Self-tuning Hamiltonian Monte Carlo for accelerated sampling.

The performance of Hamiltonian Monte Carlo simulations crucially depends on both the integration timestep and the number of integration steps. We present an adaptive general-purpose framework to automatically tune such parameters based on a local loss function that promotes the fast exploration of phase space. We show that a good correspondence between loss and autocorrelation time can be established, allowing for gradient-based optimization using a fully differentiable set-up.

Catastrophic Forgetting in Deep Graph Networks: A Graph Classification Benchmark.

In this work, we study the phenomenon of catastrophic forgetting in the graph representation learning scenario. The primary objective of the analysis is to understand whether classical continual learning techniques for flat and sequential data have a tangible impact on performances when applied to graph data. To do so, we experiment with a structure-agnostic model and a deep graph network in a robust and controlled environment on three different datasets.

A Deep Graph Network-Enhanced Sampling Approach to Efficiently Explore the Space of Reduced Representations of Proteins.

The limits of molecular dynamics (MD) simulations of macromolecules are steadily pushed forward by the relentless development of computer architectures and algorithms. The consequent explosion in the number and extent of MD trajectories induces the need for automated methods to rationalize the raw data and make quantitative sense of them. Recently, an algorithmic approach was introduced by some of us to identify the subset of a protein's atoms, or mapping, that enables the most informative description of the system.

A gentle introduction to deep learning for graphs.

The adaptive processing of graph data is a long-standing research topic that has been lately consolidated as a theme of major interest in the deep learning community. The snap increase in the amount and breadth of related research has come at the price of little systematization of knowledge and attention to earlier literature. This work is a tutorial introduction to the field of deep learning for graphs.