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Volumn 17, Issue 1, 2016, Pages

A multiple kernel learning algorithm for drug-target interaction prediction

Author keywords

Artificial intelligence; Drug discovery; Kernel methods; Multiple kernel learning; Supervised machine learning

Indexed keywords

ALGORITHMS; ARTIFICIAL INTELLIGENCE; DATA INTEGRATION; FORECASTING; LEARNING ALGORITHMS; LEARNING SYSTEMS; QUALITY CONTROL; SUPERVISED LEARNING;

EID: 84957037250     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-016-0890-3     Document Type: Article
Times cited : (190)

References (61)
  • 1
    • 84877580262 scopus 로고    scopus 로고
    • Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review
    • Csermely P, Korcsmáros T, Kiss HJM, London G, Nussinov R. Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther. 2013; 138(3):333-408. doi: 10.1016/j.pharmthera.2013.01.016.
    • (2013) Pharmacol Ther , vol.138 , Issue.3 , pp. 333-408
    • Csermely, P.1    Korcsmáros, T.2    Kiss, H.J.M.3    London, G.4    Nussinov, R.5
  • 2
    • 84928196309 scopus 로고    scopus 로고
    • Similarity-based machine learning methods for predicting drug-target interactions: a brief review.
    • Ding H, Takigawa I, Mamitsuka H, Zhu S. Similarity-based machine learning methods for predicting drug-target interactions: a brief review. Brief Bioinform. 2013. doi: 10.1093/bib/bbt056.
    • (2013) Brief Bioinform.
    • Ding, H.1    Takigawa, I.2    Mamitsuka, H.3    Zhu, S.4
  • 3
    • 84991328213 scopus 로고    scopus 로고
    • Drug - target interaction prediction : databases, web servers and computational models.
    • Chen X, Yan CC, Zhang X, Zhang X, Dai F. Drug - target interaction prediction : databases, web servers and computational models. Brief Bioinform. 2015:1-17. doi: 10.1093/bib/bbv066.
    • (2015) Brief Bioinform. , pp. 1-17
    • Chen, X.1    Yan, C.C.2    Zhang, X.3    Zhang, X.4    Dai, F.5
  • 4
    • 84871893054 scopus 로고    scopus 로고
    • Chemogenomic approaches to infer drug-target interaction networks
    • Yamanishi Y. Chemogenomic approaches to infer drug-target interaction networks. Data Min Syst Biol. 2013; 939:97-113. doi: 10.1007/978-1-62703-107-3.
    • (2013) Data Min Syst Biol , vol.939 , pp. 97-113
    • Yamanishi, Y.1
  • 5
    • 33645923096 scopus 로고    scopus 로고
    • Computational methods in developing quantitative structure-activity relationships (QSAR): a review
    • Dudek AZ, Arodz T, Gálvez J. Computational methods in developing quantitative structure-activity relationships (QSAR): a review. Comb Chem High Throughput Screen. 2006; 9(3):213-8.
    • (2006) Comb Chem High Throughput Screen , vol.9 , Issue.3 , pp. 213-218
    • Dudek, A.Z.1    Arodz, T.2    Gálvez, J.3
  • 6
    • 84915753460 scopus 로고    scopus 로고
    • Benchmarking a wide range of chemical descriptors for drug-target interaction prediction using a chemogenomic approach
    • Sawada R, Kotera M, Yamanishi Y. Benchmarking a wide range of chemical descriptors for drug-target interaction prediction using a chemogenomic approach. Mol Inform. 2014; 33(11-12):719-31. doi: 10.1002/minf.201400066.
    • (2014) Mol Inform , vol.33 , Issue.11-12 , pp. 719-731
    • Sawada, R.1    Kotera, M.2    Yamanishi, Y.3
  • 7
    • 84863695210 scopus 로고    scopus 로고
    • Prediction of drug-target interactions and drug repositioning via network-based inference
    • Cheng F, Liu C, Jiang J, Lu W, Li W, Liu G, et al. Prediction of drug-target interactions and drug repositioning via network-based inference. PLoS Comput Biol. 2012; 8(5):1002503. doi: 10.1371/journal.pcbi.1002503.
    • (2012) PLoS Comput Biol , vol.8 , Issue.5 , pp. 1002503
    • Cheng, F.1    Liu, C.2    Jiang, J.3    Lu, W.4    Li, W.5    Liu, G.6
  • 8
    • 84862215494 scopus 로고    scopus 로고
    • Drug-target interaction prediction by random walk on the heterogeneous network
    • Chen X, Liu MX, Yan GY. Drug-target interaction prediction by random walk on the heterogeneous network. Mol BioSyst. 2012; 8(7):1970-8. doi: 10.1039/c2mb00002d.
