Jeffrey Hsu's repositories
llama-hub
A library of data loaders for LLMs made by the community -- to be used with GPT Index and/or LangChain
big_vision
Official codebase used to develop Vision Transformer, MLP-Mixer, LiT and more.
bioconda-recipes
Conda recipes for the bioconda channel.
equiformer-pytorch
Implementation of the Equiformer, SE3/E3 equivariant attention network that reaches new SOTA, and adopted for use by EquiFold for protein folding
gpt_index
GPT Index is a project consisting of a set of data structures designed to make it easier to use large external knowledge bases with LLMs.
hyena-dna
Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena
scenicplus
SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
flash-attention
Fast and memory-efficient exact attention
chemcrow-public
Chemcrow
ijepa
Official codebase for I-JEPA, the Image-based Joint-Embedding Predictive Architecture. First outlined in the CVPR paper, "Self-supervised learning from images with a joint-embedding predictive architecture."
pyhamilton
Python for Hamilton liquid handling robots
flash-genomics-model
My own attempt at a long context genomics model, leveraging recent advances in long context attention modeling (Flash Attention + other hierarchical methods)
idom-dash
A custom component for Plotly Dash that uses IDOM
enformer-pytorch
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
cellpose
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
tabby
Self-hosted AI coding assistant
toolformer-pytorch
Implementation of Toolformer, Language Models That Can Use Tools, by MetaAI
skypilot
SkyPilot is a framework for easily running machine learning workloads on any cloud through a unified interface.
genomic_benchmarks
Benchmarks for classification of genomic sequences
tf-bind-transformer
A repository with exploration into using transformers to predict DNA ↔ transcription factor binding
PyDESeq2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
snakepipes
Customizable workflows based on snakemake and python for the analysis of NGS data
DNA-Diffusion
Understanding the code of life: Generative models of regulatory DNA sequences based on diffusion models.