A novel method for bridge integration (i.e. integration of partially paired single-cell multimodal data): Champollion

Code for Koblan, Yost, Zheng, Colgan, et al. Science (2025)

Co-accessibility network from single-cell ATAC-seq data. Python code with AnnData, based on Cicero algorithm.

Molecular interactions inference from single-cell multi-omics data

A novel method for single-cell diagonal integration: scConfluence

Joint trajectory and network inference via reference fitting

Code for the paper Geodesic Sinkhorn for Fast and Accurate Optimal Transport on Manifolds.

Dynamical information enables inference of gene regulation at single-cell scale

[ICCV 2025] FLOSS: Plug-in Training-free and label-free text template selection that boosts OVSS methods

Python package for the ICML 2022 paper "Unsupervised Ground Metric Learning Using Wasserstein Singular Vectors".

Global Waddington-OT

Official implementation of Inductive Moment Matching

Learning stochastic dynamics from snapshots through regularized unbalanced optimal transport (ICLR'25 oral)

A generative model to predict gene expression dynamics, cell population changes, and perturbation outcomes from time-series single-cell data

SDE Parameter Estimation from Temporal Marginals

JAX implementation of the JKOnet* architecture presented in "Learning Diffusion at Lightspeed".

[WACV 2026] An extremely simple method for validation-free efficient adaptation of CLIP-like VLMs that is robust to the learning rate.

[WACV 2025] LatteCLIP: Unsupervised CLIP Fine-Tuning via LMM-Synthetic Texts

scNODE: Generative Model for Temporal Single Cell Transcriptomic Data Prediction

Learn single-cell dynamics using neural differential equations

TorchCFM: a Conditional Flow Matching library

Learning cell fate landscapes from spatial transcriptomics using Fused Gromov-Wasserstein

Inferring Gene Regulatory Networks from single-cell data

Pytorch implementation of set transformer

A simulator for single-cell expression data guided by gene regulatory networks

[CVPR 2024] Official repository of "Material Palette: Extraction of Materials from a Single Real-world Image"

Combinatorial Complex Score-based Diffusion model using stochastic differential equations

PyTorch implementation of "Kernel Neural Optimal Transport" (ICLR 2023)