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Original Articles

Database Composition Can Affect the Structure–Activity Relationship Prediction

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Pages 1527-1540 | Received 28 Apr 2005, Accepted 28 Jul 2005, Published online: 24 Feb 2007

REFERENCES

  • Arena , V. C. , Sussman , N. B. , Mazumdar , S. , Yu , S. and Macina , O. T. 2004 . The utility of structure-activity relationship (SAR) models for prediction and covariate selection in developmental toxicity: Comparative analysis of logistic regression and decision tree models . SAR QSAR Environ. Res , 15 : 1 – 18 . [INFOTRIEVE] [CSA]
  • Benigni , R. and Giuliani , A. 2003 . Putting the predictive toxicology challenge into perspective: Reflections on the results . Bioinformatics , 19 : 1194 – 1200 . [INFOTRIEVE] [CSA] [CROSSREF]
  • Chawla , N. V. , Bowyer , K. W. , Hall , L. O. and Kegelmeyer , W. P. 2002 . SMOTE: Synthetic minority over-sampling technique . J. Artif. Intell. Res , 16 : 321 – 357 . [CSA]
  • Chen , J. J. , Tsai , C.–A. , Young , J. F. and Kodell , R. L. 2005 . Classification ensembles for unbalanced class sizes in predictive toxicology . SAR QSAR Environ. Res , 16 : 517 – 529 . [INFOTRIEVE] [CSA] [CROSSREF]
  • Gold , L. S. , Sawyer , C. B. , Magaw , R. , Backman , G. M. , de Veciana , M. , Levinson , R. , Hooper , N. K. , Havender , W. R. , Bernstein , L. , Peto , R. , Pike , M. C. and Ames , B. N. 1984 . A carcinogenic potency database of the standardized results of animal bioassays . Environ. Health Perspect , 58 : 9 – 319 . [INFOTRIEVE] [CSA]
  • Hashemi , R. R. , Le Blanc , L. A. , Rucks , C. T. and Shearry , A. . Vessel accident modeling: A comparison of neural networks, discriminant analysis and logistic regression . 30th Ann. Conf. Canadian Transportation Research Forum (CTRF), Aylmer . May , Quebec. pp. 603 – 617 .
  • Hastie , T. , Tibshirani , R. and Friedman , J. 2001 . The elements of statistical learning: Data mining, inference, and prediction , New York : Springer .
  • Klimasauskas , C. C. 1991 . Applying neural networks. Part 2: A walk through the application process . J. PC AI , March/April : 27 – 34 . [CSA]
  • Kubat , M. and Matwin , S. . Addressing the curse of imbalanced training sets: One-sided selection . Proc. 14th Int. Conf. Machine Learning . Nashville, TN. pp. 179 – 186 .
  • Liu , M. , Sussman , N. , Klopman , G. and Rosenkranz , H. S. 1996a . Structure-activity and mechanistic relationships: The effect of chemical overlap on structural overlap in data bases of varying size and composition . Mutat. Res , 372 : 79 – 85 . [INFOTRIEVE] [CSA]
  • Liu , M. , Sussman , N. , Klopman , G. and Rosenkranz , H. S. 1996b . Estimation of the optimal data base size for structure-activity analyses: The Salmonella mutagenicity data base . Mutat. Res , 358 : 63 – 72 . [INFOTRIEVE] [CSA]
  • Matthews , E. J. and Contrera , J. F. 1998 . A new highly specific method for predicting the carcinogenic potential of pharmaceuticals in rodents using enhanced MCASE QSAR-ES software . Regul. Toxicol. Pharmacol , 28 : 242 – 264 . [INFOTRIEVE] [CSA] [CROSSREF]
  • McDowell , R. M. and Jaworska , J. S. 2002 . Bayesian analysis and inference from QSAR predictive model results . SAR QSAR Environ. Res , 13 : 111 – 125 . [INFOTRIEVE] [CSA] [CROSSREF]
  • Rosenkranz , H. S. 2004 . SAR modeling of genotoxic phenomena: The consequence on predictive performance of deviation from a unity ratio of genotoxicants/non-genotoxicants . Mutat. Res , 559 : 67 – 71 . [INFOTRIEVE] [CSA]
  • Rosenkranz , H. S. and Cunningham , A. R. 2001 . SAR modeling of unbalanced data sets . SAR QSAR Environ. Res , 12 : 267 – 274 . [INFOTRIEVE] [CSA]
  • Swets , J. A. 1988 . Measuring the accuracy of diagnostic systems . Science , 240 : 1285 – 1293 . [INFOTRIEVE] [CSA]
  • Takihi , N. , Zhang , Y. P. , Klopman , G. and Rosenkranz , H. S. 1993a . Development of a method to assess the informational content of structure–activity data bases . Qual. Assur. Good Pract. Regul. Law , 2 : 255 – 264 . [CSA]
  • Takihi , N. , Zhang , Y. P. , Klopman , G. and Rosenkranz , H. S. 1993b . An approach for evaluating and increasing the informational content of mutagenicity and clastogenicity data bases . Mutagenesis , 8 : 257 – 264 . [INFOTRIEVE] [CSA]
  • Toivonen , H. , Srinivasan , A. , King , R. D. , Kramer , S. and Helma , C. 2003 . Statistical evaluation of the Predictive Toxicology Challenge 2000–2001 . Bioinformatics , 19 : 1183 – 1193 . [INFOTRIEVE] [CSA] [CROSSREF]
  • Walker , J. D. , Carlsen , L. and Jaworska , J. 2003 . Improving opportunities for regulatory acceptance of QSARs: The importance of model domain, uncertainty, validity and predictability . QSAR Comb. Sci , 22 : 346 – 350 . [CSA] [CROSSREF]
  • Young , J. F. , Tong , W. , Fang , H. , Xie , Q. , Pearce , B. , Hashemi , R. , Beger , R. D. , Cheeseman , M. A. , Chen , J. J. , Chang , Y. I. and Kodell , R. L. 2004 . Building an organ-specific carcinogenic database for SAR analyses . J. Toxicol. Environ. Health A , 67 : 1363 – 1389 . [INFOTRIEVE] [CSA] [CROSSREF]

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