AI Scientists Are Only as Good as Their Evidence: A Stratified Ablation of Proprietary Data and Reasoning Skills in Drug-Asset Valuation

Autonomous coding agents are increasingly proposed as AI-scientist systems that conduct analyses and write research reports, but executing a prescribed analysis is not the same as making a discovery. Existing benchmarks are configured for reproduction: tasks, data, and rubrics are built around a hidden target study, and recovery of its result is rewarded. We present TruthInsightBench, a benchmark configured for discovery. Its 40 blind tasks, drawn from 40 peer-reviewed studies across 10 scientific domains, expose only a neutral scientific objective and frozen data; source conclusions, expected values, and analysis paths are withheld, leaving the agent to determine what claim the data support. A fixed LLM-based judge scores the evidentiary maturity of an agent's own claims along six dimensions, operationalized as 29 artifact-grounded items, with automated, deterministic aggregation and no per-instance human grading, so evaluation can be repeated automatically as agents evolve. On one frozen base model, four coding agents form a narrow plateau (58.4-60.3 of 100) with no statistically reliable pairwise separation: they execute and document analyses competently, with comparatively strong evidence auditability and novelty, but largely lack the discriminating acts that establish a trustworthy claim (controls, robustness, falsifiability, and cross-dataset generalization). The bottleneck is scientific judgment rather than coding, and genuine discovery remains out of reach. TruthInsightBench makes this gap a measurable target; data and scoring code are at https://github.com/TruthInsight-stack/TruthInsightBench.

AI scientist systems are described as tools, coauthors, or founders, but we evaluate them as if only the final answer matters. This position paper argues that outcome-only evaluation is insufficient, and that task outcome, mechanism fidelity, and epistemic honesty must be measured separately. Our evidence comes from 28 episodes of a coding agent attempting to rediscover a known particle identification observable in a Geant4 simulation, including an 8-episode probe across two additional frontier models. In 4/20 primary-model and 3/8 cross-model episodes, agents reach right-looking results through incorrect reasoning that breaks when conditions change, which we call Correct Answer, Wrong Mechanism (CAWM). Honesty and mechanism fidelity dissociate within a single agent trajectory. When given a partially misleading prior, all five agents reject the false component on evidence, yet one defends its chosen observable with physics inconsistent with its own data. In the simulation-based discovery setting studied here, coding agents prove reliable tools but unreliable scientific co-authors for open-ended claim-making, where co-author trust requires mechanism-fidelity verification they do not reliably self-apply. The failure is detectable, and we propose a lightweight test. A one-step regime-shift check needs only the agent's claim and flags the over-generalized cases. A companion recomputation flags the remaining cases when the correct observable is known. Together, these checks flag every CAWM case in this study.

Recent advances in foundation models have enabled AI scientists to automate increasingly complete research workflows, from hypothesis generation and code execution to manuscript preparation. Yet workflow coverage alone does not provide access to the full evidence on which scientific discovery depends. Existing systems typically reason over text, code, labels, or precomputed summaries, leaving scientifically decisive spatial, temporal, cross-channel, and procedural relations unavailable to the agent. We introduce OmniScientist, an end-to-end, omni-modal AI scientist that conducts multidisciplinary research directly from heterogeneous raw evidence. A perception layer and 3 autonomous agents for ideation, experiment, and writeup operate within a deterministic pipeline, allowing observations to shape research questions, experimental decisions, and final claims throughout the research lifecycle. By running idea, rigour, and claim checks in code, the system enforces novelty screening, statistical validity, execution provenance, and numerical traceability. We evaluate OmniScientist on 36 real-data cases spanning 5 discipline families, 4 families of scientific evidence, and modalities including images, signals, audio, video, 3-D structures, trajectories, tables, formulae, and graphs. The system completes the full path from raw data to a compiled manuscript in all 36 cases and achieves a mean overall paper score of 6.3 with the reference reasoning backbone. In paired comparisons against a blind variant that receives only precomputed scalar features, direct perception improves all 7 evaluation dimensions and wins 85% of head-to-head judgments. These results show that lifecycle-wide perception is essential for evidence-grounded scientific discovery and provides a practical path toward broadly capable AI scientists.