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HFEPX · Eval paper review

MolQuest: A Benchmark for Agentic Evaluation of Abductive Reasoning in Chemical Structure Elucidation

Taolin Han, Shuang Wu, Jinghang Wang, Yuhao Zhou +3 more

Published

Mar 26, 2026

Citations

0

Trust level

Moderate

Usefulness score

37/100 (Low)

Extraction confidence

50% (Moderate)

Derived from extracted protocol signals and abstract evidence.

Rater population

Not reported

Signals refreshed

Mar 26, 2026

Should you rely on this paper?

This paper is adjacent to HFEPX scope and is best used for background context, not as a primary protocol reference.

Use this for comparison and orientation, not as your only source.

Best use

Background context only

Use if you need

A secondary eval reference to pair with stronger protocol papers.

What to verify

Validate the evaluation procedure and quality controls in the full paper before operational use.

Main weakness

No major weakness surfaced.

Human feedback signal
Not explicit
Not explicit in abstract metadata
Evaluation signal
Detected
Eval setup described
Usefulness for eval research
37/100
Adjacent candidate

Treat as adjacent context, not a core eval-method reference.

Abstract

Large language models (LLMs) hold considerable potential for advancing scientific discovery, yet systematic assessment of their dynamic reasoning in real-world research remains limited. Current scientific evaluation benchmarks predominantly rely on static, single-turn Question Answering (QA) formats, which are inadequate for measuring model performance in complex scientific tasks that require multi-step iteration and experimental interaction. To address this gap, we introduce MolQuest, a novel agent-based evaluation framework for molecular structure elucidation built upon authentic chemical experimental data. Unlike existing datasets, MolQuest formalizes molecular structure elucidation as a multi-turn interactive task, requiring models to proactively plan experimental steps, integrate heterogeneous spectral sources (e.g., NMR, MS), and iteratively refine structural hypotheses. This framework systematically evaluates LLMs' abductive reasoning and strategic decision-making abilities within a vast and complex chemical space. Empirical results reveal that contemporary frontier models exhibit significant limitations in authentic scientific scenarios: notably, even state-of-the-art (SOTA) models achieve an accuracy of only approximately 50%, while the performance of most other models remains below the 30% threshold. This work provides a reproducible and extensible framework for science-oriented LLM evaluation, our findings highlight the critical gap in current LLMs' strategic scientific reasoning, setting a clear direction for future research toward AI that can actively participate in the scientific process.

What we could verify

These are the protocol signals we could actually recover from the available paper metadata. Use them to decide whether this paper is worth deeper reading.

Human Feedback Types

missing

None explicit

No explicit feedback protocol extracted.

"Large language models (LLMs) hold considerable potential for advancing scientific discovery, yet systematic assessment of their dynamic reasoning in real-world research remains limited."

Evaluation Modes

strong

Automatic Metrics, Simulation Env

Includes extracted eval setup.

"Large language models (LLMs) hold considerable potential for advancing scientific discovery, yet systematic assessment of their dynamic reasoning in real-world research remains limited."

Quality Controls

missing

Not reported

No explicit QC controls found.

"Large language models (LLMs) hold considerable potential for advancing scientific discovery, yet systematic assessment of their dynamic reasoning in real-world research remains limited."

Benchmarks / Datasets

missing

Not extracted

No benchmark anchors detected.

"Large language models (LLMs) hold considerable potential for advancing scientific discovery, yet systematic assessment of their dynamic reasoning in real-world research remains limited."

Reported Metrics

strong

Accuracy

Useful for evaluation criteria comparison.

"Empirical results reveal that contemporary frontier models exhibit significant limitations in authentic scientific scenarios: notably, even state-of-the-art (SOTA) models achieve an accuracy of only approximately 50%, while the performance of most other models remains below the 30% threshold."

Benchmarks and datasets

No benchmark or dataset names were extracted from the available abstract.

Reported metrics

accuracy
Human feedback details
Uses human feedback
No
Feedback types
None
Rater population
Not reported
Expertise required
General
Evaluation details
Evaluation modes
Automatic Metrics, Simulation Env
Agentic eval
Long Horizon
Quality controls
Not reported
Evidence quality
Moderate
Use this page as
Background context only

Research brief

Metadata summary

Large language models (LLMs) hold considerable potential for advancing scientific discovery, yet systematic assessment of their dynamic reasoning in real-world research remains limited.

Based on abstract + metadata only. Check the source paper before making high-confidence protocol decisions.

Key takeaways

  • Large language models (LLMs) hold considerable potential for advancing scientific discovery, yet systematic assessment of their dynamic reasoning in real-world research remains limited.
  • Current scientific evaluation benchmarks predominantly rely on static, single-turn Question Answering (QA) formats, which are inadequate for measuring model performance in complex scientific tasks that require multi-step iteration and experimental interaction.
  • To address this gap, we introduce MolQuest, a novel agent-based evaluation framework for molecular structure elucidation built upon authentic chemical experimental data.

Researcher actions

  • Compare this paper against nearby papers in the same arXiv category before using it for protocol decisions.
  • Validate inferred eval signals (Automatic metrics, Long-horizon tasks) against the full paper.
  • Use related-paper links to find stronger protocol-specific references.

Caveats

  • Generated from abstract + metadata only; no PDF parsing.
  • Signals below are heuristic and may miss details reported outside the abstract.

Recommended queries

Contribution summary

  • Current scientific evaluation benchmarks predominantly rely on static, single-turn Question Answering (QA) formats, which are inadequate for measuring model performance in complex scientific tasks that require multi-step iteration and…
  • To address this gap, we introduce MolQuest, a novel agent-based evaluation framework for molecular structure elucidation built upon authentic chemical experimental data.
  • This work provides a reproducible and extensible framework for science-oriented LLM evaluation, our findings highlight the critical gap in current LLMs' strategic scientific reasoning, setting a clear direction for future research toward AI…

Why it matters for eval

  • Current scientific evaluation benchmarks predominantly rely on static, single-turn Question Answering (QA) formats, which are inadequate for measuring model performance in complex scientific tasks that require multi-step iteration and…
  • To address this gap, we introduce MolQuest, a novel agent-based evaluation framework for molecular structure elucidation built upon authentic chemical experimental data.

Researcher checklist

  • Human feedback protocol is explicit

    No explicit human feedback protocol detected.

  • Evaluation mode is explicit

    Detected: Automatic Metrics, Simulation Env

  • Quality control reporting appears

    No calibration/adjudication/IAA control explicitly detected.

  • Benchmark or dataset anchors are present

    No benchmark/dataset anchor extracted from abstract.

  • Metric reporting is present

    Detected: accuracy