메뉴 건너뛰기




Volumn 146, Issue , 2015, Pages 494-502

In silico toxicity prediction of chemicals from EPA toxicity database by kernel fusion-based support vector machines

Author keywords

Data fusion; Kernel fusion; Kernel methods; Support vector machine; Toxicity prediction

Indexed keywords

ARTICLE; BIOASSAY; CHEMICAL ANALYSIS; CLUSTER ANALYSIS; CORRELATION COEFFICIENT; DATA BASE; DISTRIBUTED STRUCTURE SEARCHABLE TOXICITY DATABASE; KERNEL METHOD; MACHINE LEARNING; PREDICTION; PRIORITY JOURNAL; PROBABILITY; QUANTITATIVE ANALYSIS; RECEIVER OPERATING CHARACTERISTIC; SUPPORT VECTOR MACHINE; TOXICITY TESTING;

EID: 84937929751     PISSN: 01697439     EISSN: 18733239     Source Type: Journal    
DOI: 10.1016/j.chemolab.2015.07.009     Document Type: Article
Times cited : (22)

References (46)
  • 2
    • 84937955398 scopus 로고    scopus 로고
    • http://guidance.echa.europa.eu/guidance:en.htm.
  • 3
    • 0037364162 scopus 로고    scopus 로고
    • ADMET in silico modelling: towards prediction paradise?
    • van de Waterbeemd H., Gifford E. ADMET in silico modelling: towards prediction paradise?. Nat. Rev. Drug Discov. 2003, 2:192-204.
    • (2003) Nat. Rev. Drug Discov. , vol.2 , pp. 192-204
    • van de Waterbeemd, H.1    Gifford, E.2
  • 4
    • 0025863682 scopus 로고
    • Computer prediction of possible toxic action from chemical structure; the DEREK system
    • Sanderson D.M., Earnshaw C.G. Computer prediction of possible toxic action from chemical structure; the DEREK system. Hum. Exp. Toxicol. 1991, 10:261-273.
    • (1991) Hum. Exp. Toxicol. , vol.10 , pp. 261-273
    • Sanderson, D.M.1    Earnshaw, C.G.2
  • 5
    • 0026778110 scopus 로고
    • MULTICASE 1. A hierarchical computer automated structure evaluation program
    • Klopman G. MULTICASE 1. A hierarchical computer automated structure evaluation program. Quant. Struct.-Act. Relat. 1992, 11:176-184.
    • (1992) Quant. Struct.-Act. Relat. , vol.11 , pp. 176-184
    • Klopman, G.1
  • 6
    • 0035144211 scopus 로고    scopus 로고
    • Evaluation of the TOPKAT system for predicting the carcinogenicity of chemicals
    • Prival M.J. Evaluation of the TOPKAT system for predicting the carcinogenicity of chemicals. Environ. Mol. Mutagen. 2001, 37:55-69.
    • (2001) Environ. Mol. Mutagen. , vol.37 , pp. 55-69
    • Prival, M.J.1
  • 7
    • 1842639169 scopus 로고    scopus 로고
    • ESP: a method to predict toxicity and pharmacological properties of chemicals using multiple MCASE databases
    • Klopman G., Chakravarti S.K., Zhu H., Ivanov J.M., Saiakhov R.D. ESP: a method to predict toxicity and pharmacological properties of chemicals using multiple MCASE databases. J. Chem. Inf. Comput. Sci. 2004, 44:704-715.
    • (2004) J. Chem. Inf. Comput. Sci. , vol.44 , pp. 704-715
    • Klopman, G.1    Chakravarti, S.K.2    Zhu, H.3    Ivanov, J.M.4    Saiakhov, R.D.5
  • 8
    • 66449094983 scopus 로고    scopus 로고
    • Prediction of antibacterial compounds by machine learning approaches
    • Xue-Gang Y., Duan C., Min W., Ying X., Yu-Zong C. Prediction of antibacterial compounds by machine learning approaches. J. Comput. Chem. 2009, 30:1202-1211.
    • (2009) J. Comput. Chem. , vol.30 , pp. 1202-1211
    • Xue-Gang, Y.1    Duan, C.2    Min, W.3    Ying, X.4    Yu-Zong, C.5
  • 9
    • 53849084171 scopus 로고    scopus 로고
    • Prediction of chemical toxicity with local support vector regression and activity-specific kernels
    • Maunz A., Helma C. Prediction of chemical toxicity with local support vector regression and activity-specific kernels. SAR QSAR Environ. Res. 2008, 19:413-431.
    • (2008) SAR QSAR Environ. Res. , vol.19 , pp. 413-431
    • Maunz, A.1    Helma, C.2
  • 10
