The lack of insight into deep learning systems hinders their systematic design. In science and engineering, modeling is a methodology used to understand complex systems whose internal processes are opaque. Modeling replaces a complex system with a simpler surrogate that is more amenable to interpretation. Drawing inspiration from this, we construct a class of surrogate models for neural networks using Gaussian processes. Rather than deriving the kernels for certain limiting cases of neural networks, we learn the kernels of the Gaussian process empirically from the naturalistic behavior of neural networks. We first evaluate our approach with two case studies inspired by previous theoretical studies of neural network behavior in which we capture neural network preferences for learning low frequencies and identify pathological behavior in deep neural networks. In two further practical case studies, we use the learned kernel to predict the generalization properties of neural networks.