In this paper we present a deep learning method to predict the time evolution of dissipative dynamical systems. We propose using both geometric and thermodynamic inductive biases to improve accuracy and generalization of the resulting integration scheme. The first is achieved with Graph Neural Networks, which induces a non-Euclidean geometrical prior and permutation invariant node and edge update functions. The second bias is forced by learning the GENERIC structure of the problem, an extension of the Hamiltonian formalism, to model more general non-conservative dynamics. Several examples are provided in both Eulerian and Lagrangian description in the context of fluid and solid mechanics respectively.