    • Jensen, D.1    Neville, J.2
  • 36
    • 53349156368 scopus 로고    scopus 로고
    • Biochemistry: Not comparable, but complementary
    • Jensen, L. J. and Bork, P. (2008). Biochemistry: Not comparable, but complementary. Science 322 56-57.
    • (2008) Science , vol.322 , pp. 56-57
    • Jensen, L.J.1    Bork, P.2
  • 37
    • 0033225865 scopus 로고    scopus 로고
    • Introduction to variational methods for graphical models
    • Jordan, M., Ghahramani, Z., Jaakkola, T. and Saul, L. (1999). Introduction to variational methods for graphical models. Machine Learning 37 183-233.
    • (1999) Machine Learning , vol.37 , pp. 183-233
    • Jordan, M.1    Ghahramani, Z.2    Jaakkola, T.3    Saul, L.4
  • 38
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • Kanehisa, M. and Goto, S. (2000). KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Research 28 27-30.
    • (2000) Nucleic Acids Research , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 40
    • 33750696648 scopus 로고    scopus 로고
    • Learning systems of concepts with an infinite relational model
    • In, MIT Press, Cambridge, MA
    • Kemp, C., Tenenbaum, J., Griffths, T., Yamada, T. and Ueda, N. (2006). Learning systems of concepts with an infinite relational model. In Proceedings of AAAI'06. MIT Press, Cambridge, MA.
    • (2006) Proceedings of AAAI'06
    • Kemp, C.1    Tenenbaum, J.2    Griffths, T.3    Yamada, T.4    Ueda, N.5
  • 43
    • 0001964443 scopus 로고
    • Structural equivalence of individuals in social networks
    • Lorrain, F. and White, H. C. (1971). Structural equivalence of individuals in social networks. Journal of Mathematical Sociology 1 49-80.
    • (1971) Journal of Mathematical Sociology , vol.1 , pp. 49-80
    • Lorrain, F.1    White, H.C.2
  • 45
    • 47949123027 scopus 로고    scopus 로고
    • Coupled clustering: A method for detecting structural correspondence
    • Marx, Z., Dagan, I., Buhmann, J. and Shamir, E. (2002). Coupled clustering: A method for detecting structural correspondence. J. Mach. Learn. Res. 3747-780.
    • (2002) J. Mach. Learn. Res , pp. 3747-3780
    • Marx, Z.1    Dagan, I.2    Buhmann, J.3    Shamir, E.4
  • 46
    • 84898999170 scopus 로고    scopus 로고
    • Multiple relational embedding
    • In, Vancouver, BC
    • Memisevic, R. and Hinton, G. (2005). Multiple relational embedding. In 18th NIPS. Vancouver, BC.
    • (2005) 18th NIPS
    • Memisevic, R.1    Hinton, G.2
  • 47
    • 9144242935 scopus 로고    scopus 로고
    • MIPS: Analysis and annotation of proteins from whole genome
    • Mewes, H. et al. (2004). MIPS: Analysis and annotation of proteins from whole genome. Nucleic Acids Research 32 D41-D44.
    • (2004) Nucleic Acids Research , vol.32
    • Mewes, H.1
  • 48
    • 84874474856 scopus 로고
    • Inverting the resolution principle
    • Muggleton, S. (1981). Inverting the resolution principle. Machine Intelligence12 93-104.
    • (1981) Machine Intelligence , vol.12 , pp. 93-104
    • Muggleton, S.1
  • 51
    • 29144442904 scopus 로고    scopus 로고
    • Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps
    • Nabieva, E., Jim, K., Agarwal, A., Chazelle, B. and Singh. M. (2005). Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. Bioinformatics 21 i302-i310.
    • (2005) Bioinformatics , vol.21
    • Nabieva, E.1    Jim, K.2    Agarwal, A.3    Chazelle, B.4    Singh, M.5
  • 52
    • 0442296603 scopus 로고    scopus 로고
    • Estimation and prediction for stochastic blockstructures
    • Nowicki, K. and Snijders, T. A. B. (2001). Estimation and prediction for stochastic blockstructures. J. Amer. Statist. Assoc. 96 1077-1087.
