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Large language model (LLM)-based systems are increasingly deployed to conduct scientific research autonomously, yet whether their reasoning adheres to the epistemic norms that make scientific inquiry self-correcting is poorly understood.…

Deep Research agents are rapidly emerging as primary consumers of modern retrieval systems. Unlike human users who issue and refine queries without documenting their intermediate thought processes, Deep Research agents generate explicit…

Computation and Language · Computer Science 2026-03-10 Zijian Chen , Xueguang Ma , Shengyao Zhuang , Jimmy Lin , Akari Asai , Victor Zhong

As single-cell RNA sequencing datasets grow in adoption, scale, and complexity, data analysis remains a bottleneck for many research groups. Although frontier AI agents have improved dramatically at software engineering and general data…

Genomics · Quantitative Biology 2026-02-11 Kenny Workman , Zhen Yang , Harihara Muralidharan , Aidan Abdulali , Hannah Le

Information retrieval is a cornerstone of modern knowledge acquisition, enabling billions of queries each day across diverse domains. However, traditional keyword-based search engines are increasingly inadequate for handling complex,…

The exponential growth of global academic output has confronted researchers and AI agents with an unprecedented ``information explosion,'' where fragmented and unstructured knowledge organization impedes deep interdisciplinary integration.…

Artificial Intelligence · Computer Science 2026-05-25 Shuofei Qiao , Yunxiang Wei , Jiazheng Fan , Bin Wu , Busheng Zhang , Mengru Wang , Yuqi Zhu , Ningyu Zhang , Keyan Ding , Qiang Zhang , Huajun Chen

Recently, AI agents are rapidly evolving in intelligence and widely used in professional research applications, such as STEM, software development, and finance. Among these AI agents, deep research agent is a key category as it can perform…

Computation and Language · Computer Science 2025-10-21 Rui Sun , Zuo Bai , Wentao Zhang , Yuxiang Zhang , Li Zhao , Shan Sun , Zhengwen Qiu

The exponential growth of scientific knowledge has created significant barriers to cross-disciplinary knowledge discovery, synthesis and research collaboration. In response to this challenge, we present BioSage, a novel compound AI…

Transcending human cognitive limitations represents a critical frontier in LLM training. Proprietary agentic systems like DeepResearch have demonstrated superhuman capabilities on extremely complex information-seeking benchmarks such as…

LLM-based reasoning models have enabled the development of agentic systems that act as co-scientists, assisting in multi-step scientific analysis. However, evaluating these systems is challenging, as it requires realistic, end-to-end…

Machine Learning · Computer Science 2026-02-24 Siba Smarak Panigrahi , Jovana Videnović , Maria Brbić

Deep Research Agents are a prominent category of LLM-based agents. By autonomously orchestrating multistep web exploration, targeted retrieval, and higher-order synthesis, they transform vast amounts of online information into…

Computation and Language · Computer Science 2025-06-16 Mingxuan Du , Benfeng Xu , Chiwei Zhu , Xiaorui Wang , Zhendong Mao

Frontier AI agents show increasing promise as scientific research assistants, and may eventually be useful for extended, open-ended research workflows. However, in order to use agents for novel research, we must first assess the underlying…

With the advancement of large language models (LLMs) in their knowledge base and reasoning capabilities, their interactive modalities have evolved from pure text to multimodality and further to agentic tool use. Consequently, their…

Artificial Intelligence · Computer Science 2026-03-31 Yipeng Yu

Large Language Models (LLMs) and LLM-based agents show great promise in accelerating scientific research. Existing benchmarks for measuring this potential and guiding future development continue to evolve from pure recall and rote knowledge…

Deep research requires reasoning over web evidence to answer open-ended questions, and it is a core capability for AI agents. Yet many deep research agents still rely on implicit, unstructured search behavior that causes redundant…

Artificial Intelligence · Computer Science 2026-04-29 Boer Zhang , Mingyan Wu , Dongzhuoran Zhou , Yuqicheng Zhu , Wendong Fan , Puzhen Zhang , Zifeng Ding , Guohao Li , Yuan He

Recent developments in Large Language Model (LLM)-based agents have shown impressive capabilities spanning multiple domains, exemplified by deep research systems that demonstrate superior performance on complex information-seeking and…

Computation and Language · Computer Science 2025-09-03 Ailing Yu , Lan Yao , Jingnan Liu , Zhe Chen , Jiajun Yin , Yuan Wang , Xinhao Liao , Zhiling Ye , Ji Li , Yun Yue , Hansong Xiao , Hualei Zhou , Chunxiao Guo , Peng Wei , Junwei Liu , Jinjie Gu

The rapid growth of scientific literature demands robust tools for automated survey-generation. However, current large language model (LLM)-based methods often lack in-depth analysis, structural coherence, and reliable citations. To address…

Artificial Intelligence · Computer Science 2025-07-22 Xiaofeng Shi , Qian Kou , Yuduo Li , Ning Tang , Jinxin Xie , Longbin Yu , Songjing Wang , Hua Zhou

The rapid advancements of AI agents have ignited the long-held ambition of leveraging them to accelerate scientific discovery. Achieving this goal requires a deep understanding of the frontiers of human knowledge. As such, Humanity's Last…

Artificial Intelligence · Computer Science 2025-07-09 Jingyi Chai , Shuo Tang , Rui Ye , Yuwen Du , Xinyu Zhu , Mengcheng Zhou , Yanfeng Wang , Weinan E , Yuzhi Zhang , Linfeng Zhang , Siheng Chen

Recent advances in large language models (LLMs) have enabled agentic systems that translate natural language intent into executable scientific visualization (SciVis) tasks. Despite rapid progress, the community lacks a principled and…

Deep research systems are widely used for multi-step web research, analysis, and cross-source synthesis, yet their evaluation remains challenging. Existing benchmarks often require annotation-intensive task construction, rely on static…

Computation and Language · Computer Science 2026-01-15 Yibo Wang , Lei Wang , Yue Deng , Keming Wu , Yao Xiao , Huanjin Yao , Liwei Kang , Hai Ye , Yongcheng Jing , Lidong Bing

Recent advancements in large language model (LLM) agents have significantly accelerated scientific discovery automation, yet concurrently raised critical ethical and safety concerns. To systematically address these challenges, we introduce…

Artificial Intelligence · Computer Science 2025-05-30 Kunlun Zhu , Jiaxun Zhang , Ziheng Qi , Nuoxing Shang , Zijia Liu , Peixuan Han , Yue Su , Haofei Yu , Jiaxuan You