Shadi's repositories
DeepSpeed
DeepSpeed is a deep learning optimization library that makes distributed training and inference easy, efficient, and effective.
pggb
the pangenome graph builder
composer
Supercharge Your Model Training
openfold
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
depmap_omics
What you need to process the Quarterly DepMap-Omics releases from Terra
foldseek
Foldseek enables fast and sensitive comparisons of large structure sets.
parquet-format
Apache Parquet
alphafold
Open source code for AlphaFold.
MVFA-AD
[CVPR2024] Adapting Visual-Language Models for Generalizable Anomaly Detection in Medical Images
Human-GEM
The generic genome-scale metabolic model of Homo sapiens
MMseqs2
MMseqs2: ultra fast and sensitive search and clustering suite
TaxDiff
The official code for "TaxDiff: Taxonomic-Guided Diffusion Model for Protein Sequence Generation"
ray
Ray is a unified framework for scaling AI and Python applications. Ray consists of a core distributed runtime and a set of AI Libraries for accelerating ML workloads.
MutDTA
Improving the precision oncology pipeline by providing binding affinity purtubations predictions on a pirori identified cancer driver genes.
latent-diffusion
High-Resolution Image Synthesis with Latent Diffusion Models
AutoDock-Vina
AutoDock Vina
GFAffix
GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.
esm
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
foldingdiff
Diffusion models of protein structure; trigonometry and attention are all you need!
RFdiffusion
Code for running RFdiffusion
IgFold
Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies
Tangram
Spatial alignment of single cell transcriptomic data.
StableDiffusionReconstruction
Takagi and Nishimoto, CVPR 2023
DGraphDTA
a novel DTA predition method using graph neural network
DLKcat
Deep learning and Bayesian approach applied to enzyme turnover number for the improvement of enzyme-constrained genome-scale metabolic models (ecGEMs) reconstruction
RDE-PPI
:mountain: Rotamer Density Estimator is an Unsupervised Learner of the Effect of Mutations on Protein-Protein Interaction (ICLR 2023)