Multi-omics Graph Knowledge Representation for Pneumonia Prognostic Prediction.

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.