# Advancing the Scientific Method with Large Language Models: From Hypothesis to Discovery

arXiv: https://arxiv.org/abs/2505.16477 · HTML: https://mlsanity.com/paper/2505.16477/

## Key facts

- Cited by 7 papers in the map (data through 14 Oct 2026).
- Builds on 119 of its 196 references that are in the map.
- First posted on arXiv 22 May 2025.

## Builds on (most cited first, 30 of 119)

- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [Chain-of-Thought Prompting Elicits Reasoning in Large Language Models](https://mlsanity.com/paper/2201.11903/) (2022)
- [DeepSeekMath: Pushing the Limits of Mathematical Reasoning in Open Language Models](https://mlsanity.com/paper/2402.03300/) (2024)
- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [ReAct: Synergizing Reasoning and Acting in Language Models](https://mlsanity.com/paper/2210.03629/) (2022)
- [Evaluating Large Language Models Trained on Code](https://mlsanity.com/paper/2107.03374/) (2021)
- [Scaling Laws for Neural Language Models](https://mlsanity.com/paper/2001.08361/) (2020)
- [Self-Consistency Improves Chain of Thought Reasoning in Language Models](https://mlsanity.com/paper/2203.11171/) (2022)
- [Zero-Shot Text-to-Image Generation](https://mlsanity.com/paper/2102.12092/) (2021)
- [Reflexion: Language Agents with Verbal Reinforcement Learning](https://mlsanity.com/paper/2303.11366/) (2023)
- [Toolformer: Language Models Can Teach Themselves to Use Tools](https://mlsanity.com/paper/2302.04761/) (2023)
- [Generative Agents: Interactive Simulacra of Human Behavior](https://mlsanity.com/paper/2304.03442/) (2023)
- [Tree of Thoughts: Deliberate Problem Solving with Large Language Models](https://mlsanity.com/paper/2305.10601/) (2023)
- [TruthfulQA: Measuring How Models Mimic Human Falsehoods](https://mlsanity.com/paper/2109.07958/) (2021)
- [Emergent Abilities of Large Language Models](https://mlsanity.com/paper/2206.07682/) (2022)
- [G-Eval: NLG Evaluation using GPT-4 with Better Human Alignment](https://mlsanity.com/paper/2303.16634/) (2023)
- [Voyager: An Open-Ended Embodied Agent with Large Language Models](https://mlsanity.com/paper/2305.16291/) (2023)
- [Survey of Hallucination in Natural Language Generation](https://mlsanity.com/paper/2202.03629/) (2022)
- [Language Models as Knowledge Bases?](https://mlsanity.com/paper/1909.01066/) (2019)
- [Improving Factuality and Reasoning in Language Models through Multiagent Debate](https://mlsanity.com/paper/2305.14325/) (2023)
- [Representation Engineering: A Top-Down Approach to AI Transparency](https://mlsanity.com/paper/2310.01405/) (2023)
- [FActScore: Fine-grained Atomic Evaluation of Factual Precision in Long Form Text Generation](https://mlsanity.com/paper/2305.14251/) (2023)
- [Large Language Models Cannot Self-Correct Reasoning Yet](https://mlsanity.com/paper/2310.01798/) (2023)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [STaR: Bootstrapping Reasoning With Reasoning](https://mlsanity.com/paper/2203.14465/) (2022)
- [Attention is not Explanation](https://mlsanity.com/paper/1902.10186/) (2019)
- [ChatGPT Outperforms Crowd-Workers for Text-Annotation Tasks](https://mlsanity.com/paper/2303.15056/) (2023)
- [Large Language Models as Optimizers](https://mlsanity.com/paper/2309.03409/) (2023)
- [DSPy: Compiling Declarative Language Model Calls into Self-Improving Pipelines](https://mlsanity.com/paper/2310.03714/) (2023)

## Built on by (most cited first, 7 of 7)

- [RECODE-H: A Benchmark for Research Code Development with Interactive Human Feedback](https://mlsanity.com/paper/2510.06186/) (2025)
- [Reinforcement Learning with Metacognitive Feedback Elicits Faithful Uncertainty Expression in LLMs](https://mlsanity.com/paper/2606.32032/) (2026)
- [LLM-Generated or Human-Written? Comparing Review and Non-Review Papers on ArXiv](https://mlsanity.com/paper/2601.17036/) (2026)
- [Can LLMs Use Linguistic Uncertainty Markers to Reliably Reflect Intrinsic Confidence?](https://mlsanity.com/paper/2605.28778/) (2026)
- [Quantifying Faithful Confidence Expression in Large Reasoning Models](https://mlsanity.com/paper/2606.03969/) (2026)
- [Metacognition in LLMs: Foundations, Progress, and Opportunities](https://mlsanity.com/paper/2607.11881/) (2026)
- [Does Less Hallucination Mean Less Creativity? An Empirical Investigation in LLMs](https://mlsanity.com/paper/2512.11509/) (2025)

## Abstract (arXiv)

With recent Nobel Prizes recognising AI contributions to science, Large Language Models (LLMs) are transforming scientific research by enhancing productivity and reshaping the scientific method. LLMs are now involved in experimental design, data analysis, and workflows, particularly in chemistry and biology. However, challenges such as hallucinations and reliability persist. In this contribution, we review how Large Language Models (LLMs) are redefining the scientific method and explore their potential applications across different stages of the scientific cycle, from hypothesis testing to discovery. We conclude that, for LLMs to serve as relevant and effective creative engines and productivity enhancers, their deep integration into all steps of the scientific process should be pursued in collaboration and alignment with human scientific goals, with clear evaluation metrics. The transition to AI-driven science raises ethical questions about creativity, oversight, and responsibility. With careful guidance, LLMs could evolve into creative engines, driving transformative breakthroughs across scientific disciplines responsibly and effectively. However, the scientific community must also decide how much it leaves to LLMs to drive science, even when associations with 'reasoning', mostly currently undeserved, are made in exchange for the potential to explore hypothesis and solution regions that might otherwise remain unexplored by human exploration alone.