Owning to the rapid development of computer technologies, an increasing number of relational data have been emerging in modern biomedical research. Many network-based learning methods have been proposed to perform analysis on such data, which provide people a deep understanding of topology and knowledge behind the biomedical networks and benefit a lot of applications for human healthcare. However, most network-based methods suffer from high computational and space cost. There remain challenges on handling high dimensionality and sparsity of the biomedical networks. The latest advances in network embedding technologies provide new effective paradigms to solve the network analysis problem. It converts network into a low-dimensional space while maximally preserves structural properties. In this way, downstream tasks such as link prediction and node classification can be done by traditional machine learning methods. In this survey, we conduct a comprehensive review of the literature on applying network embedding to advance the biomedical domain. We first briefly introduce the widely used network embedding models. After that, we carefully discuss how the network embedding approaches were performed on biomedical networks as well as how they accelerated the downstream tasks in biomedical science. Finally, we discuss challenges the existing network embedding applications in biomedical domains are faced with and suggest several promising future directions for a better improvement in human healthcare.

Objective Reducing suicidal behavior among patients in the healthcare system requires accurate and explainable predictive models of suicide risk across diverse healthcare settings. Materials and Methods We proposed a general targeted fusion learning framework that can be used to build a tailored risk prediction model for any specific healthcare setting, drawing on information fusion from a separate more comprehensive dataset with indirect sample linkage through patient similarities. As a proof of concept, we predicted suicide-related hospitalizations for pediatric patients in a limited statewide Hospital Inpatient Discharge Dataset (HIDD) fused with a more comprehensive medical All-Payer Claims Database (APCD) from Connecticut. Results We built a suicide risk prediction model for the source data (APCD) and calculated patient risk scores. Patient similarity scores between patients in the source and target (HIDD) datasets using their demographic characteristics and diagnosis codes were assessed. A fused risk score was generated for each patient in the target dataset using our proposed targeted fusion framework. With this model, the averaged sensitivities at 90% and 95% specificity improved by 67% and 171%, and the positive predictive values for the combined fusion model improved 64% and 135% compared to the conventional model. Discussion and Conclusions We proposed a general targeted fusion learning framework that can be used to build a tailored predictive model for any specific healthcare setting. Results from this study suggest we can improve the performance of predictive models in specific target settings without complete integration of the raw records from external data sources.

The coronavirus disease 2019 (COVID-19) is heterogeneous and our understanding of the biological mechanisms of host response to the viral infection remains limited. Identification of meaningful clinical subphenotypes may benefit pathophysiological study, clinical practice, and clinical trials. Here, our aim was to derive and validate COVID-19 subphenotypes using machine learning and routinely collected clinical data, assess temporal patterns of these subphenotypes during the pandemic course, and examine their interaction with social determinants of health (SDoH). We retrospectively analyzed 14418 COVID-19 patients in five major medical centers in New York City (NYC), between March 1 and June 12, 2020. Using clustering analysis, 4 biologically distinct subphenotypes were derived in the development cohort (N = 8199). Importantly, the identified subphenotypes were highly predictive of clinical outcomes (especially 60-day mortality). Sensitivity analyses in the development cohort, and rederivation and prediction in the internal (N = 3519) and external (N = 3519) validation cohorts confirmed the reproducibility and usability of the subphenotypes. Further analyses showed varying subphenotype prevalence across the peak of the outbreak in NYC. We also found that SDoH specifically influenced mortality outcome in Subphenotype IV, which is associated with older age, worse clinical manifestation, and high comorbidity burden. Our findings may lead to a better understanding of how COVID-19 causes disease in different populations and potentially benefit clinical trial development. The temporal patterns and SDoH implications of the subphenotypes may add insights to health policy to reduce social disparity in the pandemic.

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