Jie Li

Zheming Zuo, Jie Li, Han Xu et al.

Disruptive technologies provides unparalleled opportunities to contribute to the identifications of many aspects in pervasive healthcare, from the adoption of the Internet of Things through to Machine Learning (ML) techniques. As a powerful tool, ML has been widely applied in patient-centric healthcare solutions. To further improve the quality of patient care, Electronic Health Records (EHRs) are commonly adopted in healthcare facilities for analysis. It is a crucial task to apply AI and ML to analyse those EHRs for prediction and diagnostics due to their highly unstructured, unbalanced, incomplete, and high-dimensional nature. Dimensionality reduction is a common data preprocessing technique to cope with high-dimensional EHR data, which aims to reduce the number of features of EHR representation while improving the performance of the subsequent data analysis, e.g. classification. In this work, an efficient filter-based feature selection method, namely Curvature-based Feature Selection (CFS), is presented. The proposed CFS applied the concept of Menger Curvature to rank the weights of all features in the given data set. The performance of the proposed CFS has been evaluated in four well-known EHR data sets, including Cervical Cancer Risk Factors (CCRFDS), Breast Cancer Coimbra (BCCDS), Breast Tissue (BTDS), and Diabetic Retinopathy Debrecen (DRDDS). The experimental results show that the proposed CFS achieved state-of-the-art performance on the above data sets against conventional PCA and other most recent approaches. The source code of the proposed approach is publicly available at https://github.com/zhemingzuo/CFS.

Jinjiang Guo, Jie Li, Dawei Leng et al.

Multi-scale biomedical knowledge networks are expanding with emerging experimental technologies that generates multi-scale biomedical big data. Link prediction is increasingly used especially in bipartite biomedical networks to identify hidden biological interactions and relationshipts between key entities such as compounds, targets, gene and diseases. We propose a Graph Neural Networks (GNN) method, namely Graph Pair based Link Prediction model (GPLP), for predicting biomedical network links simply based on their topological interaction information. In GPLP, 1-hop subgraphs extracted from known network interaction matrix is learnt to predict missing links. To evaluate our method, three heterogeneous biomedical networks were used, i.e. Drug-Target Interaction network (DTI), Compound-Protein Interaction network (CPI) from NIH Tox21, and Compound-Virus Inhibition network (CVI). Our proposed GPLP method significantly outperforms over the state-of-the-art baselines. In addition, different network incompleteness is analysed with our devised protocol, and we also design an effective approach to improve the model robustness towards incomplete networks. Our method demonstrates the potential applications in other biomedical networks.