162 Repositories
Python medical-diagnostics Libraries
ML-based medical imaging using Azure
Disclaimer This code is provided for research and development use only. This code is not intended for use in clinical decision-making or for any other
[Arxiv preprint] Causality-inspired Single-source Domain Generalization for Medical Image Segmentation (code&data-processing pipeline)
Causality-inspired Single-source Domain Generalization for Medical Image Segmentation Arxiv preprint Repository under construction. Might still be bug
A large-scale (194k), Multiple-Choice Question Answering (MCQA) dataset designed to address realworld medical entrance exam questions.
MedMCQA MedMCQA : A Large-scale Multi-Subject Multi-Choice Dataset for Medical domain Question Answering A large-scale, Multiple-Choice Question Answe
This repository will be a summary and outlook on all our open, medical, AI advancements.
medical by LAION This repository will be a summary and outlook on all our open, medical, AI advancements. See the medical-general channel in the medic
This project aims to conduct a text information retrieval and text mining on medical research publication regarding Covid19 - treatments and vaccinations.
Project: Text Analysis - This project aims to conduct a text information retrieval and text mining on medical research publication regarding Covid19 -
Code base for "On-the-Fly Test-time Adaptation for Medical Image Segmentation"
On-the-Fly Adaptation Official Pytorch Code base for On-the-Fly Test-time Adaptation for Medical Image Segmentation Paper Introduction One major probl
A framework for GPU based high-performance medical image processing and visualization
FAST is an open-source cross-platform framework with the main goal of making it easier to do high-performance processing and visualization of medical images on heterogeneous systems utilizing both multi-core CPUs and GPUs. To achieve this, FAST use modern C++, OpenCL and OpenGL.
Multi-atlas segmentation (MAS) is a promising framework for medical image segmentation
Multi-atlas segmentation (MAS) is a promising framework for medical image segmentation. Generally, MAS methods register multiple atlases, i.e., medical images with corresponding labels, to a target image;
MEDIALpy: MEDIcal Abbreviations Lookup in Python
A small python package that allows the user to look up common medical abbreviations.
DCSAU-Net: A Deeper and More Compact Split-Attention U-Net for Medical Image Segmentation
DCSAU-Net: A Deeper and More Compact Split-Attention U-Net for Medical Image Segmentation By Qing Xu, Wenting Duan and Na He Requirements pytorch==1.1
Posterior temperature optimized Bayesian models for inverse problems in medical imaging
Posterior temperature optimized Bayesian models for inverse problems in medical imaging Max-Heinrich Laves*, Malte Tölle*, Alexander Schlaefer, Sandy
Mednlp - Medical natural language parsing and utility library
Medical natural language parsing and utility library A natural language medical
This is the source code of the 1st place solution for segmentation task (with Dice 90.32%) in 2021 CCF BDCI challenge.
1st place solution in CCF BDCI 2021 ULSEG challenge This is the source code of the 1st place solution for ultrasound image angioma segmentation task (
Python Classes: Medical Insurance Project using Object Oriented Programming Concepts
Medical-Insurance-Project-OOP Python Classes: Medical Insurance Project using Object Oriented Programming Concepts Classes are an incredibly useful pr
SegTransVAE: Hybrid CNN - Transformer with Regularization for medical image segmentation
SegTransVAE: Hybrid CNN - Transformer with Regularization for medical image segmentation This repo is the official implementation for SegTransVAE. Seg
The open-source and free to use Python package miseval was developed to establish a standardized medical image segmentation evaluation procedure
miseval: a metric library for Medical Image Segmentation EVALuation The open-source and free to use Python package miseval was developed to establish
Novel and high-performance medical image classification pipelines are heavily utilizing ensemble learning strategies
An Analysis on Ensemble Learning optimized Medical Image Classification with Deep Convolutional Neural Networks Novel and high-performance medical ima
Toward Model Interpretability in Medical NLP
Toward Model Interpretability in Medical NLP LING380: Topics in Computational Linguistics Final Project James Cross ([email protected]) and Daniel Kim
Awesome Transformers in Medical Imaging
