Joey-Xue

NeMo

A scalable generative AI framework built for researchers and developers working on Large Language Models, Multimodal, and Speech AI (Automatic Speech Recognition and Text-to-Speech)

Intro-to-rnaseq-hpc-O2

This repository has teaching materials for a 2 and 3-day Introduction to RNA-sequencing data analysis workshop using the O2 Cluster

ESM-GearNet

ESM-GearNet for Protein Structure Representation Learning (https://arxiv.org/abs/2303.06275)

GWA_tutorial

A comprehensive tutorial about GWAS and PRS

scanpy

Single-cell analysis in Python. Scales to >1M cells.

ViT-pytorch

Pytorch reimplementation of the Vision Transformer (An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale)

esm

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

speos

A positive-unlabeled ensemble learning framework for disease gene prioritization.

Exomiser

A Tool to Annotate and Prioritize Exome Variants

PEER_Benchmark

PEER Benchmark, appear at NeurIPS 2022 Dataset and Benchmark Track (https://arxiv.org/abs/2206.02096)

pytorch-tutorial

PyTorch Tutorial for Deep Learning Researchers

EVE

Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Joint collaboration between the Marks lab and the OATML group.

tuning_playbook

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

paper-reading

深度学习经典、新论文逐段精读

alphafold

Open source code for AlphaFold.

GNNPapers

Must-read papers on graph neural networks (GNN)

attention-is-all-you-need-pytorch

A PyTorch implementation of the Transformer model in "Attention is All You Need".

workshop

prospr

ProSPr: Protein Structure Prediction

deepmind-research

This repository contains implementations and illustrative code to accompany DeepMind publications

pytorch

Tensors and Dynamic neural networks in Python with strong GPU acceleration

Machine-learning-for-proteins

Listing of papers about machine learning for proteins.

awesome-machine-learning

A curated list of awesome Machine Learning frameworks, libraries and software.

deepcontact

DeepContact Software

EVcouplings

Evolutionary couplings from protein and RNA sequence alignments

d2l-pytorch

This project reproduces the book Dive Into Deep Learning (https://d2l.ai/), adapting the code from MXNet into PyTorch.

500lines

500 Lines or Less

Python-100-Days

Python - 100天从新手到大师

mgpfusion

mGPfusion is a Gaussian process based method for predicting stability changes upon single and multiple mutations of proteins that complements the available experimental data with large amounts of simulated data.

Data-Analysis

Data Science Using Python