6 accepted papers
We introduce a new framework for 2D molecular graph generation using 3D molecule generative models. Our Synthetic Coordinate Embedding (SyCo) framework maps 2D molecular graphs to 3D Euclidean point clouds via synthetic coordinates and learns the inverse map using an E($n$)-Equivariant Graph Neural…
Recent advances in machine learning for molecules exhibit great potential for facilitating drug discovery from in silico predictions. Most models for molecule generation rely on the decomposition of molecules into frequently occurring substructures (motifs), from which they generate novel compounds.…
Although recent advances in higher-order Graph Neural Networks (GNNs) improve the theoretical expressiveness and molecular property predictive performance, they often fall short of the empirical performance of models that explicitly use fragment information as inductive bias. However, for these appr…
Effectively designing molecular geometries is essential to advancing pharmaceutical innovations, a domain, which has experienced great attention through the success of generative models and, in particular, diffusion models. However, current molecular diffusion models are tailored towards a specific…
End-to-end (geometric) deep learning has seen first successes in approximating the solution of combinatorial optimization problems. However, generating data in the realm of NP-hard/-complete tasks brings practical and theoretical challenges, resulting in evaluation protocols that are too optimistic.…
Neural ordinary differential equations describe how values change in time. This is the reason why they gained importance in modeling sequential data, especially when the observations are made at irregular intervals. In this paper we propose an alternative by directly modeling the solution curves - t…