BaseCamp is an agentic AI framework that automates the decision layer of DNA sequencing pipelines by deploying six specialized AI agents for tasks such as sample intake, quality control, alignment, variant calling, annotation, cross‑stage monitoring, and reporting. The agents rely on established bioinformatics tools for actual sequence analysis, while using fine‑tuned, domain‑specialized large language models to select, configure, and interpret these tools’ outputs, ensuring reproducibility and local data privacy. Evaluation demonstrates that the agents’ configurations align with expert practice, provide an explicit filtering ledger for traceability, and detect anomalies that traditional monitoring may miss.
By Eranga Bandara, Xueping Liang, Asanga Gunaratna, Tharaka Hewa, Abdul Rahman, Peter Foytik, Safdar H. Bouk, Sachini Rajapakse, Isurunima Kularathna, Pramoda Karunarathna, Chalani Rajapakse, Ng Wee Keong, Kasun De Zoysa, Amin Hass, Wathsala Herath, Ross Gore, Ravi Mukkamala, Nihal Siriwardanagea, Gihan Siriwardanagea, Aruna Withanage, Nilaan Loganathan, Sachin Shetty
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: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: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: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:2606. 11150v1 Announce Type: new Abstract: Large language models (LLMs) are rapidly acquiring capabilities relevant to biological research, from literature synthesis to interpretation of experimental data.
By Andrew Bo Liu, Samira Nedungadi, Bryce Cai, Alex Kleinman, Harmon Bhasin, Seth Donoughe
arXiv:2605. 09366v3 Announce Type: replace Abstract: Transforming neuroimaging data into clinically actionable biomarkers is a knowledge-intensive and labor-intensive process.
By Keqi Han, Songlin Zhao, Yao Su, Xiang Li, Yixuan Yuan, Lifang He, Carl Yang
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: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
The Bioinfoysis Technical Report introduces a multi‑agent harness designed to improve long‑horizon bioinformatics tasks by maintaining persistent, artifact‑grounded analysis runs. It combines global planning with step‑wise, evidence‑driven replanning, ensuring intermediate results are tied to responsible agents and preventing stale evidence reuse. The system was evaluated on BixBench and LAB‑Bench 2, achieving state‑of‑the‑art accuracy and demonstrating that reliable bioinformatics automation relies on robust planning, execution, memory, and evidence flow.
By Qingyang Shao, Xin Zhang, Zhouyang Yuan, Xianying Chen, Yujia Xiang, Zihao Yang, Tong Ye, Yangqi Zhang, Jiakang Xu, Xiaoqing Yan, Xuan Luo, Keyi Li, Enci Fan, Kai Kang, Zhuohan Liu, Xingyu Jin, Chunran Teng, Tao Li, Xinyu Lv, Minghui Wang, Wenfeng Li, Yidan Gao, Siyu Liu, Mingrui Luo, Zhu Liang, Guanren Qiao, Zhiping Xu
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.
OSWorld-Science is a benchmark and evaluation environment for computer-using agents that use visual language models (VLMs) to perform scientific software tasks. It includes 12 VLMs and 146 high-quality tasks across domains such as molecular drawing, pathology image analysis, statistical computing, and physical simulation, with artifact-based evaluation and a harness that logs interactions and supports model comparison. The benchmark was developed through expert proposals and iterative human–AI co‑design, and results show that current VLMs still struggle with key scientific questions, offering insights into factors like language, reasoning, and context length.
By Dingyuan Dai, Heli Qi, Lei Liu, Yinxi Li, Baiding Chen, Zijun Dou, Qingcheng Zeng, Qi Kang, Oliver Sun, Eric Wang, Bo Zhou, Haixin Wang, Yufan Du, Shi Bo, Ruihan Lin, Mengqi Yuan, Dunjie Lu, Steven Dillmann, Yiming Shi, Tina Su, Amy Xin, Minghao Liu, Xi Wang, Xu Huang, Ge Zhang, Pengyu Nie, Zhen Yang, Jie Tang, Juanzi Li, Weihao Xuan, Tianyu Liu