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Information technology has profoundly altered the way humans interact with information. The vast amount of content created, shared, and disseminated online has made it increasingly difficult to access relevant information. Over the past two…

Information Retrieval · Computer Science 2025-04-14 Yu Zhang , Shutong Qiao , Jiaqi Zhang , Tzu-Heng Lin , Chen Gao , Yong Li

Large Language Model (LLM)-based search agents have shown remarkable capabilities in solving complex tasks by dynamically decomposing problems and addressing them through interleaved reasoning and retrieval. However, this interleaved…

Artificial Intelligence · Computer Science 2025-05-20 Tiannuo Yang , Zebin Yao , Bowen Jin , Lixiao Cui , Yusen Li , Gang Wang , Xiaoguang Liu

Search agents are language models (LMs) that reason and search knowledge bases (or the web) to answer questions; recent methods supervise only the final answer accuracy using reinforcement learning with verifiable rewards (RLVR). Most RLVR…

Machine Learning · Computer Science 2026-01-27 James Burgess , Jan N. Hansen , Duo Peng , Yuhui Zhang , Alejandro Lozano , Min Woo Sun , Emma Lundberg , Serena Yeung-Levy

Since the advent of various pre-trained large language models, extracting structured knowledge from scientific text has experienced a revolutionary change compared with traditional machine learning or natural language processing techniques.…

Computational Physics · Physics 2025-10-27 Aritra Roy , Enrico Grisan , John Buckeridge , Chiara Gattinoni

The number of databases as well as their size and complexity is increasing. This creates a barrier to use especially for non-experts, who have to come to grips with the nature of the data, the way it has been represented in the database,…

Computation and Language · Computer Science 2021-04-15 Adrián Bazaga , Nupur Gunwant , Gos Micklem

Effective information seeking in the vast and ever-growing digital landscape requires balancing expansive search with strategic reasoning. Current large language model (LLM)-based agents struggle to achieve this balance due to limitations…

Artificial Intelligence · Computer Science 2025-08-13 Xianghe Pang , Shuo Tang , Rui Ye , Yuwen Du , Yaxin Du , Siheng Chen

Language agents perform complex tasks by using tools to execute each step precisely. However, most existing agents are based on proprietary models or designed to target specific tasks, such as mathematics or multi-hop question answering. We…

Artificial Intelligence · Computer Science 2024-06-11 Joongwon Kim , Bhargavi Paranjape , Tushar Khot , Hannaneh Hajishirzi

We present Tongyi DeepResearch, an agentic large language model, which is specifically designed for long-horizon, deep information-seeking research tasks. To incentivize autonomous deep research agency, Tongyi DeepResearch is developed…

Protein research is crucial in various fundamental disciplines, but understanding their intricate structure-function relationships remains challenging. Recent Large Language Models (LLMs) have made significant strides in comprehending…

Computational Engineering, Finance, and Science · Computer Science 2025-01-24 Chao Wang , Hehe Fan , Ruijie Quan , Yi Yang

Understanding biological processes, drug development, and biotechnological advancements requires a detailed analysis of protein structures and functions, a task that is inherently complex and time-consuming in traditional protein research.…

Artificial Intelligence · Computer Science 2025-04-21 Yijia Xiao , Edward Sun , Yiqiao Jin , Qifan Wang , Wei Wang

TalkBank is an online database that facilitates the sharing of linguistics research data. However, the existing TalkBank's API has limited data filtering and batch processing capabilities. To overcome these limitations, this paper…

Databases · Computer Science 2023-06-23 Man Ho Wong

Query understanding is essential in modern relevance systems, where user queries are often short, ambiguous, and highly context-dependent. Traditional approaches often rely on multiple task-specific Named Entity Recognition models to…

Information Retrieval · Computer Science 2025-09-15 Ping Liu , Jianqiang Shen , Qianqi Shen , Chunnan Yao , Kevin Kao , Dan Xu , Rajat Arora , Baofen Zheng , Caleb Johnson , Liangjie Hong , Jingwei Wu , Wenjing Zhang

The advent of Large Language Models (LLMs) has significantly revolutionized web search. The emergence of LLM-based Search Agents marks a pivotal shift towards deeper, dynamic, autonomous information seeking. These agents can comprehend user…

Information Retrieval · Computer Science 2025-08-20 Yunjia Xi , Jianghao Lin , Yongzhao Xiao , Zheli Zhou , Rong Shan , Te Gao , Jiachen Zhu , Weiwen Liu , Yong Yu , Weinan Zhang

Identification and alignment of three-dimensional folding of proteins may yield useful information about relationships too remote to be detected by conventional methods, such as sequence comparison, and may potentially lead to prediction of…

Quantitative Methods · Quantitative Biology 2017-01-10 Barış Ekim

Recently, Diffusion Large Language Models (dLLMs) have demonstrated unique efficiency advantages, enabled by their inherently parallel decoding mechanism and flexible generation paradigm. Meanwhile, despite the rapid advancement of Search…

Artificial Intelligence · Computer Science 2026-02-10 Jiahao Zhao , Shaoxuan Xu , Zhongxiang Sun , Fengqi Zhu , Jingyang Ou , Yuling Shi , Chongxuan Li , Xiao Zhang , Jun Xu

Multi-agent systems powered by large language models have demonstrated remarkable capabilities across diverse domains, yet existing automated design approaches seek monolithic solutions that fail to adapt resource allocation based on query…

Artificial Intelligence · Computer Science 2025-10-06 Bo Ma , Hang Li , ZeHua Hu , XiaoFan Gui , LuYao Liu , Simon Liu

Tensor networks are efficient for extremely high-dimensional representation, but their model selection, known as tensor network structure search (TN-SS), is a challenging problem. Although several works have targeted TN-SS, most existing…

Machine Learning · Computer Science 2024-06-04 Junhua Zeng , Chao Li , Zhun Sun , Qibin Zhao , Guoxu Zhou

Directed evolution is a versatile technique in protein engineering that mimics the process of natural selection by iteratively alternating between mutagenesis and screening in order to search for sequences that optimize a given property of…

Biomolecules · Quantitative Biology 2024-05-02 Lixue Cheng , Ziyi Yang , Changyu Hsieh , Benben Liao , Shengyu Zhang

Deep neural-network-based language models (LMs) are increasingly applied to large-scale protein sequence data to predict protein function. However, being largely black-box models and thus challenging to interpret, current protein LM…

Quantitative Methods · Quantitative Biology 2024-08-06 Mai Ha Vu , Rahmad Akbar , Philippe A. Robert , Bartlomiej Swiatczak , Victor Greiff , Geir Kjetil Sandve , Dag Trygve Truslew Haug

The rise of Large Language Models (LLMs) has accelerated the long-standing goal of enabling natural language querying over complex, hybrid databases. Yet, this ambition exposes a dual challenge: reasoning jointly over structured,…

Databases · Computer Science 2025-10-22 Aymane Hassini