W. Walden
Publications
Can Coding Agents Reproduce Findings in Computational Materials Science?
Large language models are increasingly deployed as autonomous coding agents and have achieved remarkably strong performance on software engineering benchmarks. However, it is unclear whether such success transfers to computational scientific workflows, where tasks require not only strong coding ability, but also the ability to navigate complex, domain-specific procedures and to interpret results in the context of scientific claims. To address this question, we present AutoMat, a benchmark for evaluating LLM-based agents' ability to reproduce claims from computational materials science. AutoMat poses three interrelated challenges: recovering underspecified computational procedures, navigating specialized toolchains, and determining whether the resulting evidence supports a claim. By working closely with subject matter experts, we curate a set of claims from real materials science papers to test whether coding agents can recover and execute the end-to-end workflow needed to support (or undermine) such claims. We then evaluate multiple representative coding agent settings across several foundation models. Our results show that current LLM-based agents obtain low overall success rates on AutoMat, with the best-performing setting achieving a success rate of only 54.1%. Error analysis further reveals that agents perform worst when workflows must be reconstructed from paper text alone and that they fail primarily due to incomplete procedures, methodological deviations, and execution fragility. Taken together, these findings position AutoMat as both a benchmark for computational scientific reproducibility and a tool for diagnosing the current limitations of agentic systems in AI-for-science settings.
Insider Knowledge: How Much Can RAG Systems Gain from Evaluation Secrets?
RAG systems are increasingly evaluated and optimized using LLM judges, an approach that is rapidly becoming the dominant paradigm for system assessment. Nugget-based approaches in particular are now embedded not only in evaluation frameworks but also in the architectures of RAG systems themselves. While this integration can lead to genuine improvements, it also creates a risk of faulty measurements due to circularity. In this paper, we investigate this risk through comparative experiments with nugget-based RAG systems, including Ginger and Crucible, against strong baselines such as GPT-Researcher. By deliberately modifying Crucible to generate outputs optimized for an LLM judge, we show that near-perfect evaluation scores can be achieved when elements of the evaluation - such as prompt templates or gold nuggets - are leaked or can be predicted. Our results highlight the importance of blind evaluation settings and methodological diversity to guard against mistaking metric overfitting for genuine system progress.
Incorporating Q&A Nuggets into Retrieval-Augmented Generation
RAGE systems integrate ideas from automatic evaluation (E) into Retrieval-augmented Generation (RAG). As one such example, we present Crucible, a Nugget-Augmented Generation System that preserves explicit citation provenance by constructing a bank of Q&A nuggets from retrieved documents and uses them to guide extraction, selection, and report generation. Reasoning on nuggets avoids repeated information through clear and interpretable Q&A semantics - instead of opaque cluster abstractions - while maintaining citation provenance throughout the entire generation process. Evaluated on the TREC NeuCLIR 2024 collection, our Crucible system substantially outperforms Ginger, a recent nugget-based RAG system, in nugget recall, density, and citation grounding.