    • 0042355457 scopus 로고    scopus 로고
    • In silico prediction of drug toxicity
    • Dearden J.C. In silico prediction of drug toxicity. J. Comput. Aided Mol. Des. 2003, 17:119-127.
    • (2003) J. Comput. Aided Mol. Des. , vol.17 , pp. 119-127
    • Dearden, J.C.1
  • 14
    • 84925409378 scopus 로고    scopus 로고
    • Kernelmethods for large-scale genomic data analysis
    • Wang X., Xing E.P., Schaid D.J. Kernelmethods for large-scale genomic data analysis. Brief. Bioinform. 2015, 16:183-192.
    • (2015) Brief. Bioinform. , vol.16 , pp. 183-192
    • Wang, X.1    Xing, E.P.2    Schaid, D.J.3
  • 16
    • 24044461725 scopus 로고    scopus 로고
    • A novel multivariate regression approach based on kernel partial least squares with orthogonal signal correction
    • Kim K., Lee J.-M., Lee I.-B. A novel multivariate regression approach based on kernel partial least squares with orthogonal signal correction. Chemom. Intell. Lab. Syst. 2005, 79:22-30.
    • (2005) Chemom. Intell. Lab. Syst. , vol.79 , pp. 22-30
    • Kim, K.1    Lee, J.-M.2    Lee, I.-B.3
  • 17
    • 84894426130 scopus 로고    scopus 로고
    • A new kernel discriminant analysis framework for electronic nose recognition
    • Zhang L., Tian F.-C. A new kernel discriminant analysis framework for electronic nose recognition. Anal. Chim. Acta 2014, 816:8-17.
    • (2014) Anal. Chim. Acta , vol.816 , pp. 8-17
    • Zhang, L.1    Tian, F.-C.2
  • 20
    • 77952238401 scopus 로고    scopus 로고
    • A tutorial on support vector machine-based methods for classification problems in chemometrics
    • Luts J., Ojeda F., Van de Plas R., De Moor B., Van Huffel S., Suykens J.A.K. A tutorial on support vector machine-based methods for classification problems in chemometrics. Anal. Chim. Acta 2010, 665:129-145.
    • (2010) Anal. Chim. Acta , vol.665 , pp. 129-145
    • Luts, J.1    Ojeda, F.2    Van de Plas, R.3    De Moor, B.4    Van Huffel, S.5    Suykens, J.A.K.6
  • 21
    • 80053631131 scopus 로고    scopus 로고
    • A novel kernel Fisher discriminant analysis: constructing informative kernel by decision tree ensemble for metabolomics data analysis
    • Cao D.S., Zeng M.M., Yi L.Z., Wang B., Xu Q.S., Hu Q.N., Zhang L.X., Lu H.M., Liang Y.Z. A novel kernel Fisher discriminant analysis: constructing informative kernel by decision tree ensemble for metabolomics data analysis. Anal. Chim. Acta 2011, 706:97-104.
    • (2011) Anal. Chim. Acta , vol.706 , pp. 97-104
    • Cao, D.S.1    Zeng, M.M.2    Yi, L.Z.3    Wang, B.4    Xu, Q.S.5    Hu, Q.N.6    Zhang, L.X.7    Lu, H.M.8    Liang, Y.Z.9
  • 22
    • 26944486424 scopus 로고    scopus 로고
    • Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity
    • Swamidass S.J., Chen J., Phung P., Ralaivola L., Baldi P. Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity. Bioinformatics 2005, 21:I359-I368.
    • (2005) Bioinformatics , vol.21 , pp. I359-I368
    • Swamidass, S.J.1    Chen, J.2    Phung, P.3    Ralaivola, L.4    Baldi, P.5
  • 26
    • 27144489164 scopus 로고    scopus 로고
    • A tutorial on support vector machines for pattern recognition
    • Burges C.J.C. A tutorial on support vector machines for pattern recognition. Data Min. Knowl. Disc. 1998, 2:121-167.
    • (1998) Data Min. Knowl. Disc. , vol.2 , pp. 121-167
    • Burges, C.J.C.1
  • 27
    • 34848824629 scopus 로고    scopus 로고
    • Applications of support vector machines in chemistry
    • Ivanciuc O. Applications of support vector machines in chemistry. Rev. Comput. Chem. 2007, 23:291-400.
    • (2007) Rev. Comput. Chem. , vol.23 , pp. 291-400
    • Ivanciuc, O.1
  • 28
    • 28844500372 scopus 로고    scopus 로고
    • Application of support vector machine (SVM) for prediction toxic activity of different data sets
