Correcting gradient-based interpretations of deep neural networks for genomics

Abstract

Post hoc attribution methods can provide insights into the learned patterns from deep neural networks (DNNs) trained on high-throughput functional genomics data. However, in practice, their resultant attribution maps can be challenging to interpret due to spurious importance scores for seemingly arbitrary nucleotides. Here, we identify a previously overlooked attribution noise source that arises from how DNNs handle one-hot encoded DNA. We demonstrate this noise is pervasive across various genomic DNNs and introduce a statistical correction that effectively reduces it, leading to more reliable attribution maps. Our approach represents a promising step towards gaining meaningful insights from DNNs in regulatory genomics.