ownpubs.bib

Machine Learning - Main Conferences / Journals
@string{uaii="Uncertainty in Artificial Intelligence (UAI)"}
@string{icml="International Conference on Machine Learning (ICML)"}
@string{nips="Advances in Neural Information Processing Systems (NeurIPS)"}
@string{jmlr="Journal of Machine Learning Research"}
@string{iclr="International Conference on Learning Representations (ICLR)"}
@string{iclrws="International Conference on Learning Representations (ICLR), Workshop Track"}
@string{mlsp="IEEE International Workshop for Machine Learning in Signal Processing"}
@string{tmlr="Transactions on Machine Learning Research (TMLR)"}
@string{aabi="Advances in Approximate Bayesian Inference (AABI)"}

NLP
@string{acl="Proceedings of the Annual Meeting of the Association for Computational Linguistics (ACL)"}
@string{conll="SIGNLL Conference on Computational Natural Language Learning (CoNLL)"}
@string{emnlp="Conference on Empirical Methods in Natural Language Processing (EMNLP)"}
@string{tacl="Transactions of the Association for Computational Linguistics (TACL)"}

Vision
@string{cvpr="IEEE Conference on Computer Vision and Pattern Recognition (CVPR)"}
@string{ijcv="International Journal of Computer Vision"}
@string{iccv="International Conference on Computer Vision (ICCV)"}
@string{eccv="European Conference on Computer Vision (ECCV)"}
@string{siggraph="Proceedings of SIGGRAPH"}

Theory
@string{tcs="Theoretical Computer Science"}
@string{soda="SIAM-ACM Symposium on Discrete Algorithms (SODA)"}
@string{focs="IEEE Symposium on Foundations of Computer Science (FOCS)"}
@string{colt="Conference on Learning Theory (COLT)"}
@string{stoc="Symposium on Theory of Computing (STOC)"}
@string{icalp="International Colloquium on Automata, Languages and Programming (ICALP)"}

Robotics
@string{icra="IEEE International Conference on Robotics and Automation (ICRA)"}

Statistics
@string{uai="Conference on Uncertainty in Artificial Intelligence (UAI)"}

Misc AI
@string{jair="Journal or Artificial Intelligence Research"}
@string{aaai="AAAI Conference on Artificial Intelligence"}
@string{aistats="International Conference on Artificial Intelligence and Statistics (AISTATS)"}
@string{kdd="ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD)"}
@string{tpami="IEEE Transactions on Pattern Analysis and Machine Intelligence"}
@string{tog="ACM Transactions on Graphics (TOG)"}
@string{mathprog="Mathematical Programming"}
@string{infpl="Information Processing Letters"}
@string{jacm="Journal of the ACM"}
@string{tkdd="ACM Trassactions on Knowledge Discovery from Data (TKDD)"}
@string{icalp="International Colloquium on Automata, Languages, and Programming (ICALP)"}
@string{wads="Workshop on Algorithms and Data Structures (WADS)"}
@string{wadsnew="International Symposium on Algorithms and Data Structures (WADS)"}
@string{vldb="International Conference on Very Large Data Bases (VLDB)"}
@string{wsdm="ACM International Conference on Web Search and Data Mining (WSDM)"}
@string{acc="Annual Allerton Conference on Circuit and System Theory"}
@string{www="Proceedings of the International World Wide Web Conference (WWW)"}
@string{icwsm="International AAAI Conference on Web and Social Media (ICWSM)"}

# More general
@string{arxiv="arXiv Preprint"}
@string{rsc="Royal Society of Chemistry"}
@string{acspub="ACS Publications"}
@string{wol="Wiley Online Library"}
@string{spr="Springer"}
@string{npg="Nature Publishing Group"}
@string{ang="Angew. Chem., Int. Ed."}



