We formulate the problem of bipartite graph inference as a supervised learning problem, and propose a new method to solve it from the viewpoint of distance metric learning. The method involves the learning of two mappings of the heterogeneous objects to a unified Euclidean space representing the network topology of the bipartite graph, where the graph is easy to infer. The algorithm can be formulated as an optimization problem in a reproducing kernel Hilbert space. We report encouraging results on the problem of compound-protein interaction network reconstruction from chemical structure data and genomic sequence data.