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    60 repositories

    • spatialfusion

      Public
      This repository contains the package SpatialFusion, a deep-learning multimodal model for niche discovery in spatial transcritomics and histopathological data.
      Jupyter Notebook
      •
      MIT License
      •0•8•0•1•Updated Mar 25, 2026Mar 25, 2026

    • greedy-ancestral-search

      Public
      Official implementation of the Greedy Ancestral Seach (GAS) algorithm from the paper "On the Number of Conditional Independence Tests in Constraint-based Causal…
      Python
      •
      MIT License
      •0•1•0•0•Updated Mar 24, 2026Mar 24, 2026

    • MORPH

      Public
      Jupyter Notebook
      •4•11•1•0•Updated Mar 8, 2026Mar 8, 2026

    • TissueFormer

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Feb 13, 2026Feb 13, 2026

    • prt-pbmc

      Public
      Deep learning-based analysis reveals patient-level proton radiation therapy trajectories using single-cell PBMC chromatin images
      Jupyter Notebook
      •0•0•0•0•Updated Feb 5, 2026Feb 5, 2026

    • TRIM

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Jan 29, 2026Jan 29, 2026

    • strimap-tools

      Public
      Python
      •
      MIT License
      •1•1•0•0•Updated Jan 14, 2026Jan 14, 2026

    • APOLLO

      Public
      Jupyter Notebook
      •0•8•0•0•Updated Dec 10, 2025Dec 10, 2025

    • spatialfusion-analysis

      Public
      This is the repository that contains the accompanying code for the SpatialFusion manuscript.
      Jupyter Notebook
      •
      MIT License
      •0•0•1•0•Updated Dec 4, 2025Dec 4, 2025

    • neurodegeneration

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Nov 1, 2025Nov 1, 2025

    • Spatial-Gene-Imputation-Methods

      Public
      Python
      •1•1•0•0•Updated Sep 18, 2025Sep 18, 2025

    • prob_fact_design

      Public
      Code for paper "Probabilistic Factorial Experimental Design for Combinatorial Interventions"
      Jupyter Notebook
      •0•0•0•0•Updated Jun 2, 2025Jun 2, 2025

    • PUPS

      Public
      Jupyter Notebook
      •
      Other
      •4•16•1•0•Updated May 14, 2025May 14, 2025

    • DisentangledSSL

      Public
      Code for paper: "An Information Criterion for Controlled Disentanglement of Multimodal Data"
      Python
      •1•6•0•0•Updated Feb 28, 2025Feb 28, 2025

    • image2reg

      Public
      Code for the paper "Image2Reg: Linking Chromatin Images to Gene Regulation using Genetic Perturbation Screens"
      Jupyter Notebook
      •1•7•0•0•Updated Feb 18, 2025Feb 18, 2025

    • porcelan

      Public
      Detecting lineage-related gene expression patterns
      Jupyter Notebook
      •
      MIT License
      •1•3•0•0•Updated Jan 29, 2025Jan 29, 2025

    • MODES

      Public
      Decoupled multimodal representation fusion
      Python
      •0•3•0•0•Updated Jan 22, 2025Jan 22, 2025

    • bmtm-mle

      Public
      Investigating the MLE of Brownian Motion Tree Models given 1-sample
      Python
      •1•3•0•0•Updated Jan 19, 2025Jan 19, 2025

    • observational-crl

      Public
      Jupyter Notebook
      •0•2•0•0•Updated Oct 30, 2024Oct 30, 2024

    • sccvae

      Public
      Single-cell Causal VAE
      Python
      •2•8•0•0•Updated Oct 28, 2024Oct 28, 2024

    • server_tutorial

      Public
      Code for using the GPU server
      Python
      •2•0•0•0•Updated Sep 9, 2024Sep 9, 2024

    • adhesome_clustering

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Jul 12, 2024Jul 12, 2024

    • synthetic_lethality

      Public
      Jupyter Notebook
      •1•3•1•0•Updated Jun 18, 2024Jun 18, 2024

    • CCPG

      Public
      Jupyter Notebook
      •1•7•0•0•Updated Jun 10, 2024Jun 10, 2024

    • DCISprogression

      Public
      Jupyter Notebook
      •0•3•0•0•Updated May 22, 2024May 22, 2024

    • graphical_models

      Public
      Implementations of common graphical models, utilities for creating random graphs, and sampling from graphical models.
      graphical-models
      graphical-models
      HTML
      •
      Other
      •5•11•3•1•Updated Apr 22, 2024Apr 22, 2024

    • InfoCORE

      Public
      Code for paper: "Removing Biases from Molecular Representations via Information Maximization"
      Python
      •0•20•0•0•Updated Apr 4, 2024Apr 4, 2024

    • discrepancy_vae

      Public
      code for paper: Identifiability Guarantees for Causal Disentanglement from Soft Interventions
      Jupyter Notebook
      •3•15•0•0•Updated Nov 27, 2023Nov 27, 2023

    • actlearn_optint

      Public
      Active learning for optimal intervention design in causal models
      Jupyter Notebook
      •
      MIT License
      •7•16•1•0•Updated Nov 8, 2023Nov 8, 2023

    • meek_sep

      Public
      Source code for paper: Meek Separators and Their Applications in Targeted Causal Discovery
      Jupyter Notebook
      •0•0•0•0•Updated Nov 7, 2023Nov 7, 2023
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