An Optimal Self-Pruning Neural Network and Nonlinear Descriptor Selection in QSAR
Feature selection is an important but still poorly solved problem in QSAR modeling. We employ a Bayesian regularized neural network with a sparse Laplacian prior as an efficient method for supervised feature selection, and robust parsimonious nonlinear QSAR modeling. The method simultaneously select...
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| Published in | QSAR & combinatorial science Vol. 28; no. 10; pp. 1092 - 1097 |
|---|---|
| Main Authors | , |
| Format | Journal Article |
| Language | English |
| Published |
Weinheim
WILEY-VCH Verlag
01.10.2009
WILEY‐VCH Verlag |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1611-020X 1611-0218 |
| DOI | 10.1002/qsar.200810202 |
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| Abstract | Feature selection is an important but still poorly solved problem in QSAR modeling. We employ a Bayesian regularized neural network with a sparse Laplacian prior as an efficient method for supervised feature selection, and robust parsimonious nonlinear QSAR modeling. The method simultaneously selects the most relevant descriptors for model, and automatically prunes the neural network to have the architecture with optimum prediction ability. We illustrate the advantages of the method using a suite of diverse data sets, and compare the results obtained by the new method against those obtained by alternative contemporary methods. |
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| AbstractList | Feature selection is an important but still poorly solved problem in QSAR modeling. We employ a Bayesian regularized neural network with a sparse Laplacian prior as an efficient method for supervised feature selection, and robust parsimonious nonlinear QSAR modeling. The method simultaneously selects the most relevant descriptors for model, and automatically prunes the neural network to have the architecture with optimum prediction ability. We illustrate the advantages of the method using a suite of diverse data sets, and compare the results obtained by the new method against those obtained by alternative contemporary methods. |
| Author | Winkler, David A. Burden, Frank R. |
| Author_xml | – sequence: 1 givenname: Frank R. surname: Burden fullname: Burden, Frank R. email: frank.burden@scimetrics.com organization: Scimetrics, Victoria, Australia and School of Chemistry, Monash University, Australia 3800 – sequence: 2 givenname: David A. surname: Winkler fullname: Winkler, David A. email: dave.winkler@csiro.au organization: CSIRO Molecular Science, Private Bag 10, Clayton South MDC 3169, Australia; and School of Chemistry, Monash University, Australia 3800 |
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| Cites_doi | 10.1016/0006-2952(92)90472-U 10.1021/jm00346a002 10.1021/jm00113a009 10.1162/neco.1992.4.3.448 10.1021/ci990061k 10.1002/qsar.19970160406 10.1021/jm00165a028 10.1021/jm00090a019 10.1071/CH05202 10.1021/jm00085a016 10.1071/CH9942001 10.1021/jm00106a033 10.1016/j.jmgm.2004.03.010 10.1162/neco.1995.7.1.117 10.1002/(SICI)1521-3838(199801)17:01<14::AID-QSAR14>3.0.CO;2-U 10.1007/978-1-4612-0745-0 10.1021/tx010101q 10.1021/jm00100a005 10.1021/jm00006a014 10.1021/jm00063a017 10.1021/jm00091a007 10.1021/jm00117a029 10.1021/ci800290h 10.1016/0223-5234(96)85873-9 |
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| References_xml | – reference: D. A. Winkler , F. R. Burden , J. Mol. Graph. Mod. 2004, 22, 499-505 – reference: M. J. Polley , D. A. Winkler , F. R. Burden , J. Chem. Inf. Model. 2009, 49, 710. – reference: G. B. Barlin , L. P. Davies , D. R. Aavis , P. W. Harrison , Aust. J. Chem. 1994, 47, 2001-2012. – reference: F. R. Burden , D. A. Winkler , QSAR Comb. Sci.B 2008, in press; DOI: 10.1002/QSAR200810173 – reference: C-G. Wang, T. Langer, P. G. Kamath, Z-Q. Gu, P. Skolnick, R. I. Fryer, J. Med. Chem. 1995, 38, 950-957. – reference: M. S. Allen , T. J. Hagen , M. L. Trudell , P. W. Codding , P. Skolnick , J. M. Cook , J. Med. Chem. 1988, 31, 1854-1861. – reference: P. M. Williams , Neural Comput. 1995, 7, 117-143. – reference: P. Sauerberg , P. H. Olesen , S. Nielsen , S. Treppendahl , M. J. Sheardown , T. Honoré , C. H. Mitch , J. S. Ward , A. J. Pike , F. P. Bymaster , B. D. Sawyer , H. E. Shannon , J. Med. Chem. 1992, 35, 2274-2283. – reference: J. S. Ward , L. Merritt , V. J. 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| Title | An Optimal Self-Pruning Neural Network and Nonlinear Descriptor Selection in QSAR |
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