Dan Berenberg

Researcher, Mythos Scientific

Joined

February 2022

Names

Dan Berenberg (Preferred)

Daniel Berenberg

Emails

****@nyu.edu (Confirmed)

****@mythos.science (Confirmed)

Personal Links

Career & Education History

Researcher

Mythos Scientific (mythos.science)

2025 – Present

PhD student

Computer Science, New York University (nyu.edu)

2020 – 2025

Researcher

Genentech (gene.com)

2022 – 2024

Machine Learning Engineer

Genentech (gene.com)

2021 – 2022

Advisors, Relations & Conflicts

No relations added

Expertise

No areas of expertise listed

Publications

Residue-level text conditioning for protein language model mutation effect prediction
Dan Berenberg, Nate Gruver, Alan Nawzad Amin, Peter Mørch Groth, Leo Chen, Harsh R. Srivastava, Pascal Notin, Debora Susan Marks, Andrew Gordon Wilson, Kyunghyun Cho, Richard Bonneau
- GEM
- Readers: Everyone
Protein Discovery with Discrete Walk-Jump Sampling
Nathan Frey, Dan Berenberg, Karina Zadorozhny, Joseph Kleinhenz, Julien Lafrance-Vanasse, Isidro Hotzel, Yan Wu, Stephen Ra, Richard Bonneau, Kyunghyun Cho, Vladimir Gligorijevic, Saeed Saremi
- GenBio@NeurIPS2023 Spotlight
- Readers: Everyone
Protein Discovery with Discrete Walk-Jump Sampling
Nathan C. Frey, Dan Berenberg, Karina Zadorozhny, Joseph Kleinhenz, Julien Lafrance-Vanasse, Isidro Hotzel, Yan Wu, Stephen Ra, Richard Bonneau, Kyunghyun Cho, Andreas Loukas, Vladimir Gligorijevic, Saeed Saremi
- ICLR 2024 oral
- Readers: Everyone
OpenProteinSet: Training data for structural biology at scale
Gustaf Ahdritz, Nazim Bouatta, Sachin Kadyan, Lukas Jarosch, Dan Berenberg, Ian Fisk, Andrew Martin Watkins, Stephen Ra, Richard Bonneau, Mohammed AlQuraishi
- NeurIPS 2023 Datasets and Benchmarks Poster
- Readers: Everyone
Learning protein family manifolds with smoothed energy-based models
Nathan C. Frey, Dan Berenberg, Joseph Kleinhenz, Isidro Hotzel, Julien Lafrance-Vanasse, Ryan Lewis Kelly, Yan Wu, Arvind Rajpal, Stephen Ra, Richard Bonneau, Kyunghyun Cho, Andreas Loukas, Vladimir Gligorijevic, Saeed Saremi
- Published: 03 Mar 2023, Last Modified: 31 Mar 2023
- Physics4ML Spotlight
- Readers: Everyone
LEARNING PROTEIN FAMILY MANIFOLDS WITH SMOOTHED ENERGY-BASED MODELS
Nathan C. Frey, Dan Berenberg, Joseph Kleinhenz, Stephen Ra, Isidro Hotzel, Julien Lafrance-Vanasse, Ryan Lewis Kelly, Yan Wu, Arvind Rajpal, Richard Bonneau, Kyunghyun Cho, Andreas Loukas, Vladimir Gligorijevic, Saeed Saremi
- Published: 06 Mar 2023, Last Modified: 05 May 2023
- ICLR 2023 - MLDD Poster
- Readers: Everyone
OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization
Gustaf Ahdritz, Nazim Bouatta, Sachin Kadyan, Qinghui Xia, William Gerecke, Timothy J O'Donnell, Dan Berenberg, Ian Fisk, Niccolò Zanichelli, Bo Zhang, Arkadiusz Nowaczynski, Bei Wang, Marta M Stepniewska-Dziubinska, Shang Zhang, Adegoke Ojewole, Murat Efe Guney, Stella Biderman, Andrew Martin Watkins, Stephen Ra, Pablo Ribalta Lorenzo et al. (8 additional authors not shown)
- 30 Jan 2023
- OpenReview Archive Direct Upload
- Readers: Everyone
Multi-Segment Preserving Sampling for Deep Manifold Sampler
Dan Berenberg, Jae Hyeon Lee, Simon Kelow, Ji Won Park, Andrew Watkins, Richard Bonneau, Vladimir Gligorijevic, Stephen Ra, Kyunghyun Cho
- Published: 05 Apr 2022, Last Modified: 05 May 2023
- MLDD Oral
- Readers: Everyone

Co-Authors

View all 52 co-authors