    • Zhao C.Y., Zhang H.X., Zhang X.Y., Liu M.C., Hu Z.D., Fan B.T. Application of support vector machine (SVM) for prediction toxic activity of different data sets. Toxicology 2006, 217:105-119.
    • (2006) Toxicology , vol.217 , pp. 105-119
    • Zhao, C.Y.1    Zhang, H.X.2    Zhang, X.Y.3    Liu, M.C.4    Hu, Z.D.5    Fan, B.T.6
  • 29
    • 79551534528 scopus 로고    scopus 로고
    • Prediction of aqueous solubility of druglike organic compounds using partial least squares, back-propagation network and support vector machine
    • Cao D.-S., Xu Q.-S., Liang Y.-Z., Chen X., Li H.-D. Prediction of aqueous solubility of druglike organic compounds using partial least squares, back-propagation network and support vector machine. J. Chemom. 2010, 24:584-595.
    • (2010) J. Chemom. , vol.24 , pp. 584-595
    • Cao, D.-S.1    Xu, Q.-S.2    Liang, Y.-Z.3    Chen, X.4    Li, H.-D.5
  • 30
    • 79951876692 scopus 로고    scopus 로고
    • Combination of kernel PCA and linear support vector machine for modeling a nonlinear relationship between bioactivity and molecular descriptors
    • Fu G.H., Cao D.S., Xu Q.S., Li H.D., Liang Y.Z. Combination of kernel PCA and linear support vector machine for modeling a nonlinear relationship between bioactivity and molecular descriptors. J. Chemom. 2011, 25:92-99.
    • (2011) J. Chemom. , vol.25 , pp. 92-99
    • Fu, G.H.1    Cao, D.S.2    Xu, Q.S.3    Li, H.D.4    Liang, Y.Z.5
  • 31
    • 32444444605 scopus 로고    scopus 로고
    • About kernel latent variable approaches and SVM
    • Czekaj T., Wu W., Walczak B. About kernel latent variable approaches and SVM. J. Chemom. 2005, 19:341-354.
    • (2005) J. Chemom. , vol.19 , pp. 341-354
    • Czekaj, T.1    Wu, W.2    Walczak, B.3
  • 32
    • 80052261350 scopus 로고    scopus 로고
    • Support vector machines in water quality management
    • Singh K.P., Basant N., Gupta S. Support vector machines in water quality management. Anal. Chim. Acta 2011, 703:152-162.
    • (2011) Anal. Chim. Acta , vol.703 , pp. 152-162
    • Singh, K.P.1    Basant, N.2    Gupta, S.3
  • 33
    • 84870810274 scopus 로고    scopus 로고
    • A novel tree kernel support vector machine classifier for modeling the relationship between bioactivity and molecular descriptors
    • Huang X., Cao D.-S., Xu Q.-S., Shen L., Huang J.-H., Liang Y.-Z. A novel tree kernel support vector machine classifier for modeling the relationship between bioactivity and molecular descriptors. Chemom. Intell. Lab. Syst. 2013, 120:71-76.
    • (2013) Chemom. Intell. Lab. Syst. , vol.120 , pp. 71-76
    • Huang, X.1    Cao, D.-S.2    Xu, Q.-S.3    Shen, L.4    Huang, J.-H.5    Liang, Y.-Z.6
  • 34
    • 77955644255 scopus 로고    scopus 로고
    • Visualization and recovery of the (bio)chemical interesting variables in data analysis with support vector machine classification
    • Krooshof P.W.T., Uustuun B., Postma G.J., Buydens L.M.C. Visualization and recovery of the (bio)chemical interesting variables in data analysis with support vector machine classification. Anal. Chem. 2011, 82:7000-7007.
    • (2011) Anal. Chem. , vol.82 , pp. 7000-7007
    • Krooshof, P.W.T.1    Uustuun, B.2    Postma, G.J.3    Buydens, L.M.C.4
  • 35
    • 84862003752 scopus 로고    scopus 로고
    • Interpretation and visualization of non-linear data fusion in kernel space: study on metabolomic characterization of progression of multiple sclerosis
    • Smolinska A., Blanchet L., Coulier L., Ampt K.A., Luider T., Hintzen R.Q., Wijmenga S.S., Buydens L.M. Interpretation and visualization of non-linear data fusion in kernel space: study on metabolomic characterization of progression of multiple sclerosis. PLoS One 2012, 7:e38163.