    • (2001) J. Amer. Statist. Assoc , vol.96 , pp. 1077-1087
    • Nowicki, K.1    Snijders, T.A.B.2
  • 55
    • 33646018046 scopus 로고    scopus 로고
    • Evaluation of different biological data and computational classification methods for use in protein interaction prediction
    • Qi, Y., Bar-Joseph, Z. and Klein-Seetharaman, J. (2006). Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins: Structure, Function, and Bioinformatics 63 490-500.
    • (2006) Proteins: Structure, Function, and Bioinformatics , vol.63 , pp. 490-500
    • Qi, Y.1    Bar-Joseph, Z.2    Klein-Seetharaman, J.3
  • 59
    • 84870282648 scopus 로고    scopus 로고
    • SGD. Saccharomyces genome database. Available atftp://ftp.yeastgenome.org/yeast/
    • SGD. Saccharomyces genome database. Available atftp://ftp.yeastgenome.org/yeast/.
  • 64
    • 0035735751 scopus 로고    scopus 로고
    • Generalization, similarity, and Bayesian inference
    • Tenenbaum, J. and Griffiths, T. (2001). Generalization, similarity, and Bayesian inference. Behavioral and Brain Sciences 24 629-641.
    • (2001) Behavioral and Brain Sciences , vol.24 , pp. 629-641
    • Tenenbaum, J.1    Griffiths, T.2
  • 65
    • 34548104117 scopus 로고    scopus 로고
    • TRANSFAC, Available at
    • TRANSFAC. Transcription factor database. Available at http://www.gene-regulation.com/.
    • Transcription factor database
  • 66
    • 65849291551 scopus 로고    scopus 로고
    • The latent relation mapping engine: Algorithm and experiments
    • Turney, P. (2008a). The latent relation mapping engine: Algorithm and experiments. J. Artificial Intelligence Res. 33 615-655.
    • (2008) J. Artificial Intelligence Res , vol.33 , pp. 615-655
    • Turney, P.1
  • 67
    • 80053399246 scopus 로고    scopus 로고
    • A uniform approach to analogies, synonyms, antonyms, and associations
    • In, Association for Computational Linguistics, Stroudsburg, PA
    • Turney, P. (2008b). A uniform approach to analogies, synonyms, antonyms, and associations. In Proceedings of the 22nd International Conference on Computational Linguistics (COLING-08) 905-912. Association for Computational Linguistics, Stroudsburg, PA.
    • (2008) Proceedings of the 22nd International Conference on Computational Linguistics (COLING-08) , pp. 905-912
    • Turney, P.1
  • 68
    • 24044553921 scopus 로고    scopus 로고
    • Corpus-based learning of analogies and semantic relations
    • Turney, P. and Littman, M. (2005). Corpus-based learning of analogies and semantic relations. Machine Learning 60 251-278.
    • (2005) Machine Learning , vol.60 , pp. 251-278
    • Turney, P.1    Littman, M.2
  • 70
    • 0027552829 scopus 로고
    • Derivational analogy in PRODIGY: Automating case acquisition, storage and utilization
    • Veloso, M. and Carbonell, J. (1993). Derivational analogy in PRODIGY: Automating case acquisition, storage and utilization. Machine Learning 10249-278.
    • (1993) Machine Learning , pp. 10249-10278
    • Veloso, M.1    Carbonell, J.2
  • 71
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S. G., Fields, S. and Bork, P. (2002). Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417 399-403.
    • (2002) Nature , vol.417 , pp. 399-403
    • von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5    Fields, S.6    Bork, P.7
  • 76
    • 0032861774 scopus 로고    scopus 로고
    • SCPD: A promoter database of the yeast Saccharomyces cerevisiae
    • Zhu, J. and Zhang, M. Q. (1999). SCPD: A promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics 15 607-611.
    • (1999) Bioinformatics , vol.15 , pp. 607-611
    • Zhu, J.1    Zhang, M.Q.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.