arXiv AI

BioAgent Bench: An AI Agent Evaluation Suite for Bioinformatics

arXiv:2601. 21800v4 Announce Type: replace Abstract: We introduce BioAgent Bench, an evaluation suite designed for measuring the performance and robustness of AI agents in common bioinformatics tasks.

arXiv AI
Jun 9

A case study of evaluating AI agents on a neuroscience data-to-discovery pipeline

arXiv:2606. 07718v1 Announce Type: new Abstract: Agentic AI tools offer a promising path to automating software development bottlenecks in scientific research pipelines, particularly for stages that take domain experts days to months to build, where scientists care about correctness and robustness, not implementation details.

By Kai A. Horstmann, Ethan Lin, Alice A. Robie, Jennifer J. Sun, Kristin Branson
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
Jun 12

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales

arXiv:2606. 12736v1 Announce Type: new Abstract: AI agents are increasingly being developed to accelerate scientific discovery, yet their practical capabilities in real research settings remain poorly understood.

By Tianyu Liu, Allen Xin Wang, Antonia Panescu, Lisa Xinyi Chen, Wenxin Long, Xinyu Wei, Yueqian Jing, Ziyao Zeng, Jihang Chen, Sihan Jiang, Ziqing Wang, Siyi Gu, Siyu Chen, Xinyang Hu, Haoran Shao, Leqi Xu, Wangjie Zheng, Zhiyuan Cao, Ada Fang, Botao Yu, Kunyang Sun, Rex Ying, Arman Cohan, Qingyu Chen, Lingzhou Xue, Kaize Ding, Yuanqi Du, Wengong Jin, Zhuoran Yang, Marinka Zitnik, James Zou, Hua Xu, Hongyu Zhao
arXiv AI
Jun 24

BioMedArena: An Open-source Toolkit for Building and Evaluating Biomedical Deep Research Agents

arXiv:2605. 06177v2 Announce Type: replace Abstract: Reproducing and comparing deep research agents today is hard: the same backbone evaluated on the same benchmark can report different accuracies across papers because the harness and tool registry differ, and integrating a new model into a comparable evaluation surface costs weeks of model-specific engineering.

By Jinge Wu, Hongjian Zhou, Mingde Zeng, Jiayuan Zhu, Junde Wu, Jiazhen Pan, Ayush Noori, Sean Wu, Honghan Wu, Fenglin Liu, David A. Clifton
arXiv AI
Jul 1

HealthAgentBench: A Unified Benchmark Suite of Realistic Agentic Healthcare Environments for Challenging Frontier AI Agents

arXiv:2606. 31179v1 Announce Type: new Abstract: As AI agents become increasingly capable of complex, long-horizon reasoning, rigorous and holistic evaluation is essential for measuring progress toward real-world healthcare applications.

By Qianchu Liu, Sheng Zhang, Guanghui Qin, Jeya Maria Jose Valanarasu, Maximilian Rokuss, Mingyu Lu, Timothy Ossowski, Juan Manuel Zambrano Chaves, Cliff Wong, Peniel Argaw, Yashna Hasija, Mu Wei, Wen-wai Yim, Qin Liu, Zilin Jing, Jason Entenmann, Naoto Usuyama, Tristan Naumann, Hoifung Poon
arXiv AI
Jul 14

FIRE-Bench: Evaluating AI Agents on the Rediscovery of Scientific Insights

arXiv:2602. 02905v2 Announce Type: replace Abstract: Autonomous agents powered by large language models (LLMs) promise to accelerate scientific discovery end-to-end, but rigorously evaluating their capacity for verifiable discovery remains a central challenge.

By Zhen Wang, Fan Bai, Zhongyan Luo, Jinyan Su, Kaiser Sun, Xinle Yu, Jieyuan Liu, Kun Zhou, Claire Cardie, Mark Dredze, Zhiting Hu, Eric P. Xing
Hugging Face Trending Papers
Jun 30

HealthAgentBench: A Unified Benchmark Suite of Realistic Agentic Healthcare Environments for Challenging Frontier AI Agents

As AI agents become increasingly capable of complex, long-horizon reasoning, rigorous and holistic evaluation is essential for measuring progress toward real-world healthcare applications. We introduce HealthAgentBench, a suite of 54 agentic healthcare tasks across 7 categories each with its unique environment.

arXiv AI
Jun 2

AutoMedBench: Towards Medical AutoResearch with Agentic AI Models

arXiv:2606. 01961v1 Announce Type: new Abstract: Autonomous agents are increasingly expected to support end-to-end medical-AI research workflows, moving beyond isolated prediction tasks or short-form clinical question answering.

By Junqi Liu, Salena Song, Yuhan Wang, Jiawei Mao, Hardy Chen, Xiaoke Huang, Tianhao Qi, Pengfei Guo, Yucheng Tang, Yufan He, Can Zhao, Andriy Myronenko, Dong Yang, Daguang Xu, Yuyin Zhou
arXiv AI
Jun 30

meta-pipe: An LLM-agent pipeline for end-to-end automated systematic review and meta-analysis

arXiv:2606. 28363v1 Announce Type: cross Abstract: Objective: To describe the architecture and design rationale of meta-pipe, an open-source large language model (LLM)-agent pipeline that integrates the complete systematic review and meta-analysis (SR/MA) workflow -- from literature search through statistical analysis, manuscript generation, and quality assurance -- with mandatory human oversight at critical decision points.

By Hsieh-Ting Lin, Jiunn-Tyng Yeh