N. Tashi
Publications
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 their own: output structure, external knowledge, reasoning structure, and reasoning robustness. We test each lever with an inference-time method against a shared zero-shot baseline reproducing previously reported near-zero performance. Experiments with several strong reasoning LLMs yield four main findings. First, external knowledge is decisive and must precede reasoning: uniformly low closed-book performance rises sharply with open-book access, narrowing model gaps. Second, in closed-book settings, whether cascading and chain-of-thought help or hurt depends on a model's tendency to abstain. Third, once evidence is available the aggregate score of the best LLM setting is indistinguishable from simply voting the EC numbers of the nearest retrieved neighbors; that tie is an artifact of averaging, and it hides a large gain on adversarial evidence set against an equally large loss on multi-functional enzymes. Reasoning over evidence therefore acts as an arbiter of conflicting neighbors rather than as a source of knowledge, and no single-number leaderboard can see it. Fourth, accuracy obeys a law of homology availability.
SkillSight: Seeing Through Shared Descriptions for Accurate Skill Retrieval
As large language model agents gain access to increasingly large skill libraries, retrieving the right skill becomes critical to reliable capability selection and execution. Existing retrievers often treat skill descriptions as ordinary documents, overlooking their highly regular structure: shared descriptive patterns recur across many skills while providing little evidence for distinguishing the required capability. We show that this shared descriptive background systematically contributes to dense relevance scores, induces a pronounced energy gap between queries and skill documents, and obscures task-relevant signals. Based on this observation, we propose SkillSight, a training-free retrieval framework that calibrates shared background in both semantic and lexical spaces. Semantic Background Calibration estimates a background subspace from generic tokens identified by IDF, reducing similarity induced by shared descriptive patterns, while Lexical Evidence Calibration downweights shared background tokens to recover discriminative token-level evidence. Experiments on SRA-Bench and SkillBench-Supp demonstrate consistent improvements across retrieval metrics, with SkillSight improving Recall@10 by up to 20.21 percentage points over the original dense retriever. In end-to-end evaluation, SkillSight achieves the best overall performance across three agent models and outperforms LLM Selection by up to 4.97 percentage points. It is also up to 1,248 times faster than the Dense + Reranker baseline. These results identify shared descriptive background as a key source of bias in skill retrieval and demonstrate that explicitly calibrating it enables accurate and efficient skill selection without additional training. Our code is available at https://github.com/xiaojinying/SkillSight.