Large Language Models for Zero-shot Inference of Causal Structures in Biology
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arXiv
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| Format: | Preprint |
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2025
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| author | Newsham, Izzy Kovačević, Luka Moulange, Richard Ke, Nan Rosemary Mukherjee, Sach |
| author_facet | Newsham, Izzy Kovačević, Luka Moulange, Richard Ke, Nan Rosemary Mukherjee, Sach |
| contents | Genes, proteins and other biological entities influence one another via causal molecular networks. Causal relationships in such networks are mediated by complex and diverse mechanisms, through latent variables, and are often specific to cellular context. It remains challenging to characterise such networks in practice. Here, we present a novel framework to evaluate large language models (LLMs) for zero-shot inference of causal relationships in biology. In particular, we systematically evaluate causal claims obtained from an LLM using real-world interventional data. This is done over one hundred variables and thousands of causal hypotheses. Furthermore, we consider several prompting and retrieval-augmentation strategies, including large, and potentially conflicting, collections of scientific articles. Our results show that with tailored augmentation and prompting, even relatively small LLMs can capture meaningful aspects of causal structure in biological systems. This supports the notion that LLMs could act as orchestration tools in biological discovery, by helping to distil current knowledge in ways amenable to downstream analysis. Our approach to assessing LLMs with respect to experimental data is relevant for a broad range of problems at the intersection of causal learning, LLMs and scientific discovery. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2503_04347 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Large Language Models for Zero-shot Inference of Causal Structures in Biology Newsham, Izzy Kovačević, Luka Moulange, Richard Ke, Nan Rosemary Mukherjee, Sach Machine Learning Genomics Genes, proteins and other biological entities influence one another via causal molecular networks. Causal relationships in such networks are mediated by complex and diverse mechanisms, through latent variables, and are often specific to cellular context. It remains challenging to characterise such networks in practice. Here, we present a novel framework to evaluate large language models (LLMs) for zero-shot inference of causal relationships in biology. In particular, we systematically evaluate causal claims obtained from an LLM using real-world interventional data. This is done over one hundred variables and thousands of causal hypotheses. Furthermore, we consider several prompting and retrieval-augmentation strategies, including large, and potentially conflicting, collections of scientific articles. Our results show that with tailored augmentation and prompting, even relatively small LLMs can capture meaningful aspects of causal structure in biological systems. This supports the notion that LLMs could act as orchestration tools in biological discovery, by helping to distil current knowledge in ways amenable to downstream analysis. Our approach to assessing LLMs with respect to experimental data is relevant for a broad range of problems at the intersection of causal learning, LLMs and scientific discovery. |
| title | Large Language Models for Zero-shot Inference of Causal Structures in Biology |
| topic | Machine Learning Genomics |
| url | https://arxiv.org/abs/2503.04347 |