# Beyond Execution: Auditing Experimental Fidelity in LLM-Driven Scientific Research

arXiv: https://arxiv.org/abs/2608.26753 · HTML: https://mlsanity.com/paper/2608.26753/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Web, search, and research agents, one of 16 directions in LLM agents and tool use.
- Builds on 8 of its 18 references that are in the map.
- First posted on arXiv 27 Aug 2026.

## Placed in

- LLM agents and tool use / [Web, search, and research agents](https://mlsanity.com/agents/web-search-and-research-agents/)

## Builds on (most cited first, 8 of 8)

- [Program Synthesis with Large Language Models](https://mlsanity.com/paper/2108.07732/) (2021)
- [SWE-bench: Can Language Models Resolve Real-World GitHub Issues?](https://mlsanity.com/paper/2310.06770/) (2023)
- [The AI Scientist: Towards Fully Automated Open-Ended Scientific Discovery](https://mlsanity.com/paper/2408.06292/) (2024)
- [OpenHands: An Open Platform for AI Software Developers as Generalist Agents](https://mlsanity.com/paper/2407.16741/) (2024)
- [SWE-bench Multimodal: Do AI Systems Generalize to Visual Software Domains?](https://mlsanity.com/paper/2410.03859/) (2024)
- [From AI for Science to Agentic Science: A Survey on Autonomous Scientific Discovery](https://mlsanity.com/paper/2508.14111/) (2025)
- [How Safe Are AI-Generated Patches? A Large-scale Study on Security Risks in LLM and Agentic Automated Program Repair on SWE-bench](https://mlsanity.com/paper/2507.02976/) (2025)
- [Claw AI Lab: An Autonomous Multi-Agent Research Team](https://mlsanity.com/paper/2605.22662/) (2026)

## Abstract (arXiv)

LLM agents used for scientific experimentation must do more than generate executable code: they must implement the reference method faithfully, design experiments that test the paper's claims, and provide evidence supporting those claims. We show that agents often produce methodological hallucinations: silently reducing datasets or training budgets, replacing failed learning or generative components with lookup or oracle functions, or drawing conclusions from resource-limited settings where a method's claimed advantage disappears. To detect these failures, we introduce ABE-Ralph, a reference-anchored auditing framework that represents claims, protocols, required components, baselines, and metrics as structured experimental constraints, guides implementation through an 8-step workflow, and performs quantitative, qualitative, and code-level verification. Across 30 long-horizon reproduction runs covering 12 machine learning domains, ABE-Ralph achieves a 93% robust execution rate and identifies five scientific failure modes. In 23 NatureBench discovery tasks, ABE-Ralph matches or exceeds state-of-the-art performance on 5 tasks. These results show that reliable evaluation of AI scientists must assess whether the experimental design faithfully tests the intended claim and whether the resulting evidence supports it, rather than treating code execution or plausible metrics as evidence of scientific success.