评估基于Transformer的基因组语言模型DNABERT-2的事后解释 / Evaluating Post-hoc Explanations of the Transformer-based Genome Language Model DNABERT-2
1️⃣ 一句话总结
本文研究了如何为先进的基因组语言模型DNABERT-2生成可解释性分析,通过改进一种名为AttnLRP的方法,成功将模型对DNA序列的预测转化为人类可理解的生物学模式,并证明其解释质量与传统卷积神经网络模型相当。
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.
评估基于Transformer的基因组语言模型DNABERT-2的事后解释 / Evaluating Post-hoc Explanations of the Transformer-based Genome Language Model DNABERT-2
本文研究了如何为先进的基因组语言模型DNABERT-2生成可解释性分析,通过改进一种名为AttnLRP的方法,成功将模型对DNA序列的预测转化为人类可理解的生物学模式,并证明其解释质量与传统卷积神经网络模型相当。
源自 arXiv: 2604.21690