yyou1996

lightning-hydra-template

PyTorch Lightning + Hydra. A very user-friendly template for ML experimentation. ⚡🔥⚡

torchsde

Differentiable SDE solvers with GPU support and efficient sensitivity analysis.

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

pympress

Pympress is a simple yet powerful PDF reader designed for dual-screen presentations

gnina

A deep learning framework for molecular docking

chembl_webresource_client

Official Python client for accessing ChEMBL API

adahessian

ADAHESSIAN: An Adaptive Second Order Optimizer for Machine Learning

zenodo-upload

upload big files to Zenodo using cURL, jq and bash

CPA

The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.

ChatDrug

LLM for Drug Editing, ICLR 2024

cmapPy

Assorted tools for interacting with .gct, .gctx files and other Connectivity Map (Broad Institute) data/tools

cellot

Learning Single-Cell Perturbation Responses using Neural Optimal Transport

TrajectoryNet

TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics

scPerturb

scPerturb: A resource and a python/R tool for single-cell perturbation data

chemCPA

Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.

ada-hessian

Easy-to-use AdaHessian optimizer (PyTorch)

lincs-workshop-2020

CMap Notebooks for LINCS 2020 Workshop

Perturbseq_GI

Code for reproducing "Exploring genetic interaction manifolds constructed from rich single-cell phenotypes"

PerturbNet

PerturbNet is a deep generative model that can predict the distribution of cell states induced by chemical or genetic perturbation

DMSB

Official implementation of Deep Momentum Schrödinger Bridge

FR-Perturb

Factorize-Recover for Perturb-seq analysis (FR-Perturb)

NLSB

DSPIN

Code and example of the D-SPIN framework

limbcellatlas

This repository contains codes used for the human fetal limb cell atlas.

DDG

Building and Comparing a model to perform Delta DeltaG calculations

raman2rna

Raman2RNA code base.

AnimalGAN

A Generative Adversarial Network Model Alternative to Animal Studies for Clinical Pathology Assessment

Perturb-map

variational-causal-inference

This repository implements Variational Causal Inference (VCI), a variational Bayesian causal inference framework for high-dimensional treatment effect predictions and estimations.

sci-Plex-GxE

Repository of analysis code for sci-Plex-GxE analysis