Abstract
Previous methods for accelerating Tanimoto queries have been based on using bit strings for representing molecules. No work has gone into examining accelerating Tanimoto queries on real valued descriptors, even though these offer a much more fine grained measure of similarity between molecules. This study utilises a recently discovered reduction from Tanimoto queries to distance queries in Euclidean space to accelerate Tanimoto queries using standard metric data structures. The presented experiments show that it is possible to gain a significant speedup and that general metric data structures are better suited than a data structure tailored for Euclidean space on vectors generated from molecular data.
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References
Baldi, P., Hirschberg, D.S., Nasr, R.J.: Speeding up chemical database searches using a proximity filter based on the logical exclusive OR. Journal of Chemical Information and Modeling 48(7), 1367–1378 (2008)
Bentley, J.L.: Multidimensional binary search trees used for associative searching. Commun. ACM 18(9), 509–517 (1975)
Brin, S.: Near neighbor search in large metric spaces. The VLDB Journal, 574–584 (1995)
Ciaccia, P., Patella, M., Zezula, P.: M-tree: An efficient access method for similarity search in metric spaces. In: Jarke, M., Carey, M.J., Dittrich, K.R., Lochovsky, F.H., Loucopoulos, P., Jeusfeld, M.A. (eds.) VLDB 1997, Proceedings of 23rd International Conference on Very Large Data Bases, Athens, Greece, August 25-29, pp. 426–435. Morgan Kaufmann, San Francisco (1997)
Gillet, V.J., Willett, P., Bradshaw, J.: Similarity searching using reduced graphs. Journal of Chemical Information and Computer Sciences 43(2), 338–345 (2003)
Huafeng, X., Agrafiotis, D.K.: Nearest neighbor search in general metric spaces using a tree data structure with a simple heuristic. Journal of Chemical Information and Modeling 43(6), 1933–1941 (2003)
Irwin, J.J., Shoichet, B.K.: ZINC: A free database of commercially available compounds for virtual screening. Journal of Chemical Information and Modeling 45(1), 177–182 (2005)
Kristensen, T.G., Nielsen, J., Pedersen, C.N.S.: A tree-based method for the rapid screening of chemical fingerprints. Algorithms for Molecular Biology 5(1), 9 (2010)
Kristensen, T.G.: Transforming Tanimoto queries on real valued vectors to range queries in Euclidian space. Journal of Mathematical Chemistry (March 2010)
Leach, A.R., Gillet, V.J.: An Introduction to Chemoinformatics, rev. ed edn. Kluwer Academic Publishers, Dordrecht (2007)
Lipkus, A.H.: A proof of the triangle inequality for the Tanimoto distance. Journal of Mathematical Chemistry 26(1-3), 263–265 (1999)
Molegro: Molegro Virtual Docker User Manual version 3.0.0 (2008)
Späth, H.: Cluster Analysis Algorithms for Data Reduction and Classification of Objects. Ellis Horwood (1980)
Steinbeck, C., Han, Y., Kuhn, S., Horlacher, O., Luttmann, E., Willighagen, E.: The Chemistry Development Kit (CDK): an open-source Java library for chemo- and bioinformatics. Journal of Chemical Information and Computer Sciences 43(2), 493–500 (2003)
Swamidass, S.J., Baldi, P.: Bounds and algorithms for fast exact searches of chemical fingerprints in linear and sublinear time. Journal of Chemical Information and Modeling 47(2), 302–317 (2007)
Weber, R., Schek, H.J., Blott, S.: A quantitative analysis and performance study for similarity-search methods in high-dimensional spaces. In: VLDB 1998: Proceedings of the 24rd International Conference on Very Large Data Bases, pp. 194–205. Morgan Kaufmann Publishers Inc., San Francisco (1998)
Willett, P.: Similarity-based approaches to virtual screening. Biochemical Society Transactions 31(Pt 3), 603–606 (2003)
Willett, P., Barnard, J.M., Downs, G.M.: Chemical similarity searching. Journal of Chemical Information and Computer Sciences 38(6), 983–996 (1998)
Yianilos, P.N.: Data structures and algorithms for nearest neighbor search in general metric spaces. In: Proceedings of the Fourth ACM-SIAM Symposium on Discrete Algorithms (1993)
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Kristensen, T.G., Pedersen, C.N.S. (2010). Data Structures for Accelerating Tanimoto Queries on Real Valued Vectors. In: Moulton, V., Singh, M. (eds) Algorithms in Bioinformatics. WABI 2010. Lecture Notes in Computer Science(), vol 6293. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-15294-8_3
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DOI: https://doi.org/10.1007/978-3-642-15294-8_3
Publisher Name: Springer, Berlin, Heidelberg
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