This repo supplements our Survey on Transformers in Medical Imaging Fahad Shamshad, Salman Khan, Syed Waqas Zamir, Muhammad Haris Khan, Munawar Hayat,
This repository is for our EMNLP 2021 paper "Automated Generation of Accurate & Fluent Medical X-ray Reports"
Introduction: X-Ray Report Generation This repository is for our EMNLP 2021 paper "Automated Generation of Accurate & Fluent Medical X-ray Reports". O
RATCHET is a Medical Transformer for Chest X-ray Diagnosis and Reporting
RATCHET: RAdiological Text Captioning for Human Examined Thoraxes RATCHET is a Medical Transformer for Chest X-ray Diagnosis and Reporting. Based on t
Accepted at ICCV-2021: Workshop on Computer Vision for Automated Medical Diagnosis (CVAMD)
Is it Time to Replace CNNs with Transformers for Medical Images? Accepted at ICCV-2021: Workshop on Computer Vision for Automated Medical Diagnosis (C
Mixed Transformer UNet for Medical Image Segmentation
MT-UNet Update 2022/01/05 By another round of training based on previous weights, our model also achieved a better performance on ACDC (91.61% DSC). W
For medical image segmentation
LeViT_UNet For medical image segmentation Our model is based on LeViT (https://github.com/facebookresearch/LeViT). You'd better gitclone its codes. Th
This repo holds the code of TransFuse: Fusing Transformers and CNNs for Medical Image Segmentation
TransFuse This repo holds the code of TransFuse: Fusing Transformers and CNNs for Medical Image Segmentation Requirements Pytorch=1.6.0, 1.9.0 (=1.
Automated Melanoma Recognition in Dermoscopy Images via Very Deep Residual Networks
Introduction This repository contains the modified caffe library and network architectures for our paper "Automated Melanoma Recognition in Dermoscopy
Pre-trained models for a Cascaded-FCN in caffe and tensorflow that segments
Cascaded-FCN This repository contains the pre-trained models for a Cascaded-FCN in caffe and tensorflow that segments the liver and its lesions out of
This is a curated list of medical data for machine learning
Medical Data for Machine Learning This is a curated list of medical data for machine learning. This list is provided for informational purposes only,
HistoSeg : Quick attention with multi-loss function for multi-structure segmentation in digital histology images
HistoSeg : Quick attention with multi-loss function for multi-structure segmentation in digital histology images Histological Image Segmentation This
SI_EXPLAINER_tg_bot: This bot is an assistant for medical professionals in interpreting the results of patient clustering.
SI_EXPLAINER_tg_bot This bot is an assistant for medical professionals in interpreting the results of patient clustering. ABOUT This chatbot was devel
This repository provides the code for MedViLL(Medical Vision Language Learner).
MedViLL This repository provides the code for MedViLL(Medical Vision Language Learner). Our proposed architecture MedViLL is a single BERT-based model
A natural language processing model for sequential sentence classification in medical abstracts.
NLP PubMed Medical Research Paper Abstract (Randomized Controlled Trial) A natural language processing model for sequential sentence classification in
NLU Dataset Diagnostics
NLU Dataset Diagnostics This repository contains data and scripts to reproduce the results from our paper: Aarne Talman, Marianna Apidianaki, Stergios
The final project of "Applying AI to 2D Medical Imaging Data" of "AI for Healthcare" nanodegree - Udacity.
Pneumonia Detection from X-Rays Project Overview In this project, you will apply the skills that you have acquired in this 2D medical imaging course t
The final project of "Applying AI to EHR Data" of "AI for Healthcare" nanodegree - Udacity.
Patient Selection for Diabetes Drug Testing Project Overview EHR data is becoming a key source of real-world evidence (RWE) for the pharmaceutical ind
The final project of "Applying AI to 3D Medical Imaging Data" from "AI for Healthcare" nanodegree - Udacity.
Quantifying Hippocampus Volume for Alzheimer's Progression Background Alzheimer's disease (AD) is a progressive neurodegenerative disorder that result
ISBI 2022: Cross-level Contrastive Learning and Consistency Constraint for Semi-supervised Medical Image.
Cross-level Contrastive Learning and Consistency Constraint for Semi-supervised Medical Image Introduction This repository contains the PyTorch implem
Liver segmentation using MONAI and pytorch
Machine Learning use case in the field of Healthcare. In this project MONAI and pytorch frameworks are used for 3D Liver segmentation.
