Agent-driven Model Development for RNA 3D Structure Prediction

Authors

Majewski, M., Malo, L., Montero-Blay, A., Marengo, M., Gkeka, P., Minoux, H.

Abstract

Large language model (LLM) agents have shown promise in driving scientific discovery, but their effectiveness in complex, real-world biological problems remains underexplored. We ask whether a general-purpose LLM agent can drive semi-autonomous development of a model for a genuinely hard biological problem, RNA 3D structure prediction. We designed a development loop where, under a fixed budget and with human supervision, the agent iteratively proposed, implemented, trained, and evaluated model changes. Over 297 iterations, the model evolved from a randomly-initialised baseline to QuickFold, an 8.9M-parameter folding trunk that matches the strongest open-source baselines (RhoFold+, NuFold) on lDDT and TM-score within noise on a held-out test set at a fraction of their inference cost. We frame this less as a new predictor than as a case study in feedback-driven, agent-led model development.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 10 Sep 2026.

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