A randomized exhaustive propositionalization approach for molecule classification

INFORMS Journal on Computing

Volumn 23, Issue 3, 2011, Pages 331-345

  Samorani, Michele ^a   Laguna, Manuel ^a   DeLisle, Robert Kirk ^b   Weaver, Daniel C ^b  

^a UNIVERSITY OF COLORADO   (United States)

^b ARRAY BIOPHARMA INC   (United States)

Author keywords

Drug discovery; Molecule classification; Propositionalization; Relational learning

Indexed keywords

EID: 79961085816     PISSN: 10919856     EISSN: 15265528     Source Type: Journal    
DOI: 10.1287/ijoc.1100.0404     Document Type: Article

References (25)

1. Atramentov, A., H. Leiva, V. Honavar. 2003. A multi-relational decision tree learning algorithm-Implementation and experiments. T. Horváth, A. Yamamoto, eds. Inductive Logic Programming. Lecture Notes in Computer Science, Vol. 2835. Springer, Berlin, 38-56. (Pubitemid 37273925)
2. Brzozowski, A. M., A. C. W. Pike, Z. Dauter, R. E. Hubbard, T. Bonn, O. Engström, L. Ohman, G. L. Greene, J.-Å. Gustafsson, M. Carlquist. 1997. Molecular basis of agonism and antagonism in the oestrogen receptor. Nature 389(6652) 753-758. (Pubitemid 27458965)
3. Cristianini, N., J. Shawe-Taylor. 2000. An Introduction to Support Vector Machines and Other Kernel-Based Learning Methods. Cambridge University Press, Cambridge, UK.
4. DiMasi, J. A., R. W. Hansen, H. G. Grabowski. 2003. The price of innovation: New estimates of drug development costs. J. Health Econom. 22(2) 151-185. (Pubitemid 36279392)
5. Dixon, S. L., K. M. Merz Jr. 2001. One-dimensional molecular representations and similarity calculations: Methodology and validation. J. Medicinal Chemistry 44(23) 3795-3809. (Pubitemid 33051472)
6. Domingos, P. 1999. The role of Occam's razor in knowledge discovery. Data Mining Knowledge Discovery 3(4) 409-425.
7. Durant, J. L., B. A. Leland, D. R. Henry, J. G. Nourse. 2002. Reoptimization of MDL keys for use in drug discovery. J. Chemical Inform. Comput. Sci. 42(6) 1273-1280. (Pubitemid 35468313)
8. Fang, H., W. Tong, L. M. Shi, R. Blair, R. Perkins, W. Branham, B. S. Hass et al. 2001. Structure-activity relationships for a large diverse set of natural, synthetic, and environmental estrogens. Chemical Res. Toxicol. 14(3) 280-294. (Pubitemid 32238488)
9. Ferguson, L. R., W. A. Denny. 2007. Genotoxicity of non-covalent interactions: DNA intercalators. Mutation Res. 623(1-2) 14-23. (Pubitemid 47368577)
10. Finkelstein, M. B., S. Vamvakas, D. Bittner, M. W. Anders. 1994. Structure-mutagenicity and structure-cytotoxicity studies on bromine-containing cysteine S-conjugates and related compounds. Chemical Res. Toxicol. 7(2) 157-163. (Pubitemid 24105346)
11. Glover, F., M. Laguna, R. Marti. 2003. Scatter search and path relinking: Advances and applications. F. Glover, G. Kochenberger, eds. Handbook of Metaheuristics, Vol. 57. Springer, New York, 1-35.
12. Han, J., M. Kamber. 2000. Data Mining: Concepts and Techniques. Morgan Kaufmann, San Francisco.
13. Hert, J., P. Willett, D. J. Wilton, P. Acklin, K. Azzaoul, E. Jacoby, A. Schuffenhauer. 2004. Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures. Organic Biomolecular Chemistry 2(22) 3256-3266.
14. King, R. D., A. Srinivasan, L. Dehaspe. 2001. Warmr: A data mining tool for chemical data. J. Comput.-Aided Molecular Design 15(2) 173-181. (Pubitemid 32124509)
15. Knobbe, A. J., M. de Haas, A. Siebes. 2001. Propositionalisation and aggregates. L. De Raedt, A. Siebes, eds. Principles of Data Mining and Knowledge Discovery (PKDD 2001). Lecture Notes in Computer Science, Vol. 2168. Springer, Berlin, 277-288. (Pubitemid 33331868)
16. Knobbe, A. J., H. Blockeel, A. Siebes, D. M. G. van der Walle. 1999. Multi-relational data mining. Technical Report INSR9908, Centrum voor Wiskunde en Informatica, Amsterdam.
17. Matter, H., T. Pötter. 1999. Comparing 3D pharmacophore triplets and 2D fingerprints for selecting diverse compound subsets. J. Chemical Inform. Comput. Sci. 39(6) 1211-1225. (Pubitemid 129579856)
18. Rogers, D., R. D. Brown, M. Hahn. 2005. Using extendedconnectivity fingerprints with Laplacian-modified Bayesian analysis in high-throughput screening follow-up. J. Biomolecular Screening 10(7) 682-686. (Pubitemid 41476802)
19. Rokach, L., O. Maimon. 2005. Top-down induction of decision trees classifiers-A survey. IEEE Trans. Systems, Man, Cybernetics, Part C: Appl. Rev. 35(4) 476-487. (Pubitemid 41638167)
20. Serrurier, M., H. Prade. 2008. Improving inductive logic programming by using simulated annealing. Inform. Sci. 178(6) 1423-1441.
21. Svetnik, V., A. Liaw, C. Tong, J. C. Culberson, R. P. Sheridan, B. P. Feuston. 2003. Random forest: A classification and regression tool for compound classification and QSAR modeling. J. Chemical Inform. Comput. Sci. 43(6) 1947-1958.
22. Todeschini, R., V. Consonni. 2000. Handbook of Molecular Descriptors. Wiley-VCH, Weinheim, Germany.
23. Votano, J. R., M. Parham, L. H. Hall, L. B. Kier, S. Oloff, A. Tropsha, Q. Xie, W. Tong. 2004. Three new consensus QSAR models for the prediction of Ames genotoxicity. Mutagenesis 19(5) 365-377. (Pubitemid 39405973)
24. Weaver, D. C. 2004. Applying data mining techniques to library design, lead generation and lead optimization. Current Opinion Chemical Biol. 8(3) 264-270. (Pubitemid 38759401)
25. Witten, I. H., E. Frank. 2005. Data Mining: Practical Machine Learning Tools and Techniques with Java Implementations. Morgan Kaufmann, San Francisco.