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31st International Conference on Computational Linguistics, COLING 2025

作者： Liao, Xincheng Duan, Junwen Huang, Yixi Wang, Jianxin Hunan Provincial Key Lab on Bioinformatics School of Computer Science and Engineering Central South University Hunan Changsha China

ISBN: (纸本)9798891761964

Unified information extraction (UIE) aims to extract diverse structured information from unstructured text. While large language models (LLMs) have shown promise for UIE, they require significant computational resources and often struggle to generalize to unseen tasks. We propose RUIE (Retrieval-based Unified Information Extraction), a framework that leverages in-context learning for efficient task generalization. RUIE introduces a novel demonstration selection mechanism combining LLM preferences with a keyword-enhanced reward model, and employs a bi-encoder retriever trained through contrastive learning and knowledge distillation. As the first trainable retrieval framework for UIE, RUIE serves as a universal plugin for various LLMs. Experimental results on eight held-out datasets demonstrate RUIE's effectiveness, with average F1-score improvements of 19.22 and 3.22 compared to instruction-tuning methods and other retrievers, respectively. © 2025 Association for Computational Linguistics.

关键词： Data mining

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medIKAL: Integrating Knowledge Graphs as Assistants of LLMs for Enhanced Clinical Diagnosis on EMRs 31

medIKAL: Integrating Knowledge Graphs as Assistants of LLMs ...

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31st International Conference on Computational Linguistics, COLING 2025

作者： Jia, Mingyi Duan, Junwen Song, Yan Wang, Jianxin Hunan Provincial Key Lab on Bioinformatics School of Computer Science and Engineering Central South University China University of Science and Technology of China China

ISBN: (纸本)9798891761964

Electronic Medical Records (EMRs), while integral to modern healthcare, present challenges for clinical reasoning and diagnosis due to their complexity and information redundancy. To address this, we proposed medIKAL (Integrating Knowledge Graphs as Assistants of LLMs), a framework that combines Large Language Models (LLMs) with knowledge graphs (KGs) to enhance diagnostic capabilities. medIKAL assigns weighted importance to entities in medical records based on their type, enabling precise localization of candidate diseases within KGs. It innovatively employs a residual network-like approach, allowing initial diagnosis by LLMs to be merged into KG search results. Through a path-based reranking algorithm and a fill-in-the-blank style prompt template, it further refined the diagnostic process. We validated medIKAL's effectiveness through extensive experiments on a newly introduced open-sourced Chinese EMR dataset, demonstrating its potential to improve clinical diagnosis in real-world settings. The code and dataset are publicly available at https://***/CSU-NLP-Group/mediKAL. © 2025 Association for Computational Linguistics.

关键词： Knowledge graph

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PathActMarker:an R package for inferring pathway activity of complex diseases

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Frontiers of computer science 2025年第3期19卷 123-124页

作者： Xingyi LI Jun HAO Zhelin ZHAO Junming LI Xingyu LIAO Min LI Xuequn SHANG School of Computer Science Northwestern Polytechnical UniversityXi’an 710072China Research&Development Institute of Northwestern Polytechnical University in Shenzhen Shenzhen 518063China School of Software Northwestern Polytechnical UniversityXi’an 710072China Hunan Provincial Key Lab on Bioinformatics School of Computer Science and EngineeringCentral South UniversityChangsha 410083China

1 Introduction The process of complex diseases is closely linked to the disruption of key biological pathways,it is crucial to identify the dysfunctional pathways and quantify the degree of dysregulation at the indivi... 详细信息

关键词： pathway activity dysregulation complex diseases biological pathways disruption key biological pathwaysit identify dysfunctional pathways

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Multimodal Representation Learning Based on Personalized Graph-Based Fusion for Mortality Prediction Using Electronic Medical Records

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Big Data Mining and Analytics 2025年第4期8卷 933-950页

作者： Al-Dailami, Abdulrahman Kuang, Hulin Wang, Jianxin School of Computer Science and Engineering Central South University Hunan Provincial Key Lab on Bioinformatics Changsha 410083 China Sana'a University Faculty of Computer and Information Technology Sana'a 999101 Yemen

Predicting mortality risk in the Intensive Care Unit (ICU) using Electronic Medical Records (EMR) is crucial for identifying patients in need of immediate attention. However, the incompleteness and the variability of EMR features for each patient make mortality prediction challenging. This study proposes a multimodal representation learning framework based on a novel personalized graph-based fusion approach to address these challenges. The proposed approach involves constructing patient-specific modality aggregation graphs to provide information about the features associated with each patient from incomplete multimodal data, enabling the effective and explainable fusion of the incomplete features. Modality-specific encoders are employed to encode each modality feature separately. To tackle the variability and incompleteness of input features among patients, a novel personalized graph-based fusion method is proposed to fuse patient-specific multimodal feature representations based on the constructed modality aggregation graphs. Furthermore, a MultiModal Gated Contrastive Representation Learning (MMGCRL) method is proposed to facilitate capturing adequate complementary information from multimodal representations and improve model performance. We evaluate the proposed framework using the large-scale ICU dataset, MIMIC-III. Experimental results demonstrate its effectiveness in mortality prediction, outperforming several state-of-the-art methods. © 2018 Tsinghua University Press.

