Towards Autonomous Mechanistic Reasoning in Virtual Cells

Yunhui Jang, Lu Zhu, Jake Fawkes, Alisandra Kaye Denton, Dominique Beaini, Emmanuel Noutahi

Towards Autonomous Mechanistic Reasoning in Virtual Cells: 5 upvotes on Hugging Face Daily Papers, #20 of 29 papers on 2026-04-17. Day-by-day upvote history.

Large language models (LLMs) have recently gained significant attention as a promising approach to accelerate scientific discovery. However, their application in open-ended scientific domains such as biology remains limited, primarily due to the lack of factually grounded and actionable explanations. To address this, we introduce a structured explanation formalism for virtual cells that represents biological reasoning as mechanistic action graphs, enabling systematic verification and falsification. Building upon this, we propose VCR-Agent, a multi-agent framework that integrates biologically grounded knowledge retrieval with a verifier-based filtering approach to generate and validate mechanistic reasoning autonomously. Using this framework, we release VC-TRACES dataset, which consists of verified mechanistic explanations derived from the Tahoe-100M atlas. Empirically, we demonstrate that training with these explanations improves factual precision and provides a more effective supervision signal for downstream gene expression prediction. These results underscore the importance of reliable mechanistic reasoning for virtual cells, achieved through the synergy of multi-agent and rigorous verification.

Paper page on Hugging Face · arXiv

Data: hysts-bot-data/daily-papers-stats and the Daily Papers API. Open data: tardellirs/paper-pulse-data. Sister project: Model Pulse, the download history of every model on the Hub.