Identity or Evidence? Auditing Evidence Dependence in Agentic Life-Science Benchmarks

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 For each question, we build versions of its data files in which the evidence for the answer is left intact, withdrawn or reversed, check each edit with a pre-registered reference statistic, and run the same agent on every version.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measure evidence-grounded accuracy, which credits a correct answer only if the agent also responds when the evidence is withdrawn and follows it when it is reversed.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.

Agentic LLMs increasingly support scientific prediction by grounding decisions in external evidence. In biology, they promise accurate, interpretable predictions for important problems by integrating complex experimental and computational evidence. However, serialized tool results can contain hidden label shortcuts, such as dataset identifiers or template artifacts, that create apparent success without biological reasoning. To address this risk, we introduce a two-stage audit. Stage 1, Per-Tool TF-IDF Decomposition (PT2D), localizes label-predictive patterns to individual tool results while avoiding signal dilution in the concatenated tool trace. Stage 2, Token-Class Redaction, counterfactually tests whether the frozen LLM depends on the localized shortcut. We apply this audit to TCR-pMHC binding, where tool augmentation substantially outperforms a no-evidence baseline. At face value, this suggests that the LLM has learned to use scientific evidence. The audit overturns this interpretation: PT2D localizes the strongest signal to identifiers in one tool result, and redacting them reduces performance to chance. These findings show how hidden label shortcuts can masquerade as scientific reasoning or discovery, motivating source-level audits before benchmark gains are trusted.

Interactive agent benchmarks map an agent run to a binary outcome through outcome checks. When these checks rely on surface level signals or fail to capture the agent's actual action path, they cannot reliably determine whether the run succeeded. For example, a benchmark task may ask whether Alice's shipping address was changed, while the outcome check only verifies that the agent clicked "Save." This does not guarantee that the intended state change occurred, since the agent may have modified the wrong record. Treating such a run as successful therefore makes the reported score misleading. Benchmark quality thus depends not only on task design, but also on the reliability of outcome detection. We address this problem by introducing an outcome evidence reporting layer for existing benchmarks, without modifying their tasks, agents, or evaluators. The layer performs three functions. First, before scoring, it specifies which stored artifacts are required to verify the claimed outcome for each case. Second, it applies a locked checklist to each completed run and assigns one of three evidence labels: Evidence Pass, Evidence Fail, or Unknown. Third, it reports evidence supported score bounds that quantify uncertainty arising from Unknown cases. Rather than silently counting, discarding, or hiding uncertain cases inside a single aggregate success rate, the framework keeps them explicitly visible. We evaluate the outcome evidence layer on five public benchmarks: ANDROIDWORLD, AGENTDOJO, APPWORLD, tau3 bench retail, and MINIWOB. The resulting reports separate several empirically distinct failure modes.