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Retrieval-Augmented Generation (RAG) shows promise for enterprise knowledge work, yet it often underperforms in high-stakes decision settings that require deep synthesis, strict traceability, and recovery from underspecified prompts.…

Information Retrieval · Computer Science 2026-01-27 Xincheng You , Qi Sun , Neha Bora , Huayi Li , Shubham Goel , Kang Li , Sean Culatana

Translational medicine turns underspecified development goals into evidence synthesis that must combine literature, trials, patents, and quantitative multi-omics analysis while preserving identifiers, uncertainty, and retrievable…

Repurposing approved drugs offers a time-efficient and cost-effective alternative to traditional drug development. However, in silico prediction of repurposing candidates is challenging and requires the effective collaboration of…

Artificial Intelligence · Computer Science 2026-02-10 Simon Süwer , Kester Bagemihl , Sylvie Baier , Lucia Dicunta , Markus List , Jan Baumbach , Andreas Maier , Fernando M. Delgado-Chaves

Research waste in biomedical science is driven by redundant studies, incomplete reporting, and the limited scalability of traditional evidence synthesis workflows. We present an AI co-scientist for scalable and transparent knowledge…

Artificial Intelligence · Computer Science 2026-01-21 Arya Rahgozar , Pouria Mortezaagha

Computational drug repurposing for rare diseases is especially challenging when no prior associations exist between drugs and target diseases. Therefore, knowledge graph completion and message-passing GNNs have little reliable signal to…

Artificial Intelligence · Computer Science 2025-10-17 Lang Qin , Zijian Gan , Xu Cao , Pengcheng Jiang , Yankai Jiang , Jiawei Han , Kaishun Wu , Jintai Chen

Designing multi-agent workflows is especially difficult in open-ended scientific settings where tasks lack curated training sets, reliable scalar evaluation metrics, and standardized interfaces between existing tools and agents. We propose…

Artificial Intelligence · Computer Science 2026-05-21 Shuaike Shen , Wenduo Cheng , Shike Wang , Mingqian Ma , Jian Ma

Deep Research Agents (DRAs) aim to solve complex, long-horizon research tasks involving planning, retrieval, multimodal understanding, and report generation, yet their evaluation remains challenging due to dynamic web environments and…

Rare diseases affect over 300 million individuals worldwide, yet timely and accurate diagnosis remains an urgent challenge. Patients often endure a prolonged diagnostic odyssey exceeding five years, marked by repeated referrals,…

Computation and Language · Computer Science 2026-02-17 Weike Zhao , Chaoyi Wu , Yanjie Fan , Xiaoman Zhang , Pengcheng Qiu , Yuze Sun , Xiao Zhou , Yanfeng Wang , Xin Sun , Ya Zhang , Yongguo Yu , Kun Sun , Weidi Xie

Recent advances in large language models have demonstrated considerable potential in scientific domains such as drug repositioning. However, their effectiveness remains constrained when reasoning extends beyond the knowledge acquired during…

Artificial Intelligence · Computer Science 2025-08-01 Zerui Yang , Yuwei Wan , Siyu Yan , Yudai Matsuda , Tong Xie , Bram Hoex , Linqi Song

AI agents have seen widespread adoption in information retrieval for scientific research, giving rise to tools such as Deep Research. However, existing retrieval agents mainly rely on keyword- or embedding-based methods. While effective at…

Computational Engineering, Finance, and Science · Computer Science 2026-05-25 Chenyang Shao , Fengli Xu , Yong Li

Drug repurposing has attracted increasing attention from both the pharmaceutical industry and the research community. Many existing computational drug repurposing methods rely on preclinical data (e.g., chemical structures, drug targets),…

Quantitative Methods · Quantitative Biology 2020-07-28 Qianlong Wen , Ruoqi Liu , Ping Zhang

Clinical diagnosis is a complex cognitive process, grounded in dynamic cue acquisition and continuous expertise accumulation. Yet most current artificial intelligence (AI) systems are misaligned with this reality, treating diagnosis as…

Artificial Intelligence · Computer Science 2026-03-12 Ruiyang Ren , Yuhao Wang , Yunsen Liang , Lan Luo , Jing Liu , Haifeng Wang , Cong Feng , Yinan Zhang , Chunyan Miao , Ji-Rong Wen , Wayne Xin Zhao

Artificial intelligence systems for scientific discovery have demonstrated remarkable potential, yet existing approaches remain largely proprietary and operate in batch-processing modes requiring hours per research cycle, precluding…

Artificial Intelligence · Computer Science 2026-01-28 Lukas Weidener , Marko Brkić , Mihailo Jovanović , Ritvik Singh , Chiara Baccin , Emre Ulgac , Alex Dobrin , Aakaash Meduri

Drug repurposing is an effective strategy to identify new uses for existing drugs, providing the quickest possible transition from bench to bedside. Existing methods for drug repurposing that mainly focus on pre-clinical information may…

Applications · Statistics 2021-04-14 Ruoqi Liu , Lai Wei , Ping Zhang

Open-source scientific software is abundant, yet most tools remain difficult to compile, configure, and reuse, sustaining a small-workshop mode of scientific computing. This deployment bottleneck limits reproducibility, large-scale…

Software Engineering · Computer Science 2026-01-08 Yi Wang , Zhenting Huang , Zhaohan Ding , Ruoxue Liao , Yuan Huang , Xinzijian Liu , Jiajun Xie , Siheng Chen , Linfeng Zhang

Background: Identifying new indications for approved drugs is a complex and time-consuming process that requires extensive knowledge of pharmacology, clinical data, and advanced computational methods. Recently, deep learning (DL) methods…

Machine Learning · Computer Science 2025-11-13 Shuting Jin , Yi Jiang , Yimin Liu , Tengfei Ma , Dongsheng Cao , Leyi Wei , Xiangrong Liu , Xiangxiang Zeng

Identifying novel hypotheses is essential to scientific research, yet this process risks being overwhelmed by the sheer volume and complexity of available information. Existing automated methods often struggle to generate novel and…

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 fields of therapeutic application and drug research and development (R&D) both face substantial challenges, i.e., the therapeutic domain calls for more treatment alternatives, while numerous promising pre-clinical drugs have failed in…

To promote better performance-bandwidth trade-off for multi-agent perception, we propose a novel distilled collaboration graph (DiscoGraph) to model trainable, pose-aware, and adaptive collaboration among agents. Our key novelties lie in…

Computer Vision and Pattern Recognition · Computer Science 2022-01-19 Yiming Li , Shunli Ren , Pengxiang Wu , Siheng Chen , Chen Feng , Wenjun Zhang
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