Accelerated CNN-based Scans for Traces of Positive Selection

Positive natural selection is the driving force that enables species to survive and reproduce in their environment. Localizing traces of positive selection has practical applications in studying virus evolution and designing more effective drug treatments. State-of-the-art methods for the detection of positive selection combine Convolutional Neural Networks (CNN) with sliding-window algorithms to scan genomic sequences with high precision, but require prohibitively long execution times to process whole genomes with fine-grained resolution. To this end, we present an FPGA-accelerated system for efficiently scanning whole genomes with high granularity, implementing a quantized version of FAST-NN (reversed abbreviation of Neural Network for Tracing Sweeps with Allele Frequencies), a CNN that has been designed through a hardware-aware neural architecture search. FAST-NN employs a highly compact representation of genomic data as features, which eliminates potential I/O bottlenecks in hardware. Our accelerator architecture consists of a dedicated stage for each CNN layer in a pipelined datapath that integrates a specialized buffer design; this enables data reuse between overlapping sliding windows by leveraging the dilated convolutions in FAST-NN. A design point implemented onto an Alveo U250 accelerator card achieves comparable accuracy to FAST-NN, with a maximum reduction of only 2.2% due to quantization, while producing a classification outcome in each clock cycle at a frequency of 100 MHz. Scanning the entire human genome (excluding the sex chromosomes), we observed between 19.51× and 28.61× faster processing than a PyTorch implementation on a 16-core x86 CPU, and between 1.22× and 2.89× faster processing than a high-end GPU. The architecture can be adapted to other domains, beyond population genetics, where CNNs are deployed in sliding-window algorithms for large-scale data processing.