Publications

2024

1. EquiReact: An equivariant neural network for chemical reactions

   Puck Gerwen, Ksenia R Briling, Charlotte Bunne, Vignesh Ram Somnath, Ruben Laplaza, Andreas Krause, and Clemence Corminboeuf

   arXiv Preprint arXiv:2312.08307, 2024

   bibtex PDF Code

   @article{van2023equireact,
     title={EquiReact: An equivariant neural network for chemical reactions},
     author={van Gerwen, Puck and Briling, Ksenia R and Bunne, Charlotte and Somnath, Vignesh Ram and Laplaza, Ruben and Krause, Andreas and Corminboeuf, Clemence},
     journal={arXiv Preprint arXiv:2312.08307},
     year={2024},
   }

2023

1. Transition Path Sampling with Boltzmann Generator-based MCMC Moves

   Michael Plainer, Hannes Stärk, Charlotte Bunne, and Stephan Günnemann

   arXiv preprint arXiv:2312.05340, 2023

   bibtex PDF

   @article{plainer2023transition,
     title={Transition Path Sampling with Boltzmann Generator-based MCMC Moves},
     author={Plainer, Michael and Stärk, Hannes and Bunne, Charlotte and Günnemann, Stephan},
     journal={arXiv preprint arXiv:2312.05340},
     year={2023},
   }

2. Reproducible image-based profiling with Pycytominer

   Erik Serrano, Srinivas Niranj Chandrasekaran, Dave Bunten, Kenneth I Brewer, Jenna Tomkinson, Roshan Kern, Michael Bornholdt, Stephen Fleming, Ruifan Pei, John Arevalo, and others

   arXiv Preprint arXiv:2311.13417, 2023

   bibtex PDF Code

   @article{serrano2023reproducible,
     title={Reproducible image-based profiling with Pycytominer},
     author={Serrano, Erik and Chandrasekaran, Srinivas Niranj and Bunten, Dave and Brewer, Kenneth I and Tomkinson, Jenna and Kern, Roshan and Bornholdt, Michael and Fleming, Stephen and Pei, Ruifan and Arevalo, John and others},
     journal={arXiv Preprint arXiv:2311.13417},
     year={2023},
   }

3. Unbalanced Diffusion Schrödinger Bridge

   Matteo Pariset, Ya-Ping Hsieh, Charlotte Bunne, Andreas Krause, and Valentin De Bortoli

   arXiv Preprint arXiv:2306.09099, 2023

   ICML Workshop on New Frontiers for Learning, Control, and Dynamical Systems, 2023.

   bibtex PDF Code

   @article{pariset2023unbalanced,
     title={Unbalanced Diffusion Schrödinger Bridge},
     author={Pariset, Matteo and Hsieh, Ya-Ping and Bunne, Charlotte and Krause, Andreas and Bortoli, Valentin De},
     journal={arXiv Preprint arXiv:2306.09099},
     year={2023},
   }

4. Nature Methods

   Research Briefing

   Learning Single-Cell Perturbation Responses using Neural Optimal Transport

   Charlotte Bunne, Stefan Stark, Gabriele Gut, ..., Mitchell Levesque, Kjong Van Lehmann, Lucas Pelkmans, Andreas Krause, and Gunnar Rätsch

   Nature Methods, 2023

   NeurIPS Workshop on Optimal Transport and Machine Learning (OTML), 2021.

   bibtex PDF Talk Code Press Highlight

   @article{bunne2021learning,
     title={Learning Single-Cell Perturbation Responses using Neural Optimal Transport},
     author={Bunne, Charlotte and Stark, Stefan and Gut, Gabriele and ... and Levesque, Mitchell and Van Lehmann, Kjong and Pelkmans, Lucas and Krause, Andreas and Rätsch, Gunnar},
     journal={Nature Methods},
     year={2023},
   }

5. UAI

   Aligned Diffusion Schrödinger Bridges

   Vignesh Ram Somnath, Matteo Pariset, Ya-Ping Hsieh, Maria Rodriguez Martinez, Andreas Krause, and Charlotte Bunne

