# Are We Measuring Scientific Intelligence? Rethinking the Evaluation of AI Scientists

arXiv: https://arxiv.org/abs/2610.04915 · HTML: https://mlsanity.com/paper/2610.04915/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 40 of its 49 references that are in the map.
- First posted on arXiv 4 Oct 2026.

## Placed in

- LLM reasoning

## Builds on (most cited first, 30 of 40)

- [Measuring Massive Multitask Language Understanding](https://mlsanity.com/paper/2009.03300/) (2020)
- [Let's Verify Step by Step](https://mlsanity.com/paper/2305.20050/) (2023)
- [GPQA: A Graduate-Level Google-Proof Q&A Benchmark](https://mlsanity.com/paper/2311.12022/) (2023)
- [Language Models Don't Always Say What They Think: Unfaithful Explanations in Chain-of-Thought Prompting](https://mlsanity.com/paper/2305.04388/) (2023)
- [The AI Scientist: Towards Fully Automated Open-Ended Scientific Discovery](https://mlsanity.com/paper/2408.06292/) (2024)
- [Beyond Accuracy: Behavioral Testing of NLP models with CheckList](https://mlsanity.com/paper/2005.04118/) (2020)
- [Are We on the Right Way for Evaluating Large Vision-Language Models?](https://mlsanity.com/paper/2403.20330/) (2024)
- [Annotation Artifacts in Natural Language Inference Data](https://mlsanity.com/paper/1803.02324/) (2018)
- [MLE-bench: Evaluating Machine Learning Agents on Machine Learning Engineering](https://mlsanity.com/paper/2410.07095/) (2024)
- [Learning the Difference that Makes a Difference with Counterfactually-Augmented Data](https://mlsanity.com/paper/1909.12434/) (2019)
- [Reasoning Models Don't Always Say What They Think](https://mlsanity.com/paper/2505.05410/) (2025)
- [Accelerating scientific discovery with Co-Scientist](https://mlsanity.com/paper/2502.18864/) (2025)
- [Monitoring Reasoning Models for Misbehavior and the Risks of Promoting Obfuscation](https://mlsanity.com/paper/2503.11926/) (2025)
- [Entity-Based Knowledge Conflicts in Question Answering](https://mlsanity.com/paper/2109.05052/) (2021)
- [Adaptive Chameleon or Stubborn Sloth: Revealing the Behavior of Large Language Models in Knowledge Conflicts](https://mlsanity.com/paper/2305.13300/) (2023)
- [PaperBench: Evaluating AI's Ability to Replicate AI Research](https://mlsanity.com/paper/2504.01848/) (2025)
- [Hypothesis Only Baselines in Natural Language Inference](https://mlsanity.com/paper/1805.01042/) (2018)
- [Agent-as-a-Judge: Evaluate Agents with Agents](https://mlsanity.com/paper/2410.10934/) (2024)
- [ScienceAgentBench: Toward Rigorous Assessment of Language Agents for Data-Driven Scientific Discovery](https://mlsanity.com/paper/2410.05080/) (2024)
- [SciCode: A Research Coding Benchmark Curated by Scientists](https://mlsanity.com/paper/2407.13168/) (2024)
- [LAB-Bench: Measuring Capabilities of Language Models for Biology Research](https://mlsanity.com/paper/2407.10362/) (2024)
- [When Benchmarks are Targets: Revealing the Sensitivity of Large Language Model Leaderboards](https://mlsanity.com/paper/2402.01781/) (2024)
- [CORE-Bench: Fostering the Credibility of Published Research Through a Computational Reproducibility Agent Benchmark](https://mlsanity.com/paper/2409.11363/) (2024)
- [Measuring what Matters: Construct Validity in Large Language Model Benchmarks](https://mlsanity.com/paper/2511.04703/) (2025)
- [SciEval: A Multi-Level Large Language Model Evaluation Benchmark for Scientific Research](https://mlsanity.com/paper/2308.13149/) (2023)
- [DiscoveryBench: Towards Data-Driven Discovery with Large Language Models](https://mlsanity.com/paper/2407.01725/) (2024)
- [AgentRewardBench: Evaluating Automatic Evaluations of Web Agent Trajectories](https://mlsanity.com/paper/2504.08942/) (2025)
- [BixBench: a Comprehensive Benchmark for LLM-based Agents in Computational Biology](https://mlsanity.com/paper/2503.00096/) (2025)
- [How Much Reading Does Reading Comprehension Require? A Critical Investigation of Popular Benchmarks](https://mlsanity.com/paper/1808.04926/) (2018)
- [BLADE: Benchmarking Language Model Agents for Data-Driven Science](https://mlsanity.com/paper/2408.09667/) (2024)

## Abstract (arXiv)

AI agents can now carry out data-driven scientific analyses end to end, and benchmarks assess them by giving an agent a question and a dataset and scoring its final answer against a fixed key. These benchmarks assume that a correct answer was derived from the supplied data, a property we call evidence grounding. However, an agent can also reach the key from prior knowledge or by ruling out the other options, and a score based on a single run cannot tell these cases apart. We show how to test this assumption and find that it often fails. For each question, we build versions of its data files in which the evidence for the answer is left intact, withdrawn or reversed, check each edit with a pre-registered reference statistic, and run the same agent on every version. We then measure evidence-grounded accuracy, which credits a correct answer only if the agent also responds when the evidence is withdrawn and follows it when it is reversed. We evaluate three agent scaffolds and five models on 18 single-cell questions from BAISBench and four synthetic problems from GeneBench-Pro. On the single-cell questions, the Claude agents are 95% accurate and answer 83% correctly without any data, but their evidence-grounded accuracy is only 41%. Hiding gene names raises the share of runs that follow reversed evidence from 58% to 93% on ten gene tasks, suggesting that prior knowledge competes with the supplied data. The benchmark score and LLM judges can also reward answers that ignore the changed evidence. Measuring scientific intelligence rather than recall therefore requires checking whether answers follow the evidence and whether scores reward them for it.