    • (2012) Mol BioSyst , vol.8 , Issue.7 , pp. 1970-1978
    • Chen, X.1    Liu, M.X.2    Yan, G.Y.3
  • 9
    • 77954230951 scopus 로고    scopus 로고
    • Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework
    • Yamanishi Y, Kotera M, Kanehisa M, Goto S. Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework. Bioinformatics (Oxford, England). 2010; 26(12):246-54. doi: 10.1093/bioinformatics/btq176.
    • (2010) Bioinformatics (Oxford, England) , vol.26 , Issue.12 , pp. 246-254
    • Yamanishi, Y.1    Kotera, M.2    Kanehisa, M.3    Goto, S.4
  • 10
    • 80054881553 scopus 로고    scopus 로고
    • Gaussian interaction profile kernels for predicting drug-target interaction
    • van Laarhoven T, Nabuurs SB, Marchiori E. Gaussian interaction profile kernels for predicting drug-target interaction. Bioinformatics (Oxford, England). 2011; 27(21):3036-43. doi: 10.1093/bioinformatics/btr500.
    • (2011) Bioinformatics (Oxford, England) , vol.27 , Issue.21 , pp. 3036-3043
    • van Laarhoven, T.1    Nabuurs, S.B.2    Marchiori, E.3
  • 12
    • 84884286350 scopus 로고    scopus 로고
    • Efficient regularized least-squares algorithms for conditional ranking on relational data
    • Pahikkala T, Airola A, Stock M, Baets BD, Waegeman W. Efficient regularized least-squares algorithms for conditional ranking on relational data. Mach Learn. 2013; 93:321-356. arXiv:1209.4825v2.
    • (2013) Mach Learn. , vol.93 , pp. 321-356
    • Pahikkala, T.1    Airola, A.2    Stock, M.3    Baets, B.D.4    Waegeman, W.5
  • 13
    • 80052213499 scopus 로고    scopus 로고
    • Multiple kernel learning algorithms
    • Gönen M, Alpaydin E. Multiple kernel learning algorithms. J Mach Learn Res. 2011; 12:2211-268.
    • (2011) J Mach Learn Res , vol.12 , pp. 2211-2268
    • Gönen, M.1    Alpaydin, E.2
  • 14
    • 79951729882 scopus 로고    scopus 로고
    • Combining drug and gene similarity measures for drug-target elucidation
    • Perlman L, Gottlieb A, Atias N, Ruppin E, Sharan R. Combining drug and gene similarity measures for drug-target elucidation. J Comput Biol. 2011; 18(2):133-45. doi: 10.1089/cmb.2010.0213.
    • (2011) J Comput Biol , vol.18 , Issue.2 , pp. 133-145
    • Perlman, L.1    Gottlieb, A.2    Atias, N.3    Ruppin, E.4    Sharan, R.5
  • 15
    • 80155156908 scopus 로고    scopus 로고
    • Kernel-based data fusion improves the drug-protein interaction prediction
    • Wang YC, Zhang CH, Deng NY, Wang Y. Kernel-based data fusion improves the drug-protein interaction prediction. Comput Biol Chem. 2011; 35(6):353-62. doi: 10.1016/j.compbiolchem.2011.10.003.
    • (2011) Comput Biol Chem , vol.35 , Issue.6 , pp. 353-362
    • Wang, Y.C.1    Zhang, C.H.2    Deng, N.Y.3    Wang, Y.4
  • 16
    • 84892907298 scopus 로고    scopus 로고
    • Drug repositioning by kernel-based integration of molecular structure, molecular activity, and phenotype data
    • Wang Y, Chen S, Deng N, Wang Y. Drug repositioning by kernel-based integration of molecular structure, molecular activity, and phenotype data. PLoS ONE. 2013; 8(11):78518. doi: 10.1371/journal.pone.0078518.
    • (2013) PLoS ONE , vol.8 , Issue.11 , pp. 78518
    • Wang, Y.1    Chen, S.2    Deng, N.3    Wang, Y.4
  • 17
    • 24744435534 scopus 로고    scopus 로고
    • Kernel methods for predicting protein-protein interactions
    • Ben-Hur A, Noble WS. Kernel methods for predicting protein-protein interactions,. Bioinformatics (Oxford, England). 2005; 21 Suppl 1:38-46. doi: 10.1093/bioinformatics/bti1016.
