Multimodal AI predicts clinical outcomes of drug combinations from preclinical data

Yepeng Huang; Xiaorui Su; Varun Ullanat; Intae Moon; Ivy Liang; Lindsay Clegg; Damilola Olabode; Ruthie Johnson; Nicholas Ho; Megan Gibbs; Alexander Gusev; Bino John; Marinka Zitnik

arXiv · 2503.02781

Multimodal AI predicts clinical outcomes of drug combinations from preclinical data

Yepeng Huang·Xiaorui Su·Varun Ullanat·Intae Moon·Ivy Liang·Lindsay Clegg·Damilola Olabode·Ruthie Johnson·Nicholas Ho·Megan Gibbs·Alexander Gusev·Bino John·Marinka Zitnik

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Abstract

Predicting clinical outcomes from preclinical data is essential for identifying safe and effective drug combinations, reducing late-stage clinical failures, and accelerating the development of precision therapies. Current AI models rely on structural or target-based features but fail to incorporate the multimodal data necessary for accurate, clinically relevant predictions. Here, we introduce Madrigal, a multimodal AI model that learns from structural, pathway, cell viability, and transcriptomic data to predict drug-combination effects across 953 clinical outcomes and 21,842 compounds, including combinations of approved drugs and novel compounds in development. Madrigal uses an attention bottleneck module to unify preclinical drug data modalities while handling missing data during training and inference, a major challenge in multimodal learning. It outperforms single-modality methods and state-of-the-art models in predicting adverse drug interactions, and ablations show both modality alignment and multimodality are necessary. It captures transporter-mediated interactions and aligns with head-to-head clinical trial differences for neutropenia, anemia, alopecia, and hypoglycemia. In type 2 diabetes and MASH, Madrigal supports polypharmacy decisions and prioritizes resmetirom among safer candidates. Extending to personalization, Madrigal improves patient-level adverse-event prediction in a longitudinal EHR cohort and an independent oncology cohort, and predicts ex vivo efficacy in primary acute myeloid leukemia samples and patient-derived xenograft models. Madrigal links preclinical multimodal readouts to safety risks of drug combinations and offers a generalizable foundation for safer combination design.

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q-bio.QM cs.AI cs.LG

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BibTeX RIS

Yepeng Huang, Xiaorui Su, Varun Ullanat, Intae Moon, Ivy Liang, Lindsay Clegg, Damilola Olabode, Ruthie Johnson, Nicholas Ho, Megan Gibbs, Alexander Gusev, Bino John, Marinka Zitnik. 2025-03-04. Multimodal AI predicts clinical outcomes of drug combinations from preclinical data. https://arxiv.org/abs/2503.02781

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