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[Submitted on 23 Sep 2026] Title:SMILESGNN: Interpretable Clinical Toxicity Prediction via SMILES-Graph Cross-Attention Fusion View a PDF of the paper titled SMILESGNN: Interpretable Clinical Toxicity Prediction via SMILES-Graph Cross-Attention Fusion, by Quang Minh Nguyen and 5 other authors View PDF HTML (experimental) Abstract:Drug toxicity prediction is critical for reducing late-stage attrition in drug discovery, yet remains challenging due to severe class imbalance, scaffold-based generalization, and the clinical need for interpretable predictions. Single-modality approaches-SMILES Transformers or graph neural networks capture complementary aspects of molecular structure, while sequence-only models cannot directly provide graph-attributed explanations. We present SMILESGNN, a multimodal architecture that fuses a SMILES Transformer encoder and a GATv2 graph encoder via cross-attention, and SMILESGNN-PT, a variant using a ChemBERTa-2 pretrained backbone. The design retains an explicit graph branch within the predictive pipeline, supporting GNNExplainer-based analysis of substructures associated with toxic predictions. On ClinTox, SMILESGNN achieves AUC-ROC 0.987 and F1 0.906 with only 0.4M parameters, performing competitively with a strong SMILESTransformer and a larger ChemBERTa-2/GATv2 concat-fusion baseline. On Tox21 (12 tasks), SMILESGNN-PT obtains mean AUC-ROC 0.750, comparable to ChemBERTa-2 alone and the same-backbone concat-fusion baseline. Overall, the results suggest that cross-attention is a practical fusion alternative that preserves competitive predictive performance while enabling graph-based interpretability support. Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI) Cite as: arXiv:2609.28553 [cs.LG] (or arXiv:2609.28553v1 [cs.LG] for this version) https://doi.org/10.48550/arXiv.2609.28553 arXiv-issued DOI via DataCite Journal reference: 2026 International Conference on Multimedia Analysis and Pattern Recognition (MAPR) Related DOI: https://doi.org/10.1109/MAPR72750.2026.11685822 DOI(s) linking to related resources Submission history From: Nghia Nguyen Trong [view email] [v1] Wed, 23 Sep 2026 07:51:46 UTC (1,956 KB) Full-text links: Access Paper: View a PDF of the paper titled SMILESGNN: Interpretable Clinical Toxicity Prediction via SMILES-Graph Cross-Attention Fusion, by Quang Minh Nguyen and 5 other authors View PDF HTML (experimental) TeX Source view license Current browse context: cs.LG new | recent | 2026-09 Change to browse by: cs cs.AI References & Citations NASA ADS Google Scholar Semantic Scholar Loading... Data provided by: Bibliographic Tools Bibliographic and Citation Tools Bibliographic Explorer Toggle Bibliographic Explorer (What is the Explorer?) Connected Papers Toggle Connected Papers (What is Connected Papers?) Litmaps Toggle Litmaps (What is Litmaps?) scite.ai Toggle scite Smart Citations (What are Smart Citations?) Code, Data, Media Code, Data and Media Associated with this Article alphaXiv Toggle alphaXiv (What is alphaXiv?) Links to Code Toggle CatalyzeX Code Finder for Papers (What is CatalyzeX?) DagsHub Toggle DagsHub (What is DagsHub?) GotitPub Toggle Gotit.pub (What is GotitPub?) Huggingface Toggle Hugging Face (What is Huggingface?) ScienceCast Toggle ScienceCast (What is ScienceCast?) Demos Demos Replicate Toggle Replicate (What is Replicate?) Spaces Toggle Hugging Face Spaces (What is Spaces?) Spaces Toggle TXYZ.AI (What is TXYZ.AI?) Related Papers Recommenders and Search Tools Link to Influence Flower Influence Flower (What are Influence Flowers?) Core recommender toggle CORE Recommender (What is CORE?) IArxiv recommender toggle IArxiv Recommender (What is IArxiv?) Author Venue Institution Topic About arXivLabs arXivLabs: experimental projects with community collaborators arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website. Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them. Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs. Which authors of this paper are endorsers? | Disable MathJax (What is MathJax?)