Similarity searching effectiveness

Gardiner EJ, Gillet VJ, Haranczyk M, Hert J, Holliday JD, Malim N, Patel Y, Willett P (2009) Turbo similarity searching effect of FP and dataset on virtual-screening performance. Stat Anal Data Mining 2 103-114... 

Hert J, WiUett P, Wilton DJ, Addin P, Azzaoui K, Jacoby E, Schuffenhauer A. (2005) New Methods for Ligand-Based Virtual Screening Use of Data-Fusion and Machine-Learning Techniques to Enhance the Effectiveness of Similarity Searching. /. Chem. Inf. Model, (in the press). 

This chapter reviews the techniques available for quantifying the effectiveness of methods for molecular similarity and molecular diversity, focusing in particular on similarity searching and on compound selection procedures. The evaluation criteria considered are based on biological activity data, both qualitative and quantitative, with rather different criteria needing to be used depending on the type of data available. 

The relationship between IR and chemical similarity searching is discussed in detail by Edgar et al. (11) who summarize the various effectiveness measures in terms of the 2 x 2 contingency table shown in Table 1. In this table, it is assumed that a search has been carried out resulting in the retrieval of the n nearest neighbors at the top of the ranked output. Assume that these n nearest neighbors include a of the A active molecules in the complete database, which contains a total of N molecules. Then the recall, R, is defined to be the fraction of the active molecules that are retrieved, i.e.,... 

It is inconvenient to have to specify two measures, i.e., recall and precision, to quantify the effectiveness of a search. The Merck group have made extensive use of the enrichment factor, i.e., the number of actives retrieved relative to the number that would have been retrieved if compounds had been picked from the database at random (12). Thus, using the notation of Table 1, the enrichment factor at some point, n, in the ranking resulting from a similarity search is given by... 

Edgar, S. J., Holliday, J. D., and Willett, P. (2000) Effectiveness of retrieval in similarity searches of chemical databases a review of performance measures. 

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