ToolGate: An Executable Acceptance Pipeline for Tool-Dependent Scientific Benchmark Construction
Authors: Ke Zhang, Yankang Liu, Roya Zandi, Maziar Raissi
Abstract
Scientific benchmarks are commonly built by domain experts who write tasks and cross-check one another's work, or who adapt existing material from textbooks, published papers, and online resources. These routes can produce strong evaluations, but they require substantial per-item labor. Language models can reduce this repeated work by proposing candidates quickly. The remaining problem is acceptance. We target scientific questions whose answers require computations with specialist software rather than unaided reasoning alone. A candidate is invalid if its script fails or returns a different answer, or trivial if a model answers it without the software. We present ToolGate, which treats every generated item as a proposal and keeps it only if three gates pass. First, an executable solution script must reproduce the proposed answer when run with the scientific software. Second, randomized no-tool screening rejects candidates that models can already solve from the prompt alone. Third, a tool-using agent must solve each survivor within a fixed time limit. We instantiate ToolGate in FEniCSx with 500 generation attempts. The local-verification gate retains 478 candidates. For final reporting, we rescreen this pool after generation: two randomized no-tool screens exclude 222 from the reported pool, and direct GPT-5.5 API calls at medium reasoning (the API default) exclude another 121. Of the remaining 135, a GPT-5.5 Codex CLI agent with access to FEniCSx solves 130; exact deduplication leaves 128 unique protocol survivors. ToolGate turns repeated answer checking and difficulty screening into an auditable process while leaving domain design and final review to experts.
As benchmarks grow in complexity, many apparent agent failures are not failures of the agent at all - they are failures of the benchmark itself: broken specifications, implicit assumptions, and rigid evaluation scripts that penalize valid alternative approaches. We propose employing frontier LLMs as systematic auditors of evaluation infrastructure, and realize this vision through BenchGuard, the first automated auditing framework for task-oriented, execution-based agent benchmarks. BenchGuard cross-verifies all benchmark artifacts via structured LLM protocols, optionally incorporating agent solutions or execution traces as additional diagnostic evidence. Deployed on two prominent scientific benchmarks, BenchGuard identified 12 author-confirmed issues in ScienceAgentBench - including fatal errors rendering tasks unsolvable - and exactly matched 83.3% of expert-identified issues on the BIXBench Verified-50 subset, catching defects that prior human review missed entirely. A full audit of 50 complex bioinformatics tasks costs under USD 15, making automated benchmark auditing a practical and valuable complement to human review. These findings point toward AI-assisted benchmark development, where frontier models serve not only as subjects of evaluation but as active participants in validating the evaluation infrastructure itself.
Large language model agents are increasingly connected to scientific software, yet it remains unclear when tool access makes scientific computation more reliable rather than merely more complex. We introduce PHREEQC-MCQ-200, a benchmark for evaluating tool-augmented agents on deterministic aqueous-geochemistry simulations. The benchmark contains 200 multiple-choice questions derived from 21 validated PHREEQC scenarios, requiring agents to construct simulator inputs, execute PHREEQC, inspect structured outputs, and commit to final answers. Across multiple frontier and mid-tier model families, simulator access substantially improves aggregate accuracy, confirming that grounded execution is necessary for many scientific-computation tasks. However, the gains are not monotonic: tool-augmented agents also lose items they answered correctly without tools, revealing regressions that average accuracy alone hides. We further show that output-access protocol matters. A table-of-contents interface can reduce token cost while preserving or improving accuracy for stronger models, but it degrades performance for mid-tier models that cannot reliably navigate structured simulator outputs. PHREEQC-MCQ-200 therefore frames scientific tool use as an end-to-end diagnostic problem rather than a simple tool-calling capability. We argue that evaluations of scientific agents should report not only accuracy, but also item-level retention, output-access sensitivity, trajectory failures, and where the computation chain breaks.
SciCode is the standard measure of the scientific-coding ability of language models: research-level problems that demand both frontier scientific theory and its implementation as working numerical code. It is a component of the Artificial Analysis Intelligence Index and a standing evaluation in government and national-laboratory suites. Yet its scores have recently plateaued: the strongest 2026 models cluster tightly around 60% subproblem accuracy, and a successor model ties its predecessor. We trace this stagnation to defects in the benchmark itself. A per-problem, domain-expert audit of all 65 test problems uncovers 263 defects; 192 of them, spread across 91% of the main problems, cause correct, instruction-following solutions to be wrongly rejected---through non-reproducible gold answers, over-tight tolerances, or self-contradictory specifications. Critically, 78% of these score-suppressing defects require specialized physics or mathematics knowledge to detect, not mere clerical proofreading. We corrected every confirmable defect to produce SciCode-Verified. The corrections add only the specifications a well-posed problem requires, repair grading, and tighten the tests that were too lenient; every change is recorded with its justification and independently re-checked by a second domain expert. We re-evaluate twelve frontier model snapshots on the corrected benchmark and find a substantial recovery: subproblem accuracy rises from 45--60% to 84--98%, and main-problem accuracy from 9--27% to 69--92%. State-of-the-art models are far more proficient in scientific coding than SciCode has suggested---the bottleneck was not model capability, but the quality of the evaluation instrument. We release SciCode-Verified with its complete audit trail as the corrected public standard.