Support vector inductive logic programming outperforms the Naive Bayes Classifier and inductive logic programming for the classification of bioactive chemical compounds

Journal of Computer-Aided Molecular Design

Volumn 21, Issue 5, 2007, Pages 269-280

  Cannon, Edward O ^a   Amini, Ata ^a,b   Bender, Andreas ^a,c   Sternberg, Michael J E ^a,b   Muggleton, Stephen H ^a,b   Glen, Robert C ^a   Mitchell, John B O ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

^c NOVARTIS INSTITUTES FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

Classification; Feature selection; Machine learning; Molecular similarity; Screening

Indexed keywords

BENCHMARKING; CLASSIFIERS; COMPUTER CIRCUITS; FEATURE SELECTION; INDUCTIVE LOGIC PROGRAMMING (ILP); LEARNING SYSTEMS;

BAYES CLASSIFIER; F MEASURE; FEATURES SELECTION; INDUCTIVE LOGIC; LOGIC-PROGRAMMING; MACHINE-LEARNING; MOLECULAR SIMILARITY; NAIVE BAYES CLASSIFIERS; PERFORMANCE; SUPPORT VECTOR;

CLASSIFICATION (OF INFORMATION);

ANGIOTENSIN RECEPTOR ANTAGONIST; DOPAMINE 2 RECEPTOR BLOCKING AGENT; PROSTAGLANDIN SYNTHASE INHIBITOR; PROTEIN KINASE C INHIBITOR; PROTEINASE INHIBITOR; RENIN INHIBITOR; SEROTONIN 1A AGONIST; SEROTONIN 3 ANTAGONIST; SEROTONIN UPTAKE INHIBITOR; SUBSTANCE P ANTAGONIST; THROMBIN INHIBITOR;

ACCURACY; AREA UNDER THE CURVE; ARTICLE; BAYES THEOREM; COMPUTER PROGRAM; CONTROLLED STUDY; CORRELATION COEFFICIENT; DRUG CLASSIFICATION; INTERMETHOD COMPARISON; MATHEMATICAL ANALYSIS; MCNEMAR TEST; PREDICTION; PRIORITY JOURNAL; QUALITY CONTROL; RECALL; RECEIVER OPERATING CHARACTERISTIC; SENSITIVITY AND SPECIFICITY; STATISTICAL ANALYSIS; STATISTICAL SIGNIFICANCE; STRUCTURE ANALYSIS; SUPPORT VECTOR MACHINE;

EID: 34247386376     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-007-9113-3     Document Type: Article

References (41)

