arXiv Computation and Language

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

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.

arXiv AI
Jul 8

Prompt-to-Paper: Agentic AI System for Bioinformatics

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 AI
Jul 21

AI for Auto-Research: Roadmap & User Guide

arXiv:2605. 18661v2 Announce Type: replace Abstract: AI-assisted research is crossing a threshold: fully automated systems can now generate research papers for as little as $15, while long-horizon agents can execute experiments, draft manuscripts, and simulate critique with minimal human input.

By Lingdong Kong, Xian Sun, Wei Chow, Linfeng Li, Kevin Qinghong Lin, Xuan Billy Zhang, Song Wang, Rong Li, Qing Wu, Wei Gao, Yingshuo Wang, Shaoyuan Xie, Jiachen Liu, Leigang Qu, Shijie Li, Lai Xing Ng, Benoit R. Cottereau, Ziwei Liu, Tat-Seng Chua, Wei Tsang Ooi
arXiv AI
Oct 16

Do Agents Need a New Kind of Paper? SPRA: Structured Paper Representation for Agents

The paper introduces SPRA (Structured Paper Representation for Agents), a comprehensive representation of AI research papers that organizes key research elements—Problems, Contributions, Components, ExperimentSetups, Measures, and Findings—into typed relations for easier querying, traversal, and reuse. SPRA includes paper-level citation relations that capture dependencies, component usage, and comparisons, and it has been instantiated across more than one million AI papers, yielding millions of research units and internal relations. Empirical evaluations show that SPRA improves source-conditioned scientific QA and directed cross-paper reasoning over passage retrieval while significantly reducing input and output token counts, demonstrating its practicality for scientific workflows.

By Yutong Leng, Haojiong Chen, Fukai Shang, Xiaoyang Wang, Mindong Liu, Runyuan Ma, Jiantao Qiu
arXiv AI
Sep 3

Can Coding Agents Reproduce Findings in Computational Materials Science?

The paper introduces AutoMat, a benchmark designed to test large language model (LLM) coding agents on their ability to reproduce claims from computational materials science. AutoMat presents three challenges: reconstructing underspecified procedures, navigating specialized toolchains, and assessing whether the evidence supports a claim. Experiments show that current LLM agents achieve low success rates, with the best setting reaching only 53%, and failures stem mainly from incomplete procedures, methodological deviations, and execution fragility.

By Ziyang Huang, Yi Cao, Ali K. Shargh, Jing Luo, Ruidong Mei, Mohd Zaki, Zhan Liu, Wyatt Bunstine, William Jurayj, Somdatta Goswami, Tyrel McQueen, Michael Shields, Jaafar El-Awady, Paulette Clancy, Benjamin Van Durme, Nicholas Andrews, William Walden, Daniel Khashabi