Charlotte Bunne

• PhD Student
• External Website
• bunnec@inf.ethz.ch
• CAB G65
• +41 44 632 31 83
• I am a PhD student in Computer Science at ETH Zurich under the supervision of Andreas Krause and Marco Cuturi. I am part of the Institute for Machine Learning and the ETH AI Center. Before, I worked with Stefanie Jegelka as a Master student at MIT. My research focuses on dynamic optimal transport and optimal transport across incomparable domains with applications in single-cell genomics and protein design.

---

Publications

2023

Neural Unbalanced Optimal Transport via Cycle-Consistent Semi-Couplings F. Lübeck*, C. Bunne*, G. Gut, J. S. del Castillo, L. Pelkmans, D. Alvarez-Melis In arXiv preprint arXiv:2209.15621, 2023 [bibtex] [abstract] [pdf]

The Schrödinger Bridge between Gaussian Measures has a Closed Form C. Bunne, Y. P. Hsieh, M. Cuturi, A. Krause In Proc. International Conference on Artificial Intelligence and Statistics (AISTATS), 2023 Oral presentation [bibtex] [abstract] [pdf]

Aligned Diffusion Schrödinger Bridges V. R. Somnath, M. Pariset, Y. P. Hsieh, M. R. Martinez, A. Krause, C. Bunne In arXiv preprint arXiv:2302.11419, 2023 [bibtex] [abstract] [pdf]

2022

Supervised Training of Conditional Monge Maps C. Bunne, A. Krause, M. Cuturi In Proc. Neural Information Processing Systems (NeurIPS), 2022 [bibtex] [abstract] [pdf]

Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking O. E. Ganea*, X. Huang*, C. Bunne, Y. Bian, R. Barzilay, T. S. Jaakkola, A. Krause In Proc. International Conference on Learning Representations (ICLR), 2022 Spotlight presentation [bibtex] [abstract] [pdf]

Proximal Optimal Transport Modeling of Population Dynamics C. Bunne, L. Meng-Papaxanthos, A. Krause, M. Cuturi In Proc. International Conference on Artificial Intelligence and Statistics (AISTATS), 2022 Best Paper Award at ICML Time-Series Workshop [bibtex] [abstract] [pdf]

Machine intelligence for chemical reaction space P. Schwaller, A. C. Vaucher, R. Laplaza, C. Bunne, A. Krause, C. Corminboeuf, T. Laino In WIREs Computational Molecular Science Advanced Reviews, 2022 [bibtex] [abstract] [pdf] [doi]

2021

Multi-Scale Representation Learning on Proteins V. R. Somnath*, C. Bunne*, A. Krause In Proc. Neural Information Processing Systems (NeurIPS), 2021 [bibtex] [abstract] [pdf] [code]

Learning Graph Models for Retrosynthesis Prediction V. R. Somnath, C. Bunne, C. W. Coley, A. Krause, R. Barzilay In Proc. Neural Information Processing Systems (NeurIPS), 2021 Best Paper Award at ICML on Graph Representation Learning and Beyond [bibtex] [abstract] [pdf] [code]

Learning Single-Cell Perturbation Responses using Neural Optimal Transport C. Bunne, S. G. Stark, G. Gut, K. V. Lehmann, L. Pelkmans, A. Krause, G. Ratsch In NeurIPS Optimal Transport and Machine Learning Workshop, 2021 [bibtex] [abstract] [pdf]

2019

Learning Generative Models across Incomparable Spaces C. Bunne, D. Alvarez-Melis, A. Krause, S. Jegelka In Proc. International Conference on Machine Learning (ICML), 2019 Best Paper Award at NeurIPS Workshop on Relational Representation Learning [bibtex] [abstract] [pdf]