William Jurayj
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.
Many-Tier Instruction Hierarchy in LLM Agents
Large language model agents receive instructions from many sources-system messages, user prompts, tool outputs, and more-each carrying different levels of trust and authority. When these instructions conflict, models must reliably follow the highest-privilege instruction to remain safe and effective. The dominant paradigm, instruction hierarchy (IH), assumes a fixed, small set of privilege levels (typically fewer than five) defined by rigid role labels (e.g., system > user). This is inadequate for real-world agentic settings, where conflicts can arise across far more sources and contexts. In this work, we propose Many-Tier Instruction Hierarchy (ManyIH), a paradigm for resolving instruction conflicts among instructions with arbitrarily many privilege levels. We introduce ManyIH-Bench, the first benchmark for ManyIH. ManyIH-Bench requires models to navigate up to 12 levels of conflicting instructions with varying privileges, comprising 853 agentic tasks (427 coding and 426 instruction-following). ManyIH-Bench composes constraints developed by LLMs and verified by humans to create realistic and difficult test cases spanning 46 real-world agents. Our experiments show that even the current frontier models perform poorly (~40% accuracy) when instruction conflict scales. This work underscores the urgent need for methods that explicitly target fine-grained, scalable instruction conflict resolution in agentic settings.
Conformal Thinking: Risk Control for Reasoning on a Compute Budget
Reasoning Large Language Models (LLMs) enable test-time scaling, with dataset-level accuracy improving as the token budget increases, motivating adaptive reasoning -- spending tokens when they improve reliability and stopping early when additional computation is unlikely to help. However, setting the token budget, as well as the threshold for adaptive reasoning, is a practical challenge that entails a fundamental risk-accuracy trade-off. We re-frame the budget setting problem as risk control, limiting the error rate while minimizing compute. Our framework introduces an upper threshold that stops reasoning when the model is confident (risking incorrect output) and a novel parametric lower threshold that preemptively stops unsolvable instances (risking premature stoppage). Given a target risk and a validation set, we use distribution-free risk control to optimally specify these stopping mechanisms. For scenarios with multiple budget controlling criteria, we incorporate an efficiency loss to select the most computationally efficient exiting mechanism. Empirical results across diverse reasoning tasks and models demonstrate the effectiveness of our risk control approach, demonstrating computational efficiency gains from the lower threshold and ensemble stopping mechanisms while adhering to the user-specified risk target.