A flexible ML framework built to simplify medical image reconstruction and analysis experimentation.

Overview

meddlr

Getting Started

Meddlr is a config-driven ML framework built to simplify medical image reconstruction and analysis problems.

Installation

To avoid cuda-related issues, downloading torch, torchvision, and cupy (optional) must be done prior to downloading other requirements.

# Create and activate the environment.
conda create -n meddlr_env python=3.7
conda activate meddlr_env

# Install cuda-dependant libraries. Change cuda version as needed.
# Below we show examples for cuda-10.1
conda install pytorch torchvision cudatoolkit=10.1 -c pytorch
pip install cupy-cuda101

# Install as package in virtual environment (recommended):
git clone https://github.com/ad12/meddlr.git
cd dl-ss-recon && python -m pip install -e '.[dev]'

# For all contributors, install development packages.
make dev

Contributing

See CONTRIBUTING.md for more information.

Acknowledgements

Meddlr's design for rapid experimentation and benchmarking is inspired by detectron2.

About

If you use Meddlr for your work, please consider citing the following work:

@article{desai2021noise2recon,
  title={Noise2Recon: A Semi-Supervised Framework for Joint MRI Reconstruction and Denoising},
  author={Desai, Arjun D and Ozturkler, Batu M and Sandino, Christopher M and Vasanawala, Shreyas and Hargreaves, Brian A and Re, Christopher M and Pauly, John M and Chaudhari, Akshay S},
  journal={arXiv preprint arXiv:2110.00075},
  year={2021}
}
Owner
Arjun Desai
Arjun Desai
PyTorch implementation of paper "StarEnhancer: Learning Real-Time and Style-Aware Image Enhancement" (ICCV 2021 Oral)

StarEnhancer StarEnhancer: Learning Real-Time and Style-Aware Image Enhancement (ICCV 2021 Oral) Abstract: Image enhancement is a subjective process w

IDKiro 133 Dec 28, 2022
DziriBERT: a Pre-trained Language Model for the Algerian Dialect

DziriBERT DziriBERT is the first Transformer-based Language Model that has been pre-trained specifically for the Algerian Dialect. It handles Algerian

117 Jan 07, 2023
Hcaptcha-challenger - Gracefully face hCaptcha challenge with Yolov5(ONNX) embedded solution

hCaptcha Challenger 🚀 Gracefully face hCaptcha challenge with Yolov5(ONNX) embe

593 Jan 03, 2023
Baleen: Robust Multi-Hop Reasoning at Scale via Condensed Retrieval (NeurIPS'21)

Baleen Baleen is a state-of-the-art model for multi-hop reasoning, enabling scalable multi-hop search over massive collections for knowledge-intensive

Stanford Future Data Systems 22 Dec 05, 2022
This is a model made out of Neural Network specifically a Convolutional Neural Network model

This is a model made out of Neural Network specifically a Convolutional Neural Network model. This was done with a pre-built dataset from the tensorflow and keras packages. There are other alternativ

9 Oct 18, 2022
Asterisk is a framework to generate high-quality training datasets at scale

Asterisk is a framework to generate high-quality training datasets at scale

Mona Nashaat 44 Apr 25, 2022
Space robot - (Course Project) Using the space robot to capture the target satellite that is disabled and spinning, then stabilize and fix it up

Space robot - (Course Project) Using the space robot to capture the target satellite that is disabled and spinning, then stabilize and fix it up

Mingrui Yu 3 Jan 07, 2022
This is the code of "Multi-view Contrastive Graph Clustering" in NeurlPS 2021.

MCGC Description This is the code of "Multi-view Contrastive Graph Clustering" in NeurlPS 2021. Datasets Results ACM DBLP IMDB Amazon photos Amazon co

31 Nov 14, 2022
Caffe-like explicit model constructor. C(onfig)Model

cmodel Caffe-like explicit model constructor. C(onfig)Model Installation pip install git+https://github.com/bonlime/cmodel Usage In order to allow usi

1 Feb 18, 2022
Create time-series datacubes for supervised machine learning with ICEYE SAR images.

ICEcube is a Python library intended to help organize SAR images and annotations for supervised machine learning applications. The library generates m

ICEYE Ltd 65 Jan 03, 2023
Accuracy Aligned. Concise Implementation of Swin Transformer

Accuracy Aligned. Concise Implementation of Swin Transformer This repository contains the implementation of Swin Transformer, and the training codes o

FengWang 77 Dec 16, 2022
A geometric deep learning pipeline for predicting protein interface contacts.

A geometric deep learning pipeline for predicting protein interface contacts.

44 Dec 30, 2022
"Learning Free Gait Transition for Quadruped Robots vis Phase-Guided Controller"

PhaseGuidedControl The current version is developed based on the old version of RaiSim series, and possibly requires further modification. It will be

X-Mechanics 12 Oct 21, 2022
An open source app to help calm you down when needed.

By: Seanpm2001, Et; Al. Top README.md Read this article in a different language Sorted by: A-Z Sorting options unavailable ( af Afrikaans Afrikaans |

Sean P. Myrick V19.1.7.2 2 Oct 24, 2022
Official Implementation of DE-DETR and DELA-DETR in "Towards Data-Efficient Detection Transformers"

DE-DETRs By Wen Wang, Jing Zhang, Yang Cao, Yongliang Shen, and Dacheng Tao This repository is an official implementation of DE-DETR and DELA-DETR in

Wen Wang 61 Dec 12, 2022
Code for ViTAS_Vision Transformer Architecture Search

Vision Transformer Architecture Search This repository open source the code for ViTAS: Vision Transformer Architecture Search. ViTAS aims to search fo

46 Dec 17, 2022
ST++: Make Self-training Work Better for Semi-supervised Semantic Segmentation

ST++ This is the official PyTorch implementation of our paper: ST++: Make Self-training Work Better for Semi-supervised Semantic Segmentation. Lihe Ya

Lihe Yang 147 Jan 03, 2023
Robust Lane Detection via Expanded Self Attention (WACV 2022)

Robust Lane Detection via Expanded Self Attention (WACV 2022) Minhyeok Lee, Junhyeop Lee, Dogyoon Lee, Woojin Kim, Sangwon Hwang, Sangyoun Lee Overvie

Min Hyeok Lee 18 Nov 12, 2022
Deep learning model for EEG artifact removal

DeepSeparator Introduction Electroencephalogram (EEG) recordings are often contaminated with artifacts. Various methods have been developed to elimina

23 Dec 21, 2022
Hippocampal segmentation using the UNet network for each axis

Hipposeg Hippocampal segmentation using the UNet network for each axis, inspired by https://github.com/MICLab-Unicamp/e2dhipseg Red: False Positive Gr

Juan Carlos Aguirre Arango 0 Sep 02, 2021