# PaperDoctor: Evidence-Grounded and Actionable Feedback for Scientific Papers in Progress

arXiv: https://arxiv.org/abs/2609.16995 · HTML: https://mlsanity.com/paper/2609.16995/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Web, search, and research agents, one of 16 directions in LLM agents and tool use.
- Builds on 44 of its 50 references that are in the map.
- First posted on arXiv 15 Sep 2026.

## Placed in

- LLM agents and tool use / [Web, search, and research agents](https://mlsanity.com/agents/web-search-and-research-agents/)

## Builds on (most cited first, 30 of 44)

- [SWE-bench: Can Language Models Resolve Real-World GitHub Issues?](https://mlsanity.com/paper/2310.06770/) (2023)
- [The AI Scientist: Towards Fully Automated Open-Ended Scientific Discovery](https://mlsanity.com/paper/2408.06292/) (2024)
- [Enabling Large Language Models to Generate Text with Citations](https://mlsanity.com/paper/2305.14627/) (2023)
- [MLE-bench: Evaluating Machine Learning Agents on Machine Learning Engineering](https://mlsanity.com/paper/2410.07095/) (2024)
- [Agent Laboratory: Using LLM Agents as Research Assistants](https://mlsanity.com/paper/2501.04227/) (2025)
- [The AI Scientist-v2: Workshop-Level Automated Scientific Discovery via Agentic Tree Search](https://mlsanity.com/paper/2504.08066/) (2025)
- [MLAgentBench: Evaluating Language Agents on Machine Learning Experimentation](https://mlsanity.com/paper/2310.03302/) (2023)
- [PaperBench: Evaluating AI's Ability to Replicate AI Research](https://mlsanity.com/paper/2504.01848/) (2025)
- [RARR: Researching and Revising What Language Models Say, Using Language Models](https://mlsanity.com/paper/2210.08726/) (2022)
- [DeepSeek-Prover-V2: Advancing Formal Mathematical Reasoning via Reinforcement Learning for Subgoal Decomposition](https://mlsanity.com/paper/2504.21801/) (2025)
- [ScienceAgentBench: Toward Rigorous Assessment of Language Agents for Data-Driven Scientific Discovery](https://mlsanity.com/paper/2410.05080/) (2024)
- [Can large language models provide useful feedback on research papers? A large-scale empirical analysis](https://mlsanity.com/paper/2310.01783/) (2023)
- [RE-Bench: Evaluating frontier AI R&D capabilities of language model agents against human experts](https://mlsanity.com/paper/2411.15114/) (2024)
- [CycleResearcher: Improving Automated Research via Automated Review](https://mlsanity.com/paper/2411.00816/) (2024)
- [CORE-Bench: Fostering the Credibility of Published Research Through a Computational Reproducibility Agent Benchmark](https://mlsanity.com/paper/2409.11363/) (2024)
- [Attributed Question Answering: Evaluation and Modeling for Attributed Large Language Models](https://mlsanity.com/paper/2212.08037/) (2022)
- [MARG: Multi-Agent Review Generation for Scientific Papers](https://mlsanity.com/paper/2401.04259/) (2024)
- [DeepReview: Improving LLM-based Paper Review with Human-like Deep Thinking Process](https://mlsanity.com/paper/2503.08569/) (2025)
- [AI-Researcher: Autonomous Scientific Innovation](https://mlsanity.com/paper/2505.18705/) (2025)
- [AgentReview: Exploring Peer Review Dynamics with LLM Agents](https://mlsanity.com/paper/2406.12708/) (2024)
- [ML-Bench: Evaluating Large Language Models and Agents for Machine Learning Tasks on Repository-Level Code](https://mlsanity.com/paper/2311.09835/) (2023)
- [Large language models for automated scholarly paper review: A survey](https://mlsanity.com/paper/2501.10326/) (2025)
- [Hilbert: Recursively Building Formal Proofs with Informal Reasoning](https://mlsanity.com/paper/2509.22819/) (2025)
- [Can LLM feedback enhance review quality? A randomized study of 20K reviews at ICLR 2025](https://mlsanity.com/paper/2504.09737/) (2025)
- [Peer Review as A Multi-Turn and Long-Context Dialogue with Role-Based Interactions](https://mlsanity.com/paper/2406.05688/) (2024)
- [SciReplicate-Bench: Benchmarking LLMs in Agent-driven Algorithmic Reproduction from Research Papers](https://mlsanity.com/paper/2504.00255/) (2025)
- [ResearchCodeBench: Benchmarking LLMs on Implementing Novel Machine Learning Research Code](https://mlsanity.com/paper/2506.02314/) (2025)
- [HALoGEN: Fantastic LLM Hallucinations and Where to Find Them](https://mlsanity.com/paper/2501.08292/) (2025)
- [AutoReproduce: Automatic AI Experiment Reproduction with Paper Lineage](https://mlsanity.com/paper/2505.20662/) (2025)
- [TreeReview: A Dynamic Tree of Questions Framework for Deep and Efficient LLM-based Scientific Peer Review](https://mlsanity.com/paper/2506.07642/) (2025)

## Abstract (arXiv)

Autoresearch agents are reshaping the research ecosystem, but they can also let flawed claims enter the literature at scale. Human advisors catch such issues in drafts through careful, traceable feedback, yet advisor-style assessment requires extensive manual effort and does not scale. To shift automated paper assessment from a judge to a diagnostician, we introduce PaperDoctor, an agent framework for pre-submission feedback with three key innovations. First, a holistic hierarchical framework evaluates writing, layout, references, code, theory, prior work, and experiments through three layers: L1 surface screening, L2 typed verifiers that route each claim to the appropriate evidence, and L3 reproducers that rerun experiments by priority. Second, each finding contains an observation, a pointer to specific evidence such as a sentence, equation, or code line, and a revision suggestion, making critiques auditable and actionable. Third, PaperDoctor selectively rebuilds and reruns experiments based on claim importance and compute budget, surfacing reproducibility gaps and quantitative limitations that are invisible from the manuscript alone. We evaluate PaperDoctor on 30 in-progress papers, yielding 70.6% agreement and all positive holistic scores, and on 40 manuscripts across machine learning, natural science, and social science, covering human- and AI-authored papers with code. Overall, PaperDoctor produces more auditable feedback than human and other agentic reviewers, pairs critiques with concrete suggestions by design, and complements dimensions often overlooked by human reviewers. We also develop an interactive interface that lets authors browse findings grounded in their paper. PaperDoctor reframes automated paper assessment as diagnosis rather than verdict, taking a concrete step toward AI advisors for more rigorous AI-assisted scientific discovery.