mlsanityData to 7 Oct 2026

Chaining thoughts and LLMs to learn DNA structural biophysics

arXiv 2403.01332 ↗First posted 2 Mar 2024q-bio.QM cs.AI cs.LGcited by 1

On the map: LLM reasoning → Clinical and biomedical applications

Abstract (arXiv)

The future development of an AI scientist, a tool that is capable of integrating a variety of experimental data and generating testable hypotheses, holds immense potential. So far, bespoke machine learning models have been created to specialize in singular scientific tasks, but otherwise lack the flexibility of a general purpose model. Here, we show that a general purpose large language model, chatGPT 3.5-turbo, can be fine-tuned to learn the structural biophysics of DNA. We find that both fine-tuning models to return chain-of-thought responses and chaining together models fine-tuned for subtasks have an enhanced ability to analyze and design DNA sequences and their structures.

Key facts. Cited by 1 paper in the map (data through 7 Oct 2026). Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning. Builds on 3 of its 14 references that are in the map. First posted on arXiv 2 Mar 2024.

Builds on

3 of 14 references.

References · 3

  1. 2022Chain-of-Thought Prompting Elicits Reasoning in Large Language Modelscited by 12,302
  2. 2023Mathematical Capabilities of ChatGPTcited by 263
  3. 2021Machine Learning in the Search for New Fundamental Physicscited by 50

Built on by

Cited by year (2026 to 7 Oct)

Citing papers per year: 2026: 1.

1 paper.

  1. 2026Reasoning4Sciences: Bridging Reasoning Language Models to All Scientific Branchescited by 0

Similar, not cited

Close in wording, no citation either way

  1. 2026The limits of bio-molecular modeling with large language models : a cross-scale evaluation
  2. 2024Structural Reasoning Improves Molecular Understanding of LLM
  3. 2025BioMedGPT-Mol: Multi-task Learning for Molecular Understanding and Generation
  4. 2024DNAHLM -- DNA sequence and Human Language mixed large language Model
  5. 2025Reflection Pretraining Enables Token-Level Self-Correction in Biological Sequence Models
  6. 2026BioPhys-Bridge: A Benchmark for Interdisciplinary Scientific Reasoning in Physics-Grounded Biological Research
  7. 2025BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model
  8. 2025Lost in Tokenization: Context as the Key to Unlocking Biomolecular Understanding in Scientific LLMs