关键词： Electronic Medical Records (EMR) Graph Neural Network (GNN) Intensive Care Unit (ICU) mortality prediction multimodal representation learning

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FIND: Fine-grained Information Density Guided Adaptive Retrieval-Augmented Generation for Disease Diagnosis

arXiv

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arXiv 2025年

Retrieval-Augmented Large Language Models (LLMs), which integrate external knowledge into LLMs, have shown remarkable performance in various medical domains, including clinical diagnosis. However, existing RAG methods struggle to effectively assess task difficulty to make retrieval decisions, thereby failing to meet the clinical requirements for balancing efficiency and accuracy. So in this paper, we propose FIND (Fine-grained Information Density Guided Adaptive RAG), a novel framework that improves the reliability of RAG in disease diagnosis scenarios. FIND incorporates a fine-grained adaptive control module to determine whether retrieval is necessary based on the information density of the input. By optimizing the retrieval process and implementing a knowledge filtering module, FIND ensures that the retrieval is better suited to clinical scenarios. Experiments on three Chinese electronic medical record datasets demonstrate that FIND significantly outperforms various baseline methods, highlighting its effectiveness in clinical diagnosis tasks. Copyright © 2025, The Authors. All rights reserved.

关键词： Disease control

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FedComDist: Towards Effective Personalized Federated Learning for Patient Outcome Prediction Using Multi-Center Electronic Medical Records

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IEEE Journal of Biomedical and Health Informatics 2025年 PP卷 PP页

作者： Al-Dailami, Abdulrahman Kuang, Hulin Wang, Jianxin Central South University Hunan Provincial Key Lab on Bioinformatics School of Computer Science and Engineering Changsha410083 China Sana'a University Faculty of Computer and Information Technology Sana'a1247 Yemen

Accurate patient outcome predictions are essential for healthcare improvement, yet utilizing diverse medical data raises privacy and security concerns. Federated learning enables collaborative model training while preserving data privacy. However, the heterogeneity of clinical features among hospitals poses a challenge, leading to suboptimal performance in conventional federated learning. In response, we propose FedComDist, a personalized federated learning approach designed to maximize the use of heterogeneous features across hospitals for patient outcome prediction. Our approach incorporates a novel method for optimizing common global and distinct local parameters. We categorize input clinical features into two main groups—common and distinct—based on their presence across all hospitals and decouple the model parameters into common and distinct accordingly. The common features are used to train common global parameters, which are aggregated and optimized on the server, making them trainable across all hospitals. Meanwhile, the distinct features are used to train local parameters and optimized using the local dataset of each hospital. Our approach is evaluated on the eICU dataset, a publicly available multi-center clinical dataset, to predict patient clinical outcomes, specifically mortality and Length of Stay (LoS). The experimental results demonstrate the effectiveness of our approach compared to various federated learning methods and provide enhanced privacy through parameter decoupling. © 2013 IEEE.

关键词： Personalized medicine

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Multi-Modal Multi-Kernel Graph Learning for Autism Prediction and Biomarker Discovery

IEEE Transactions on Computational Biology and Bioinformatic...

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IEEE Transactions on Computational Biology and bioinformatics 2025年第2期22卷 842-854页

作者： Jin Liu Junbin Mao Hanhe Lin Hulin Kuang Shirui Pan Xusheng Wu Shan Xie Fei Liu Yi Pan Hunan Provincial Key Lab on Bioinformatics School of Computer Science and Engineering Central South University Changsha China Xinjiang Engineering Research Center of Big Data and Intelligent Software School of software Xinjiang University Wulumuqi China Hunan Province Key Lab on Bioinformatics School of Computer Science and Engineering Central South University Changsha China School of Science and Engineering University of Dundee Dundee U.K. School of Information and Communication Technology Griffith University Gold Coast QLD Australia Shenzhen Health Development Research and Data Management Center Shenzhen China Faculty of Computer Science and Control Engineering Shenzhen University of Advanced Technology Shenzhen China Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen China

Graph learning-based multi-modal integration and classification is one of the most challenging tasks for disease prediction. To effectively offset the negative impact among modalities in the process of multi-modal integration and heterogeneous information extractions from graphs, we propose a novel method called Multi-modal Multi-Kernel Graph Learning (MMKGL). To solve the problem of negative impact among modalities, we propose a multi-modal graph embedding module to construct a multi-modal graph. Different from conventional methods that manually construct static graphs for all modalities, each modality generates a separate graph by adaptive learning, where a function graph and a supervision graph are introduced for optimization during the multi-graph fusion embedding process. We then propose a multi-kernel graph learning module to extract heterogeneous information from the multi-modal graph. The information in the multi-modal graph at different levels is aggregated by convolutional kernels with different receptive field sizes, followed by generating a cross-kernel discovery tensor for disease prediction. Our method is evaluated on the benchmark Autism Brain Imaging Data Exchange (ABIDE) dataset and outperforms the state-of-the-art methods. In addition, discriminative brain regions associated with autism are identified by our model, providing guidance for the study of autism pathology.

