Charlotte Bunne

32 papers A* 6A 4Journal 21
YearRankTypeTitle / Venue / Authors
2026 J jnl
Latent Causal Diffusions for Single-Cell Perturbation Modeling.
CoRR
Lars Lorch, Jiaqi Zhang, Charlotte Bunne, Andreas Krause, Bernhard Schölkopf, Caroline Uhler
2025 J jnl
AI-powered virtual tissues from spatial proteomics for clinical diagnostics and biomedical discovery.
CoRR
Johann Wenckstern, Eeshaan Jain, Kiril Vasilev, Matteo Pariset, Andreas Wicki, Gabriele Gut, Charlotte Bunne
2025 A conf
Cross-modality Matching and Prediction of Perturbation Responses with Labeled Gromov-Wasserstein Optimal Transport.
AISTATS
Jayoung Ryu, Charlotte Bunne, Luca Pinello, Aviv Regev, Romain Lopez
2025 J jnl
MTBBench: A Multimodal Sequential Clinical Decision-Making Benchmark in Oncology.
CoRR
Kiril Vasilev, Alexandre Misrahi, Eeshaan Jain, Phil F. Cheng, Petros Liakopoulos, Olivier Michielin, Michael Moor, Charlotte Bunne
2025 A* conf
Modeling Complex System Dynamics with Flow Matching Across Time and Conditions.
ICLR
Martin Rohbeck, Edward De Brouwer, Charlotte Bunne, Jan-Christian Huetter, Anne Biton, Kelvin Y. Chen, Aviv Regev, Romain Lopez
2024 J jnl
3DReact: Geometric Deep Learning for Chemical Reactions.
J. Chem. Inf. Model.
Puck van Gerwen, Ksenia R. Briling, Charlotte Bunne, Vignesh Ram Somnath, Rubén Laplaza, Andreas Krause, Clémence Corminboeuf
2024 J jnl
How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities.
CoRR
Charlotte Bunne, Yusuf H. Roohani, Yanay Rosen, Ankit Gupta, Xikun Zhang, Marcel Roed, Theo Alexandrov, Mohammed AlQuraishi, Patricia Brennan, Daniel B. Burkhardt, Andrea Califano, Jonah Cool, Abby F. Dernburg, Kirsty Ewing, Emily B. Fox, Matthias Haury, Amy E. Herr, Eric Horvitz, Patrick D. Hsu, Viren Jain, Gregory R. Johnson, Thomas Kalil, David R. Kelley, Shana O. Kelley, Anna Kreshuk, Tim Mitchison, Stephani Otte, Jay Shendure, Nicolas J. Sofroniew, Fabian J. Theis, Christina V. Theodoris, Srigokul Upadhyayula, Marc Valer, Bo Wang, Eric Xing, Serena Yeung-Levy, Marinka Zitnik, Theofanis Karaletsos, Aviv Regev, Emma Lundberg, Jure Leskovec, Stephen R. Quake
2023 A conf
Aligned Diffusion Schrödinger Bridges.
UAI
Vignesh Ram Somnath, Matteo Pariset, Ya-Ping Hsieh, María Rodríguez Martínez, Andreas Krause, Charlotte Bunne
2023 J jnl
Aligned Diffusion Schrödinger Bridges.
CoRR
Vignesh Ram Somnath, Matteo Pariset, Ya-Ping Hsieh, María Rodríguez Martínez, Andreas Krause, Charlotte Bunne
2023 J jnl
EquiReact: An equivariant neural network for chemical reactions.
CoRR
Puck van Gerwen, Ksenia R. Briling, Charlotte Bunne, Vignesh Ram Somnath, Rubén Laplaza, Andreas Krause, Clémence Corminboeuf
2023 — —
Neural Optimal Transport for Dynamical Systems: Methods and Applications in Biomedicine.
Charlotte Bunne
2023 A conf
The Schrödinger Bridge between Gaussian Measures has a Closed Form.
AISTATS
Charlotte Bunne, Ya-Ping Hsieh, Marco Cuturi, Andreas Krause
2023 J jnl
Transition Path Sampling with Boltzmann Generator-based MCMC Moves.
