Hi! I am currently a 3rd year Ph.D. student at ETH Zurich, supervised by Andreas Krause and Kjell Jorner. The first 1.5 years of my PhD were spent at IBM Research Zurich, under Maria Rodriguez Martinez. Previously, I obtained my Masters degree in Computational Biology and Bioinformatics at ETH Zurich, and had the fortune of doing my Master Thesis with Regina Barzilay and Klavs Jensen at MIT.
My research aims to develop machine learning methods in scientific domains such as structural biology and chemistry. I enjoy learning the science behind the problem, and developing algorithms that strike a balance between being methodologically interesting yet practically applicable. I also am interested in finding connections between different fields that could provide a different perspective on the problem being investigated. My past experience revolves around the following domains:
In addition, I also value a strong software engineering component to my research, trying to maintain readability and ease of extension in the code associated with my projects.
Most recent publications on Google Scholar.
‡ indicates equal contribution.
DockGame: Cooperative Games for Multimeric Rigid Protein Docking
Vignesh Ram Somnath‡, Pier Giuseppe Sessa‡, Maria Rodriguez Martinez, Andreas Krause
arXiv
Aligned Diffusion Schrödinger Bridges
Vignesh Ram Somnath‡, Matteo Pariset‡, Ya-Ping Hsieh, Maria Rodriguez Martinez, Andreas Krause, Charlotte Bunne
Conference on Uncertainty in Artificial Intelligence (UAI) 2023. Spotlight Presentation.
Isotropic Gaussian Processes on Spaces of Graphs
Viacheslav Borovitskiy‡, Mohammad Reza Karimi‡, Vignesh Ram Somnath‡, Andreas Krause
Artificial Intelligence and Statistics (AISTATS) 2023
Multi-Scale Representation Learning on Proteins
Vignesh Ram Somnath‡, Charlotte Bunne‡, Andreas Krause
Neural Information Processing Systems (NeurIPS) 2021.
Learning Graph Models for Retrosynthesis Prediction
Vignesh Ram Somnath, Charlotte Bunne, Connor W. Coley, Andreas Krause, Regina Barzilay
Neural Information Processing Systems (NeurIPS) 2021.
Best Paper Award at ICML 2020 Graph Representation Learning & Beyond Workshop
Mixture-of-Experts Variational Autoencoder for Clustering and Generating from Similarity-Based Representations on Single Cell Data
Andreas Kopf, Vincent Fortuin, Vignesh Ram Somnath, Manfred Claassen
PLoS Computational Biology 2021
EquiReact: An equivariant neural network for chemical reactions
Puck van Gerwen, Ksenia R Briling, Charlotte Bunne, Vignesh Ram Somnath, Ruben Laplaza, Andreas Krause, Clemence Corminboeuf
arXiv
DockGame: Cooperative Games for Multimeric Rigid Protein Docking
Vignesh Ram Somnath‡, Pier Giuseppe Sessa‡, Maria Rodriguez Martinez, Andreas Krause
arXiv
Aligned Diffusion Schrödinger Bridges
Vignesh Ram Somnath‡, Matteo Pariset‡, Ya-Ping Hsieh, Maria Rodriguez Martinez, Andreas Krause, Charlotte Bunne
Conference on Uncertainty in Artificial Intelligence (UAI) 2023. Spotlight Presentation.
Isotropic Gaussian Processes on Spaces of Graphs
Viacheslav Borovitskiy‡, Mohammad Reza Karimi‡, Vignesh Ram Somnath‡, Andreas Krause
Artificial Intelligence and Statistics (AISTATS) 2023
ChromFormer: A transformed-based model for 3D genome structure prediction
Henry Valeyre, Pushpak Pati, Federico Gossi, Vignesh Ram Somnath, Adriano Martinelli, Marianna Rapsomaniki
Learning Meaningful Representations of Life workshop, NeurIPS 2022
Multi-Scale Representation Learning on Proteins
Vignesh Ram Somnath‡, Charlotte Bunne‡, Andreas Krause
Neural Information Processing Systems (NeurIPS) 2021.
Learning Graph Models for Retrosynthesis Prediction
Vignesh Ram Somnath, Charlotte Bunne, Connor W. Coley, Andreas Krause, Regina Barzilay
Neural Information Processing Systems (NeurIPS) 2021.
Best Paper Award at ICML 2020 Graph Representation Learning & Beyond Workshop
Mixture-of-Experts Variational Autoencoder for Clustering and Generating from Similarity-Based Representations on Single Cell Data
Andreas Kopf, Vincent Fortuin, Vignesh Ram Somnath, Manfred Claassen
PLoS Computational Biology 2021
A PDF version of my CV can be found here.