    • (2005) Bioinformatics (Oxford, England) , vol.21 , pp. 38-46
    • Ben-Hur, A.1    Noble, W.S.2
  • 18
    • 77952305592 scopus 로고    scopus 로고
    • Large-scale prediction of protein-protein interactions from structures
    • Hue M, Riffle M, Vert J-p, Noble WS. Large-scale prediction of protein-protein interactions from structures. BMC Bioinforma. 2010; 11:144.
    • (2010) BMC Bioinforma. , vol.11 , pp. 144
    • Hue, M.1    Riffle, M.2    Vert, J.-P.3    Noble, W.S.4
  • 21
    • 84928711013 scopus 로고    scopus 로고
    • Integrating multiple networks for protein function prediction
    • Yu G, Zhu H, Domeniconi C, Guo M. Integrating multiple networks for protein function prediction. BMC Syst Biol. 2015; 9(Suppl 1):3. doi: 10.1186/1752-0509-9-S1-S3.
    • (2015) BMC Syst Biol , vol.9 , pp. 3
    • Yu, G.1    Zhu, H.2    Domeniconi, C.3    Guo, M.4
  • 23
    • 46249090791 scopus 로고    scopus 로고
    • Prediction of drug-target interaction networks from the integration of chemical and genomic spaces
    • Yamanishi Y, Araki M, Gutteridge A, Honda W, Kanehisa M. Prediction of drug-target interaction networks from the integration of chemical and genomic spaces. Bioinformatics (Oxford, England). 2008; 24(13):232-40. doi: 10.1093/bioinformatics/btn162.
    • (2008) Bioinformatics (Oxford, England) , vol.24 , Issue.13 , pp. 232-240
    • Yamanishi, Y.1    Araki, M.2    Gutteridge, A.3    Honda, W.4    Kanehisa, M.5
  • 24
    • 84870805181 scopus 로고    scopus 로고
    • Flaws in evaluation schemes for pair-input computational predictions
    • Park Y, Marcotte EM. Flaws in evaluation schemes for pair-input computational predictions. Nat Methods. 2012; 9(12):1134-6. doi: 10.1038/nmeth.2259.
    • (2012) Nat Methods , vol.9 , Issue.12 , pp. 1134-1136
    • Park, Y.1    Marcotte, E.M.2
  • 25
    • 77956953029 scopus 로고    scopus 로고
    • Semi-supervised drug-protein interaction prediction from heterogeneous biological spaces
    • Xia Z, Wu LY, Zhou X, Wong STC. Semi-supervised drug-protein interaction prediction from heterogeneous biological spaces. BMC Syst Biol. 2010; 4 Suppl 2(Suppl 2):6. doi: 10.1186/1752-0509-4-S2-S6.
    • (2010) BMC Syst Biol , vol.4 , pp. 6
    • Xia, Z.1    Wu, L.Y.2    Zhou, X.3    Wong, S.T.C.4
  • 26
    • 69849094133 scopus 로고    scopus 로고
    • Supervised prediction of drug-target interactions using bipartite local models
    • Bleakley K, Yamanishi Y. Supervised prediction of drug-target interactions using bipartite local models. Bioinformatics (Oxford, England). 2009; 25(18):2397-403. doi: 10.1093/bioinformatics/btp433.
    • (2009) Bioinformatics (Oxford, England) , vol.25 , Issue.18 , pp. 2397-2403
    • Bleakley, K.1    Yamanishi, Y.2
  • 27
    • 52749085437 scopus 로고    scopus 로고
    • Protein-ligand interaction prediction: an improved chemogenomics approach
    • Jacob L, Vert JP. Protein-ligand interaction prediction: an improved chemogenomics approach. Bioinformatics (Oxford, England). 2008; 24(19):2149-56. doi: 10.1093/bioinformatics/btn409.
    • (2008) Bioinformatics (Oxford, England) , vol.24 , Issue.19 , pp. 2149-2156
    • Jacob, L.1    Vert, J.P.2
  • 30
    • 0015000439 scopus 로고
    • Some results on Tchebycheffian spline functions
    • Kimeldorf G, Wahba G. Some results on Tchebycheffian spline functions. J Math Anal Appl. 1971; 33(1):82-95.
    • (1971) J Math Anal Appl , vol.33 , Issue.1 , pp. 82-95
    • Kimeldorf, G.1    Wahba, G.2
  • 31
    • 67650705012 scopus 로고    scopus 로고
    • On pairwise kernels: an efficient alternative and generalization analysis
    • Kashima H, Oyama S, Yamanishi Y, Tsuda K. On pairwise kernels: an efficient alternative and generalization analysis. Adv Data Min Knowl Disc. 2009; 5476:1030-7.
