What Molecular Structure Cannot Tell Us: A Taxonomy of Explainability Gaps in GNN-Based Drug Toxicity Prediction
arXiv:2605.26183v1 Announce Type: cross Abstract: Graph Neural Networks (GNNs) have emerged as a structurally natural approach for molecular toxicity prediction, operating directly on atomic connectivity without the information loss inherent to fixed-length fingerprints. However, the fraction of a drug's known pharmacological profile that is actually encodable in its molecular structure remains systematically underexplored. This study addresses this question through a systematic case study using acetylsalicylic acid (ASA, Aspirin) - one of the most comprehensively characterized drugs in pharmacology - as a model compound. A Message Passing Neural Network (MPNN) is trained on the Tox21 benchmark and GNNExplainer is applied to characterize atom-level attribution. Results indicate that molecular structure explains approximately 45% (5/11) of known ASA adverse effects. A four-category Gap Taxonomy (GAP-1 through GAP-4) is introduced distinguishing between principally non-encodable effects,