A graph is a data structure that represents a set of objects and their relationships. Graphs can be used to represent and analyze big data such as search engine problems, social media, knowledge discovery, network systems, and others. Graph Neural Networks (GNNs) is a type of Neural Network that operates directly on a graph structure. The GNNs working system is the classification of points on a graph structure by Labelling the node. Graph neural networks (GNNs) is a continuous study of developing the concept of neural networks. Artificial Neural Networks, abbreviated as artificial neural networks, is an information processing system that is appropriate for biological neural networks. This research focus on Applying neural network graphs to the problem of protein interaction of diabetes mellitus