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    45 repositories

    • causalspyne

      Public
      Python data generation tool with unobserved confounding as testbed for causal discovery and causal abstraction
      Python
      •0•3•1•0•Updated Dec 20, 2024Dec 20, 2024

    • DomainLab

      Public
      modular domain generalization: https://pypi.org/project/domainlab/
      domain-generalization-causality-deep-learning
      Python
      •
      MIT License
      •2•43•20•18•Updated Dec 11, 2024Dec 11, 2024

    • MLL23

      Public
      A large publicly available single-cell peripheral blood dataset for domain generalized hematological disease diagnostics
      Jupyter Notebook
      •0•0•0•0•Updated Nov 29, 2024Nov 29, 2024

    • cAItomorph

      Public
      cAItomorph: Hematological Diagnostics from Peripheral Blood Cytomorphology
      MIT License
      •0•0•0•0•Updated Nov 5, 2024Nov 5, 2024

    • HistoGPT

      Public
      A vision language model for gigapixel whole slide images in histopathology
      Jupyter Notebook
      •
      Apache License 2.0
      •6•28•2•0•Updated Sep 25, 2024Sep 25, 2024

    • WBC-NCA

      Public
      Jupyter Notebook
      •0•2•1•0•Updated Aug 20, 2024Aug 20, 2024

    • DinoBloom

      Public
      Blood Cell Foundation Model based on DINOv2
      Python
      •
      Apache License 2.0
      •6•33•1•0•Updated Jun 18, 2024Jun 18, 2024

    • MILPLE

      Public
      Python
      •0•0•0•0•Updated Apr 8, 2024Apr 8, 2024

    • RedTell

      Public
      Python
      •3•5•1•0•Updated Mar 1, 2024Mar 1, 2024

    • initial-data-point-selection

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Feb 20, 2024Feb 20, 2024

    • pxpermute

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jan 12, 2024Jan 12, 2024

    • SHAPR_torch

      Public
      SHAPR: Code for "Capturing Shape Information with Multi-Scale Topological Loss Terms for 3D Reconstruction"
      image-reconstructionpersistent-homologytopological-data-analysistopological-machine-learningcubical-complexesdeep-learningpytorchsegmentation
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •9•39•0•0•Updated Oct 28, 2023Oct 28, 2023

    • BatchDetect

      Public
      BatchDetect: a python package for detect systematic batch effects in datasets
      Python
      •
      MIT License
      •0•2•0•0•Updated Oct 17, 2023Oct 17, 2023

    • scifAI-notebooks

      Public
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Oct 11, 2023Oct 11, 2023

    • scifAI

      Public
      scifAI: An explainable AI python framework for the analysis of multi-channel imaging data
      Python
      •
      MIT License
      •0•8•0•0•Updated Oct 11, 2023Oct 11, 2023

    • AE-CFE

      Public
      Python
      •4•3•2•0•Updated Jul 10, 2023Jul 10, 2023

    • AE-CFE-1

      Public
      Python
      •4•0•0•0•Updated Jul 4, 2023Jul 4, 2023

    • DISPR

      Public
      A Diffusion Model Predicts 3D Shapes from 2D Microscopy Images
      Python
      •
      Apache License 2.0
      •4•34•4•0•Updated May 31, 2023May 31, 2023

    • SHAPR

      Public
      SHAPR - An AI approach to predict 3D cell shapes from 2D microscopic images
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •7•14•0•0•Updated May 31, 2023May 31, 2023

    • Bright2Nuc

      Public
      Preprint: https://www.biorxiv.org/content/10.1101/2022.08.30.505835v1.full.pdf
      Python
      •
      MIT License
      •1•1•0•0•Updated May 31, 2023May 31, 2023

    • InstantDL

      Public
      InstantDL: An easy and convenient deep learning pipeline for image segmentation and classification
      dockerdeep-learninggpuregressionsemantic-segmentationinstance-segmentationpixel-wise-regressionclassificationimage-segmentation
      Python
      •
      MIT License
      •8•42•1•2•Updated Mar 24, 2023Mar 24, 2023

    • SCEMILA

      Public
      Single cell based explainable multiple instance learning algorithm (SCEMILA) for genetic acute myeloid leukemia subtype classification.
      Python
      •
      MIT License
      •1•5•0•0•Updated Mar 16, 2023Mar 16, 2023

    • percollFFT

      Public
      Python
      •1•1•0•0•Updated Mar 16, 2023Mar 16, 2023

    • attMIL

      Public
      Attention Based Multiple Instance Learning (attMIL)
      Python
      •0•4•0•0•Updated Feb 15, 2023Feb 15, 2023

    • CAR_T_TargetIdentification

      Public
      Computational identification of targets for CAR-T cell therapy in AML
      Jupyter Notebook
      •
      MIT License
      •3•16•2•0•Updated Dec 25, 2022Dec 25, 2022

    • patch-visualization

      Public
      0•0•0•0•Updated Nov 3, 2022Nov 3, 2022

    • Gal1repression

      Public
      Modeling Gal1 repression kinetics in single budding yeast cells
      MATLAB
      •0•1•0•0•Updated Oct 11, 2022Oct 11, 2022

    • Recap-Friday

      Public
      In this repository we maintain the material for recap fridays at marr lab
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 1, 2022Aug 1, 2022

    • HematoFatePrediction

      Public
      Code accompanying "Prospective identification of hematopoietic lineage choice by deep learning", Nature methods 2017, DOI:10.1038/nmeth.4182
      MATLAB
      •6•20•0•1•Updated Jul 13, 2022Jul 13, 2022

    • Anomaly-aware-MIL

      Public
      A simple pooling method for multiple instance learning based on attention and anomaly scores of instances.
      Python
      •
      MIT License
      •0•6•0•0•Updated Jun 30, 2022Jun 30, 2022