2021/09/13 by Hongwu Peng, Shiyang Chen, Peng, Hongwu +21
Biochemistry, Genetics and Molecular Biology · Chemistry · Computer Science · #Analytical Chemistry and Chromatography #B.0 #Computational Drug Discovery Methods #FOS: Computer and information sciences #Hardware Architecture (cs.AR) #I.0 #Machine Learning in Bioinformatics
paper · pdf · doi:10.48550/arxiv.2109.06355
openalex publication_date 2021/09/13 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Molecular similarity search has been widely used in drug discovery to identify structurally similar compounds from large molecular databases rapidly. With the increasing size of chemical libraries, there is growing interest in the efficient acceleration of large-scale similarity search. Existing works mainly focus on CPU and GPU to accelerate the computation of the Tanimoto coefficient in measuring the pairwise similarity between different molecular fingerprints. In this paper, we propose and optimize an FPGA-based accelerator design on exhaustive and approximate search algorithms. On exhaustive search using BitBound & folding, we analyze the similarity cutoff and folding level relationship with search speedup and accuracy, and propose a scalable on-the-fly query engine on FPGAs to reduce the resource utilization and pipeline interval. We achieve a 450 million compounds-per-second processing throughput for a single query engine. On approximate search using hierarchical navigable small world (HNSW), a popular algorithm with high recall and query speed. We propose an FPGA-based graph traversal engine to utilize a high throughput register array based priority queue and fine-grained distance calculation engine to increase the processing capability. Experimental results show that the proposed FPGA-based HNSW implementation has a 103385 query per second (QPS) on the Chembl database with 0.92 recall and achieves a 35x speedup than the existing CPU implementation on average. To the best of our knowledge, our FPGA-based implementation is the first attempt to accelerate molecular similarity search algorithms on FPGA and has the highest performance among existing approaches.