VictorLee94

pytorch-grad-cam

Advanced AI Explainability for computer vision. Support for CNNs, Vision Transformers, Classification, Object detection, Segmentation, Image similarity and more.

shap

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

tcga-glioma

Machine learning project classifying glioma gradings in R. Somatic mutation data collected from The Cancer Genome Atlas. Algorithms include logistic regression, Adaptive Boosting, Linear SVM, Random Forest, and Naive Bayes

tcga-cancer-classification

A deep learning approach to classify cancer type from TCGA data.

PORPOISE

Pan-Cancer Integrative Histology-Genomic Analysis via Multimodal Deep Learning - Cancer Cell

fast-stain-normalization

:star2: GPU-accelerated stain normalization command line tool

RandStainNA

RandStainNA: Simple and efficient augmentations for histology [MICCAI 2022]

StainTools

Tools for tissue image stain normalisation and augmentation in Python 3

Lung-Cancer-Risk-Prediction

Lung cancer risk prediction from CT using fine-tuned I3D neural network

lifelines

Survival analysis in Python

PyMethylProcess

Preprocessing methylation pipeline, written in python. Easy to use and highly parallelized.

3D-genome-risk-prediction

[ACM-BCB 2023 Oral Presentation] Official repository of "Deep learning-based survival prediction using DNA methylation-derived 3D genomic information"

MethylNet

Modular framework for deep learning predictions on methylation data.

TransPath

slideflow

Powerful, open-source AI tools for digital pathology.

JARVIS

JARVIS: a comprehensive deep learning framework to prioritise non-coding variants in whole genomes

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

PathomicFusion

Fusing Histology and Genomics via Deep Learning - IEEE TMI

GenNet

Framework for Interpretable Neural Networks

TIDEpy

TIDE (Tumor Immune Dysfunction and Exclusion), a gene expression biomarker to predict the clinical response to immune checkpoint blockade in Python.

CLAM

Data-efficient and weakly supervised computational pathology on whole slide images - Nature Biomedical Engineering

tensorflow-huge-model-support

This library is designed to speed up huge model training on unified memory.

whole-slide-cnn

This repository provides scripts to reproduce the results in the paper "An annotation-free whole-slide training approach to pathological classification of lung cancer types by deep learning".

deepslide

Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for classification of high resolution whole-slide images, often microscopy or histopathology images.

IDHmut

Deep learning aids prediction of IDH mutation status from histopathological whole slide images (WSI)

Image-Cleaning

This repository is created to contain code that could be used to pre- and post-process histology images.

google-research

Google Research