Large language model research agents can connect literature retrieval, analysis code, and manuscript preparation, but coherent output does not establish scientific validity. We developed Plato-Bio, a biology-routed extension of the open Plato/Denario architecture that couples explicit workflow states with provenance records, citation checks, claim-to-evidence links, scoped file writes, and publication gates.
arXiv:2607. 09349v1 Announce Type: cross Abstract: Retrieval-augmented generation evaluation checks whether model claims are factually grounded in retrieved documents.
By Cedric Caruzzo, Donggeun Yoo, Tae Soo Kim
arXiv:2606. 11208v1 Announce Type: cross Abstract: Biomedical findings often seem to conflict across studies, but many of these differences are context-dependent rather than true contradictions.
By Elias Hossain, Sanjeda Sara Jennifer, Sabera Akter Bushra, Niloofar Yousefi
arXiv:2606. 19245v1 Announce Type: new Abstract: Artificial intelligence (AI) agents promise to accelerate drug discovery by compressing interpretation and decision-making loops, but practical deployment requires trusted evaluation on realistic program decisions.
By Hannah Le, Ramesh Ramasamy, Alex Urrutia, Mahsa Yazdani, Tim Proctor, Kenny Workman
arXiv:2607. 24878v1 Announce Type: cross Abstract: Phenotype-driven diagnostic benchmarks usually report the rank of the reference disease, but they rarely reveal which plausible alternatives are ranked above it or what evidence a tool-using model examines before making its decision.
By Guiling Guo, Jia Yang, Jiahao Xu, Shuyuan Zheng, Zhonghai Sun, Qiyuan Li
arXiv:2606. 09500v1 Announce Type: new Abstract: Objective.
By Yoojin Nam, Jinhoon Jeong, Namkug Kim
Frontier large language models (LLMs) are increasingly integrated into scientific workflows, yet their growing biological capabilities may outpace current safeguards. To assess the biological risks of frontier models, we develop Intern-BioBreaker, a specialized bio-red-teaming model, together with an integrated computational-to-physical framework that couples model-level stress testing with wet-lab validation.
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: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. 16149v1 Announce Type: new Abstract: Most medical AI systems improve by scaling additional machinery: more fine-tuning data, more agents, and/or larger retrieval databases.
By Minh-Ha Nguyen, Erica Gray, Chih-Ting Yang, Rizwan Hamid, Lingyao Li, Siyuan Ma, Thomas A. Cassini, Cathy Shyr
arXiv:2607. 19262v1 Announce Type: new Abstract: As pathogen genomic surveillance scales, the bottleneck is shifting from data generation to analysis.
By Harmon Bhasin, Kevin Flyangolts, Dianzhuo Wang, Evan Seeyave, Arjun Banerjee, Amanda Darling, Joshua Stallings, David Stern, Shawn Higdon, Claire Duvallet, Bryan Tegomoh, Kenny Workman
arXiv:2606. 11830v1 Announce Type: new Abstract: Background.
By Qianyu Yao, Fei Sun, Bocheng Huang, Wei Chen, Jiarui Jiang, Shu Quan, Yifei Chen, Wenjie Xu, Bo li, Liping Su, Ruoqiong Wu, Huhai Hong, Huimei Wang