Synergistic Disease Similarity Measurement via Unifying Hierarchical Relation Perception and Association Capturing

Zihao Gao, Huifang Ma, Yike Wang, Zhixin Li, Liang Chang

Abstract: Quantifying similarities among human diseases is crucial to enhance our understanding of disease biology. Deep learning efforts have been devoted to quantifying disease similarity by integrating multi-view data sources from disparate biological data. However, disease data are often sparse, leading to suboptimal representation of disease given biological entity relationships and labeled disease data are not adequately modeled. In this paper, we propose an effective Synergistic disease Similarity measurement model called SynerSim. SynerSim possesses two key components: a hierarchical biological entity relation perception module to capture disease features from various biological entities, and a disease association capturing module based on signed random walk to model precious disease data. Additionally, SynerSim leverages dual granularity contrastive learning to enhance the representation of diverse biological entities, owing to the ability to enable the synergistic supervision of diseases represented by both homogeneous and heterogeneous information. Experimental results demonstrate that SynerSim achieves outstanding performance in the disease similarity measurement.