Knowledge distillation for fast and accurate DNA sequence correction

Anastasiya Belyaeva, Joel Shor, Daniel E Cook, Kishwar Shafin, Daniel Liu, Armin Töpfer, Aaron M Wenger, William J Rowell, Howard Yang, Alexey Kolesnikov, Cory Y McLean, Maria Nattestad, Andrew Carroll, Pi-Chuan Chang

Keywords: DNA sequencing, transformers, variant calling, genome assembly

Abstract: Accurate genome sequencing can improve our understanding of biology and the genetic basis of disease. The standard approach for generating DNA sequences from PacBio instruments relies on HMM-based models. Here, we introduce Distilled DeepConsensus - a distilled transformer–encoder model for sequence correction, which improves upon the HMM-based methods with runtime constraints in mind. Distilled DeepConsensus is 1.3x faster and 1.5x smaller than its larger counterpart while improving the yield of high quality reads (Q30) over the HMM-based method by 1.69x (vs. 1.73x for larger model). With improved accuracy of genomic sequences, Distilled DeepConsensus improves downstream applications of genomic sequence analysis such as reducing variant calling errors by 39% (34% for larger model) and improving genome assembly quality by 3.8% (4.2% for larger model). We show that the representations learned by Distilled DeepConsensus are similar between faster and slower models.