Python Medical-datasets Resources

Mask-RCNN on Mycobacterium tuberculosis This is an example of object detection on Mycobacterium Tuberculosis using Mask RCNN. Implement of Mask R-CNN

normalizer This python module is an easy-to-use port of the text normalization used in the paper "Not low-resource anymore: Aligner ensembling, batch

EasyDatas An easy way to build PyTorch datasets. Modularly build datasets and automatically cache processed results Installation pip install git+https

WobblyStitcher Introduction A scalable implementation of WobblyStitcher Dependencies $ python -m pip install numpy scikit-image Visualization ImageJ

Medical image preprocessing and augmentation toolkit for deep learning. Part of the PyTorch Ecosystem.

[Japanese/English] GrabCut-Annotation-Tool GrabCut-Annotation-Tool.mp4 OpenCVのGrabCut()を利用したアノテーションツールです。 セマンティックセグメンテーション向けのデータセット作成にご使用いただけます。 ※Grab

About This repository provides data and code for the paper: Scalable Data Annotation Pipeline for High-Quality Large Speech Datasets Development (subm

Thermostat is a large collection of NLP model explanations and accompanying analysis tools. Combines explainability methods from the captum library wi

Codebase for training transformers on systematic generalization datasets. The official repository for our EMNLP 2021 paper The Devil is in the Detail:

GraphGT: Machine Learning Datasets for Graph Generation and Transformation Dataset Website | Paper Installation Using pip To install the core environm

This is a playground for pytorch beginners, which contains predefined models on popular dataset. Currently we support mnist, svhn cifar10, cifar100 st

PyTorch Image Classifier Updates As for many users request, I released a new version of standared pytorch immage classification example at here: http:

Simple tool/toolkit for evaluating NLG (Natural Language Generation) offering various automated metrics. Jury offers a smooth and easy-to-use interface. It uses datasets for underlying metric computation, and hence adding custom metric is easy as adopting datasets.Metric.

THU模式识别2021春 -- Jittor 医学图像分割 模型列表 本仓库收录了课程作业中同学们采用jittor框架实现的如下模型： UNet SegNet DeepLab V2 DANet EANet HarDNet及其改动HarDNet_alter PSPNet OCNet OCRNet DL

CaraNet: Context Axial Reverse Attention Network for Small Medical Objects Segmentation This repository contains the implementation of a novel attenti

An Effective Loss Function for Generating 3D Models from Single 2D Image without Rendering Papers with code | Paper Nikola Zubić Pietro Lio University

Meeting Summarization Dataset Meeting plays an essential part in our daily life, which allows us to share information and collaborate with others. Wit

Common Sense Beyond English: Evaluating and Improving Multilingual LMs for Commonsense Reasoning This is the Github repository of our paper, "Common S

Deep Automatic Natural Image Matting [IJCAI-21] This is the official repository of the paper Deep Automatic Natural Image Matting. Introduction | Netw

A curated list of amazingly awesome Cybersecurity datasets

PyTorch Remote Sensing (torchrs) (WIP) PyTorch implementation of popular datasets and models in remote sensing tasks (Change Detection, Image Super Re

Deduplicating Training Data Makes Language Models Better This repository contains code to deduplicate language model datasets as descrbed in the paper

Deep Neural Networks Improve Radiologists' Performance in Breast Cancer Screening Introduction This is an implementation of the model used for breast

The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.

UACANet: Uncertainty Aware Context Attention for Polyp Segmentation Official pytorch implementation of UACANet: Uncertainty Aware Context Attention fo

MONAI Label is a server-client system that facilitates interactive medical image annotation by using AI. It is an open-source and easy-to-install ecosystem that can run locally on a machine with one or two GPUs. Both server and client work on the same/different machine. However, initial support for multiple users is restricted. It shares the same principles with MONAI.

Rapid Neural Architecture Search by Learning to Generate Graphs from Datasets This is the official PyTorch implementation for the paper Rapid Neural A

Project page for the paper Semi-Supervised Raw-to-Raw Mapping 2021.

RSG: A Simple but Effective Module for Learning Imbalanced Datasets (CVPR 2021) A Pytorch implementation of our CVPR 2021 paper "RSG: A Simple but Eff

PyMedPhys is an open-source Medical Physics python library built by an open community that values and prioritises code sharing, review, improvement, and learning from each other. I

Swin-Unet The codes for the work "Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation"(https://arxiv.org/abs/2105.05537). A validatio

What is nnDetection? Simultaneous localisation and categorization of objects in medical images, also referred to as medical object detection, is of hi

Meerkat makes it easier for ML practitioners to interact with high-dimensional, multi-modal data. It provides simple abstractions for data inspection, model evaluation and model training supported by efficient and robust IO under the hood.

