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