Learning Drug Synergy through Environment-Conditioned Feature Modulation

Abstract Motivation Drug combinations are crucial for overcoming resistance in cancer therapy. Although deep learning has achieved strong performance in synergy prediction, existing models often treat cell-specific features and paired drugs as a static background and fail to capture how the specific cell-drug environment dynamically modulates drug representations, thereby hindering the modeling of environment-specific synergistic effects. Results We propose Env-Syn, a framework for modeling drug-drug-cell interactions through Environment-Conditioned Feature Modulation, which incorporates a Residual Feature-wise Linear Modulation (R-FiLM) module to perform precise affine transformations on drug representations conditioned on paired drugs and cellular environments. Benchmark evaluations show that Env-Syn consistently outperforms state-of-the-art methods. Notably, the model exhibits exceptional generalization performance in rigorous inductive scenarios. It maintains high predictive accuracy for unseen drugs with AUROC and AUPRC exceeding 0.81 in the Leave-drug-out setting, and further demonstrates strong cross-dataset reliability by surpassing a recall of 0.7 on independent test set. Furthermore, among 15 novel predicted drug combinations, eight are directly supported by literature evidence. These results demonstrate that Env-Syn is an effective computational tool for drug synergy discovery. Availability The source code is available at https://github.com/AnQi-87/Env-Syn. Supplementary information Supplementary data is available at Bioinformatics online.