There is described a neural network system implemented by one or more computers for determining graph similarity. The neural network system comprises one or more neural networks configured to process an input graph to generate a node state representation vector for each node of the input graph and an edge representation vector for each edge of the input graph; and process the node state representation vectors and the edge representation vectors to generate a vector representation of the input graph. The neural network system further comprises one or more processors configured to: receive a first graph; receive a second graph; generate a vector representation of the first graph; generate a vector representation of the second graph; determine a similarity score for the first graph and the second graph based upon the vector representations of the first graph and the second graph.