Berger, Bonnie

29 publications

NeurIPS 2025 Evaluating Multiple Models Using Labeled and Unlabeled Data Divya M Shanmugam, Shuvom Sadhuka, Manish Raghavan, John Guttag, Bonnie Berger, Emma Pierson
ICLRW 2025 Recovery-on-the-Line: Linear Trends in Post-Quantization Performance Recovery Shashata Sawmya, Shuvom Sadhuka, Ragulan Sivakumar, Nir N Shavit, Dan Alistarh, Bonnie Berger
ICLRW 2025 Reframing Retreival-Augmented Generation for *in Silico* Optimization of Antibody Solubility Lena Erlach, Rohit Singh, Bonnie Berger, Sai T. Reddy
ICML 2024 AlphaFold Meets Flow Matching for Generating Protein Ensembles Bowen Jing, Bonnie Berger, Tommi Jaakkola
ICML 2024 Dirichlet Flow Matching with Applications to DNA Sequence Design Hannes Stark, Bowen Jing, Chenyu Wang, Gabriele Corso, Bonnie Berger, Regina Barzilay, Tommi Jaakkola
ICLRW 2024 Dirichlet Flow Matching with Applications to DNA Sequence Design Hannes Stark, Bowen Jing, Chenyu Wang, Gabriele Corso, Bonnie Berger, Regina Barzilay, Tommi Jaakkola
ICLR 2024 Equivariant Scalar Fields for Molecular Docking with Fast Fourier Transforms Bowen Jing, Tommi S. Jaakkola, Bonnie Berger
NeurIPS 2024 Generative Modeling of Molecular Dynamics Trajectories Bowen Jing, Hannes Stärk, Tommi Jaakkola, Bonnie Berger
ICMLW 2024 Generative Modeling of Molecular Dynamics Trajectories Bowen Jing, Hannes Stark, Tommi Jaakkola, Bonnie Berger
ICLRW 2024 Multi-Model Evaluation with Labeled & Unlabeled Data Divya M Shanmugam, Shuvom Sadhuka, Manish Raghavan, John Guttag, Bonnie Berger, Emma Pierson
NeurIPSW 2023 AlphaFold Meets Flow Matching for Generating Protein Ensembles Bowen Jing, Bonnie Berger, Tommi Jaakkola
NeurIPSW 2023 AlphaFold Meets Flow Matching for Generating Protein Ensembles Bowen Jing, Bonnie Berger, Tommi Jaakkola
NeurIPSW 2023 AlphaFold Meets Flow Matching for Generating Protein Ensembles Bowen Jing, Bonnie Berger, Tommi Jaakkola
TMLR 2023 Causally-Guided Regularization of Graph Attention Improves Generalizability Alexander P Wu, Thomas Markovich, Bonnie Berger, Nils Yannick Hammerla, Rohit Singh
ICLRW 2023 EigenFold: Generative Protein Structure Prediction with Diffusion Models Bowen Jing, Ezra Erives, Peter Pao-Huang, Gabriele Corso, Bonnie Berger, Tommi S. Jaakkola
NeurIPSW 2023 Learning Scalar Fields for Molecular Docking with Fast Fourier Transforms Bowen Jing, Tommi Jaakkola, Bonnie Berger
NeurIPSW 2023 Learning Scalar Fields for Molecular Docking with Fast Fourier Transforms Bowen Jing, Tommi Jaakkola, Bonnie Berger
NeurIPSW 2023 Scalable Multimer Structure Prediction Using Diffusion Models Peter Pao-Huang, Bowen Jing, Bonnie Berger
NeurIPSW 2023 Scalable Multimer Structure Prediction Using Diffusion Models Peter Pao-Huang, Bowen Jing, Bonnie Berger
ICLR 2022 Granger Causal Inference on DAGs Identifies Genomic Loci Regulating Transcription Alexander P Wu, Rohit Singh, Bonnie Berger
ICCV 2021 CryoDRGN2: Ab Initio Neural Reconstruction of 3D Protein Structures from Real Cryo-EM Images Ellen D. Zhong, Adam Lerer, Joseph H. Davis, Bonnie Berger
ICLR 2021 Multi-Resolution Modeling of a Discrete Stochastic Process Identifies Causes of Cancer Adam Uri Yaari, Maxwell Sherman, Oliver Clarke Priebe, Po-Ru Loh, Boris Katz, Andrei Barbu, Bonnie Berger
NeurIPS 2020 Learning Mutational Semantics Brian Hie, Ellen Zhong, Bryan Bryson, Bonnie Berger
ICLR 2020 Reconstructing Continuous Distributions of 3D Protein Structure from Cryo-EM Images Ellen D. Zhong, Tristan Bepler, Joseph H. Davis, Bonnie Berger
NeurIPS 2019 Explicitly Disentangling Image Content from Translation and Rotation with Spatial-VAE Tristan Bepler, Ellen Zhong, Kotaro Kelley, Edward Brignole, Bonnie Berger
AISTATS 2019 Large-Margin Classification in Hyperbolic Space Hyunghoon Cho, Benjamin DeMeo, Jian Peng, Bonnie Berger
ICLR 2019 Learning Protein Sequence Embeddings Using Information from Structure Tristan Bepler, Bonnie Berger
ICML 2008 Inverting the Viterbi Algorithm: An Abstract Framework for Structure Design Michael Schnall-Levin, Leonid Chindelevitch, Bonnie Berger
ICML 2005 Active Learning for Sampling in Time-Series Experiments with Application to Gene Expression Analysis Rohit Singh, Nathan P. Palmer, David K. Gifford, Bonnie Berger, Ziv Bar-Joseph