   Conference on Uncertainty in Artificial Intelligence (UAI), 2023

   ICML Workshop on New Frontiers for Learning, Control, and Dynamical Systems, 2023.

   bibtex PDF Code

   @inproceedings{somnath2023aligned,
     title={Aligned Diffusion Schrödinger Bridges},
     author={Somnath, Vignesh Ram and Pariset, Matteo and Hsieh, Ya-Ping and Martinez, Maria Rodriguez and Krause, Andreas and Bunne, Charlotte},
     booktitle={Conference on Uncertainty in Artificial Intelligence (UAI)},
     year={2023},
   }

6. Neural Unbalanced Optimal Transport via Cycle-Consistent Semi-Couplings

   Frederike Lübeck, Charlotte Bunne, Gabriele Gut, Jacobo Sarabia Castillo, Lucas Pelkmans, and David Alvarez Melis

   arXiv Preprint arXiv:2209.15621, 2023

   Spotlight Talk at NeurIPS Meaningful Representations of Life Workshop, 2022.

   bibtex PDF Code

   @article{luebeck2023neural,
     title={Neural Unbalanced Optimal Transport via Cycle-Consistent Semi-Couplings},
     author={Lübeck, Frederike and Bunne, Charlotte and Gut, Gabriele and del Castillo, Jacobo Sarabia and Pelkmans, Lucas and Alvarez Melis, David},
     journal={arXiv Preprint arXiv:2209.15621},
     year={2023},
   }

7. AISTATS

   Oral

   The Schrödinger Bridge between Gaussian Measures has a Closed Form

   Charlotte Bunne, Ya-Ping Hsieh, Marco Cuturi, and Andreas Krause

   International Conference on Artificial Intelligence and Statistics (AISTATS), 2023

   ICML Workshop on Continuous Time Methods for Machine Learning, 2022.

   Oral Presentation at AISTATS (Top 1.9% of Submitted Papers).

   bibtex PDF

   @inproceedings{bunne2023the,
     title={The Schrödinger Bridge between Gaussian Measures has a Closed Form},
     author={Bunne, Charlotte and Hsieh, Ya-Ping and Cuturi, Marco and Krause, Andreas},
     booktitle={International Conference on Artificial Intelligence and Statistics (AISTATS)},
     year={2023},
   }

2022

1. NeurIPS

   Supervised Training of Conditional Monge Maps

   Charlotte Bunne, Andreas Krause, and Marco Cuturi

   Advances in Neural Information Processing Systems (NeurIPS), 2022

   ICML Workshop on Interpretable Machine Learning in Healthcare (IMLH), 2022.

   bibtex PDF Code

   @inproceedings{bunne2022supervised,
     title={Supervised Training of Conditional Monge Maps},
     author={Bunne, Charlotte and Krause, Andreas and Cuturi, Marco},
     booktitle={Advances in Neural Information Processing Systems (NeurIPS)},
     year={2022},
   }

2. AISTATS

   Best Paper Award

   Proximal Optimal Transport Modeling of Population Dynamics

   Charlotte Bunne, Laetitia Meng-Papaxanthos, Andreas Krause, and Marco Cuturi

   International Conference on Artificial Intelligence and Statistics (AISTATS), 2022

   Best Paper Award and Contributed Talk at ICML Time Series Workshop, 2021.

   bibtex PDF Talk Short Talk Code

   @inproceedings{bunne2022proximal,
     title={Proximal Optimal Transport Modeling of Population Dynamics},
     author={Bunne, Charlotte and Meng-Papaxanthos, Laetitia and Krause, Andreas and Cuturi, Marco},
     booktitle={International Conference on Artificial Intelligence and Statistics (AISTATS)},
     year={2022},
   }

3. ICLR

   Independent SE (3)-Equivariant Models for End-to-End Rigid Protein Docking

   Octavian-Eugen Ganea, Xinyuan Huang, Charlotte Bunne, Yatao Bian, Regina Barzilay, Tommi Jaakkola, and Andreas Krause

   International Conference on Learning Representations (ICLR), 2022

   Contributed Talk at ELLIS Machine Learning for Molecule Discovery Workshop, 2021.

