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[Submitted on 4 Oct 2026] Title:State-Aware Interaction MIL for Rare Joint Molecular Phenotype Prediction in Colorectal Cancer and Lung Adenocarcinoma View a PDF of the paper titled State-Aware Interaction MIL for Rare Joint Molecular Phenotype Prediction in Colorectal Cancer and Lung Adenocarcinoma, by Dasari Naga Raju and 1 other authors View PDF HTML (experimental) Abstract:Joint molecular phenotype prediction is complicated by small joint-positive populations and overlapping histological features across alternative molecular states. Existing computational pathology approaches typically predict biomarkers independently or formulate the joint-positive phenotype as a binary endpoint. Independent prediction does not model interactions between biomarker-specific histological representations, whereas binary joint prediction collapses the double-negative and two single-positive configurations into a single negative class. We propose State-Aware Interaction MIL, a weakly supervised method that preserves biomarker-specific histological representations, models their interaction, and supervises the complete four-state molecular configuration. We evaluate the proposed approach for joint BRAF+/MSI+ prediction in colorectal cancer and EGFR+/TP53+ prediction in lung adenocarcinoma using frozen UNI2-h and CONCH pathology foundation-model representations. With UNI2-h, State-Aware Interaction MIL achieved an average precision of 0.5566 in colorectal cancer (joint-positive prevalence 6.8%) compared with 0.5161 for NaiveMTL, and 0.2784 in lung adenocarcinoma (joint-positive prevalence 8.6%) compared with 0.2525 for IndependentPair. With CONCH, State-Aware achieved an average precision of 0.4410 compared with 0.3932 for DirectJoint in colorectal cancer and 0.1659 compared with 0.1226 for DirectJoint in lung adenocarcinoma. These results indicate that pathology foundation-model representations contain predictive information for rare joint molecular phenotypes and that preserving biomarker-specific representations within a structured molecular-state formulation can improve prediction of these phenotypes from histopathology. Comments: Accepted at the NeurIPS 2026 Workshop on AI at Scale for Clinical Impact (ASCI): Cancer Pathology Foundation Models Subjects: Computer Vision and Pattern Recognition (cs.CV) Cite as: arXiv:2610.06991 [cs.CV] (or arXiv:2610.06991v1 [cs.CV] for this version) https://doi.org/10.48550/arXiv.2610.06991 arXiv-issued DOI via DataCite (pending registration) Submission history From: Dasari Naga Raju [view email] [v1] Sun, 4 Oct 2026 07:29:06 UTC (1,321 KB) Full-text links: Access Paper: View a PDF of the paper titled State-Aware Interaction MIL for Rare Joint Molecular Phenotype Prediction in Colorectal Cancer and Lung Adenocarcinoma, by Dasari Naga Raju and 1 other authors View PDF HTML (experimental) TeX Source view license Additional Features Audio Summary Current browse context: cs.CV new | recent | 2026-10 Change to browse by: cs 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?) 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?)