Table 2.

Research on network-based methods for resolving multi-omics data

Method category	Modeling methods	Input	Application	Refs
Multi-layer integration	Dimensionality reduction	Multi-layer network	Multi-layer clustering	52
Multi-layer integration	Similarity measurement	Multi-layer network	Multi-layer clustering	57
Multi-layer integration	Network structure analysis	Multi-layer network	Multi-level biological network construction and resolution	59
Multi-layer integration	Network structure analysis and machine learning	Multi-layer network	Multi-level biological network construction and disease gene prediction	61
Dynamic feature identification	Representation learning	Dynamic network	Network topology dynamic representation	63
Dynamic feature identification	Dynamic embedding	Dynamic network	Dynamic features identification and anomaly detection	65
Dynamic feature identification	State transition simulation	Dynamic biological network	Dynamic features identification, early warning signals	66
Dynamic feature identification	Multiscale modeling	Dynamic biological data	Simulation of tumorigenesis	67