   Spotlight Talk at ICLR and Ranked Top 15 among 3326 Submissions (Top 0.4%).

   bibtex PDF Code Press

   @inproceedings{ganea2021independent,
     title={Independent SE (3)-Equivariant Models for End-to-End Rigid Protein Docking},
     author={Ganea, Octavian-Eugen and Huang, Xinyuan and Bunne, Charlotte and Bian, Yatao and Barzilay, Regina and Jaakkola, Tommi and Krause, Andreas},
     booktitle={International Conference on Learning Representations (ICLR)},
     year={2022},
   }

4. Featured Cover

   Machine intelligence for chemical reaction space

   Philippe Schwaller, Alain C Vaucher, Ruben Laplaza, Charlotte Bunne, Andreas Krause, Clemence Corminboeuf, and Teodoro Laino

   Wiley Interdisciplinary Reviews: Computational Molecular Science, 2022

   Selected as Featured Cover of Volume 12, Issue 5.

   bibtex PDF

   @article{schwaller2022machine,
     title={Machine intelligence for chemical reaction space},
     author={Schwaller, Philippe and Vaucher, Alain C and Laplaza, Ruben and Bunne, Charlotte and Krause, Andreas and Corminboeuf, Clemence and Laino, Teodoro},
     journal={Wiley Interdisciplinary Reviews: Computational Molecular Science},
     year={2022},
   }

5. Optimal Transport Tools (OTT): A JAX Toolbox for all things Wasserstein

   Marco Cuturi, Laetitia Meng-Papaxanthos, Yingtao Tian, Charlotte Bunne, Geoff Davis, and Olivier Teboul

   arXiv Preprint arXiv:2201.12324, 2022

   bibtex PDF Code

   @article{cuturi2022optimal,
     title={Optimal Transport Tools (OTT): A JAX Toolbox for all things Wasserstein},
     author={Cuturi, Marco and Meng-Papaxanthos, Laetitia and Tian, Yingtao and Bunne, Charlotte and Davis, Geoff and Teboul, Olivier},
     journal={arXiv Preprint arXiv:2201.12324},
     year={2022},
   }

6. Invariant Causal Mechanisms through Distribution Matching

   Mathieu Chevalley, Charlotte Bunne, Andreas Krause, and Stefan Bauer

   arXiv Preprint arXiv:2206.11646, 2022

   bibtex PDF

   @article{chevalley2022invariant,
     title={Invariant Causal Mechanisms through Distribution Matching},
     author={Chevalley, Mathieu and Bunne, Charlotte and Krause, Andreas and Bauer, Stefan},
     journal={arXiv Preprint arXiv:2206.11646},
     year={2022},
   }

2021

1. NeurIPS

   Multi-Scale Representation Learning on Proteins

   Charlotte Bunne, Vignesh Ram Somnath, and Andreas Krause

   Advances in Neural Information Processing Systems (NeurIPS), 2021

   Spotlight Talk at ICML Computational Biology Workshop, 2021.

   bibtex PDF Talk Short Talk Code

   @inproceedings{somnath2021multi,
     title={Multi-Scale Representation Learning on Proteins},
     author={Bunne, Charlotte and Somnath, Vignesh Ram and Krause, Andreas},
     booktitle={Advances in Neural Information Processing Systems (NeurIPS)},
     year={2021},
   }

2. NeurIPS

   Best Paper Award

   Learning Graph Models for Retrosynthesis Prediction

   Vignesh Ram Somnath, Charlotte Bunne, Connor Coley, Andreas Krause, and Regina Barzilay

   Advances in Neural Information Processing Systems (NeurIPS), 2021

   Best Paper Award and Contributed Talk at ICML Workshop on Graph Representation Learning and Beyond, 2019.

   bibtex PDF Talk Code

   @inproceedings{somnath2021learning,
     title={Learning Graph Models for Retrosynthesis Prediction},
     author={Somnath, Vignesh Ram and Bunne, Charlotte and Coley, Connor and Krause, Andreas and Barzilay, Regina},
     booktitle={Advances in Neural Information Processing Systems (NeurIPS)},
     year={2021},
   }

