Multi-Task Topological Laplacian deep learning model that predicts binding free energy changes upon mutation

SAASBO: a package for high-dimensional bayesian optimization

My implementation of the original GAT paper (Veličković et al.). I've additionally included the playground.py file for visualizing the Cora dataset, GAT embeddings, an attention mechanism, and entr…

MDAnalysis is a Python library to analyze molecular dynamics trajectories.

SwarmCG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization

Multi-View Spectral Graph Convolution with Consistent Edge Attention for Molecular Modeling

A settings-free global optimization method based on PSO and fuzzy logic

Fast EMD for Python: a wrapper for Pele and Werman's C++ implementation of the Earth Mover's Distance metric