Improving the Hit Rates of Virtual Screening by Active Learning from Bioactivity Feedback

Virtual screening has been widely used to identify potential hit candidates that can bind to the target protein in drug discovery. Contemporary screening methods typically rely on oversimplified scoring functions, frequently yielding one-digit hit rates (or even zero) among top-ranked candidates. The substantial cost of laboratory validation further constrains the exploration of candidate molecules. We find that test-time prediction refinement is almost blank in this area, which means bioactivity feedback in the wet-lab experiments is neglected. Here, we introduce an Active Learning from Bioactivity Feedback (ALBF) framework to enhance the weak hit rate of current virtual screening methods. ALBF spends the budget of wet-lab experiments iteratively and leverages the target-specific bioactivity insights from current wet-lab tests to refine the score results (i.e., rankings). Our framework consists of two components: a novel query strategy that considers the evaluation quality and its overall influence on other top-scored molecules; and an efficient score optimization strategy that propagates the bioactivity feedback to structurally similar molecules. We evaluated ALBF on diverse subsets of the well-known DUD-E and LIT-PCBA benchmarks. Our active learning protocol averagely enhances top-100 hit rates by 60% and 30% on DUD-E and LIT-PCBA with 50 to 200 bioactivity queries on the selected molecules that are deployed in ten rounds. The consistently superior performance demonstrates ALBF's potential to enhance both the accuracy and cost-effectiveness of active learning-based laboratory testing.