1. Johnson AM, Maggiora GM (1990) Concepts and applications of molecular similarity, eds. Wiley, New York
2. Bender A, Jenkins JL, Li Q, Adams SE, Cannon EO, Glen RC (2006) Molecular similarity: Advances in methods, applications and validations in virtual screening and QSAR. In: Annual reports in computational chemistry, vol 2, pp 141-168
3. Patterson DE, Cramer RD, Ferguson AM, Clark RD, Weinberger LE (1996) J Med Chem 39:3049
4. Bohm HJ, Schneider G (2000) Virtual screening for bioactive molecules ed. Wiley-VCH
5. Downs GM, Willett P, Fisanick W (1994) J Chem Inf Comput Sci 34:1094
6. Estrada E, Uriarte E (2001) Curr Med Chem 8:1573
7. Mason JS, Good AC, Martin EJ (2001) Curr Pharm Des 7:567
8. Leach AR, Gillet VJ (2003) An introduction to chemoinformatics. Kluwer, Dordrecht
9. Gasteiger J (2003) Handbook of chemoinformatics, eds. Wiley-VCH, Weinheim
10. Scitegic Inc. Retrieved from http://www.scitegic.com/
11. Hert J, Willett P, Wilton DJ, Acklin P, Azzaoui K, Jacoby E, Schuffenhauer A (2004) Org Biomol Chem 2:3256
12. Elsevier MDL, 2440 Camino Ramon, Suite 300, San Ramon, CA 94583, USA. http://www.mdl.com/
13. Glen RC, Bender A, Arnby CH, Carlsson L, Boyer S, Smith J (2006) IDrugs 9:199
14. Bender A, Mussa HY, Glen RC, Reiling S (2004) J Chem Inf Comput Sci 44:170
15. Mitchell TM (1997) Machine learning, ed. McGraw-Hill, New York
16. Liu YA (2004) J Chem Inf Comput Sci 44:1823
17. Muggleton SH, Lodhi H, Amini A, Sternberg MJE (2006) In: Holmes D, Jain LC (eds) Innovations in machine learning. Springer-Verlag, pp 113-135
18. Muggleton SH, Lodhi H, Amini A, Sternberg MJE (2005) Proceedings of the 8th international conference on discovery science. Springer-Verlag, 3735:163 163,
19. Briem H, Lessel UF (2000) Persepect Drug Discovery Design 20:231
20. Bender A, Mussa HY, Glen RC, Reiling S (2004) J Chem Inf Comput Sci 44:1708
21. Hert J, Willett P, Wilton DJ, Acklin P, Azzaoui K, Jacoby E, Schuffenhauer A (2004) J Chem Inf Comput Sci 44:1177
22. Cannon EO, Bender A, Palmer DS, Mitchell JBO (2006) J Chem Inf Model 46:2369
23. World Anti-Doping Agency (WADA), Stock Exchange Tower, 800 Place Victoria, (Suite 1700), P.O. Box 120, Montreal, Quebec, H4Z 1B7, Canada. Retrieved from http://www.wada.ama.org
24. Rodgers S, Glen RC, Bender A (2006) J Chem Inf Model 46:569
25. King RD, Muggleton SH, Lewis R, Sternberg MJE (1992) Proc Natl Acad Sci 89:11322
26. King RD, Muggleton SH, Srinivasan A, Sternberg MJE (1996) Proc Natl Acad Sci 93:438
27. Buttingsrud B, Ryeng E, King RD, Alsberg BK (2006) J Comput Aid Mol Des 20:361
28. Pompe U, Kononenko I (1995) Proceedings of the 5th international workshop on inductive logic programming, pp 417-436
29. Dutra I, Page D, Santos Costa V, Shavlik J (2003) In: Matwin S, Sammut C (eds) Proceedings of the 12th international conference on inductive logic programming, vol 2583. Lecture Notes in Computer Science, Springer-Verlag, pp 48-65
30. Hoche S, Wrobel S (2001) In: Rouveirol C, Sebag M (eds) Proceedings of the 11th interational conference on inductive logic programming, vol 2157. Lecture Notes In Computer Science, Springer-Verlag, pp 51-64
31. Bender A, Glen RC (2004) Org Biomol Chem 2:3204
32. Barrett SJ, Langdon WB (2006) In: Tiwari A, Knowles J (eds) Applications of soft computing: Recent trends, vol 19. Springer-Verlag, pp 99-110
33. Guha R, Howard MT, Hutchison GR, Murray-Rust P, Rzepa H, Steinbeck C, Wegner J, Willighagen EL (2006) J Chem Inf Model 46(3):991. The Open Babel Package (2006), version 2.0.1. Retrieved from http:// openbabel.sourceforge.net/
34. Quinlan JR (1986) Mach Learn 1:81
35. A-Razzak M, Glen RC (1992) J Comput Aided Mol Des 6:349
36. Muggleton SH (1995) New Generation Comput 13:245
37. Muggleton SH, Bryant CH (2000) In: Cussens J, Frisch AM (eds) Proceedings of the 10th international conference on inductive logic programming. Springer-Verlag, pp 130-146
38. Joachims T (1999) Making large-Scale SVM learing practical. In: Schölkopf B, Burges C, Smola A (eds) Advances in Kernel Methods-Support Vector Learing, MIT-press, http://svmlight.joachims.org
39. Siegel S, Castellan NJ Jr (1988) Nonparametric statistics for the behavioral sciences. Boston, MA, McGraw-Hill
40. McNemar Q (1947) Psychometrica 12:153
41. Bender A, Glen RC (2005) J Chem Inf Model 45:1369