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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