Publications

Publications by categories in reversed chronological order.

2022

  1. Neural Unbalanced Optimal Transport via Cycle-Consistent Semi-Couplings
    Frederike Lübeck*, Charlotte Bunne*, Gabriele Gut, Jacobo Sarabia Castillo, Lucas Pelkmans, and David Alvarez Melis
    Under Review, 2022
    Spotlight Talk at NeurIPS Meaningful Representations of Life Workshop, 2022.
  2. 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.
  3. Nature Methods
    Submission
    Learning Single-Cell Perturbation Responses using Neural Optimal Transport
    Charlotte Bunne*, Stefan Stark*, Gabriele Gut*, Jacobo Sarabia Castillo, Mitchell Levesque, Kjong Van Lehmann, Lucas Pelkmans, Andreas Krause, and Gunnar Rätsch
    Under Review at Nature Methods, 2022
    NeurIPS Workshop on Optimal Transport and Machine Learning (OTML), 2021.
  4. Recovering Stochastic Dynamics via Gaussian Schrödinger Bridges
    Charlotte Bunne*, Ya-Ping Hsieh*, Marco Cuturi, and Andreas Krause
    In Submission (arXiv:2202.05722), 2022
    ICML Workshop on Continuous Time Methods for Machine Learning, 2022.
  5. 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.
  6. 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%).
  7. 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.
  8. 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
    In Submission (arXiv:2201.12324), 2022
  9. Invariant Causal Mechanisms through Distribution Matching
    Mathieu Chevalley, Charlotte Bunne, Andreas Krause, and Stefan Bauer
    In Submission (arXiv:2206.11646), 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.
  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.

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

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.
  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, 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