关键词： Diseases Autism Random access memory Data mining Kernel Electronic mail Training Neuroimaging Graph convolutional networks bioinformatics

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Improved Approximation Algorithm for Individual Fairness k-Median 17th

Improved Approximation Algorithm for Individual Fairness k-...

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17th International Conference on Combinatorial Optimization and Applications, COCOA 2024

作者： Wu, Di Feng, Qilong Xu, Jinhui Wang, Jianxin School of Computer Science and Engineering Central South University Changsha China Xiangjiang Laboratory Changsha 410205 China Department of Computer Science and Engineering State University of New York at Buffalo Buffalo NY United States The Hunan Provincial Key Lab of Bioinformatics Central South University Changsha China

ISBN: (纸本)9789819644445

The individual fairness k-median problem is a frequently encountered problem in applications involving center location, which generalizes the standard k-median problem by assigning each point a neighborhood radius, allowing connections only to centers within a constant factor of this radius. In this paper, we present a randomized polynomial-time approximation scheme (PTAS) framework with (2+O(ϵ))-fairness violation for the individual fairness k-median problem, improving upon the previous best approximation ratio of (7.081+ϵ) and fairness violation of 3. We propose a new dynamic programming approach to deal with the challenges caused by the individual fairness requirements, which is the crucial step in getting the improved ratio. © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2025.

关键词： approximation algorithm clustering k-median

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Modeling Multilevel Business Process Monitoring via BPMN Extension

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Concurrency and Computation: Practice and Experience 2025年第12-14期37卷

作者： Kang, Guosheng Wang, Zhen Cheng, Hangyu Liu, Jianxun Wen, Yiping Peng, Jun School of Computer Science and Engineering Hunan University of Science and Technology Xiangtan China Hunan Provincial Key Lab. for Services Computing and Novel Software Technology Hunan University of Science and Technology Xiangtan China School of Computer Science and Technology Xi'an Jiaotong University Xi'an China School of Computer Science Fudan University Shanghai China

Business process monitoring involves real-time supervision of a series of activities carried out by an organization to achieve specific objectives. Process event monitoring points (PEMP) are used to pinpoint specific locations within a process model where expected events are anticipated to occur. However, in general business process modeling languages, such as business process model and notation (BPMN), there is a lack of explicit modeling for PEMPs. This article proposes a method for modeling pairwise event monitoring points in business process models to track the execution status of specific activities or process segments via BPMN extension. Specifically, process monitoring points are designed by expanding the modeling element of sequence flow. Moreover, the business process model is decomposed using the refined process structure tree (RPST) to verify the soundness of the designed pairwise monitoring points. The proposed method allows flexible monitoring at the process segment level. And the process monitoring data could be used for a clear understanding of business progress, especially useful in heterogeneous business process model to support decision-making. Through case study from real-world business processes, the effectiveness and usefulness of the proposed process monitoring modeling method is validated. © 2025 John Wiley & Sons Ltd.

关键词： Electronic trading

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MKMGCN-DDI: Predicting Drug-Drug Interactions via Magnetic Graph Convolutional Network With Multiple Kernels

IEEE Transactions on Computational Biology and Bioinformatic...

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IEEE Transactions on Computational Biology and bioinformatics 2025年第2期22卷 469-480页

作者： Ming Chen Yunhan Pan Xiujuan Lei Chunyan Ji Yinglong Dai Yi Pan Department of Artificial Intelligence Hunan Normal University Changsha Hunan China School of Computer Science Shaanxi Normal University Xi’an China Computer Science Department BNU-HKBU United International College Zhuhai China Shenzhen Key Laboratory of Intelligent Bioinformatics Shenzhen Institute of Advanced Technology Shenzhen China Faculty of Computer Science and Control Engineering Shenzhen University of Advanced Technology Shenzhen China

Polypharmacy is a common means of clinical treatments, but detecting drug-drug interactions (DDIs) behind unexpected effects can be costly and faces clinical limitations. Recently, graph neural networks (GNNs) have demonstrated encouraging performance in predicting DDIs. However, most studies overlook the comprehensive aspects of DDIs, such as the coexistence of types of pharmacological changes and the asymmetric roles of drugs. In this article, we define new prediction tasks, taking into account both enhancive or depressive changes and the roles of drugs, and then establish spectral GNNs to predict comprehensive information of DDIs. First, we formally define several tasks, including joint prediction tasks designed to leverage both types and directions. These tasks deduce to sub-tasks in previous studies. Then, we propose a unified framework, the MKMGCN-DDI, via introducing two Magnetic Laplacian matrices to encode comprehension information within DDIs, defining multiple graph filters, and designing multiple-kernel based Magnetic graph convolutional networks (MKMGCN). Experiments across three datasets show that it not only has good adaptability to multiple tasks but also significantly improves results on simple tasks. Case studies on breast neoplasms and lung neoplasms verify its feasibility, as over half of top-10 items are supported.

关键词： Drugs Predictive models Magnetic separation Laplace equations bioinformatics Sodium Market research Graph convolutional networks computer science Computational modeling

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