{"title":"Multi-omics Graph Knowledge Representation for Pneumonia Prognostic Prediction.","authors":"Wenyu Xing, Miao Li, Yiwen Liu, Xin Liu, Yifang Li, Yanping Yang, Jing Bi, Jiangang Chen, Dongni Hou, Yuanlin Song, Dean Ta","doi":"10.1109/JBHI.2024.3488735","DOIUrl":null,"url":null,"abstract":"<p><p>Early prognostic prediction is crucial for determining appropriate clinical interventions. Previous single-omics models had limitations, such as high contingency and overlooking complex physical conditions. In this paper, we introduced multi-omics graph knowledge representation to predict in-hospital outcomes for pneumonia patients. This method utilizes CT imaging and three non-imaging omics information, and explores a knowledge graph for modeling multi-omics relations to enhance the overall information representation. For imaging omics, a multichannel pyramidal recursive MLP and Longformer-based 3D deep learning module was developed to extract depth features in lung window, while radiomics features were simultaneously extracted in both lung and mediastinal windows. Non-imaging omics involved the adoption of laboratory, microbial, and clinical indices to complement the patient's physical condition. Following feature screening, the similarity fusion network and graph convolutional network (GCN) were employed to determine omics similarity and provide prognostic prediction. The results of comparative experiments and generalization validation demonstrat that the proposed multi-omics GCN-based prediction model has good robustness and outperformed previous single-type omics, classical machine learning, and previous deep learning methods. Thus, the proposed multi-omics graph knowledge representation model enhances early prognostic prediction performance in pneumonia, facilitating a comprehensive assessment of disease severity and timely intervention for high-risk patients.</p>","PeriodicalId":13073,"journal":{"name":"IEEE Journal of Biomedical and Health Informatics","volume":null,"pages":null},"PeriodicalIF":6.7000,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"IEEE Journal of Biomedical and Health Informatics","FirstCategoryId":"5","ListUrlMain":"https://doi.org/10.1109/JBHI.2024.3488735","RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"COMPUTER SCIENCE, INFORMATION SYSTEMS","Score":null,"Total":0}
引用次数: 0
Abstract
Early prognostic prediction is crucial for determining appropriate clinical interventions. Previous single-omics models had limitations, such as high contingency and overlooking complex physical conditions. In this paper, we introduced multi-omics graph knowledge representation to predict in-hospital outcomes for pneumonia patients. This method utilizes CT imaging and three non-imaging omics information, and explores a knowledge graph for modeling multi-omics relations to enhance the overall information representation. For imaging omics, a multichannel pyramidal recursive MLP and Longformer-based 3D deep learning module was developed to extract depth features in lung window, while radiomics features were simultaneously extracted in both lung and mediastinal windows. Non-imaging omics involved the adoption of laboratory, microbial, and clinical indices to complement the patient's physical condition. Following feature screening, the similarity fusion network and graph convolutional network (GCN) were employed to determine omics similarity and provide prognostic prediction. The results of comparative experiments and generalization validation demonstrat that the proposed multi-omics GCN-based prediction model has good robustness and outperformed previous single-type omics, classical machine learning, and previous deep learning methods. Thus, the proposed multi-omics graph knowledge representation model enhances early prognostic prediction performance in pneumonia, facilitating a comprehensive assessment of disease severity and timely intervention for high-risk patients.
期刊介绍:
IEEE Journal of Biomedical and Health Informatics publishes original papers presenting recent advances where information and communication technologies intersect with health, healthcare, life sciences, and biomedicine. Topics include acquisition, transmission, storage, retrieval, management, and analysis of biomedical and health information. The journal covers applications of information technologies in healthcare, patient monitoring, preventive care, early disease diagnosis, therapy discovery, and personalized treatment protocols. It explores electronic medical and health records, clinical information systems, decision support systems, medical and biological imaging informatics, wearable systems, body area/sensor networks, and more. Integration-related topics like interoperability, evidence-based medicine, and secure patient data are also addressed.