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Understanding mechanistic relationships among genes and their impacts on biological pathways is essential for elucidating disease mechanisms and advancing precision medicine. Despite the availability of extensive molecular interaction and…

Molecular Networks · Quantitative Biology 2026-03-24 Fujian Jia , Jiwen Gu , Cheng Lu , Dezhi Zhao , Mengjiang Huang , Yuanzhi Lu , Xin Liu , Kang Liu

Temporal knowledge graph reasoning aims to predict future events with knowledge of existing facts and plays a key role in various downstream tasks. Previous methods focused on either graph structure learning or semantic reasoning, failing…

Computation and Language · Computer Science 2025-06-18 Yimin Deng , Yuxia Wu , Yejing Wang , Guoshuai Zhao , Li Zhu , Qidong Liu , Derong Xu , Zichuan Fu , Xian Wu , Yefeng Zheng , Xiangyu Zhao , Xueming Qian

In recent years, large language models (LLMs) have revolutionized the field of natural language processing. However, they often suffer from knowledge gaps and hallucinations. Graph retrieval-augmented generation (GraphRAG) enhances LLM…

Artificial Intelligence · Computer Science 2025-03-19 Kai Guo , Harry Shomer , Shenglai Zeng , Haoyu Han , Yu Wang , Jiliang Tang

Graph-based Retrieval-Augmented Generation (GraphRAG) extends traditional RAG by using knowledge graphs (KGs) to give large language models (LLMs) a structured, semantically coherent context, yielding more grounded answers. However,…

Artificial Intelligence · Computer Science 2026-04-28 Zhuoling Li , Ha Linh Hong Tran Nguyen , Valeria Bladinieres , Maxim Romanovsky

Graph Neural Networks (GNNs) have recently become increasingly popular due to their ability to learn complex systems of relations or interactions arising in a broad spectrum of problems ranging from biology and particle physics to social…

Machine Learning · Computer Science 2020-10-12 Emanuele Rossi , Ben Chamberlain , Fabrizio Frasca , Davide Eynard , Federico Monti , Michael Bronstein

Recommender systems are pivotal in enhancing user experiences across various web applications by analyzing the complicated relationships between users and items. Knowledge graphs(KGs) have been widely used to enhance the performance of…

Information Retrieval · Computer Science 2024-07-02 Guangsi Shi , Xiaofeng Deng , Linhao Luo , Lijuan Xia , Lei Bao , Bei Ye , Fei Du , Shirui Pan , Yuxiao Li

We propose a scalable and cost-efficient framework for deploying Graph-based Retrieval-Augmented Generation (GraphRAG) in enterprise environments. While GraphRAG has shown promise for multi- hop reasoning and structured retrieval, its…

Artificial Intelligence · Computer Science 2025-12-19 Congmin Min , Sahil Bansal , Joyce Pan , Abbas Keshavarzi , Rhea Mathew , Amar Viswanathan Kannan

Large Language Models (LLMs) show strong reasoning ability in open-domain question answering, yet their reasoning processes are typically linear and often logically inconsistent. In contrast, real-world reasoning requires integrating…

Computation and Language · Computer Science 2026-01-21 Yingjian Chen , Haoran Liu , Yinhong Liu , Sherry T. Tong , Aosong Feng , Jinghui Lu , Juntao Zhang , Yusuke Iwasawa , Yutaka Matsuo , Irene Li

Knowledge graphs (KGs) are the cornerstone of the semantic web, offering up-to-date representations of real-world entities and relations. Yet large language models (LLMs) remain largely static after pre-training, causing their internal…

Computation and Language · Computer Science 2026-03-24 Songlin Zhai , Guilin Qi , Yue Wang , Yuan Meng

Knowledge graph embedding, which aims to learn the low-dimensional representations of entities and relationships, has attracted considerable research efforts recently. However, most knowledge graph embedding methods focus on the structural…

Machine Learning · Computer Science 2020-07-23 Yonghui Xu , Shengjie Sun , Yuan Miao , Dong Yang , Xiaonan Meng , Yi Hu , Ke Wang , Hengjie Song , Chuanyan Miao

Temporal knowledge graph (TKG) reasoning has become a hot topic due to its great value in many practical tasks. The key to TKG reasoning is modeling the structural information and evolutional patterns of the TKGs. While great efforts have…

Social and Information Networks · Computer Science 2025-01-07 Yuwei Du , Xinyue Liu , Wenxin Liang , Linlin Zong , Xianchao Zhang

In real-world scenarios, most of the data obtained from the information retrieval (IR) system is unstructured. Converting natural language sentences into structured Knowledge Graphs (KGs) remains a critical challenge. We identified three…

Computation and Language · Computer Science 2025-09-29 Haoyu Huang , Chong Chen , Zeang Sheng , Yang Li , Wentao Zhang

Graph neural networks (GNNs) have advanced recommender systems by modeling interaction relationships. However, existing graph-based recommenders rely on sparse ID features and do not fully exploit textual information, resulting in low…

Information Retrieval · Computer Science 2025-11-24 Hailong Luo , Bin Wu , Hongyong Jia , Qingqing Zhu , Lianlei Shan

The quality of graph-structured data is fundamental to the success of modern graph analysis techniques such as Graph Neural Networks (GNNs). However, real-world graph data is often suboptimal, suffering from issues such as noise and…

Machine Learning · Computer Science 2026-05-19 Shen Han , Zhiyao Zhou , Jiawei Chen , Sheng Zhou , Canghong Jin , Hai Lin , Da Zhong Li , Bingde Hu , Can Wang

Temporal graph neural network has recently received significant attention due to its wide application scenarios, such as bioinformatics, knowledge graphs, and social networks. There are some temporal graph neural networks that achieve…

Machine Learning · Computer Science 2023-01-23 Mingyi Liu , Zhiying Tu , Xiaofei Xu , Zhongjie Wang

Interpretable Graph Neural Networks (GNNs) aim to reveal the underlying reasoning behind model predictions, attributing their decisions to specific subgraphs that are informative. However, existing subgraph-based interpretable methods…

Machine Learning · Computer Science 2025-05-02 Jie Yang , Yuwen Wang , Kaixuan Chen , Tongya Zheng , Yihe Zhou , Zhenbang Xiao , Ji Cao , Mingli Song , Shunyu Liu

Large Language Models (LLMs) achieve excellent performance in natural language reasoning tasks through pre-training on vast unstructured text, enabling them to understand the logic in natural language and generate logic-consistent…

Computation and Language · Computer Science 2025-11-12 Songze Li , Zhiqiang Liu , Zhaoyan Gong , Xiaoke Guo , Zhengke Gui , Huajun Chen , Wen Zhang

Recent large language model (LLM) reasoning, despite its success, suffers from limited domain knowledge, susceptibility to hallucinations, and constrained reasoning depth, particularly in small-scale models deployed in resource-constrained…

Artificial Intelligence · Computer Science 2025-03-04 Wenjie Wu , Yongcheng Jing , Yingjie Wang , Wenbin Hu , Dacheng Tao

Well-designed open-source software drives progress in Machine Learning (ML) research. While static graph ML enjoys mature frameworks like PyTorch Geometric and DGL, ML for temporal graphs (TG), networks that evolve over time, lacks…

Large Language Models (LLMs) have shown strong inductive reasoning ability across various domains, but their reliability is hindered by the outdated knowledge and hallucinations. Retrieval-Augmented Generation mitigates these issues by…

Computation and Language · Computer Science 2025-06-12 Tianjun Yao , Haoxuan Li , Zhiqiang Shen , Pan Li , Tongliang Liu , Kun Zhang