atong01

conditional-flow-matching

TorchCFM: a Conditional Flow Matching library

diffusion_schrodinger_bridge

PyTorch Implementation of DSB for Score Based Generative Modeling. Experiments managed using Hydra.

Imagenet-Tensorflow

Single Command Docker container to test imagenet classifier

MultiscaleEMD

Multiscale earth mover's distance methods for tree and manifold structured data

ot-icnn-minimal

A minimal example of optimal transport with Input Convex Neural Networks in Pytorch

FoldFlow

FoldFlow: SE(3)-Stochastic Flow Matching for Protein Backbone Generation

DEM

Code for the paper Iterated Denoising Energy Matching for Sampling from Boltzmann Densities.

DiffusionEMD

Code corresponding to the paper Diffusion Earth Mover's Distance and Distribution Embeddings

TrajectoryNet

TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics

dyn-gfn

DynGFN: Bayesian Dynamic Causal Discovery using Generative Flow Networks

atong01/conditional-flow-matching

TorchCFM: a Conditional Flow Matching library

atong01/MultiscaleEMD

Multiscale earth mover's distance methods for tree and manifold structured data

atong01/coinshuffle

Coin Shuffle implementation

atong01/trainable_symmetry

Implementation of learnable generalized geometric scattering transforms on graphs

atong01/AlphaFold3

Open source implementation of AlphaFold3

atong01/fab-torch

Flow Annealed Importance Sampling Bootstrap (FAB). ICLR 2023.

atong01/flora-opt

This is the official repository for the paper "Flora: Low-Rank Adapters Are Secretly Gradient Compressors" in ICML 2024.

atong01/website

📝 Easily create a beautiful website using Academic, Hugo, and Netlify

atong01/action-matching

atong01/Cell-Dynamics-Pipeline

atong01/chroma

A generative model for programmable protein design

atong01/esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

atong01/FLeCS

Flexible and Learnable Cell Simulator

atong01/genie

De Novo Protein Design by Equivariantly Diffusing Oriented Residue Clouds

atong01/genie2

Protein structure diffusion model for unconditional protein generation and motif scaffolding

atong01/guided-diffusion

atong01/lightning-hydra-template

PyTorch Lightning + Hydra. A very user-friendly template for rapid and reproducible ML experimentation with best practices. ⚡🔥⚡

atong01/MELD

Quantifying experimental perturbations at single cell resolution

atong01/moscot

https://moscot.readthedocs.io/en/latest/

atong01/moscot_notebooks

Analysis notebooks using the moscot package

atong01/navigator-hugo

Navigator Business theme powered by Hugo. It also could be used for a personal portfolio.

atong01/ott

Optimal Transport tools implemented with the JAX framework, to get auto-diff, parallel and jit-able computations.

atong01/papers_for_protein_design_using_DL

List of papers about Proteins Design using Deep Learning

atong01/personal

Personal configuration files

atong01/PHATE

PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.

atong01/POT

Python Optimal Transport library

atong01/Protenix

A trainable PyTorch reproduction of AlphaFold 3.

atong01/safari

Convolutions for Sequence Modeling

atong01/SCOT

Gromov-Wasserstein based optimal transport for aligning single-cell multi-omics data

atong01/torchdyn

A PyTorch library entirely dedicated to neural differential equations, implicit models and related numerical methods.