Uncovering Internal Prediction Mechanisms of Transformer-Based Chemical Foundation Models
Year: 2025
Type: preprint
Abstract: Supervised deep learning has become a standard approach to deliver competitive predictive tools that allow relating the structure of molecules and their physicochemical features to properties such as binding to protein targets, performance as electronic materials, and reactivity. However, efforts to understand how these models learn and how specific predictions can be explained are still limited in chemistry, which hinders trust in these predictions. To overcome both the current widespread approach of considering supervised deep learning models as black boxes and the limitations of explainable deep learning based on feature attribution, we introduce two general methods from the field of mechanistic interpretability to molecular property prediction. Specifically, we leverage ablation and adapt existing techniques into the regression lens to inspect model predictions of the Transformer-based ChemBERTa foundation model. Our results for 3 ChemBERTa-based models finetuned on distinct datasets allow us to propose the internal mechanisms operable within each of the corresponding model layers that lead to the final predictions. Our results are a stepping stone towards more trustworthy deep learning models in the molecular domain.
Source: ChemRxiv
Authors: Alexander Müller, Juan Cardenas-Cartagena, Robert Pollice
Institution: University of Groningen
Language: English
Subfield: Computational Theory and Mathematics
Field: Computer Science
Domain: Physical Sciences
Open Access status: green
OpenAlex ID: W4416228101
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