Supervised 3D Pre-training on Large-scale 2D Natural Image Datasets for 3D Medical Image Analysis
Introduction This is an implementation of our paper Supervised 3D Pre-training on Large-scale 2D Natural Image Datasets for 3D Medical Image Analysis.
prior-based-losses-for-medical-image-segmentation
Repository for papers: Benchmark: Effect of Prior-based Losses on Segmentation Performance: A Benchmark Midl: A Surprisingly Effective Perimeter-based
Time series annotation library.
CrowdCurio Time Series Annotator Library The CrowdCurio Time Series Annotation Library implements classification tasks for time series. Features Suppo
Medical appointments No-Show classifier
Medical Appointments No-shows Why do 20% of patients miss their scheduled appointments? A person makes a doctor appointment, receives all the instruct
Using BERT+Bi-LSTM+CRF
Chinese Medical Entity Recognition Based on BERT+Bi-LSTM+CRF Step 1 I share the dataset on my google drive, please download the whole 'CCKS_2019_Task1
An open-source project for applying deep learning to medical scenarios
Auto Vaidya An open source solution for creating end-end web app for employing the power of deep learning in various clinical scenarios like implant d
ESMAC diags - Earth System Model Aerosol-Cloud Diagnostics Package
Earth System Model Aerosol-Cloud Diagnostics Package This Earth System Model (ES
Medical Insurance Cost Prediction using Machine earning
Medical-Insurance-Cost-Prediction-using-Machine-learning - Here in this project, I will use regression analysis to predict medical insurance cost for people in different regions, and based on several aspects like : Smoking, Number of children, BMI...etc.
Code for NeurIPS 2020 article "Contrastive learning of global and local features for medical image segmentation with limited annotations"
Contrastive learning of global and local features for medical image segmentation with limited annotations The code is for the article "Contrastive lea
Medical-Image-Triage-and-Classification-System-Based-on-COVID-19-CT-and-X-ray-Scan-Dataset
Medical-Image-Triage-and-Classification-System-Based-on-COVID-19-CT-and-X-ray-Sc
BisQue is a web-based platform designed to provide researchers with organizational and quantitative analysis tools for 5D image data. Users can extend BisQue by implementing containerized ML workflows.
Overview BisQue is a web-based platform specifically designed to provide researchers with organizational and quantitative analysis tools for up to 5D
Build a medical knowledge graph based on Unified Language Medical System (UMLS)
UMLS-Graph Build a medical knowledge graph based on Unified Language Medical System (UMLS) Requisite Install MySQL Server 5.6 and import UMLS data int
The official start-up code for paper "FFA-IR: Towards an Explainable and Reliable Medical Report Generation Benchmark."
FFA-IR The official start-up code for paper "FFA-IR: Towards an Explainable and Reliable Medical Report Generation Benchmark." The framework is inheri
An End-to-End Machine Learning Library to Optimize AUC (AUROC, AUPRC).
Logo by Zhuoning Yuan LibAUC: A Machine Learning Library for AUC Optimization Website | Updates | Installation | Tutorial | Research | Github LibAUC a
MISSFormer: An Effective Medical Image Segmentation Transformer
MISSFormer Code for paper "MISSFormer: An Effective Medical Image Segmentation Transformer". Please read our preprint at the following link: paper_add
CPPE - 5 (Medical Personal Protective Equipment) is a new challenging object detection dataset
CPPE - 5 CPPE - 5 (Medical Personal Protective Equipment) is a new challenging dataset with the goal to allow the study of subordinate categorization
WORD: Revisiting Organs Segmentation in the Whole Abdominal Region
WORD: Revisiting Organs Segmentation in the Whole Abdominal Region (Paper and DataSet). [New] Note that all the emails about the download permission o
Mixed Transformer UNet for Medical Image Segmentation
MT-UNet Update 2021/11/19 Thank you for your interest in our work. We have uploaded the code of our MTUNet to help peers conduct further research on i
Clustergram - Visualization and diagnostics for cluster analysis in Python
Clustergram Visualization and diagnostics for cluster analysis Clustergram is a diagram proposed by Matthias Schonlau in his paper The clustergram: A
Hypernetwork-Ensemble Learning of Segmentation Probability for Medical Image Segmentation with Ambiguous Labels
Hypernet-Ensemble Learning of Segmentation Probability for Medical Image Segmentation with Ambiguous Labels The implementation of Hypernet-Ensemble Le
📜Generate poetry with gcc diagnostics
gado (gcc awesome diagnostics orchestrator) is a wrapper of gcc that outputs its errors and warnings in a more poetic format.
