egurapha

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New York, NY

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RosettaCommons

Raphael Eguchi's starred repositories

tuning_playbook

A playbook for systematically maximizing the performance of deep learning models.

NOASSERTION25994 281 39

vim-airline

lean & mean status/tabline for vim that's light as air

Language:Vim ScriptMIT17704 223 1779

alphafold

Open source code for AlphaFold.

Language:PythonApache-2.012160 224 840

mamba

Mamba SSM architecture

Language:PythonApache-2.011963 98 449

awesome-tmux

A list of awesome resources for tmux

evil

The extensible vi layer for Emacs.

Language:Emacs LispGPL-3.03298 43 1358

ColabFold

Making Protein folding accessible to all!

Language:Jupyter NotebookMIT1818 46 537

voyager

🛰️ An approximate nearest-neighbor search library for Python and Java with a focus on ease of use, simplicity, and deployability.

Language:C++Apache-2.01238 14 24

DeepPurpose

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

Language:Jupyter NotebookBSD-3-Clause940 31 130

DiffuSeq

[ICLR'23] DiffuSeq: Sequence to Sequence Text Generation with Diffusion Models

Language:PythonMIT699 26 79

surgeon-pytorch

A library to inspect and extract intermediate layers of PyTorch models.

Language:PythonMIT468 4 3

torchani

Accurate Neural Network Potential on PyTorch

Language:PythonMIT452 31 167

pdbfixer

PDBFixer fixes problems in PDB files

Language:PythonNOASSERTION446 13 191

python-blosc

A Python wrapper for the extremely fast Blosc compression library

Language:PythonNOASSERTION348 16 112

awesome-molecular-generation

Awesome papers related to generative molecular modeling and design.

pyTorchChamferDistance

Implementation of the Chamfer Distance as a module for pyTorch

Language:C++MIT268 40

tmux-nova

tmux theme

Language:ShellMIT170 3 29

deeprank

This repository has been integrated in https://github.com/DeepRank/deeprank2

Language:PythonApache-2.0145 14 167

bgflow

Boltzmann Generators and Normalizing Flows in PyTorch

Language:Jupyter NotebookMIT129 5 23

arpeggio

Calculation of interatomic interactions in molecular structures

Language:PythonGPL-3.066 8 23

cubenet

3D Roto-translation equivariant convolutions

Language:PythonMIT55 5 2

Rosetta-DL

A bundle of deep-learning packages for biomolecular structure prediction and design contributed to the Rosetta Commons

NOASSERTION29 7 1

BLISS

Large Scale Search Index

Language:PythonApache-2.022 2 1

geometric_algebra_attention

Geometric algebra attention mechanism for tensorflow, keras, pytorch, and jax

Language:PythonMIT19 3 4

QuickSES

Tool to compute molecular Solvent Excluded Surface meshes on the GPU using CUDA

Language:C++MIT14 5 3

vim-color-scheme-screenshots

A collection of screenshots for vim color schemes

1100

tmux-doom-one-dark

doom-one-dark theme for tmux

Language:ShellMIT9 30

g2g_optimization

graph-to-graph translation using hierarchical graph structure with iterations

Language:PythonMIT8 20

coordinates-compression

This repository contains the compression methods described in the paper "Towards an efficient compression of 3D coordinates of macromolecular structures".

Language:JavaApache-2.0200

cath-funfhmmer

Split GeMMA clusters into functionally coherent alignments (FunFams)

Language:Perl200