Relation mining experiments in the pharmacogenomics domain
Journal of Biomedical Informatics
| Hi-index | 3.84 |
Motivation: Since database retrieval is a fundamental operation, the measurement of retrieval efficacy is critical to progress in bioinformatics. This article points out some issues with current methods of measuring retrieval efficacy and suggests some improvements. In particular, many studies have used the pooled receiver operating characteristic for n irrelevant records (ROCn) score, the area under the ROC curve (AUC) of a ‘pooled’ ROC curve, truncated at n irrelevant records. Unfortunately, the pooled ROCn score does not faithfully reflect actual usage of retrieval algorithms. Additionally, a pooled ROCn score can be very sensitive to retrieval results from as little as a single query. Methods: To replace the pooled ROCn score, we propose the Threshold Average Precision (TAP-k), a measure closely related to the well-known average precision in information retrieval, but reflecting the usage of E-values in bioinformatics. Furthermore, in addition to conditions previously given in the literature, we introduce three new criteria that an ideal measure of retrieval efficacy should satisfy. Results: PSI-BLAST, GLOBAL, HMMER and RPS-BLAST provided examples of using the TAP-k and pooled ROCn scores to evaluate sequence retrieval algorithms. In particular, compelling examples using real data highlight the drawbacks of the pooled ROCn score, showing that it can produce evaluations skewing far from intuitive expectations. In contrast, the TAP-k satisfies most of the criteria desired in an ideal measure of retrieval efficacy. Availability and Implementation: The TAP-k web server and downloadable Perl script are freely available at http://www.ncbi.nlm.nih.gov/CBBresearch/Spouge/html.ncbi/tap/ Contact: spouge@ncbi.nlm.nih.gov Supplementary Information:Supplementary data are available at Bioinformatics online.