Interpreting Attention Mechanisms in Genomic Transformer Models: A Framework for Biological Insights

Abstract

Transformer models have shown strong performance on biological sequence prediction tasks, but the interpretability of their internal mechanisms remains underexplored. Given their application in biomedical research, understanding the mechanisms behind these models predictions is crucial for their widespread adoption. We introduce a method to interpret attention heads in genomic transformers by correlating per-token attention scores with curated biological annotations, and we use GPT-4 to summarize each heads focus. Applying this to DNABERT, Nucleotide Transformer, and scGPT, we find that attention heads learn biologically meaningful associations during self-supervised pre-training and that these associations shift with fine-tuning. We show that interpretability varies with tokenization scheme, and that context-dependence plays a key role in head behaviour. Through ablation, we demonstrate that heads strongly associated with biological features are more important for task performance than uninformative heads in the same layers. In DNABERT trained for TATA promoter prediction, we observe heads with positive and negative associations reflecting positive and negative learning dynamics. Our results offer a framework to trace how biological features are learned from random initialization to pre-training to fine-tuning, enabling insight into how genomic foundation models represent nucleotides, genes, and cells.