71 citations · 126 across the 9 of their papers we have counts for
7 papers · 1 filter
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…
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…
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…