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Drug repurposing is often framed as a candidate identification task, but existing approaches provide limited guidance for distinguishing biologically plausible candidates from historically well-connected ones. Here we introduce DrugKLM, a…

Large Language Models (LLMs) have grown exponentially since the release of ChatGPT. These models have gained attention due to their robust performance on various tasks, including language processing tasks. These models achieve understanding…

Computation and Language · Computer Science 2025-08-11 Ali Sarabadani , Maryam Abdollahi Shamami , Hamidreza Sadeghsalehi , Borhan Asadi , Saba Hesaraki

This survey investigates the synergistic relationship between Large Language Models (LLMs) and Knowledge Graphs (KGs), which is crucial for advancing AI's capabilities in understanding, reasoning, and language processing. It aims to address…

The growing trend of Large Language Models (LLM) development has attracted significant attention, with models for various applications emerging consistently. However, the combined application of Large Language Models with semantic…

Computation and Language · Computer Science 2023-05-09 Milena Trajanoska , Riste Stojanov , Dimitar Trajanov

Electronic health record (EHR) systems present clinicians with vast repositories of clinical information, creating a significant cognitive burden where critical details are easily overlooked. While Large Language Models (LLMs) offer…

Computation and Language · Computer Science 2026-03-17 Samuel Thio , Matthew Lewis , Spiros Denaxas , Richard JB Dobson

Large Language Models (LLMs) integrated with Retrieval-Augmented Generation (RAG) techniques have exhibited remarkable performance across a wide range of domains. However, existing RAG approaches primarily operate on unstructured data and…

Artificial Intelligence · Computer Science 2026-04-22 Ge Chang , Jinbo Su , Jiacheng Liu , Pengfei Yang , Yuhao Shang , Huiwen Zheng , Hongli Ma , Yan Liang , Yuanchun Li , Yunxin Liu

Large language models (LLMs) in biomedicine face a fundamental conflict between static parameter knowledge and the dynamic nature of clinical evidence. Retrieval-Augmented Generation (RAG) addresses this by grounding generation in external…

Other Quantitative Biology · Quantitative Biology 2025-12-19 Jiawei He , Boya Zhang , Hossein Rouhizadeh , Yingjian Chen , Rui Yang , Jin Lu , Xudong Chen , Nan Liu , Douglas Teodoro

Despite the strong abilities, large language models (LLMs) still suffer from hallucinations and reliance on outdated knowledge, raising concerns in knowledge-intensive tasks. Graph-based retrieval-augmented generation (GRAG) enriches LLMs…

Computation and Language · Computer Science 2026-01-14 Derong Xu , Pengyue Jia , Xiaopeng Li , Yingyi Zhang , Maolin Wang , Qidong Liu , Xiangyu Zhao , Yichao Wang , Huifeng Guo , Ruiming Tang , Enhong Chen , Tong Xu

The rapid advancement of large language models (LLMs) has opened new boundaries in the extraction and synthesis of medical knowledge, particularly within evidence synthesis. This paper reviews the state-of-the-art applications of LLMs in…

Generative AI, especially through large language models (LLMs), is transforming how technical knowledge can be accessed, reused, and extended. PETSc, a widely used numerical library for high-performance scientific computing, has accumulated…

While pioneering deep learning methods have made great strides in analyzing electronic health record (EHR) data, they often struggle to fully capture the semantics of diverse medical codes from limited data. The integration of external…

Machine Learning · Computer Science 2024-08-26 Zhihao Yu , Yujie Jin , Yongxin Xu , Xu Chu , Yasha Wang , Junfeng Zhao

Large language models (LLMs) often suffer from hallucination, generating factually incorrect statements when handling questions beyond their knowledge and perception. Retrieval-augmented generation (RAG) addresses this by retrieving…

Computation and Language · Computer Science 2025-11-18 Shengyuan Chen , Chuang Zhou , Zheng Yuan , Qinggang Zhang , Zeyang Cui , Hao Chen , Yilin Xiao , Jiannong Cao , Xiao Huang

Traditional methods of linking large language models (LLMs) to knowledge bases via the semantic similarity search often fall short of capturing complex relational dynamics. To address these limitations, we introduce AutoKG, a lightweight…

Computation and Language · Computer Science 2023-11-28 Bohan Chen , Andrea L. Bertozzi

Large language models (LLMs) have demonstrated remarkable in-context reasoning capabilities across a wide range of tasks, particularly with unstructured inputs such as language or images. However, LLMs struggle to handle structured data,…

Machine Learning · Computer Science 2025-02-20 Jintang Li , Ruofan Wu , Yuchang Zhu , Huizhe Zhang , Liang Chen , Zibin Zheng

Current medical language models, adapted from large language models (LLMs), typically predict ICD code-based diagnosis from electronic health records (EHRs) because these labels are readily available. However, ICD codes do not capture the…

Computation and Language · Computer Science 2025-12-09 Wenhao Li , Hongkuan Zhang , Hongwei Zhang , Zhengxu Li , Zengjie Dong , Yafan Chen , Niranjan Bidargaddi , Hong Liu

Extensive research has investigated the integration of large language models (LLMs) with knowledge graphs to enhance the reasoning process. However, understanding how models perform reasoning utilizing structured graph knowledge remains…

Computation and Language · Computer Science 2025-02-24 Han Zhang , Langshi Zhou , Hanfang Yang

The application of Artificial Intelligence (AI) in healthcare has been revolutionary, especially with the recent advancements in transformer-based Large Language Models (LLMs). However, the task of understanding unstructured electronic…

Computation and Language · Computer Science 2023-08-08 Shivani Shekhar , Simran Tiwari , T. C. Rensink , Ramy Eskander , Wael Salloum

The rapid expansion of e-commerce platforms generates vast amounts of unstructured product data, creating significant challenges for information retrieval, recommendation systems, and data analytics. Knowledge Graphs (KGs) offer a…

Artificial Intelligence · Computer Science 2025-11-17 Dimitar Peshevski , Riste Stojanov , Dimitar Trajanov

Teaching large language models (LLMs) to use tools is crucial for improving their problem-solving abilities and expanding their applications. However, effectively using tools is challenging because it requires a deep understanding of tool…

Machine Learning · Computer Science 2025-06-27 Jingwei Wang , Zai Zhang , Hao Qian , Chunjing Gan , Binbin Hu , Ziqi Liu , Zhiqiang Zhang , Jun Zhou , Bin Shi , Bo Dong

Large Language Models (LLMs) have shown promising performance on diverse medical benchmarks, highlighting their potential in supporting real-world clinical tasks. Retrieval-Augmented Generation (RAG) has emerged as a key approach for…

Computation and Language · Computer Science 2025-09-30 Kaishuai Xu , Wenjun Hou , Yi Cheng , Wenjie Li