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HEST: Bringing Spatial Transcriptomics and Histopathology together - NeurIPS 2024 (Spotlight)

Python 206 19 Updated Dec 14, 2024

Meta Lingua: a lean, efficient, and easy-to-hack codebase to research LLMs.

Python 4,400 230 Updated Jan 14, 2025
Jupyter Notebook 7 1 Updated Nov 8, 2024

Practical associated to the class given within the IMALIS Master of ENS Paris

Shell 1 Updated Sep 18, 2019
Python 1 1 Updated Sep 18, 2023

A Shrek inspired package with colors and quotes

R 2 Updated Dec 1, 2023

Tool to download/merge RNASeq data from the GDC Portal in matrices identified by TCGA barcode

Python 35 14 Updated May 18, 2020

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

Python 614 70 Updated Jan 14, 2025

Compute gradients on mesh and unstructured data objects.

Jupyter Notebook 1 Updated Apr 2, 2021

Sparse Convolutional Context-Aware Multiple Instance Learning for Whole Slide Image Classification | https://arxiv.org/abs/2105.02726

Python 26 2 Updated Oct 11, 2021

Individual Coefficient Approximation for Risk Estimation (ICARE) model

Jupyter Notebook 17 1 Updated Sep 9, 2023

P-NET, Biologically informed deep neural network for prostate cancer classification and discovery

HTML 148 59 Updated Nov 15, 2021

Python package for multi-view machine learning

Python 208 22 Updated Oct 29, 2023

pyComBat is a Python 3 implementation of ComBat, one of the most widely used tool for correcting technical biases, called batch effects, in microarray expression data.

Python 81 23 Updated Feb 24, 2024

This data-centric AI repository implements a robust deep learning method (LFBNet) for fully automated tumor segmentation in whole-body [18]F-FDG PET/CT images.

Python 32 10 Updated May 29, 2024
Python 19 7 Updated Nov 7, 2023

PyTorch deep learning projects made easy.

Python 4,807 1,089 Updated Jun 4, 2024

A framework for Medical Image Segmentation with Convolutional Neural Networks and Deep Learning

Python 408 117 Updated May 10, 2023

Hierarchical approach to Stabilised Independent Component Analysis

Jupyter Notebook 7 3 Updated Sep 28, 2023

Code for ICE-BeeM paper - NeurIPS 2020

Python 86 18 Updated Aug 31, 2021

Computational framework for dataset integration

Jupyter Notebook 11 2 Updated Jul 21, 2023

Implementation of Attention-based Deep Multiple Instance Learning in PyTorch

Python 850 191 Updated Jan 8, 2024

Deep probabilistic analysis of single-cell and spatial omics data

Python 1,314 372 Updated Jan 17, 2025

Nextflow pipeline for RNA-seq pre-analysis (quality controls, genes/isoforms expression, isoform de-novo identification)

HTML 6 3 Updated Oct 23, 2024

Open-source python package for the extraction of Radiomics features from 2D and 3D images and binary masks. Support: https://discourse.slicer.org/c/community/radiomics

Jupyter Notebook 1,197 503 Updated Oct 21, 2024

Preconditioned ICA for Real Data

Python 108 13 Updated Nov 18, 2024

PyTorch Tutorial for Deep Learning Researchers

Python 30,599 8,157 Updated Aug 15, 2023

A game theoretic approach to explain the output of any machine learning model.

Jupyter Notebook 23,247 3,319 Updated Jan 16, 2025

A Tree based feature selection tool which combines both the Boruta feature selection algorithm with shapley values.

Python 601 91 Updated Feb 19, 2024
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