Modeling variable guide efficiency in pooled CRISPR screens with ContrastiveVI+

A deep generative model for single-cell methylation data

Files needed to replicate my research blog

Evaluation metrics for scvi-tools models

This repository contains the implementation of Label-Free XAI, a new framework to adapt explanation methods to unsupervised models. For more details, please read our ICML 2022 paper: 'Label-Free Ex…

PyTorch implementation of BasisVAE: Translation-invariant feature-level clustering with Variational Autoencoders

generalized principal component analysis (GLM-PCA) implemented in python

Models and datasets for perturbational single-cell omics

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

Contrastive Poisson latent variable models (CPLVMs)

Template repository for creating novel models with scvi-tools

Feature selection for deep learning models.

Archetypal Analysis network (AAnet)

TriMap: Large-scale Dimensionality Reduction Using Triplets

A Collection of Variational Autoencoders (VAE) in PyTorch.

Code for paper "Transferable representations of single-cell transcriptomic data"

POT : Python Optimal Transport

CellBox: Interpretable Machine Learning for Perturbation Biology

scPretrain: Multi-task self-supervised learning for cell type classification

Deep probabilistic analysis of single-cell and spatial omics data

Morpho-MNIST: Quantitative Assessment and Diagnostics for Representation Learning (http://jmlr.org/papers/v20/19-033.html)

Reference mapping for single-cell genomics

Single-cell analysis in Python. Scales to >100M cells.

Differentiable Unsupervised Feature Selection

Python/R library for feature selection in neural nets. ("Feature selection using Stochastic Gates", ICML 2020)