# When Stability Fails: Hidden Failure Modes Of LLMS in Data-Constrained Scientific Decision-Making

arXiv: https://arxiv.org/abs/2603.15840 · HTML: https://mlsanity.com/paper/2603.15840/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 4 of its 12 references that are in the map.
- First posted on arXiv 16 Mar 2026.

## Builds on (most cited first, 4 of 4)

- [Survey of Hallucination in Natural Language Generation](https://mlsanity.com/paper/2202.03629/) (2022)
- [Large Language Models Encode Clinical Knowledge](https://mlsanity.com/paper/2212.13138/) (2022)
- [Beyond Accuracy: Behavioral Testing of NLP models with CheckList](https://mlsanity.com/paper/2005.04118/) (2020)
- [A Computational Inflection for Scientific Discovery](https://mlsanity.com/paper/2205.02007/) (2022)

## Abstract (arXiv)

Large language models (LLMs) are increasingly used as decision-support tools in data-constrained scientific workflows, where correctness and validity are critical. However, evaluation practices often emphasize stability or reproducibility across repeated runs. While these properties are desirable, stability alone does not guar- antee agreement with statistical ground truth when such references are available. We introduce a controlled behavioral evaluation framework that explicitly sep- arates four dimensions of LLM decision-making: stability, correctness, prompt sensitivity, and output validity under fixed statistical inputs. We evaluate multi- ple LLMs using a statistical gene prioritization task derived from differential ex- pression analysis across prompt regimes involving strict and relaxed significance thresholds, borderline ranking scenarios, and minor wording variations. Our ex- periments show that LLMs can exhibit near-perfect run-to-run stability while sys- tematically diverging from statistical ground truth, over-selecting under relaxed thresholds, responding sharply to minor prompt wording changes, or producing syntactically plausible gene identifiers absent from the input table. Although sta- bility reflects robustness across repeated runs, it does not guarantee agreement with statistical ground truth in structured scientific decision tasks. These findings highlight the importance of explicit ground-truth validation and output validity checks when deploying LLMs in automated or semi-automated scientific work- flows.