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Single-cell RNA-seq foundation models achieve strong performance on downstream tasks but remain black boxes, limiting their utility for biological discovery. Recent work has shown that sparse dictionary learning can extract concepts from…

基因组学 · 定量生物学 2025-10-31 Charlotte Claye , Pierre Marschall , Wassila Ouerdane , Céline Hudelot , Julien Duquesne

Large language models (LLMs) have demonstrated significant potential in clinical decision support. Yet LLMs still suffer from hallucinations and lack fine-grained contextual medical knowledge, limiting their high-stake healthcare…

计算与语言 · 计算机科学 2025-04-22 Pengcheng Jiang , Cao Xiao , Minhao Jiang , Parminder Bhatia , Taha Kass-Hout , Jimeng Sun , Jiawei Han

Multi-hop question answering (MHQA) requires integrating knowledge scattered across multiple passages to derive the correct answer. Traditional retrieval-augmented generation (RAG) methods primarily focus on coarse-grained textual semantic…

计算与语言 · 计算机科学 2025-08-18 Changjian Wang , Weihong Deng , Weili Guan , Quan Lu , Ning Jiang

Rare genetic disease diagnosis faces critical challenges: insufficient patient data, inaccessible full genome sequencing, and the immense number of possible causative genes. These limitations cause prolonged diagnostic journeys,…

机器学习 · 计算机科学 2025-10-13 Premt Cara , Kamilia Zaripova , David Bani-Harouni , Nassir Navab , Azade Farshad

Existing medical RAG systems mainly leverage knowledge from medical knowledge bases, neglecting the crucial role of experiential knowledge derived from similar patient cases -- a key component of human clinical reasoning. To bridge this…

计算与语言 · 计算机科学 2025-05-27 Yuxing Lu , Gecheng Fu , Wei Wu , Xukai Zhao , Sin Yee Goi , Jinzhuo Wang

In biomedical research, unified access to up-to-date domain-specific knowledge is crucial, as such knowledge is continuously accumulated in scientific literature and structured resources. Identifying and extracting specific information is a…

信息检索 · 计算机科学 2020-06-03 Anastasios Nentidis , Konstantinos Bougiatiotis , Anastasia Krithara , Georgios Paliouras

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…

人工智能 · 计算机科学 2025-10-17 Lang Qin , Zijian Gan , Xu Cao , Pengcheng Jiang , Yankai Jiang , Jiawei Han , Kaishun Wu , Jintai Chen

Large language models (LLMs) offer new opportunities for constructing knowledge graphs (KGs) from unstructured clinical narratives. However, existing approaches often rely on structured inputs and lack robust validation of factual accuracy…

人工智能 · 计算机科学 2026-01-06 Udiptaman Das , Krishnasai B. Atmakuri , Duy Ho , Chi Lee , Yugyung Lee

Despite initial successes and a variety of architectures, retrieval-augmented generation systems still struggle to reliably retrieve and connect the multi-step evidence required for complicated reasoning tasks. Most of the standard RAG…

人工智能 · 计算机科学 2026-05-26 Jovan Pavlović , Miklós Krész , László Hajdu

The rapidly growth of biomedical literature creates challenges acquiring specific medical information. Current biomedical question-answering systems primarily focus on short-form answers, failing to provide comprehensive explanations…

Schizophrenia is a serious psychiatric disorder. Its pathogenesis is not completely clear, making it difficult to treat patients precisely. Because of the complicated non-Euclidean network structure of the human brain, learning critical…

计算机视觉与模式识别 · 计算机科学 2024-08-28 Yuhong Jiao , Jiaqing Miao , Jinnan Gong , Hui He , Ping Liang , Cheng Luo , Ying Tan

Accurate and interpretable image-based diagnosis remains a fundamental challenge in medical AI, particularly under domain shifts and rare-class conditions. Deep learning models often struggle with real-world distribution changes, exhibit…

机器学习 · 计算机科学 2025-12-13 Midhat Urooj , Ayan Banerjee , Farhat Shaikh , Kuntal Thakur , Sandeep Gupta

Automated question-answering (QA) systems increasingly rely on retrieval-augmented generation (RAG) to ground large language models (LLMs) in authoritative medical knowledge, ensuring clinical accuracy and patient safety in Artificial…

计算与语言 · 计算机科学 2026-03-05 Aswini Sivakumar , Vijayan Sugumaran , Yao Qiang

Rare diseases represent the long tail of medical imaging, where AI models often fail due to the scarcity of representative training data. In clinical workflows, radiologists frequently consult case reports and literature when confronted…

Network topology excels at structural predictions but fails to capture functional semantics encoded in biomedical literature. We present RAG-GNN, an end-to-end trainable retrieval-augmented graph neural network framework that integrates GNN…

分子网络 · 定量生物学 2026-05-14 Hasi Hays , William J. Richardson

Knowledge Graph Retrieval-Augmented Generation (KG-RAG) extends the RAG paradigm by incorporating structured knowledge from knowledge graphs, enabling Large Language Models (LLMs) to perform more precise and explainable reasoning. While…

计算与语言 · 计算机科学 2026-02-04 Jing Ren , Bowen Li , Ziqi Xu , Xikun Zhang , Haytham Fayek , Xiaodong Li

Knowledge graphs and large language models (LLMs) are key tools for biomedical knowledge integration and reasoning, facilitating structured organization of scientific articles and discovery of complex semantic relationships. However,…

计算与语言 · 计算机科学 2025-04-01 Yichun Feng , Jiawei Wang , Ruikun He , Lu Zhou , Yixue Li

Large language models (LLMs) often struggle with knowledge-intensive tasks due to hallucinations and outdated parametric knowledge. While Retrieval-Augmented Generation (RAG) addresses this by integrating external corpora, its effectiveness…

计算与语言 · 计算机科学 2026-02-04 Su Dong , Qinggang Zhang , Yilin Xiao , Shengyuan Chen , Chuang Zhou , Xiao Huang

Artificial Intelligence has revolutionised critical care for common conditions. Yet, rare conditions in the intensive care unit (ICU), including recognised rare diseases and low-prevalence conditions in the ICU, remain underserved due to…

机器学习 · 计算机科学 2025-07-10 Mingcheng Zhu , Yu Liu , Zhiyao Luo , Tingting Zhu

We introduce a novel graph-based Retrieval-Augmented Generation (RAG) framework specifically designed for the medical domain, called \textbf{MedGraphRAG}, aimed at enhancing Large Language Model (LLM) capabilities for generating…

计算机视觉与模式识别 · 计算机科学 2024-10-17 Junde Wu , Jiayuan Zhu , Yunli Qi , Jingkun Chen , Min Xu , Filippo Menolascina , Vicente Grau
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