Authors: Jiacheng Miao, Jonathan K Pritchard, James Zou
Organizations: Department of Biomedical Data Science, Stanford University · Department of Genetics, Stanford University · Department of Biology, Stanford University · Department of Electrical Engineering, Stanford University · Department of Computer Science, Stanford University
Abstract
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.
The deployment of LLM-based agents in scientific analysis raises opposing concerns: that agents may reduce methodological diversity, or that they may amplify the analytic flexibility through which researchers reach motivated conclusions. We argue these worries target two empirically separable layers: a design layer of methodological choices, and a verdict layer in which a decision rule maps estimates to a substantive claim. We test both by running 20 independent executions of Claude Code and Codex on a prominent immigration and social-policy against a many-analysts human baseline. At the design layer, Codex matches human methodological diversity and Claude Code produces nearly three times as many specifications; both agents' effect estimates remain broadly aligned with the human consensus, and no agent model exactly matches any human model. A prompt-induced anti-immigration researcher prior reorganizes each agent's methodological decisions but, unlike for biased human analysts in the same data, does not shift aggregate estimates or final verdicts; nor do agents reroute along the methodological axes humans use to bias their estimates. At the verdict layer, an explicit confirmatory prompt flips Claude Code's verdicts from 10% to 90% support while leaving its coefficient distribution essentially unchanged, operating through rule omission rather than rule softening. AI agents can rival or exceed human methodological diversity at the design layer while remaining vulnerable at the verdict layer. In our setting, the locus of AI bias is not estimation but interpretation.
Multi-agent AI systems improve inference by spawning agents and synthesizing reports. But another agent is not another observation: apparently independent reports may descend from the same evidence, and genuinely independent evidence can produce nearly identical reports. We formalize this as an epistemic Sybil problem. A report Z is an epistemic Sybil extension relative to reports R when I(Theta; Z | R) = 0. No report-only aggregator can generally distinguish replication from independent corroboration: identical reports can warrant different posteriors under unobserved ancestry. A Gaussian shared-root model shows common ancestry does not imply complete redundancy. Repeated extraction adds information toward a source-level ceiling, and correlated extraction errors, which a shared base model can induce among independent agents, lower that ceiling further. We test these predictions with more than 20,000 controlled LLM-agent report and extraction calls on synthetic evidentiary documents. Holding one evidence root fixed while report multiplicity rises from 1 to 32 collapses naive posterior coverage from 0.940 to 0.263. Holding report count fixed while evidence-root multiplicity rises from 1 to 16 closes the gap, and the aggregators are statistically indistinguishable at k = 16. The agent's replicate extraction errors are correlated (gamma_cal = 0.719, estimated out of sample), and a correlated-extraction aggregator restores calibration accordingly. A controlled manipulation isolates representation similarity from evidential ancestry. It changes a report-space deduplication mechanism's mean inferred cluster count by 1.425 (95% CI [1.363, 1.485]), whereas a fourfold change in true ancestry changes it by only 0.040 ([-0.045, 0.120]). Collective inference should therefore track evidential ancestry and dependence, not agent or report multiplicity or similarity.
Forecasts of explosive AI progress hinge on AI agents automating AI research. But evidence on whether agents can carry out open-ended AI research is thin. Current evaluations either test agents on narrow, verifiable tasks, which excludes open-ended research, or submit AI-generated papers to blind peer review, which is overstretched, stochastic, and suffers from poor review quality. We introduce a third way to measure progress towards AI R&D automation. An agent takes on the central, open-ended research question of a high-quality unpublished paper, and the paper's original authors grade its output. We call these shadow evaluations. We ran shadow evaluations on two unpublished NeurIPS 2026 submissions, giving frontier agents six days and thousands of dollars of compute. The agents completed all of the engineering without human help, yet could not make substantial progress towards answering the research questions. As a result, both papers were unambiguously rejected by the authors. We identify five recurring failure modes: poor judgment about the bar for publishable research, uncreative responses to shortcomings in the research design, ineffective backtracking from dead ends, poor resource awareness, and instruction drift. A robustness check with a second model and scaffold reproduced these failures. We release the expert reviews, survey responses, agent repositories, and logs. Our results provide early evidence that today's agents can do the engineering of AI research, but struggle with critical parts of the research lifecycle.