A Scientific Claim Stability Framework for Evaluating MRI Morphometry Pipelines

Scientific coding agents produce interdependent code, results, figures, and claims, yet evaluating final outputs alone does not establish whether their conclusions are scientifically supported. We formulate evidence-grounded multimodal scientific analysis, requiring agents to produce executable analyses and claims supported by results and visualizations from the same run. We introduce SciRIGOR, an evaluation framework and benchmark comprising 100 cases from scientific articles across six domains and 17 subfields. The framework reconstructs typed evidence graphs, separates artifact fidelity from relational validity, and scores complete claim-support paths while localizing the earliest unsupported relation. Source-grounded alternative paths accommodate scientifically equivalent analyses and visualizations. We evaluate 11 agent/model configurations. On full-benchmark runs, claims agree with faithful and unfaithful results at nearly identical rates (91.8% versus 91.0%). Yet no system exceeds 62.6% on the soft evidence-chain score or 18.0% strict whole-chain success. These findings show that internal coherence does not establish scientific correctness: evaluation must verify support along the complete data-to-claim path.

Evaluating scientific arguments requires assessing the strict consistency between a claim and its underlying multimodal evidence. However, existing benchmarks lack the scale, domain diversity, and visual complexity needed to evaluate this alignment realistically. To address this gap, we introduce M2-Verify, a large-scale multimodal dataset for checking scientific claim consistency. Sourced from PubMed and arXiv, M2-Verify provides over 469K instances across 16 domains, rigorously validated through expert audits. Extensive baseline experiments show that state-of-the-art models struggle to maintain robust consistency. While top models achieve up to 85.8% Micro-F1 on low-complexity medical perturbations, performance drops to 61.6% on high-complexity challenges like anatomical shifts. Furthermore, expert evaluations expose hallucinations when models generate scientific explanations for their alignment decisions. Finally, we demonstrate our dataset's utility and provide comprehensive usage guidelines.

Large language model (LLM) agents can autonomously run neuroimaging analyses from research questions to reported findings. Existing agentic systems use tools to check that code runs and reported values match its output, but rely on LLM judgment to decide which results warrant scientific reporting. We show that LLM judges endorse site-confounded findings even when the confound is presented as evidence. We present CONFIRM, a framework that separates running an analysis from deciding which findings to report. CONFIRM encodes each hypothesis as a machine-readable, pre-specified analysis plan that fixes the claim and its pass criteria before computing results. It then filters results through five deterministic gates (search history and multiplicity, confounds, power, analytic stability, and replication) under three configurable reporting standards, from least to most demanding: Screen, Replicate, and Full. Failed claims receive diagnoses that guide follow-up analyses. To evaluate reporting decisions at the claim level, we introduce NeuroClaimBench, comprising 489 executable neuroimaging claims with frozen data, including literature-supported findings and 150 controls designed to violate individual methodological requirements. On NeuroClaimBench, CONFIRM falsely supports at most 3% of controls, compared with 23--38% for the baselines, while recovering up to 61% of literature-supported claims. When auditing an existing agent, CONFIRM reduces false support on controls from 23% to 0% while retaining the agent's literature-supported claims. Its diagnostic feedback also produces more supported revisions than Self-Refine with fewer LLM calls. Together, CONFIRM and NeuroClaimBench show that basing reporting decisions on pre-specified analysis plans and deterministic gates is essential for trustworthy autonomous scientific discovery.