2020

1. COSIFER: a Python package for the consensus inference of molecular interaction networks

   Matteo Manica, Charlotte Bunne, Roland Mathis, Joris Cadow, Mehmet Eren Ahsen, Gustavo A Stolovitzky, and Maria Rodriguez Martinez

   Bioinformatics, 2020

   bibtex PDF Code

   @article{manica2021cosifer,
     title={COSIFER: a Python package for the consensus inference of molecular interaction networks},
     author={Manica, Matteo and Bunne, Charlotte and Mathis, Roland and Cadow, Joris and Ahsen, Mehmet Eren and Stolovitzky, Gustavo A and Martinez, Maria Rodriguez},
     journal={Bioinformatics},
     year={2020},
   }

2019

1. ICML

   Best Paper Award

   Learning Generative Models across Incomparable Spaces

   Charlotte Bunne, David Alvarez-Melis, Andreas Krause, and Stefanie Jegelka

   International Conference on Machine Learning (ICML), 2019

   Best Paper Award and Contributed Talk at NeurIPS Workshop on Relational Representation Learning, 2018.

   bibtex PDF Code

   @inproceedings{bunne2019learning,
     title={Learning Generative Models across Incomparable Spaces},
     author={Bunne, Charlotte and Alvarez-Melis, David and Krause, Andreas and Jegelka, Stefanie},
     booktitle={International Conference on Machine Learning (ICML)},
     year={2019},
   }

2. Exponential Growth of Glioblastoma In Vivo Driven by Rapidly Dividing and Outwardly Migrating Cancer Stem Cells

   Lisa Buchauer, Muhammad Amir Khan, Yue Zhuo, Chunxuan Shao, Peng Zou, Weijun Feng, Mengran Qian, Gözde Bekki, Charlotte Bunne, Anna Neuerburg, Azer Aylin Acikgöz, Mona Tomaschko, Zhe Zhu, Heike Alter, Katharina Hartmann, Olga Friesen, Klaus Hexel, Thomas Höfer, and Hai-Kun Liu

   bioRxiv Preprint bioRxiv:10.1101/723601v1, 2019

   bibtex PDF

   @article{buchauer2019exponential,
     title={Exponential Growth of Glioblastoma In Vivo Driven by Rapidly Dividing and Outwardly Migrating Cancer Stem Cells},
     author={Buchauer, Lisa and Khan, Muhammad Amir and Zhuo, Yue and Shao, Chunxuan and Zou, Peng and Feng, Weijun and Qian, Mengran and Bekki, Gözde and Bunne, Charlotte and Neuerburg, Anna and Acikgöz, Azer Aylin and Tomaschko, Mona and Zhu, Zhe and Alter, Heike and Hartmann, Katharina and Friesen, Olga and Hexel, Klaus and Höfer, Thomas and Liu, Hai-Kun},
     journal={bioRxiv Preprint bioRxiv:10.1101/723601v1},
     year={2019},
   }

2015

1. Backbone circularization of Bacillus subtilis family 11 xylanase increases its thermostability and its resistance against aggregation

   Max C Waldhauer, Silvan N Schmitz, Constantin Ahlmann-Eltze, Jan G Gleixner, Carolin C Schmelas, Anna G Huhn, Charlotte Bunne, Magdalena Büscher, Max Horn, Nils Klughammer, and others

   Molecular BioSystems, 2015

   bibtex PDF

   @article{waldhauer2015backbone,
     title={Backbone circularization of Bacillus subtilis family 11 xylanase increases its thermostability and its resistance against aggregation},
     author={Waldhauer, Max C and Schmitz, Silvan N and Ahlmann-Eltze, Constantin and Gleixner, Jan G and Schmelas, Carolin C and Huhn, Anna G and Bunne, Charlotte and Büscher, Magdalena and Horn, Max and Klughammer, Nils and others},
     journal={Molecular BioSystems},
     year={2015},
   }