CoRR
Michael Plainer, Hannes Stärk, Charlotte Bunne, Stephan Günnemann
2023 J jnl
Unbalanced Diffusion Schrödinger Bridge.
CoRR
Matteo Pariset, Ya-Ping Hsieh, Charlotte Bunne, Andreas Krause, Valentin De Bortoli
2022 A* conf
Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking.
ICLR
Octavian-Eugen Ganea, Xinyuan Huang, Charlotte Bunne, Yatao Bian, Regina Barzilay, Tommi S. Jaakkola, Andreas Krause
2022 J jnl
Invariant Causal Mechanisms through Distribution Matching.
CoRR
Mathieu Chevalley, Charlotte Bunne, Andreas Krause, Stefan Bauer
2022 J jnl
Multi-Scale Representation Learning on Proteins.
CoRR
Vignesh Ram Somnath, Charlotte Bunne, Andreas Krause
2022 J jnl
Neural Unbalanced Optimal Transport via Cycle-Consistent Semi-Couplings.
CoRR
Frederike Lübeck, Charlotte Bunne, Gabriele Gut, Jacobo Sarabia del Castillo, Lucas Pelkmans, David Alvarez-Melis
2022 J jnl
Optimal Transport Tools (OTT): A JAX Toolbox for all things Wasserstein.
CoRR
Marco Cuturi, Laetitia Meng-Papaxanthos, Yingtao Tian, Charlotte Bunne, Geoff Davis, Olivier Teboul
2022 A conf
Proximal Optimal Transport Modeling of Population Dynamics.
AISTATS
Charlotte Bunne, Laetitia Papaxanthos, Andreas Krause, Marco Cuturi
2022 J jnl
Recovering Stochastic Dynamics via Gaussian Schrödinger Bridges.
CoRR
Charlotte Bunne, Ya-Ping Hsieh, Marco Cuturi, Andreas Krause
2022 A* conf
Supervised Training of Conditional Monge Maps.
NeurIPS
Charlotte Bunne, Andreas Krause, Marco Cuturi
2022 J jnl
Supervised Training of Conditional Monge Maps.
CoRR
Charlotte Bunne, Andreas Krause, Marco Cuturi
2021 J jnl
COSIFER: a Python package for the consensus inference of molecular interaction networks.
Bioinform.
Matteo Manica, Charlotte Bunne, Roland Mathis, Joris Cadow, Mehmet Eren Ahsen, Gustavo A. Stolovitzky, María Rodríguez Martínez
2021 J jnl
Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking.
CoRR
Octavian-Eugen Ganea, Xinyuan Huang, Charlotte Bunne, Yatao Bian, Regina Barzilay, Tommi S. Jaakkola, Andreas Krause
2021 J jnl
JKOnet: Proximal Optimal Transport Modeling of Population Dynamics.
CoRR
Charlotte Bunne, Laetitia Meng-Papaxanthos, Andreas Krause, Marco Cuturi
2021 A* conf
Learning Graph Models for Retrosynthesis Prediction.
NeurIPS
Vignesh Ram Somnath, Charlotte Bunne, Connor W. Coley, Andreas Krause, Regina Barzilay
2021 A* conf
Multi-Scale Representation Learning on Proteins.
NeurIPS
Vignesh Ram Somnath, Charlotte Bunne, Andreas Krause
2020 J jnl
Learning Graph Models for Template-Free Retrosynthesis.
CoRR
Vignesh Ram Somnath, Charlotte Bunne, Connor W. Coley, Andreas Krause, Regina Barzilay
2019 A* conf
Learning Generative Models across Incomparable Spaces.
ICML
Charlotte Bunne, David Alvarez-Melis, Andreas Krause, Stefanie Jegelka
2019 J jnl
Learning Generative Models across Incomparable Spaces.
CoRR
Charlotte Bunne, David Alvarez-Melis, Andreas Krause, Stefanie Jegelka
2018 J jnl
Studying Invariances of Trained Convolutional Neural Networks.
CoRR
Charlotte Bunne, Lukas Rahmann, Thomas Wolf