Mar 2026· arXiv.org· Vol abs/2603.03517· 1 citation· 61 references
Computer Science
TL;DR
Across essential drug discovery tasks - including molecular optimization, ADMET property prediction, retrosynthesis, drug-target activity prediction, and functional group reasoning - the resulting model achieves near specialist-level performance and, in the majority of settings, surpasses larger models, while remaining more efficient and broadly applicable in the domain.
Abstract
General-purpose large language models (LLMs) that rely on in-context learning do not reliably deliver the scientific understanding and performance required for drug discovery tasks. Simply increasing model size or introducing reasoning tokens does not yield significant performance gains. To address this gap, we introduce the MMAI Gym for Science, a one-stop shop molecular data formats and modalities as well as task-specific reasoning, training, and benchmarking recipes designed to teach foundation models the'language of molecules'in order to solve practical drug discovery problems. We use MMAI Gym to train an efficient Liquid Foundation Model (LFM) for these applications, demonstrating that smaller, purpose-trained foundation models can outperform substantially larger general-purpose or specialist models on molecular benchmarks. Across essential drug discovery tasks - including molecular optimization, ADMET property prediction, retrosynthesis, drug-target activity prediction, and functional group reasoning - the resulting model achieves near specialist-level performance and, in the majority of settings, surpasses larger models, while remaining more efficient and broadly applicable in the domain.
This work investigates whether LLMs can learn molecular design strategies from cheaper synthetic tasks that generalize to expensive molecular lead optimization settings and suggests that scaling post-training using synthetic tasks is an effective strategy for adapting LLMs to high-cost experimental scenarios that are t...
Frank Hu, Shriram Chennakesavalu, Zi-Cheng Wang et al.· 0 citations
Monroe is presented, a new MFM with several innovations over the existing state of the art: increased scale allowing pre-training on over 81 million molecules from the PM6 quantum chemistry dataset; improved graph representation of stereochemistry; improved training losses including conformer denoising and embedding de...
Błażej Banaszewski, Andrew W. Fitzgibbon· 1 citation
This work presents a model validation framework consisting of five recommendations that would enable the community to move beyond aggregate metrics toward understanding where and why molecular property prediction models fail, and connects evaluation choices to real-world applications and case studies encountered in pha...
Srijit Seal, Akshat Shirish Zalte, David Alencar Araripe et al.· bioRxiv· 0 citations
Two deep learning-based computational protocols designed to address drug mechanisms of action and predicting drug-target interactions are presented, offering scalable, cost-effective tools for accelerating therapeutic development by bridging chemical structure, molecular interactions, and systems-level biological respo...
Y. Sun, Cheng-You Liu, Zi-Hao Jing et al.· Methods in molecular biology· 0 citations
Large language models (LLMs) have significantly revolutionized natural language processing through their strong capabilities in text generation and reasoning. Yet, their applicability to bioinformatics applications remains largely unexplored. Here, we systematically evaluate state‐of‐the‐art LLMs across six represent...
Hengchuang Yin, Zi-Wen Cui, Dong-Xu Li et al.· Advanced Computing· 0 citations
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