Mohammed AlQuraishi

Assistant Professor, Systems Biology, Columbia University

Joined

October 2018

Names

Mohammed AlQuraishi (Preferred)

Emails

****@hms.harvard.edu (Confirmed)

****@cumc.columbia.edu (Confirmed)

Personal Links

Homepage

Career & Education History

Assistant Professor

Systems Biology, Columbia University (columbia.edu)

2020 – Present

Postdoc

Systems Biology, Harvard University (harvard.edu)

2013 – 2020

PhD student

Genetics, Stanford University (stanford.edu)

2005 – 2013

Advisors, Relations & Conflicts

No relations added

Expertise

No areas of expertise listed

Publications

GREmLN: A Cellular Graph Structure Aware Transcriptomics Foundation Model
Mingxuan Zhang, Vinay S Swamy, Rowan Cassius, Léo Dupire, Charilaos I. Kanatsoulis, Evan Paull, Mohammed AlQuraishi, Theofanis Karaletsos, Andrea Califano
- MLGenX 2026 Poster
- Readers: Everyone
GREmLN: A Cellular Graph Structure Aware Transcriptomics Foundation Model
Mingxuan Zhang, Vinay S Swamy, Léo Dupire, Rowan Cassius, Charilaos I. Kanatsoulis, Evan Paull, Mohammed AlQuraishi, Theofanis Karaletsos, Andrea Califano
- Submitted to ICLR 2026
- Readers: Everyone
From Mechanistic Interpretability to Mechanistic Biology: Training, Evaluating, and Interpreting Sparse Autoencoders on Protein Language Models
Etowah Adams, Liam Bai, Minji Lee, Yiyang Yu, Mohammed AlQuraishi
- ICLR 2025 Workshop LMRL
- Readers: Everyone
From Mechanistic Interpretability to Mechanistic Biology: Training, Evaluating, and Interpreting Sparse Autoencoders on Protein Language Models
Etowah Adams, Liam Bai, Minji Lee, Yiyang Yu, Mohammed AlQuraishi
- ICML 2025 spotlightposter
- Readers: Everyone
Disconnecting The Dots: Creating Leakage-Free Protein Datasets by Removal of Densely Connected Data Points
Charlotte Rochereau, Arthur Valentin, Gergo Nikolenyi, Mohammed AlQuraishi
- Submitted to ICLR 2025
- Readers: Everyone
Out of Many, One: Designing and Scaffolding Proteins at the Scale of the Structural Universe with Genie 2
Yeqing Lin, Minji Lee, Zhao Zhang, Mohammed AlQuraishi
- Submitted to ICLR 2025
- Readers: Everyone
Benchmarking out-of-the-box forecasters of varying scales in biology
Anthony E Culos, Mohammed AlQuraishi
- NeurIPS 2024 TSALM Workshop Spotlight
- Readers: Everyone
DeepSpeed4Science Initiative: Enabling Large-Scale Scientific Discovery through Sophisticated AI System Technologies
Shuaiwen Leon Song, Bonnie Kruft, Minjia Zhang, Conglong Li, Shiyang Chen, Chengming Zhang, Masahiro Tanaka, Xiaoxia Wu, Mohammed AlQuraishi, Gustaf Ahdritz, Christina Floristean, Rick L. Stevens, Venkatram Vishwanath, Arvind Ramanathan, Sam Foreman, Kyle Hippe, Prasanna Balaprakash, Yuxiong He
- NeurIPS2023-AI4Science Poster
- 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
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

View all 11 publications

Co-Authors

View all 67 co-authors