Evaluating Post-hoc Explanations of the Transformer-based Genome Language Model DNABERT-2

TL;DR

This paper evaluates the explainability of Transformer-based genome language models, specifically DNABERT-2, using adapted relevance propagation methods to produce biologically meaningful explanations.

Contribution

It introduces an adaptation of layer-wise relevance propagation for Transformer models in genomics and compares explanations between DNABERT-2 and CNN baselines.

Findings

AttnLRP provides reliable explanations aligned with biological patterns

gLMs like DNABERT-2 can be used to derive biological insights

The method enables comparison of relevance attributions across architectures

Abstract

Explaining deep neural network predictions on genome sequences enables biological insight and hypothesis generation-often of greater interest than predictive performance alone. While explanations of convolutional neural networks (CNNs) have been shown to capture relevant patterns in genome sequences, it is unclear whether this transfers to more expressive Transformer-based genome language models (gLMs). To answer this question, we adapt AttnLRP, an extension of layer-wise relevance propagation to the attention mechanism, and apply it to the state-of-the-art gLM DNABERT-2. Thereby, we propose strategies to transfer explanations from token and nucleotide level. We evaluate the adaption of AttnLRP on genomic datasets using multiple metrics. Further, we provide an extensive comparison between the explanations of DNABERT-2 and a baseline CNN. Our results demonstrate that AttnLRP yields reliable explanations corresponding to known biological patterns. Hence, like CNNs, gLMs can also help derive biological insights. This work contributes to the explainability of gLMs and addresses the comparability of relevance attributions across different architectures.