71 citations · 126 across the 9 of their papers we have counts for
9 papers
SynCoGen: Synthesizable 3D Molecule Generation via Joint Reaction and Coordinate Modeling
Andrei Rekesh, Miruna Cretu, Dmytro Shevchuk +6
Synthesizability remains a critical bottleneck in generative molecular design. While recent advances have addressed synthesizability in 2D graphs, extending these constraints to 3D…
3DReact: Geometric deep learning for chemical reactions
Puck van Gerwen, Ksenia R. Briling, Charlotte Bunne +4
Geometric deep learning models, which incorporate the relevant molecular symmetries within the neural network architecture, have considerably improved the accuracy and data efficie…
DockGame: Cooperative Games for Multimeric Rigid Protein Docking
Vignesh Ram Somnath, Pier Giuseppe Sessa, Maria Rodriguez Martinez +1
Protein interactions and assembly formation are fundamental to most biological processes. Predicting the assembly structure from constituent proteins -- referred to as the protein…
Aligned Diffusion Schrödinger Bridges
Vignesh Ram Somnath, Matteo Pariset, Ya-Ping Hsieh +3
Diffusion Schrödinger bridges (DSB) have recently emerged as a powerful framework for recovering stochastic dynamics via their marginal observations at different time points. Despi…
Isotropic Gaussian Processes on Finite Spaces of Graphs
Viacheslav Borovitskiy, Mohammad Reza Karimi, Vignesh Ram Somnath +1
We propose a principled way to define Gaussian process priors on various sets of unweighted graphs: directed or undirected, with or without loops. We endow each of these sets with…
BaCaDI: Bayesian Causal Discovery with Unknown Interventions
Alexander Hägele, Jonas Rothfuss, Lars Lorch +3
Inferring causal structures from experimentation is a central task in many domains. For example, in biology, recent advances allow us to obtain single-cell expression data under mu…
Multi-Scale Representation Learning on Proteins
Vignesh Ram Somnath, Charlotte Bunne, Andreas Krause
Proteins are fundamental biological entities mediating key roles in cellular function and disease. This paper introduces a multi-scale graph construction of a protein -- HoloProt -…
Learning Graph Models for Retrosynthesis Prediction
Vignesh Ram Somnath, Charlotte Bunne, Connor W. Coley +2
Retrosynthesis prediction is a fundamental problem in organic synthesis, where the task is to identify precursor molecules that can be used to synthesize a target molecule. A key c…
Mixture-of-Experts Variational Autoencoder for Clustering and Generating from Similarity-Based Representations on Single Cell Data
Andreas Kopf, Vincent Fortuin, Vignesh Ram Somnath +1
Clustering high-dimensional data, such as images or biological measurements, is a long-standingproblem and has been studied extensively. Recently, Deep Clustering has gained popula…