    • (2009) Adv Data Min Knowl Disc. , vol.5476 , pp. 1030-1037
    • Kashima, H.1    Oyama, S.2    Yamanishi, Y.3    Tsuda, K.4
  • 34
    • 0033471382 scopus 로고    scopus 로고
    • An interior point algorithm for large-scale nonlinear programming
    • Byrd RH, Hribar ME, Nocedal J. An interior point algorithm for large-scale nonlinear programming. SIAM J Optim. 1999; 9(4):877-900. doi: 10.1137/S1052623497325107.
    • (1999) SIAM J Optim , vol.9 , Issue.4 , pp. 877-900
    • Byrd, R.H.1    Hribar, M.E.2    Nocedal, J.3
  • 35
    • 84957028162 scopus 로고    scopus 로고
    • version 8.1.0 (R2013a). Natick, Massachusetts: The MathWorks Inc
    • MATLAB. version 8.1.0 (R2013a). Natick, Massachusetts: The MathWorks Inc.; 2013.
    • (2013)
  • 41
    • 0036358995 scopus 로고    scopus 로고
    • The spectrum kernel: a string kernel for SVM protein classification
    • Leslie CS, Eskin E, Noble WS. The spectrum kernel: a string kernel for SVM protein classification. In: Pac Symp Biocomput vol. 7: 2002. p. 566-575.
    • (2002) Pac Symp Biocomput , vol.7 , pp. 566-575
    • Leslie, C.S.1    Eskin, E.2    Noble, W.S.3
  • 42
    • 84943638759 scopus 로고    scopus 로고
    • KeBABS - an R package for kernel-based analysis of biological sequences
    • Palme J, Hochreiter S, Bodenhofer U. KeBABS - an R package for kernel-based analysis of biological sequences. Bioinformatics. 2015; 31(15):2574-2576. doi: 10.1093/bioinformatics/btv176.
    • (2015) Bioinformatics , vol.31 , Issue.15 , pp. 2574-2576
    • Palme, J.1    Hochreiter, S.2    Bodenhofer, U.3
  • 43
    • 84979860632 scopus 로고    scopus 로고
    • The BioMart community portal: an innovative alternative to large, centralized data repositories.
    • Smedley D, Haider S, Durinck S, Al E. The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Res. 2015. doi: 10.1093/nar/gkv350.
    • (2015) Nucleic Acids Res.
    • Smedley, D.1    Haider, S.2    Durinck, S.3    Al, E.4
  • 44
    • 67849110934 scopus 로고    scopus 로고
    • Fast Gene Ontology based clustering for microarray experiments
    • Ovaska K, Laakso M, Hautaniemi S. Fast Gene Ontology based clustering for microarray experiments. BioData Min. 2008; 1(1):11.
    • (2008) BioData Min , vol.1 , Issue.1 , pp. 11
    • Ovaska, K.1    Laakso, M.2    Hautaniemi, S.3
  • 45
    • 0002016474 scopus 로고    scopus 로고
    • Semantic Similarity in a Taxonomy: An Information Based Measure and Its Application to Problems of Ambiguity in Natural Language
    • Resnik P. Semantic Similarity in a Taxonomy: An Information Based Measure and Its Application to Problems of Ambiguity in Natural Language. J Artif Intell Res. 1999; 11:95-130.
    • (1999) J Artif Intell Res , vol.11 , pp. 95-130
    • Resnik, P.1
  • 47
    • 0141843591 scopus 로고    scopus 로고
    • Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways
    • Hattori M, Okuno Y, Goto S, Kanehisa M. Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. J Am Ceram Soc. 2003; 125(39):11853-65.
    • (2003) J Am Ceram Soc , vol.125 , Issue.39 , pp. 11853-11865
    • Hattori, M.1    Okuno, Y.2    Goto, S.3    Kanehisa, M.4
  • 48
    • 84947703462 scopus 로고    scopus 로고
    • Rchemcpp: a web service for structural analoging in ChEMBL, Drugbank and the Connectivity Map.
    • Klambauer G, Wischenbart M, Mahr M, Unterthiner T, Mayr A, Hochreiter S. Rchemcpp: a web service for structural analoging in ChEMBL, Drugbank and the Connectivity Map. Bioinformatics. 2015. Advance access doi: 10.1093/bioinformatics/btv373.
    • (2015) Bioinformatics.
