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
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:2608. 06961v1 Announce Type: new Abstract: Early-stage molecular design is an iterative process, not just a task of generating molecules.
By Zhu Wang, Jiangyu Chen, Yingjun Shang, Yuhui Yao, Laiao Lu, Tianfan Fu, Na Zou
arXiv:2606. 12674v1 Announce Type: new Abstract: Compact language models (LMs) reduce cost, latency, and deployment risk for tool agents.
By Kushal Raj Bhandari, Ling Yue, Ching-Yun Ko, Dhaval Patel, Shaowu Pan, Pin-Yu Chen, Jianxi Gao
arXiv:2609.01045v1 Announce Type: new
Abstract: Large Language Models (LLMs) have demonstrated remarkable capabilities as powerful components in agentic systems, enabling sophisticated reasoning and...
By Enci Zhang, Haofeng Wang, Yuesheng Zhu, Xiaole Cui, Guibo Luo
arXiv:2607. 16038v1 Announce Type: new Abstract: Scientific work increasingly spans heterogeneous artifacts -- papers, code, datasets, scientific file formats, model outputs, figures, manuscripts, and team decisions -- yet general-purpose AI assistants rarely preserve these objects as a coherent, auditable research state.
By SciForge Team, Zhangyang Gao, Minghao Fang, Yifei Liu, Hanhui Yang, Xinyu Gu, Shixiang Tang, Siqi Sun, Lei Bai, Cheng Tan, Mengdi Liu, Hao Wu, Shuizhou Chen
arXiv:2608. 03468v1 Announce Type: new Abstract: Historical tool-use trajectories provide valuable experience for large language model (LLM) agents to plan and coordinate tool usage.
By Xiuhui You, Jiayi Luo, Zichao Shen, Qingyun Sun, Ziwei Zhang
arXiv:2608. 10039v1 Announce Type: new Abstract: Agentic workflows have become an important abstraction for building reliable LLM-based automation systems by organizing large language models (LLMs), tools, and control logic into explicit execution structures.
By Shuo Hao, You Lu, Bihuan Chen, Xin Peng
DAGent introduces an Evaluate‑then‑Grow planning approach for deep research agents, building directed acyclic graphs incrementally based on confidence and uncertainty from completed tasks. The framework includes a hierarchical context layer for efficient query handling and a structural reinforcement learning component, DAGRPO, that rewards topology‑conditioned execution. Experiments on BrowseComp‑Plus, GAIA, and xbench‑DeepSearch show DAGent outperforming strong baselines across multiple backbones and scaling to large language models.
By Hanwen Liu, Yuanfu Sun, Qiaoyu Tan
Hybrid Semantic Tool Discovery for Enterprise MCP Gateway presents SCOUT, a system that addresses two major challenges in large language model (LLM) agent tool usage: a context‑engineering bottleneck and a tool discoverability barrier. SCOUT reframes tool exposure as a context‑selection problem, injecting only relevant tools into the model’s context window and providing two MCP meta‑tools—tool_search and execute_tool—to perform hybrid retrieval via BM25 and dense vector search. In production at PayPal, SCOUT cuts MCP tool‑token consumption by 99%, dramatically reducing per‑query inference cost while remaining model‑agnostic and requiring no client‑side changes.
By Olympia Saha, Amy Wang, Srinivasan Manoharan
arXiv:2607. 14642v1 Announce Type: new Abstract: As Model Context Protocol (MCP) servers emerge as the core infrastructure for connecting LLMs with external tools, existing benchmarks leverage real-world MCP servers to evaluate LLM agents' tool-using capabilities.
By Huanxi Liu, Kun Hu, Jiaqi Liao, Qiang Wang, Pengfei Qian, YuanZhao Zhai, Dawei Feng, Bo Ding, Huaimin Wang
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