[2604.00739] BioCOMPASS: Integrating Biomarkers into Transformer-Based Immunotherapy Response Prediction

Computer Science > Machine Learning arXiv:2604.00739 (cs) [Submitted on 1 Apr 2026] Title:BioCOMPASS: Integrating Biomarkers into Transformer-Based Immunotherapy Response Prediction Authors:Sayed Hashim, Frank Soboczenski, Paul Cairns View a PDF of the paper titled BioCOMPASS: Integrating Biomarkers into Transformer-Based Immunotherapy Response Prediction, by Sayed Hashim and 2 other authors View PDF HTML (experimental) Abstract:Datasets used in immunotherapy response prediction are typically small in size, as well as diverse in cancer type, drug administered, and sequencer used. Models often drop in performance when tested on patient cohorts that are not included in the training process. Recent work has shown that transformer-based models along with self-supervised learning show better generalisation performance than threshold-based biomarkers, but is still suboptimal. We present BioCOMPASS, an extension of a transformer-based model called COMPASS, that integrates biomarkers and treatment information to further improve its generalisability. Instead of feeding biomarker data as input, we built loss components to align them with the model's intermediate representations. We found that components such as treatment gating and pathway consistency loss improved generalisability when evaluated with Leave-one-cohort-out, Leave-one-cancer-type-out and Leave-one-treatment-out strategies. Results show that building components that exploit biomarker and treatment information can help ...