Graph machines and their applications to computer-aided drug design: A new approach to learning from structured data

Abstract

The recent developments of statistical learning focused on vector machines, which learn from examples that are described by vectors of features. However, there are many fields where structured data must be handled; therefore, it would be desirable to learn from examples described by graphs. Graph machines leam real numbers from graphs. Basically, for each graph, a separate learning machine is built, whose algebraic structure contains the same information as the graph. We describe the training of such machines, and show that virtual leave-one-out, a powerful method for assessing the generalization capabilities of conventional vector machines, can be extended to graph machines. Academic examples are described, together with applications to the prediction of pharmaceutical activities of molecules and to the classification of properties; the potential of graph machines for computer-aided drug design are highlighted. © Springer-Verlag Berlin Heidelberg 2006.