The easiest tool for extracting radiomics features and training ML models on them.
Simple pipeline for experimenting with radiomics features Installation git clone https://github.com/piotrekwoznicki/ClassyRadiomics.git cd classrad pi
U-Net Brain Tumor Segmentation
U-Net Brain Tumor Segmentation 🚀 :Feb 2019 the data processing implementation in this repo is not the fastest way (code need update, contribution is
PyTorch implementation of MICCAI 2018 paper "Liver Lesion Detection from Weakly-labeled Multi-phase CT Volumes with a Grouped Single Shot MultiBox Detector"
Grouped SSD (GSSD) for liver lesion detection from multi-phase CT Note: the MICCAI 2018 paper only covers the multi-phase lesion detection part of thi
Self-Supervised Generative Style Transfer for One-Shot Medical Image Segmentation
Self-Supervised Generative Style Transfer for One-Shot Medical Image Segmentation This repository contains the Pytorch implementation of the proposed
Code for A Volumetric Transformer for Accurate 3D Tumor Segmentation
VT-UNet This repo contains the supported pytorch code and configuration files to reproduce 3D medical image segmentaion results of VT-UNet. Environmen
Diagnostic tests for linguistic capacities in language models
LM diagnostics This repository contains the diagnostic datasets and experimental code for What BERT is not: Lessons from a new suite of psycholinguist
Official implementation of the method ContIG, for self-supervised learning from medical imaging with genomics
ContIG: Self-supervised Multimodal Contrastive Learning for Medical Imaging with Genetics This is the code implementation of the paper "ContIG: Self-s
Official Keras Implementation for UNet++ in IEEE Transactions on Medical Imaging and DLMIA 2018
UNet++: A Nested U-Net Architecture for Medical Image Segmentation UNet++ is a new general purpose image segmentation architecture for more accurate i
Code for A Volumetric Transformer for Accurate 3D Tumor Segmentation
VT-UNet This repo contains the supported pytorch code and configuration files to reproduce 3D medical image segmentaion results of VT-UNet. Environmen
A system used to detect whether a person is wearing a medical mask or not.
Mask_Detection_System A system used to detect whether a person is wearing a medical mask or not. To open the program, please follow these steps: Make
R interface to fast.ai
R interface to fastai The fastai package provides R wrappers to fastai. The fastai library simplifies training fast and accurate neural nets using mod
Extension to fastai for volumetric medical data
FAIMED 3D use fastai to quickly train fully three-dimensional models on radiological data Classification from faimed3d.all import * Load data in vari
Additional functionality for use with fastai’s medical imaging module
fmi Adding additional functionality to fastai's medical imaging module To learn more about medical imaging using Fastai you can view my blog Install g
Open-source python package for the extraction of Radiomics features from 2D and 3D images and binary masks.
pyradiomics v3.0.1 Build Status Linux macOS Windows Radiomics feature extraction in Python This is an open-source python package for the extraction of
Repo for the paper "DiLBERT: Cheap Embeddings for Disease Related Medical NLP"
DiLBERT Repo for the paper "DiLBERT: Cheap Embeddings for Disease Related Medical NLP" Pretrained Model The pretrained model presented in the paper is
TransMorph: Transformer for Medical Image Registration
TransMorph: Transformer for Medical Image Registration keywords: Vision Transformer, Swin Transformer, convolutional neural networks, image registrati
Implementation of GGB color space
GGB Color Space This package is implementation of GGB color space from Development of a Robust Algorithm for Detection of Nuclei and Classification of
A keras-based real-time model for medical image segmentation (CFPNet-M)
CFPNet-M: A Light-Weight Encoder-Decoder Based Network for Multimodal Biomedical Image Real-Time Segmentation This repository contains the implementat
AI Toolkit for Healthcare Imaging
Medical Open Network for AI MONAI is a PyTorch-based, open-source framework for deep learning in healthcare imaging, part of PyTorch Ecosystem. Its am
MRQy is a quality assurance and checking tool for quantitative assessment of magnetic resonance imaging (MRI) data.
