Does Learning Protein Folding Generalize to Broader Reasoning?
On the map: LLM reasoning → Knowledge- and tool-augmented reasoning also fits: Clinical and biomedical applications
Abstract (arXiv)
Large language models rely heavily on human text, which often conveys surface answers rather than the spatial and structural logic behind them. Protein folding is a natural testbed, because one solved structure yields thousands of exactly checkable spatial and topological statements. We ask: can learning to fold proteins teach general models reusable reasoning capabilities? To answer this, we build FoldingCorpus, a protein-derived question-answer dataset, and Fold2Reason, a recipe that post-trains on it through two complementary signals: discrete structural answers predicted via the model's native language head, and continuous 3D geometry decoded from the same shared representations. On FoldBench, Fold2Reason achieves structure prediction scores 2.7 to 3.5 times those of Qwen3.5-9B. Beyond protein structure prediction, it improves performance on all 10 benchmarks spanning spatial, graph, scientific, and general reasoning, raising macro-average accuracy from 45.09% to 48.33% (+3.23 pp), with positive gains on all 10 benchmarks, while matched controls built from random, synthetic, and shuffled structure yield substantially smaller or negative gains. Our work shows that non-linguistic, structure-dense scientific data can systematically improve broad reasoning in language models, making a solved scientific problem a practical source of post-training supervision.
Key facts. No citing papers in the map yet (data through 7 Oct 2026). Placed in Knowledge- and tool-augmented reasoning, one of 17 directions in LLM reasoning. Builds on 21 of its 66 references that are in the map. First posted on arXiv 30 Sep 2026.
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References · 21
- 2025DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learningcited by 6,146
- 2020The Pile: An 800GB Dataset of Diverse Text for Language Modelingcited by 2,346
- 2022Challenging BIG-Bench Tasks and Whether Chain-of-Thought Can Solve Themcited by 1,767
- 2025InternVL3.5: Advancing Open-Source Multimodal Models in Versatility, Reasoning, and Efficiencycited by 1,419
- 2024Tulu 3: Pushing Frontiers in Open Language Model Post-Trainingcited by 988
- 2025SFT Memorizes, RL Generalizes: A Comparative Study of Foundation Model Post-trainingcited by 655
- 2023Scaling Data-Constrained Language Modelscited by 391
- 2026Gemma 4 Technical Reportcited by 187
- 2023Talk like a Graph: Encoding Graphs for Large Language Modelscited by 175
- 2024LAB-Bench: Measuring Capabilities of Language Models for Biology Researchcited by 138
- 2025General-Reasoner: Advancing LLM Reasoning Across All Domainscited by 132
- 2025Does Math Reasoning Improve General LLM Capabilities? Understanding Transferability of LLM Reasoningcited by 101
9 more
- 2024ChemLLM: A Chemical Large Language Modelcited by 100
- 2023At Which Training Stage Does Code Data Help LLMs Reasoning?cited by 82
- 2024ProteinGPT: Multimodal LLM for Protein Property Prediction and Structure Understandingcited by 23
- 2025Language Models Improve When Pretraining Data Matches Target Taskscited by 18
- 2025SpatialViz-Bench: A Cognitively-Grounded Benchmark for Diagnosing Spatial Visualization in MLLMscited by 11
- 2026Paying Less Generalization Tax: A Cross-Domain Generalization Study of RL Training for LLM Agentscited by 6
- 2024Aligning Large Language Models and Geometric Deep Models for Protein Representationcited by 3
- 2026Towards Next-Generation LLM Training: From the Data-Centric Perspectivecited by 3
- 2025Structure-Aligned Protein Language Modelcited by 1
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- 2026Protein Language Models Diverge from Natural Language: Comparative Analysis and Improved Inference
- 2025SimpleFold: Folding Proteins is Simpler than You Think
- 2026Proteo-R1: Reasoning Foundation Models for De Novo Protein Design
- 2025ProtTeX: Structure-In-Context Reasoning and Editing of Proteins with Large Language Models
- 2024Reinforcement learning on structure-conditioned categorical diffusion for protein inverse folding