@Article{	  ownbunne2021learning,
  title		= {{Learning Single-Cell Perturbation Responses using Neural
		  Optimal Transport}},
  author	= {Bunne, Charlotte and Stark, Stefan G and Gut, Gabriele and
		  del Castillo, Jacobo Sarabia and Lehmann, Kjong-Van and
		  Pelkmans, Lucas and Krause, Andreas and R{\"a}tsch, Gunnar},
  journal	= {Nature Methods},
  year		= {2023},
  publisher	= {Nature Publishing Group}
}

@InProceedings{	  ownbunne2022proximal,
  title		= {{Proximal Optimal Transport Modeling of Population
		  Dynamics}},
  author	= {Bunne, Charlotte and Meng-Papaxanthos, Laetitia and
		  Krause, Andreas and Cuturi, Marco},
  booktitle	= aistats,
  year		= {2022},
  volume	= {25}
}

@InProceedings{	  ownbunne2022recovering,
  title		= {{The Schr\"odinger Bridge between Gaussian Measures has a
		  Closed Form}},
  author	= {Bunne, Charlotte and Hsieh, Ya-Ping and Cuturi, Marco and
		  Krause, Andreas},
  booktitle	= aistats,
  year		= {2023},
  volume	= {206}

}

@InProceedings{	  ownbunne2022supervised,
  title		= {{Supervised Training of Conditional Monge Maps}},
  author	= {Bunne, Charlotte and Krause, Andreas and Cuturi, Marco},
  booktitle	= nips,
  year		= {2022},
  volume	= {35},

}

@Article{	  owncuturi2022optimal,
  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}
}

@InProceedings{	  ownganea2022independent,
  title		= {{Independent {SE}(3)-Equivariant Models for End-to-End
		  Rigid Protein Docking}},
  author	= {Octavian-Eugen Ganea and Xinyuan Huang and Charlotte Bunne
		  and Yatao Bian and Regina Barzilay and Tommi S. Jaakkola
		  and Andreas Krause},
  booktitle	= iclr,
  year		= {2022}
}


@Article{	  ownlubeck2022neural,
  title		= {{Neural Unbalanced Optimal Transport via Cycle-Consistent
		  Semi-Couplings}},
  author	= {L{\"u}beck, 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		= {2022}
}

@Article{	  ownschwaller2022machine,
  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},
  publisher	= {Wiley Online Library}
}


@InProceedings{	  ownsomnath2023aligned,
  title		= {{Aligned Diffusion Schr\"odinger Bridges}},
  author	= {Somnath, Vignesh Ram and Pariset, Matteo and Hsieh, Ya-Ping and Martinez, Maria Rodriguez and Krause, Andreas and Bunne, Charlotte},
  booktitle	= uai,
  year		= {2023}
}

@InProceedings{	  ownsomnath2021multi,
  title		= {{Multi-Scale Representation Learning on Proteins}},
  author	= {Somnath, Vignesh Ram and Bunne, Charlotte and Krause, Andreas},
  booktitle	= nips,
  year		= {2021},
  volume	= {34}
}

@InProceedings{	  ownsomnath2021learning,
  title		= {{Learning Graph Models for Retrosynthesis Prediction}},
  author	= {Somnath, Vignesh Ram and Bunne, Charlotte and Coley, Connor and Krause, Andreas and Barzilay, Regina},
  booktitle	= nips,
  year		= {2021},
  volume	= {34}
}

@InProceedings{	  ownbunne2019learning,
  title		= {{Learning Generative Models across Incomparable Spaces}},
  author	= {Bunne, Charlotte and Alvarez-Melis, David and Krause, Andreas and Jegelka, Stefanie},
  booktitle	= icml,
  year		= {2019},
  volume	= {97},
}

@Article{	  ownpariset2023unbalanced,
  title		= {{Unbalanced Diffusion Schr{\"o}dinger Bridge}},
  author	= {Pariset, Matteo and Hsieh, Ya-Ping and Bunne, Charlotte and Krause, Andreas and De Bortoli, Valentin},
  journal	= {arXiv Preprint arXiv:2306.09099},
  year		= {2023}
}

@Article{	  ownmanica2021cosifer,
  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},
  volume	= {37},
  number	= {14},
  year		= {2020}
}