SciTrace: Trajectory-Aware Safety Reasoning for Scientific Discovery Agents

Large language models (LLMs) increasingly support science, but they can also convert hazardous scientific knowledge into actionable misuse guidance. Existing benchmarks often rely on templated queries disconnected from real-world hazards, and employ LLM-as-a-Judge paradigms without domain grounding. To address this, we introduce SciHazard, a real-world-grounded benchmark for scientific risks and a dataset agnostic evaluation framework for measuring harmfulness. SciHazard contains 2400 hazardous questions and 600 oversafety questions across 12 disciplines, with both queries grounded in regulated entities and documented failure scenarios. To compute \textsc{DeHarm-Score} , we develop a decomposed evaluating procedure that combines query hazard severity, refusal behavior, and response-level risk. For non-refused responses, it further decomposes response-level harm into \textsc{Executability}, quantified via dynamic checklists with importance weighting, and \textsc{Net-new risk}, assessed through retrieval-augmented claim extraction and synthesis-barrier verification. An expert-validation study shows that \textsc{DeHarm-Score} improves agreement with expert annotations by 90.17% over the strongest baseline. We benchmark 31 frontier LLMs and deep research agents in an extensive scientific safety evaluation. Notably, deep research agents yield 32.3% higher mean \textsc{DeHarm-Score} than standard LLMs, exposing autonomous agents as a critical blind spot in current safety defenses. Code and dataset are available at https://anonymous.4open.science/r/DeharmScore-7B55.

Existing benchmarks for autonomous AI scientists evaluate only final outputs---generated code, hypotheses, or papers---yet discard the reasoning process by which those outputs were obtained. This makes it impossible to audit scientific methodology, diagnose failure modes, or distinguish systematic reasoning from fortunate guessing. We present \textbf{OpenDiscoveryTrace}, a public dataset of 558 complete AI scientific agent trajectories that captures how models reason, not just what they produce. Each trajectory records a structured 9-field-per-step trace---including thoughts, tool calls, observations, errors, revision triggers, and self-reported confidence---as models execute 124 scientific tasks spanning drug discovery, materials science, genomics, and scientific literature analysis. The dataset covers seven models: three frontier models (GPT-5.4, Claude Opus 4.6, and Gemini 3.1 Pro; 124 trajectories each, fully balanced across domains and difficulty levels) and four open-weight models (Qwen2.5-7B, Mistral-7B-v0.3, Phi-3.5-mini, and Qwen2.5-1.5B; 30 each), plus 60 live-retrieval variant trajectories. Pilot analysis on 363 LLM-judged trajectories reveals that process traces expose behavioral differences invisible to output-only evaluation: all three frontier models achieve comparable success rates (84--89%), yet Claude Opus 4.6 produces 30$\times$ more errors than GPT-5.4 (2.5 vs. 0.08 per trajectory, $p < 0.0001$, Cliff's $\delta = 0.613$), with qualitatively different error profiles---66.7% tool misuse for Claude versus 83.6% reasoning errors for GPT-5.4. We define five benchmark tasks with baselines from logistic regression, random forests, LSTMs, and Transformer models. The dataset, trace schema, agent harness, and benchmark definitions are publicly available under CC BY 4.0 to support research on process-level evaluation, scientific agent auditing, and AI governance.

Large language models (LLMs) are increasingly embedded in AI for Science (AI4Science) workflows, from scientific question answering and literature analysis to laboratory planning and autonomous discovery. This progress creates an urgent need for safety benchmarks that evaluate not only scientific competence, but also whether models recognize and avoid risks in high-stakes scientific contexts. Existing AI4Science safety datasets cover several disciplines and task formats, leaving the underlying risk dimensions underspecified. We introduce \textbf{SciRisk-Bench}, a benchmark designed to evaluate AI4Science safety from two complementary perspectives: explicit risk dimensions and scientific disciplines. SciRisk-Bench covers 7 disciplines, 31 subdisciplines and 10 risk dimensions. In the experimental section, we evaluate both mainstream LLMs and science-oriented LLMs across risk dimensions, disciplines, and sub-disciplines, enabling fine-grained diagnosis of where scientific models remain unsafe.