Studying Invariances of Trained Convolutional Neural Networks. - Charlotte Bunne; Lukas Rahmann; Thomas Wolf 010 (CoRR, 2018)

Learning Generative Models across Incomparable Spaces. - Charlotte Bunne; David Alvarez-Melis; Andreas Krause 001; Stefanie Jegelka (ICML, 2019)

Learning Graph Models for Template-Free Retrosynthesis. - Vignesh Ram Somnath; Charlotte Bunne; Connor W. Coley; Andreas Krause 001; Regina Barzilay (CoRR, 2020)

Learning Graph Models for Retrosynthesis Prediction. - Vignesh Ram Somnath; Charlotte Bunne; Connor W. Coley; Andreas Krause 001; Regina Barzilay (NeurIPS, 2021)

Multi-Scale Representation Learning on Proteins. - Vignesh Ram Somnath; Charlotte Bunne; Andreas Krause 001 (NeurIPS, 2021)

JKOnet: Proximal Optimal Transport Modeling of Population Dynamics. - Charlotte Bunne; Laetitia Meng-Papaxanthos; Andreas Krause 001; Marco Cuturi (CoRR, 2021)

Proximal Optimal Transport Modeling of Population Dynamics. - Charlotte Bunne; Laetitia Papaxanthos; Andreas Krause 001; Marco Cuturi (AISTATS, 2022)

Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking. - Octavian-Eugen Ganea; Xinyuan Huang; Charlotte Bunne; Yatao Bian; Regina Barzilay; Tommi S. Jaakkola; Andreas Krause 001 (ICLR, 2022)

Supervised Training of Conditional Monge Maps. - Charlotte Bunne; Andreas Krause 001; Marco Cuturi (NeurIPS, 2022)

Optimal Transport Tools (OTT): A JAX Toolbox for all things Wasserstein. - Marco Cuturi; Laetitia Meng-Papaxanthos; Yingtao Tian; Charlotte Bunne; Geoff Davis; Olivier Teboul (CoRR, 2022)

Recovering Stochastic Dynamics via Gaussian Schrödinger Bridges. - Charlotte Bunne; Ya-Ping Hsieh; Marco Cuturi; Andreas Krause 001 (CoRR, 2022)

Invariant Causal Mechanisms through Distribution Matching. - Mathieu Chevalley; Charlotte Bunne; Andreas Krause 001; Stefan Bauer (CoRR, 2022)

Neural Unbalanced Optimal Transport via Cycle-Consistent Semi-Couplings. - Frederike Lübeck; Charlotte Bunne; Gabriele Gut; Jacobo Sarabia del Castillo; Lucas Pelkmans; David Alvarez-Melis (CoRR, 2022)

The Schrödinger Bridge between Gaussian Measures has a Closed Form. - Charlotte Bunne; Ya-Ping Hsieh; Marco Cuturi; Andreas Krause 001 (AISTATS, 2023)

Aligned Diffusion Schrödinger Bridges. - Vignesh Ram Somnath; Matteo Pariset; Ya-Ping Hsieh; María Rodríguez Martínez; Andreas Krause 001; Charlotte Bunne (UAI, 2023)

Unbalanced Diffusion Schrödinger Bridge. - Matteo Pariset; Ya-Ping Hsieh; Charlotte Bunne; Andreas Krause 001; Valentin De Bortoli (CoRR, 2023)

Transition Path Sampling with Boltzmann Generator-based MCMC Moves. - Michael Plainer; Hannes Stärk; Charlotte Bunne; Stephan Günnemann (CoRR, 2023)

EquiReact: An equivariant neural network for chemical reactions. - Puck van Gerwen; Ksenia R. Briling; Charlotte Bunne; Vignesh Ram Somnath; Rubén Laplaza; Andreas Krause 001; Clémence Corminboeuf (CoRR, 2023)

Neural Optimal Transport for Dynamical Systems: Methods and Applications in Biomedicine. - Charlotte Bunne (2023)

How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities. - Charlotte Bunne; Yusuf H. Roohani; Yanay Rosen; Ankit Gupta; Xikun Zhang 001; Marcel Roed; Theo Alexandrov; Mohammed AlQuraishi; Patricia Brennan; Daniel B. Burkhardt; Andrea Califano; Jonah Cool; et al. (CoRR, 2024)

3DReact: Geometric Deep Learning for Chemical Reactions. - Puck van Gerwen; Ksenia R. Briling; Charlotte Bunne; Vignesh Ram Somnath; Rubén Laplaza; Andreas Krause 001; Clémence Corminboeuf (J. Chem. Inf. Model., 2024)

Cross-modality Matching and Prediction of Perturbation Responses with Labeled Gromov-Wasserstein Optimal Transport. - Jayoung Ryu; Charlotte Bunne; Luca Pinello; Aviv Regev; Romain Lopez (AISTATS, 2025)

Modeling Complex System Dynamics with Flow Matching Across Time and Conditions. - Martin Rohbeck; Edward De Brouwer; Charlotte Bunne; Jan-Christian Huetter; Anne Biton; Kelvin Y. Chen; Aviv Regev; Romain Lopez (ICLR, 2025)

AI-powered virtual tissues from spatial proteomics for clinical diagnostics and biomedical discovery. - Johann Wenckstern; Eeshaan Jain; Kiril Vasilev; Matteo Pariset; Andreas Wicki; Gabriele Gut; Charlotte Bunne (CoRR, 2025)