PaperDoctor is an agent framework that provides evidence‑grounded, actionable feedback for scientific papers before submission. It evaluates writing, layout, references, code, theory, prior work, and experiments through a three‑layer hierarchical system, linking each critique to specific evidence and revision suggestions. The system selectively rebuilds and reruns experiments to uncover reproducibility gaps, and an interactive interface lets authors explore findings tied to their manuscript.
By Kevin Qinghong Lin, Siyuan Hu, Pan Lu, Yu Chen, Yanzhe Chen, Owen Queen, Yupeng Chen, Jialin Yu, Junchi Yu, Zifeng Ding, Yuanfeng Ji, Sheng Liu, Jindong Gu, Linjie Li, Mike Zheng Shou, Philip Torr, James Zou
arXiv:2608.28596v1 Announce Type: new
Abstract: Large language model (LLM) agents are increasingly embedded in scientific workflows for literature analysis, drafting, and review. Existing systems adv...
By Nidhi Jha, Siddharth Chaudhary, Ajinkya Kulkarni
arXiv:2607. 02520v1 Announce Type: cross Abstract: Automated research agents increasingly generate code, retrieve literature, and draft scientific artifacts, but they often fail to verify whether generated experiments execute correctly or whether cited sources support generated claims.
By Rajesh Kumar, Waqar Ali, Junaid Ahmed, Abdullah Aman Khan, Shaoning Zeng
arXiv:2608. 04738v1 Announce Type: new Abstract: Autonomous research agents can generate hypotheses, execute experiments, and draft manuscripts, yet their outputs often contain unsupported claims and inconsistencies between research questions, experiments, results, and conclusions.
By Zhenjiang Ren, Ruiji Li, Xujing Zhang, Ziliang Pang, Shuo Ren, Jiajun Zhang
The paper explores whether natural‑language documentation aids coding agents in fixing software bugs and introduces a roundtrip benchmark that evaluates code descriptions by regenerating code and testing it. It finds that description completeness, not length, determines fidelity, and presents an optimizer that can produce fully faithful descriptions that generalize to new files. However, experiments across two model families and ten repositories show that such compact documentation does not improve an agent’s ability to resolve real repository issues compared to using the issue alone.
By Md Shohel Arman, Igor Molybog
arXiv:2606. 21005v2 Announce Type: replace Abstract: Scientific discovery workflows often depend on structured curation from the literature.
By Sheng Zhang, Qin Liu, Renqian Luo, Shufang Xie, Reuben Tan, Sean Hayes, Gregory Bryman, Wendong Ge, Ruilian Zhang, Oluwaseun Egbelowo, Kelly Yee, Hoifung Poon
arXiv:2609.06192v1 Announce Type: new
Abstract: Scientific coding agents produce interdependent code, results, figures, and claims, yet evaluating final
outputs alone does not establish whether the...
By Bowen Liu, Shuo Nie, Bodong Du, Xiaomeng Li
arXiv:2606. 31478v1 Announce Type: new Abstract: Autonomous research agents can now draft hypotheses, write code, run experiments, and produce papers, but they remain brittle when experiments fail.
By Jie Ma, Binfei Chu, Jie Gao, Jinlu Zhang, Yiwei Ma, Yi Tan, Jiayi Ji, Xiaoshuai Sun, Rongrong Ji
arXiv:2607. 05456v1 Announce Type: new Abstract: While recent advances in large language models have enabled end-to-end automated manuscript generation, existing systems suffer from three critical deficiencies: (i) generated claims are not deterministically grounded in verifiable literature, (ii) experimental results are frequently fabricated rather than executed, and (iii) there exists no standardized, multi-dimensional framework to assess whether AI-generated manuscripts meet the quality and rigor required for real-world publication.
By Ramsha Kamran, Maheera Amjad, Zartasha Mustansar, Arsalan Shaukat, Salma Sherbaz, Muhammad U. S. Khan
arXiv:2608. 05179v1 Announce Type: cross Abstract: Large language model (LLM) agents are increasingly used across the scientific research lifecycle: ideation, literature search, experiment design and execution, analysis, manuscript drafting, and review.
By Tianyu Ding, Aditya Nannapaneni, Bingfan Liu, Ling Zhang
The paper "Beyond Execution: Auditing Experimental Fidelity in LLM-Driven Scientific Research" argues that large language model agents must faithfully implement reference methods, design experiments that truly test claims, and provide supporting evidence. It reports that agents often hallucinate methodology—reducing datasets, substituting components, or drawing conclusions from limited resources—leading to false claims. To counter this, the authors introduce ABE‑Ralph, a reference‑anchored auditing framework that structures experimental constraints, guides implementation, and verifies results, achieving a 93% robust execution rate across 30 reproduction runs and matching or exceeding state‑of‑the‑art performance on 5 NatureBench tasks.
"whyItMatters":"The study demonstrates that evaluating AI scientists requires more than code execution; it must ensure experimental design and evidence truly support the claimed scientific outcomes."
By Lezhi Yu, Xiaogang Xu, Yuhua Zhou, Shuibing He, Aimin Pan
arXiv:2607. 07980v1 Announce Type: cross Abstract: Coding agents now author entire pull requests, and practitioners sharply disagree about what this does to code review: whether it becomes the bottleneck, whether human review is still necessary, and whether it quietly erodes the understanding that it once built.
By Shyam Agarwal, Courtney Miller, Christian K\"astner, Bogdan Vasilescu