Uncovering Complicated Plant Biological Networks through the Assistance of Artificial Intelligence Tools

Plant biological networks, comprising gene regulatory, protein–protein interaction (PPI), and metabolic pathways, are intricate systems fundamental to understanding plant development and physiology. The advent of artificial intelligence (AI) offers promising tools to unravel these complex networks, allowing for more precise insights into regulatory mechanisms, functional annotation, and multi-omics data integration. This chapter explores how AI techniques, including machine learning and deep learning, are transforming the analysis of plant biological networks. It delves into AI’s role in gene regulatory network inference, PPI predictions, and metabolic network reconstruction and also highlights AI-driven approaches for analyzing spatial and temporal dynamics in plant systems. Through integrative network analysis, AI enables the synthesis of diverse data types, driving advancements in plant biology. Case studies illustrate practical applications of these AI tools, offering valuable perspectives for future research.