    • (2012) PLoS One , vol.7 , pp. e38163
    • Smolinska, A.1    Blanchet, L.2    Coulier, L.3    Ampt, K.A.4    Luider, T.5    Hintzen, R.Q.6    Wijmenga, S.S.7    Buydens, L.M.8
  • 36
    • 34250882118 scopus 로고    scopus 로고
    • Visualisation and interpretation of Support Vector Regression models
    • Ustun B., Melssen W.J., Buydens L.M.C. Visualisation and interpretation of Support Vector Regression models. Anal. Chim. Acta 2007, 595:299-309.
    • (2007) Anal. Chim. Acta , vol.595 , pp. 299-309
    • Ustun, B.1    Melssen, W.J.2    Buydens, L.M.C.3
  • 37
    • 33646023117 scopus 로고    scopus 로고
    • An introduction to ROC analysis
    • Fawcett T. An introduction to ROC analysis. Pattern Recogn. Lett. 2006, 27:861-874.
    • (2006) Pattern Recogn. Lett. , vol.27 , pp. 861-874
    • Fawcett, T.1
  • 38
    • 79954628072 scopus 로고    scopus 로고
    • In silico classification of human maximum recommended daily dose based on modified random forest and substructure fingerprint
    • Cao D.-S., Hu Q.-N., Xu Q.-S., Yang Y.-N., Zhao J.-C., Lu H.-M., Zhang L.-X., Liang Y.-Z. In silico classification of human maximum recommended daily dose based on modified random forest and substructure fingerprint. Anal. Chim. Acta 2011, 692:50-56.
    • (2011) Anal. Chim. Acta , vol.692 , pp. 50-56
    • Cao, D.-S.1    Hu, Q.-N.2    Xu, Q.-S.3    Yang, Y.-N.4    Zhao, J.-C.5    Lu, H.-M.6    Zhang, L.-X.7    Liang, Y.-Z.8
  • 39
    • 79954494823 scopus 로고    scopus 로고
    • Feature importance sampling-based adaptive random forest as a useful tool to screen underlying lead compounds
    • Cao D.-S., Liang Y.-Z., Xu Q.-S., Zhang L.-X., Hu Q.-N., Li H.-D. Feature importance sampling-based adaptive random forest as a useful tool to screen underlying lead compounds. J. Chemom. 2011, 25:201-207.
    • (2011) J. Chemom. , vol.25 , pp. 201-207
    • Cao, D.-S.1    Liang, Y.-Z.2    Xu, Q.-S.3    Zhang, L.-X.4    Hu, Q.-N.5    Li, H.-D.6
  • 40
    • 84888593703 scopus 로고    scopus 로고
    • PyDPI: freely available python package for chemoinformatics, bioinformatics, and chemogenomics studies
    • Cao D.S., Liang Y.Z., Yan J., Tan G.S., Xu Q.S., Liu S. PyDPI: freely available python package for chemoinformatics, bioinformatics, and chemogenomics studies. J. Chem. Inf. Model. 2013, 53:3086-3096.
    • (2013) J. Chem. Inf. Model. , vol.53 , pp. 3086-3096
    • Cao, D.S.1    Liang, Y.Z.2    Yan, J.3    Tan, G.S.4    Xu, Q.S.5    Liu, S.6
  • 41
    • 30844443282 scopus 로고    scopus 로고
    • Molecular similarity and diversity in chemoinformatics: from theory to applications
    • Maldonado A., Doucet J., Petitjean M., Fan B.-T. Molecular similarity and diversity in chemoinformatics: from theory to applications. Mol. Divers. 2006, 10:39-79.
    • (2006) Mol. Divers. , vol.10 , pp. 39-79
    • Maldonado, A.1    Doucet, J.2    Petitjean, M.3    Fan, B.-T.4
  • 42
    • 33646266941 scopus 로고    scopus 로고
    • Toxicity-indicating structural patterns
    • von Korff M., Sander T. Toxicity-indicating structural patterns. J. Chem. Inf. Model. 2006, 46:536-544.
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 536-544
    • von Korff, M.1    Sander, T.2
  • 43
    • 84876266543 scopus 로고    scopus 로고
    • ChemoPy: freely available python package for computational biology and chemoinformatics
    • Cao D.S., Xu Q.S., Hu Q.N., Liang Y.Z. ChemoPy: freely available python package for computational biology and chemoinformatics. Bioinformatics 2013, 29:1092-1094.
    • (2013) Bioinformatics , vol.29 , pp. 1092-1094
    • Cao, D.S.1    Xu, Q.S.2    Hu, Q.N.3    Liang, Y.Z.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.