Front-end View Backend View Table of Contents Description Prerequisites Running Basic Information Measurements User Interface Feedback and usage Descr
AI-powered literature discovery and review engine for medical/scientific papers
AI-powered literature discovery and review engine for medical/scientific papers paperai is an AI-powered literature discovery and review engine for me
Effect of Deep Transfer and Multi task Learning on Sperm Abnormality Detection
Effect of Deep Transfer and Multi task Learning on Sperm Abnormality Detection Introduction This repository includes codes and models of "Effect of De
Official implementation of UTNet: A Hybrid Transformer Architecture for Medical Image Segmentation
UTNet (Accepted at MICCAI 2021) Official implementation of UTNet: A Hybrid Transformer Architecture for Medical Image Segmentation Introduction Transf
Official Keras Implementation for UNet++ in IEEE Transactions on Medical Imaging and DLMIA 2018
UNet++: A Nested U-Net Architecture for Medical Image Segmentation UNet++ is a new general purpose image segmentation architecture for more accurate i
Code for our paper "Multi-scale Guided Attention for Medical Image Segmentation"
Medical Image Segmentation with Guided Attention This repository contains the code of our paper: "'Multi-scale self-guided attention for medical image
Implementation for paper LadderNet: Multi-path networks based on U-Net for medical image segmentation
Implementation for paper LadderNet: Multi-path networks based on U-Net for medical image segmentation This implementation is based on orobix implement
Use of Attention Gates in a Convolutional Neural Network / Medical Image Classification and Segmentation
Attention Gated Networks (Image Classification & Segmentation) Pytorch implementation of attention gates used in U-Net and VGG-16 models. The framewor
U-Net: Convolutional Networks for Biomedical Image Segmentation
Deep Learning Tutorial for Kaggle Ultrasound Nerve Segmentation competition, using Keras This tutorial shows how to use Keras library to build deep ne
A collection of random and hastily hacked together scripts for investigating EU-DCC
A collection of random and hastily hacked together scripts for investigating EU-DCC
A Japanese Medical Information Extraction Toolkit
JaMIE: a Japanese Medical Information Extraction toolkit Joint Japanese Medical Problem, Modality and Relation Recognition The Train/Test phrases requ
Code for Recurrent Mask Refinement for Few-Shot Medical Image Segmentation (ICCV 2021).
Recurrent Mask Refinement for Few-Shot Medical Image Segmentation Steps Install any missing packages using pip or conda Preprocess each dataset using
A flexible ML framework built to simplify medical image reconstruction and analysis experimentation.
meddlr Getting Started Meddlr is a config-driven ML framework built to simplify medical image reconstruction and analysis problems. Installation To av
WORD: Revisiting Organs Segmentation in the Whole Abdominal Region
WORD: Revisiting Organs Segmentation in the Whole Abdominal Region. This repository provides the codebase and dataset for our work WORD: Revisiting Or
A collection of tools for biomedical research assay analysis in Python.
waltlabtools A collection of tools for biomedical research assay analysis in Python. Key Features Analysis for assays such as digital ELISA, including
Distributing Deep Learning Hyperparameter Tuning for 3D Medical Image Segmentation
DistMIS Distributing Deep Learning Hyperparameter Tuning for 3D Medical Image Segmentation. DistriMIS Distributing Deep Learning Hyperparameter Tuning
Explainable Medical ImageSegmentation via GenerativeAdversarial Networks andLayer-wise Relevance Propagation
MedAI: Transparency in Medical Image Segmentation What is this repo This repo contains the code and experiments that are implemented to contribute in
Bayesian Optimization Library for Medical Image Segmentation.
bayesmedaug: Bayesian Optimization Library for Medical Image Segmentation. bayesmedaug optimizes your data augmentation hyperparameters for medical im
How to Leverage Multimodal EHR Data for Better Medical Predictions?
How to Leverage Multimodal EHR Data for Better Medical Predictions? This repository contains the code of the paper: How to Leverage Multimodal EHR Dat
A general, feasible, and extensible framework for classification tasks.
Pytorch Classification A general, feasible and extensible framework for 2D image classification. Features Easy to configure (model, hyperparameters) T
[v1 (ISBI'21) + v2] MedMNIST: A Large-Scale Lightweight Benchmark for 2D and 3D Biomedical Image Classification
MedMNIST Project (Website) | Dataset (Zenodo) | Paper (arXiv) | MedMNIST v1 (ISBI'21) Jiancheng Yang, Rui Shi, Donglai Wei, Zequan Liu, Lin Zhao, Bili
This repository contains scripts that help you validate QR codes.
Validation tools This repository contains scripts that help you validate QR codes. It's hacky, and a warning for Apple Silicon users: the dependencies