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This research addresses the critical bottleneck of evaluating agentic LLMs in drug discovery by establishing a human-aligned framework that outperforms traditional metrics like BLEU and ROUGE. By optimizing models such as GPT-5 and Claude Opus through few-shot learning, the study demonstrates how to achieve high fidelity with expert annotators while scaling evaluation speeds for iterative scientific workflows. The work provides a reusable template for validating tool-augmented agents in complex domains where semantic correctness is paramount.
Designing a Robust LLM-Based Evaluation System for Agentic AI in Drug Discovery Through Human Alignment
arXiv:2608.21057v1 Announce Type: new Abstract: Agentic large language model (LLM) systems are reshaping scientific workflows in chemistry and drug discovery, but evaluating their open-ended, tool-augmented outputs remains a fundamental bottleneck. Reference-based metrics such as BLEU and ROUGE fail to capture semantic correctness, while expert human evaluation does not scale to the iteration speed these systems demand. The LLM-as-a-Judge paradigm has emerged as a scalable alternative, but existing drug discovery benchmarks deploy LLM judges without validating their alignment with human experts. In this work, we present an LLM-as-a-Judge evaluation framework for ChatInvent, an agentic drug discovery assistant deployed at AstraZeneca, with four contributions. First, we define four output-quality evaluation dimensions---Completeness, Relevancy, Structural Clarity, and Scope Adherence---alongside deterministic Tool Call Correctness checks. Second, we validate the judge through a human alignment study with five expert annotators, comparing Gemini 3.1 Pro, Claude Opus 4.7, GPT-5, and Llama 3.1 70B as candidate judges. Third, we optimize the best-performing judge using few-shot demonstrations of human-annotated examples, improving alignment with the human majority vote from 0.80 to 0.86. Fourth, applying the optimized judge to 70 held-out questions, we surface concrete limitations and find that informal phrasings do not systematically degrade output quality; if anything, it is helpful to have the LLM rewrite the original question before querying the agent. Our framework provides a reusable template for human-aligned evaluation of agentic systems in scientific domains.
Abstract:Agentic large language model (LLM) systems are reshaping scientific workflows in chemistry and drug discovery, but evaluating their open-ended, tool-augmented outputs remains a fundamental bottleneck. Reference-based metrics such as BLEU and ROUGE fail to capture semantic correctness, while expert human evaluation does not scale to the iteration speed these systems demand. The LLM-as-a-Judge paradigm has emerged as a scalable alternative, but existing drug discovery benchmarks deploy LLM judges without validating their alignment with human experts. In this work, we present an LLM-as-a-Judge evaluation framework for ChatInvent, an agentic drug discovery assistant deployed at AstraZeneca, with four contributions. First, we define four output-quality evaluation dimensions---Completeness, Relevancy, Structural Clarity, and Scope Adherence---alongside deterministic Tool Call Correctness checks. Second, we validate the judge through a human alignment study with five expert annotators, comparing Gemini 3.1 Pro, Claude Opus 4.7, GPT-5, and Llama 3.1 70B as candidate judges. Third, we optimize the best-performing judge using few-shot demonstrations of human-annotated examples, improving alignment with the human majority vote from 0.80 to 0.86. Fourth, applying the optimized judge to 70 held-out questions, we surface concrete limitations and find that informal phrasings do not systematically degrade output quality; if anything, it is helpful to have the LLM rewrite the original question before querying the agent. Our framework provides a reusable template for human-aligned evaluation of agentic systems in scientific domains.
Machine Learning (cs.LG)
arXiv:2608.21057 [cs.LG]
(or arXiv:2608.21057v1 [cs.LG] for this version)
https://doi.org/10.48550/arXiv.2608.21057 Focus to learn more arXiv-issued DOI via DataCite (pending registration)
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