When Do Biological Reasoning Models Use Their Biological Inputs?
Biological reasoning models use post-training to connect LLMs to biological foundation model representations and biological text. Their benchmark accuracy is taken as evidence that LLMs reason over these inputs. We test this assumption in six biological reasoning models across DNA, protein, and single-cell tasks. We perturb one biological input while holding the query and other inputs fixed, construct evidence conflicts that pair the foundation model representation of one genome, protein, or cell with the text of another, fit linear probes to the representations the language model receives, and analyze reasoning traces against the biological inputs. Evo2 and ESM3 contribute little to BioR...
| Authors | Ada Fang, Nikitha Thoduguli, Lukas Fesser et al. |
|---|---|
| Primary category | cs.LG |
| Published | 1 October 2026 |
| Last updated at source | 1 October 2026 |
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