NoW Evaluation This is the official repository for evaluation on the NoW Benchmark Dataset. The goal of the NoW benchmark is to introduce a standard e

Unified Multimodal Transformer (UMT) for Multimodal Named Entity Recognition (MNER) Two MNER Datasets and Codes for our ACL'2020 paper: Improving Mult

UmlsBERT: Clinical Domain Knowledge Augmentation of Contextual Embeddings Using the Unified Medical Language System Metathesaurus General info This is

PTR Code and datasets for our paper "PTR: Prompt Tuning with Rules for Text Classification" If you use the code, please cite the following paper: @art

Deep Active Learning for Biased Datasets via Fisher Kernel Self-Supervision https://arxiv.org/abs/2003.00393 Abstract Active learning (AL) aims to min

Ozeu Ozeu is the toolkit to autolabal dataset for instance segmentation. You can generate datasets labaled with segmentation mask and bounding box fro

Clairvoyance: A Pipeline Toolkit for Medical Time Series Authors: van der Schaar Lab This repository contains implementations of Clairvoyance: A Pipel

Medical Image Segmentation using Squeeze-and-Expansion Transformers Introduction This repository contains the code of the IJCAI'2021 paper 'Medical Im

This repository contains 20 annotated datasets of Automatic Keyphrase Extraction made available by the research community. Following are the datasets and the original papers that proposed them. If you know more datasets, and want to contribute, please, notify me.

TSForecasting This repository contains the implementations related to the experiments of a set of publicly available datasets that are used in the tim

Covid-QA Fine tuned models for question answering on Covid-19 data. Hosted Inference This model has been contributed to huggingface.Click here to see

PosteriorStacker Combines Bayesian analyses from many datasets. Introduction Method Tutorial Output plot and files Introduction Fitting a model to a d

BOOKSUM: A Collection of Datasets for Long-form Narrative Summarization Authors: Wojciech Kryściński, Nazneen Rajani, Divyansh Agarwal, Caiming Xiong,

tfds-korean A collection of Korean Text Datasets ready to use using Tensorflow-Datasets. TensorFlow-Datasets를 이용한 한국어/한글 데이터셋 모음입니다. Dataset Catalog |

Public Datasets Pipelines Cloud-native, data pipeline architecture for onboarding datasets to the Google Cloud Public Datasets Program. Overview Requi

PRAnCER (Platform enabling Rapid Annotation for Clinical Entity Recognition) is a web platform that enables the rapid annotation of medical terms within clinical notes. A user can highlight spans of text and quickly map them to concepts in large vocabularies within a single, intuitive platform.

ViT-V-Net: Vision Transformer for Volumetric Medical Image Registration keywords: vision transformer, convolutional neural networks, image registratio

A curated list of awesome anomaly detection works in medical imaging, inspired by the other awesome-* initiatives.

Awesome Video Datasets

Towards Good Practices for Efficiently Annotating Large-Scale Image Classification Datasets This is the official implementation of "Towards Good Pract

SeqIO: Task-based datasets, preprocessing, and evaluation for sequence models. SeqIO is a library for processing sequential data to be fed into downst

Combining Events and Frames using Recurrent Asynchronous Multimodal Networks for Monocular Depth Prediction This is the code for the paper Combining E

Graph Evolving Meta-Learning for Low-resource Medical Dialogue Generation Code to be further cleaned... This repo contains the code of the following p

🤗 The largest hub of ready-to-use NLP datasets for ML models with fast, easy-to-use and efficient data manipulation tools

Debiasing Item-to-Item Recommendations With Small Annotated Datasets This is the code for our RecSys '20 paper. Other materials can be found here: Ful

PyKale is a PyTorch library for multimodal learning and transfer learning as well as deep learning and dimensionality reduction on graphs, images, texts, and videos. By adopting a unified pipeline-based API design, PyKale enforces standardization and minimalism, via reusing existing resources, reducing repetitions and redundancy, and recycling learning models across areas.

Repository on the collaborative IVADO medical imaging project between the Mila and NeuroPoly labs.

