Knowledge before Reasoning: EC-Reason-Bench, a Training-Free Diagnostic Benchmark for LLM Enzyme Classification
Enzyme function prediction is a hierarchical, knowledge-intensive form of protein function classification. Existing benchmarks expose an anomaly: general LLMs often get the coarse first level right, yet once asked for a complete EC number their accuracy at levels two through four drops to almost zero, while specialized models and tools stay usable. We propose EC-Reason-Bench, a training-free, diagnostic evaluation protocol built to answer two questions: why general LLMs score close to nothing on EC number prediction, and how much of that loss can be recovered without updating a single weight. We break enzyme classification ability into four orthogonal levers that can each be measured on t...
| Authors | Linyu Li, Zhi Jin, Yichi Zhang et al. |
|---|---|
| Primary category | cs.CL |
| Published | 29 July 2026 |
| Last updated at source | 29 July 2026 |
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