ChongWu-Biostat

AutoGPT

AutoGPT is the vision of accessible AI for everyone, to use and to build on. Our mission is to provide the tools, so that you can focus on what matters.

transformers

🤗 Transformers: State-of-the-art Machine Learning for Pytorch, TensorFlow, and JAX.

pytorch

Tensors and Dynamic neural networks in Python with strong GPU acceleration

FastChat

An open platform for training, serving, and evaluating large language models. Release repo for Vicuna and Chatbot Arena.

stanford_alpaca

Code and documentation to train Stanford's Alpaca models, and generate the data.

MiniGPT-4

Open-sourced codes for MiniGPT-4 and MiniGPT-v2 (https://minigpt-4.github.io, https://minigpt-v2.github.io/)

mtheme

A modern LaTeX Beamer theme

hyperas

Keras + Hyperopt: A very simple wrapper for convenient hyperparameter optimization

deeplearning-biology

A list of deep learning implementations in biology

benchm-ml

A minimal benchmark for scalability, speed and accuracy of commonly used open source implementations (R packages, Python scikit-learn, H2O, xgboost, Spark MLlib etc.) of the top machine learning algorithms for binary classification (random forests, gradient boosted trees, deep neural networks etc.).

talos

Hyperparameter Experiments with TensorFlow and Keras

DNABERT

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

nucleotide-transformer

🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

plink-ng

A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Development is now focused on building out support for multiallelic, phased, and dosage data in PLINK 2.0.

basenji

Sequential regulatory activity predictions with deep convolutional neural networks.

TwoSampleMR

R package for performing 2-sample MR using MR-Base database

keras_lr_finder

Plots the change of the loss function of a Keras model when the learning rate is exponentially increasing.

RcppArmadillo

Rcpp integration for the Armadillo templated linear algebra library

PRSice

A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores

keras-adamw

Keras/TF implementation of AdamW, SGDW, NadamW, Warm Restarts, and Learning Rate multipliers

ExPecto

predicting expression effects of human genome variants ab initio from sequence

ipython

ipython notebooks for machine learning, code behind work at the blog

lassosum

LASSO for GWAS with summary statistics

keras-cosine-annealing

Keras implementation of Cosine Annealing Scheduler

aSPU

An R package for adaptive sum of powered score test(ASPU) in genetic association studies.

SUMMIT

Summary-level Unified Method for Modeling Integrated Transcriptome

simus-PRS

Simulations and comparisons of Polygenic Risk Scores methods.

penRegSum

R Package that implements penalized regression methods for genetic data using summary statistics and a reference panel

TScML

For 2ScML method.

iTMLE