DoDNet This repo holds the pytorch implementation of DoDNet: DoDNet: Learning to segment multi-organ and tumors from multiple partially labeled datase

Datasets from Instructions (DINO 🦕 ) This repository contains the code for Generating Datasets with Pretrained Language Models. The paper introduces

drawdata This small python app allows you to draw a dataset in a jupyter notebook. This should be very useful when teaching machine learning algorithm

Trove Trove is a research framework for building weakly supervised (bio)medical named entity recognition (NER) and other entity attribute classifiers

Welcome to MedicalTorch MedicalTorch is an open-source framework for PyTorch, implementing an extensive set of loaders, pre-processors and datasets fo

This tutorial's purpose is to introduce Pythonistas to methods for scaling their data science and machine learning work to larger datasets and larger models, using the tools and APIs they know and love from the PyData stack (such as numpy, pandas, and scikit-learn).

rio-tiler User friendly Rasterio plugin to read raster datasets. Documentation: https://cogeotiff.github.io/rio-tiler/ Source Code: https://github.com

USGS API USGS is a python module for interfacing with the US Geological Survey's API. It provides submodules to interact with various endpoints, and c

rasterstats rasterstats is a Python module for summarizing geospatial raster datasets based on vector geometries. It includes functions for zonal stat

wav2vec-toolkit A collection of scripts to preprocess ASR datasets and finetune language-specific Wav2Vec2 XLSR models This repository accompanies the

CheXbert: Combining Automatic Labelers and Expert Annotations for Accurate Radiology Report Labeling Using BERT CheXbert is an accurate, automated dee

UA-GEC: Grammatical Error Correction and Fluency Corpus for the Ukrainian Language This repository contains UA-GEC data and an accompanying Python lib

A collection of loss functions for medical image segmentation

P-tuning A novel method to tune language models. Codes and datasets for paper ``GPT understands, too''. How to use our code We have released the code

SASSnet Code for paper: Shape-aware Semi-supervised 3D Semantic Segmentation for Medical Images(MICCAI 2020) Our code is origin from UA-MT You can fin

Domain Generalization for Medical Imaging Classification with Linear Dependency Regularization The code release of paper 'Domain Generalization for Me

imbalanced-learn imbalanced-learn is a python package offering a number of re-sampling techniques commonly used in datasets showing strong between-cla

Petastorm Contents Petastorm Installation Generating a dataset Plain Python API Tensorflow API Pytorch API Spark Dataset Converter API Analyzing petas

matrixprofile-ts matrixprofile-ts is a Python 2 and 3 library for evaluating time series data using the Matrix Profile algorithms developed by the Keo

Technical Analysis Library in Python It is a Technical Analysis library useful to do feature engineering from financial time series datasets (Open, Cl

Rasterio Rasterio reads and writes geospatial raster data. Geographic information systems use GeoTIFF and other formats to organize and store gridded,

Maths from examples - Learning advanced mathematical computations from examples This is the source code and data sets relevant to the paper Learning a

FedDG: Federated Domain Generalization on Medical Image Segmentation via Episodic Learning in Continuous Frequency Space by Quande Liu, Cheng Chen, Ji

OCR Resources This repository contains a collection of resources (including the papers and datasets) of OCR (Optical Character Recognition). Contents

Dataset Cartography Code for the paper Dataset Cartography: Mapping and Diagnosing Datasets with Training Dynamics at EMNLP 2020. This repository cont

TrajNet++ : The Trajectory Forecasting Framework PyTorch implementation of Human Trajectory Forecasting in Crowds: A Deep Learning Perspective TrajNet

Datasette An open source multi-tool for exploring and publishing data Datasette is a tool for exploring and publishing data. It helps people take data

CoTr: Efficient 3D Medical Image Segmentation by bridging CNN and Transformer This is the official pytorch implementation of the CoTr: Paper: CoTr: Ef

BatchFlow BatchFlow helps you conveniently work with random or sequential batches of your data and define data processing and machine learning workflo

torchvision The torchvision package consists of popular datasets, model architectures, and common image transformations for computer vision. Installat

imbalanced-learn imbalanced-learn is a python package offering a number of re-sampling techniques commonly used in datasets showing strong between-cla

Simple multi-dataset detection An object detector trained on multiple large-scale datasets with a unified label space; Winning solution of E

InVesalius InVesalius generates 3D medical imaging reconstructions based on a sequence of 2D DICOM files acquired with CT or MRI equipments. InVesaliu

Xpublish Publish Xarray Datasets via a REST API. Serverside: Publish a Xarray Dataset through a rest API ds.rest.serve(host="0.0.0.0", port=9000) Clie

Medical-Transformer Pytorch Code for the paper "Medical Transformer: Gated Axial-Attention for Medical Image Segmentation" About this repo: This repo

TransUNet This repo holds code for TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation Usage

xarray is an open source project and Python package that makes working with labelled multi-dimensional arrays simple, efficient, and fun!

NeuralQA: A Usable Library for (Extractive) Question Answering on Large Datasets with BERT Still in alpha, lots of changes anticipated. View demo on n

ParlAI (pronounced “par-lay”) is a python framework for sharing, training and testing dialogue models, from open-domain chitchat, to task-oriented dia

ivis Implementation of the ivis algorithm as described in the paper Structure-preserving visualisation of high dimensional single-cell datasets. Ivis