Alexander Tong's repositories
AlphaFold3
Open source implementation of AlphaFold3
genie2
Protein structure diffusion model for unconditional protein generation and motif scaffolding
conditional-flow-matching
TorchCFM: a Conditional Flow Matching library
personal
Personal configuration files
chroma
A generative model for programmable protein design
torchdyn
A PyTorch library entirely dedicated to neural differential equations, implicit models and related numerical methods.
POT
Python Optimal Transport library
SCOT
Gromov-Wasserstein based optimal transport for aligning single-cell multi-omics data
safari
Convolutions for Sequence Modeling
MELD
Quantifying experimental perturbations at single cell resolution
papers_for_protein_design_using_DL
List of papers about Proteins Design using Deep Learning
MultiscaleEMD
Multiscale earth mover's distance methods for tree and manifold structured data
esm
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
genie
De Novo Protein Design by Equivariantly Diffusing Oriented Residue Clouds
FLeCS
Flexible and Learnable Cell Simulator
trainable_symmetry
Implementation of learnable generalized geometric scattering transforms on graphs
PHATE
PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.
navigator-hugo
Navigator Business theme powered by Hugo. It also could be used for a personal portfolio.
lightning-hydra-template
PyTorch Lightning + Hydra. A very user-friendly template for rapid and reproducible ML experimentation with best practices. ⚡🔥⚡
coinshuffle
Coin Shuffle implementation
ott
Optimal Transport tools implemented with the JAX framework, to get auto-diff, parallel and jit-able computations.
moscot
https://moscot.readthedocs.io/en/latest/
moscot_notebooks
Analysis notebooks using the moscot package
statements
Successful Job Applications and Grants