Distance phenomena in high-dimensional chemical descriptor spaces: Consequences for similarity-based approaches

Journal of Computational Chemistry

Volumn 30, Issue 14, 2009, Pages 2285-2296

  Rupp, Matthias ^a   Schneider, Petra ^b   Schneider, Gisbert ^a  

^a GOETHE UNIVERSITY   (Germany)

^b Schneider Consulting GbR   (Germany)

Author keywords

Chemical descriptors; Distance concentration; Distances; High dimensional data

Indexed keywords

CHEMICAL DESCRIPTORS; CHEMINFORMATICS; DESCRIPTORS; DISTANCE CONCENTRATION; DISTANCES; EMPTY SPACE; HIGH-DIMENSIONAL; HIGH-DIMENSIONAL DATA; INNER PRODUCT; MATHEMATICAL CONCEPTS; PROPERTY PREDICTIONS; SIMILARITY COEFFICIENTS; SIMILARITY MEASURE; THREE DIMENSIONS; VECTOR REPRESENTATIONS; VECTOR SPACES;

DRUG;

ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; FACTUAL DATABASE;

COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; MOLECULAR STRUCTURE; PHARMACEUTICAL PREPARATIONS;

EID: 70349464514     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21218     Document Type: Article

References (39)

1. Johnson, M.; Maggiora, G., Eds. Concepts and Applications of Molecular Similarity; Wiley: New York, 1990.
2. Willett, P. J Chem Inform Comput Sci 1998, 38, 983.
3. Böhm, H.-J.; Schneider, G. Virtual Screening for Bioactive Molecules: Wiley-VCH, New York, USA, 2000.
4. Willett, P. Curr Opin Biotechnol 2000, 11, 85.
5. Clark, R. In Combinatorial Library Design and Evaluation; Ghose, A.; Viswanadhan, New York, USA, V., Eds.; CRC Press: 2001 pp. 337-362.
6. Gillet, V.; Willett, P. In Combinatorial Library Design and Evaluation; Ghose, A.; Viswanadhan, V., Eds.; CRC Press: 2001 pp. 379-398.
7. Todeschini, R.; Consonni, V. Handbook of Molecular Descriptors, 1st ed.; Wiley-VCH: Weinheim, Germany, 2000.
8. Meyer, C. Matrix Analysis and Applied Linear Algebra; Society for Industrial and Applied Mathematics, Philadelphia, USA, 2001.
9. Topliss, J.; Edwards, R. J Med Chem 1979, 22, 1238.
10. Mager, P. Med Res Rev 1982, 2, 93.
11. Hubálek, Z. Biol Rev Cambridge Philos Soc 1982, 57, 669.
12. Flower, D. J Chem Inform Comput Sci .1998, 38, 379.
13. Willett, P. Drug Discov Today 2006, 11, 1046.
14. Willett, P.; Barnard, J.; Downs, G. J Chem. Inform Comput Sci 1998, 38, 983.
15. François, D. High-Dimensional Data Analysis: Optimal Metrics and Feature Selection. PhD Thesis, Université Catholique de Louvain, Louvain-la-Neuve, Belgium, 2007.
16. François, D.; Weitz, V.; Verleysen, M. IEEE Trans Knowl Data Eng 2007, 19, 873.
17. Fechner, U.; Schneider, G. ChemBioChem 2004, 5, 538.
18. Schneider, P.; Schneider, G. QSAR Comb Sci 2003, 22, 713.
19. Schneider, G.; Neidhart, W.; Giller, T.; Schmid, G. Angew Chem Int Ed 1999, 38, 2894.
20. Fechner, U.; Franke, L.; Renner, S.; Schneider, P.; Schneider, G. J Comput Aided Mol Des 2003, 17, 687.
21. Scott, D.; Thompson, J. In Computer Science and Statistics: Proceedings of the 15th Symposium on the Interface (Interface 1983); Gentle, J., Ed.; North-Holland Publishing Company: Houston, TX, March 17-18, pp. 173-179.
22. Weisgerber, D. J Am Soc Inform Sci 1997, 48, 349.
23. Xue, L.; Godden, J.; Bajorath, J. J Chem. Inform. Comput Sci 1999, 39, 881.
24. Xue, L.; Godden, J.; Bajorath, J. J Chem Inform. Comput Sci 2000, 40, 1227.
25. Cruciani, G.; Crivori, P.; Carrupt, P.-A.; Testa, B. J Mol Struct 2000, 503, 17.
26. Viswanadhan, V.; Ghose, A.; Revankar, G.; Robins, R. J Chem Inform Comput Sci 1989, 29, 163.
27. Guyon, I.; Elisseeff, A. J Mach Learn Res 2003, 3, 1157.
28. Fodor, I. A survey of dimension reduction, techniques. Tech. Rep. UCRL-ID-148494, Lawrence Livermore National Laboratory, Livermore, California, USA, 2002.
29. Hamming, R. Coding and Information Theory; Prentice-Hall, 1980.
30. Abramowitz, M.; Stegun, I. Handbook of Mathematical Functions; Dover, New York, USA, 1972.
31. Beyer, K.; Goldstein, J.; Ramakrishnan, R.; Shaft, U. In Proceedings of the 7th International Conference on Database Theory (ICDT 1999), Jerusalem, Israel, January 10-12, Lecture Notes in Computer Science, New York, USA, vol.1540, pp. 217-235.
32. Hinneburg, A. ; Aggarwal, C. ; Keim, D. In Proceedings of the 26th International Conference on Very Large Databases (VLDB 2000); Abbadi, A. E.; Brodie, M.; Chakravarthy, S.; Dayal, U.; Kamel, N.; Schlageter, G.; Whang, K.-Y., Eds.; Morgan Kaufmann: Cairo, Egypt; September 10-14, pp. 506-515.
33. Aggarwal, C.; Hinneburg, A.; Keim, D. In Proceedings of the 8th International Conference on Database Theory (ICDT 2001); den Bussche, J. V.; Vianu, V., Eds.; Springer: London, United Kingdom, January 4-6, Lecture Notes in Computer Science, Vol.1973. pp. 420-434.
34. Press, W.; Teukolsky, S.; Vetterling, W.; Flannery, B. Numerical Recipes in C., 3rd ed.; Cambridge University Press, New York, USA, 2007.
35. Schneider, G.; Schneider, P.; Renner, S. QSAR Comb Sci 2006, 25, 1162.
36. Xing, E.; Ng, A.; Jordan, M.; Russell, S. In Advances in Neural Information Processing Systems 15 (NIPS 2002); Becker, S.; Thrun, S.; Obermayer, K., Eds.; MIT Press: Cambridge, MA; December 10-12, pp. 505-512.
37. Weinberger, K.; Saul, L. In Proceedings of the 25th International Conference on Machine Learning (ICML 2008); McCallum, A.; Roweis, S., Eds.; Omnipress: Helsinki, Finland; July 5-9, pp. 1160-1167.
38. Weinberger, K.; Blitzer, J.; Saul, L. In Advances in Neural Information Processing Systems 18 (NIPS 2005); Weiss, Y.; Schölkopf, B.; Platt, J., Eds.; MIT Press: Cambridge MA; December 5-8, pp. 1473-1480.
39. Tversky, A. Psychol Rev 1977, 84, 327.