Machine learning is changing the way we simulate matter. In particular, Graph Neural Networks (GNNs), which describe a molecule as a network of interacting atoms, can now predict the energy of molecular systems with high accuracy, enabling fast and reliable simulations. This accuracy, however, comes at the price of transparency: unlike classical force fields, in which each term has a clear physical meaning, a trained GNN is a complex, high-dimensional function whose predictions are hard to trace back to the underlying physical interactions. Existing interpretability tools typically explain the model one configuration at a time, with a cost that grows quickly with the size of the system and with the number of configurations to be analyzed. In this contribution we present a different strategy: rather than analyzing the network on a given unique input, we use a kernel method (in essence, a linear regression performed after a nonlinear embedding of the data) to distill what the GNN has learned into a compact analytical potential. The resulting expression provides a transparent global approximation of the original model, in which the relevant interactions can be read directly, much as in a classical force field. Although illustrated here for molecular potentials, the approach is not tied to this specific application and can be extended to other neural architectures and learning tasks. In this way, a typically opaque object such as a GNN becomes physically inspectable, opening a very effective window into the so-called black box.
Nov 12, 2026 4:30 PM
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