4 accepted papers
Can we train a 3D molecule generator using data from dense regions to generate samples in sparse regions? This challenge can be framed as an out-of-distribution (OOD) generation problem. While prior research on OOD generation predominantly targets property shifts, structural shifts, such as differen
Geometric graph neural networks (Geo-GNNs) have revolutionized molecular dynamics (MD) simulations by providing accurate and fast energy and force predictions. However, minor prediction errors could still destabilize MD trajectories in real MD simulations due to the limited coverage of molecular con…
Large-scale molecular dynamics simulations are essential in understanding chemical and biological processes, necessitating the accurate and efficient modeling of interatomic interactions. Existing learning-based methods generally are based on message passing mechanisms; they are either not scalable …
This paper proposes a new 3D molecule generation framework, called GOAT, for fast and effective 3D molecule generation based on the flow-matching optimal transport objective. Specifically, we formulate a geometric transport formula for measuring the cost of mapping multi-modal features (e.g., contin…