Large language models (LLMs) are increasingly used for scientific hypothesis generation. However, evaluating generated hypotheses remains a challenge for trustworthy AI-enabled scientific workflows.

Existing approaches often use LLMs as judges or rely on semantic similarity, which can favor familiar ideas over novel ones. We propose a logit-based energy scoring method that evaluates hypotheses using a language model's intrinsic confidence rather than comparative judgment.

We benchmarked seven language models on 1,323 papers across 12 disciplines. Each paper was paired with its hypothesis and fifteen incorrect alternatives.

Intrinsic scoring reached 33.0% Hit@1 pooled across both scorers, compared with 16.6% for prompted listwise ranking. The strongest configuration, a 1-billion-parameter model using logit-based energy scoring, reached 53.1%, though this was the maximum across 14 model-by-scorer combinations selected post hoc.

Overall, intrinsic model confidence shows potential for scientific hypothesis evaluation. This study also motivates future research on confidence-based methods for trustworthy AI-enabled scientific discovery.