Bringing analytic rigor to agentic AI for science: The Brain Researcher platform for neuroimaging data analysis

AI agents can execute scientific analyses, but an analytic output becomes a defensible claim only after alternatives are weighed and the claim is limited to what the evidence supports. Agents may reproduce failures including selective analysis, premature declarations of success and optimization of imperfect criteria. We present Brain Researcher, an agentic research harness operating in a neuroimaging researcher's computational environment under rules for admissible analyses, required checks and claim scope. In benchmarks, Brain Researcher increased first-choice tool-selection accuracy across seven models by 70.2 percentage points (23.3% without it versus 93.6% with it) and verifiable grounding from 4.6% to 22.0%. In collaborator-led and self-evolving studies, multiverse analyses exposed analytic-choice sensitivity, and scientific review classified claims as accepted, qualified, revised, blocked, rejected or deferred. By linking decisions to evidence and provenance, Brain Researcher embeds methodological judgment within the workflow, not after it.

The Agentic Garden of Forking Paths

Empirical research rarely admits a unique analysis. Different analytical choices can lead to different conclusions from the same data, yet these hidden forking paths are difficult to observe. We show that AI agents capture much of the analytical variation among human researchers while making these paths explicit. Across four high-stakes domains, assigning different personas is sufficient for AI agents to report divergent, often opposing, conclusions from the same data and question, with findings systematically aligned with those beliefs. In a study in which 42 human research teams analyzed the same immigration dataset, AI agents reproduced 72% of the human ideological gap in reported effect estimates. Despite reaching opposing conclusions, it is difficult to identify clear issues in each analysis based on the final AI reports: 86% passed independent AI review and 78% passed majority human expert review. These findings suggest that the central challenge is often not flawed analyses, but selective exploration and reporting from a large space of methodologically defensible analyses. AI agents may amplify this longstanding problem by making such exploration inexpensive and scalable. To address this, we introduce the m-value (multiverse value), the probability that an analysis path would produce a claim at least as extreme as the reported one. We further introduce Agentic Bootstrap, which estimates the m-value by using AI agents to sample plausible analysis paths. Applied to the human immigration study, 13.5% of reported human analyses fell in the most extreme 5% of the analysis space (m<0.05). Scientific evidence should therefore be evaluated not only by a single reported analysis but also by its position within the distribution of analyses that could reasonably have been reported. Agentic Bootstrap makes this distribution observable and turns it into a criterion for scientific credibility.