PyTorch implementations of algorithms from "Reinforcement Learning: An Introduction by Sutton and Barto", along with various RL research papers.

A language agent gym with challenging scientific tasks

Biomni: a general-purpose biomedical AI agent

List of AI Residency Programs

systematic explanation of attribution-based mechanisms for regulatory genomics

GWAS Tutorial for Beginners

Collections of library structure and sequence of popular single cell genomic methods

Implementation of AlphaGenome, Deepmind's updated genomic attention model

Machine learning metrics for distributed, scalable PyTorch applications.

Modeling complex perturbations with CellFlow

Python package to perform enrichment analysis from omics data.

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

Single-cell perturbation analysis

LLM agents for working with the SRA and associated bioinformatics databases.

Official repository of "Multi-level Interaction Modeling for Protein Mutational Effect Prediction"

Dataset and package for working with protein-protein interactions in 3D

Inference and numerics for multi-hybrid AI model architectures

A library for mechanistic interpretability of GPT-style language models

Implementation of the BatchTopK activation function for training sparse autoencoders (SAEs)

MMseqs2: ultra fast and sensitive search and clustering suite

Foldseek enables fast and sensitive comparisons of large structure sets.

Chai-1, SOTA model for biomolecular structure prediction

An implementation of local windowed attention for language modeling

AlphaFold 3 inference pipeline.

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

Implementation of Vision Transformer, a simple way to achieve SOTA in vision classification with only a single transformer encoder, in Pytorch

RNA-seq prediction with deep convolutional neural networks.