    • Klambauer, G.1    Wischenbart, M.2    Mahr, M.3    Unterthiner, T.4    Mayr, A.5    Hochreiter, S.6
  • 49
    • 1942516986 scopus 로고    scopus 로고
    • Marginalized kernels between labeled graphs
    • Kashima H, Tsuda K, Inokuchi A. Marginalized kernels between labeled graphs. In: ICML, vol. 3: 2003. p. 321-328.
    • (2003) ICML , vol.3 , pp. 321-328
    • Kashima, H.1    Tsuda, K.2    Inokuchi, A.3
  • 50
    • 23844480138 scopus 로고    scopus 로고
    • Graph kernels for chemical informatics
    • Ralaivola L, Swamidass SJ, Saigo H, Baldi P. Graph kernels for chemical informatics. Neural Netw. 2005; 18(8):1093-110. doi: 10.1016/j.neunet.2005.07.009.
    • (2005) Neural Netw , vol.18 , Issue.8 , pp. 1093-1110
    • Ralaivola, L.1    Swamidass, S.J.2    Saigo, H.3    Baldi, P.4
  • 51
    • 84866446560 scopus 로고    scopus 로고
    • Drug target prediction using adverse event report systems: A pharmacogenomic approach
    • Takarabe M, Kotera M, Nishimura Y, Goto S, Yamanishi Y. Drug target prediction using adverse event report systems: A pharmacogenomic approach. Bioinformatics. 2012; 28(18):611-8. doi: 10.1093/bioinformatics/bts413.
    • (2012) Bioinformatics , vol.28 , Issue.18 , pp. 611-618
    • Takarabe, M.1    Kotera, M.2    Nishimura, Y.3    Goto, S.4    Yamanishi, Y.5
  • 52
  • 53
    • 67549113661 scopus 로고    scopus 로고
    • A framework for multiple kernel support vector regression and its applications to siRNA efficacy prediction
    • Qiu S, Lane T. A framework for multiple kernel support vector regression and its applications to siRNA efficacy prediction. IEEE/ACM Trans Comput Biol Bioinf. 2009; 6(2):190-9.
    • (2009) IEEE/ACM Trans Comput Biol Bioinf , vol.6 , Issue.2 , pp. 190-199
    • Qiu, S.1    Lane, T.2
  • 55
    • 84866459051 scopus 로고    scopus 로고
    • Predicting drug-target interactions from chemical and genomic kernels using Bayesian matrix factorization
    • Gönen M. Predicting drug-target interactions from chemical and genomic kernels using Bayesian matrix factorization. Bioinformatics (Oxford, England). 2012; 28(18):2304-10. doi: 10.1093/bioinformatics/bts360.
    • (2012) Bioinformatics (Oxford, England) , vol.28 , Issue.18 , pp. 2304-2310
    • Gönen, M.1
  • 57
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: kyoto encyclopedia of genes and genomes
    • Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000; 28(1):27-30.
    • (2000) Nucleic Acids Res , vol.28 , Issue.1 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 59
    • 0031844094 scopus 로고    scopus 로고
    • Topical tretinoin in acne therapy
    • Webster GF. Topical tretinoin in acne therapy. J Am Acad Dermatol. 1998; 39(2):38-44.
    • (1998) J Am Acad Dermatol , vol.39 , Issue.2 , pp. 38-44
    • Webster, G.F.1
  • 60
    • 0036181028 scopus 로고    scopus 로고
    • Sulfonylurea receptor-1 (sur1): Genetic and metabolic evidences for a role in the susceptibility to type 2 diabetes mellitus
    • REIS A, VELHO G. Sulfonylurea receptor-1 (sur1): Genetic and metabolic evidences for a role in the susceptibility to type 2 diabetes mellitus. Diabetes Metab. 2002; 28(1):14-19.
    • (2002) Diabetes Metab , vol.28 , Issue.1 , pp. 14-19
    • REIS, A.1    VELHO, G.2
  • 61
    • 33845865582 scopus 로고    scopus 로고
    • Diazoxide prevents diabetes through inhibiting pancreatic β-cells from apoptosis via bcl-2/bax rate and p38- β mitogen-activated protein kinase
    • Huang Q, Bu S, Yu Y, Guo Z, Ghatnekar G, Bu M, et al. Diazoxide prevents diabetes through inhibiting pancreatic β-cells from apoptosis via bcl-2/bax rate and p38- β mitogen-activated protein kinase. Endocrinology. 2007; 148(1):81-91.
    • (2007) Endocrinology , vol.148 , Issue.1 , pp. 81-91
    • Huang, Q.1    Bu, S.2    Yu, Y.3    Guo, Z.4    Ghatnekar, G.5    Bu, M.6


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