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
Implementation of Rotary Embeddings, from the Roformer paper, in Pytorch

Rotary Embeddings - Pytorch A standalone library for adding rotary embeddings to transformers in Pytorch, following its success as relative positional

Phil Wang 110 Dec 30, 2022
Type4Py: Deep Similarity Learning-Based Type Inference for Python

Type4Py: Deep Similarity Learning-Based Type Inference for Python This repository contains the implementation of Type4Py and instructions for re-produ

Software Analytics Lab 45 Dec 15, 2022
Source code for From Stars to Subgraphs

GNNAsKernel Official code for From Stars to Subgraphs: Uplifting Any GNN with Local Structure Awareness Visualizations GNN-AK(+) GNN-AK(+) with Subgra

44 Dec 19, 2022
Unsupervised Real-World Super-Resolution: A Domain Adaptation Perspective

Unofficial pytorch implementation of the paper "Unsupervised Real-World Super-Resolution: A Domain Adaptation Perspective"

16 Nov 21, 2022
code for "Feature Importance-aware Transferable Adversarial Attacks"

Feature Importance-aware Attack(FIA) This repository contains the code for the paper: Feature Importance-aware Transferable Adversarial Attacks (ICCV

Hengchang Guo 44 Nov 24, 2022
Karate Club: An API Oriented Open-source Python Framework for Unsupervised Learning on Graphs (CIKM 2020)

Karate Club is an unsupervised machine learning extension library for NetworkX. Please look at the Documentation, relevant Paper, Promo Video, and Ext

Benedek Rozemberczki 1.8k Jan 07, 2023
PyTorch implementation of our CVPR2021 (oral) paper "Prototype Augmentation and Self-Supervision for Incremental Learning"

PASS - Official PyTorch Implementation [CVPR2021 Oral] Prototype Augmentation and Self-Supervision for Incremental Learning Fei Zhu, Xu-Yao Zhang, Chu

67 Dec 27, 2022
Face Mask Detection System built with OpenCV, TensorFlow using Computer Vision concepts

Face mask detection Face Mask Detection System built with OpenCV, TensorFlow using Computer Vision concepts in order to detect face masks in static im

Vaibhav Shukla 1 Oct 27, 2021
This project helps to colorize grayscale images using multiple exemplars.

Multiple Exemplar-based Deep Colorization (Pytorch Implementation) Pretrained Model [Jitendra Chautharia](IIT Jodhpur)1,3, Prerequisites Python 3.6+ N

jitendra chautharia 3 Aug 05, 2022
A minimalist implementation of score-based diffusion model

sdeflow-light This is a minimalist codebase for training score-based diffusion models (supporting MNIST and CIFAR-10) used in the following paper "A V

Chin-Wei Huang 89 Dec 20, 2022
SMD-Nets: Stereo Mixture Density Networks

SMD-Nets: Stereo Mixture Density Networks This repository contains a Pytorch implementation of "SMD-Nets: Stereo Mixture Density Networks" (CVPR 2021)

Fabio Tosi 115 Dec 26, 2022
A multi-entity Transformer for multi-agent spatiotemporal modeling.

baller2vec This is the repository for the paper: Michael A. Alcorn and Anh Nguyen. baller2vec: A Multi-Entity Transformer For Multi-Agent Spatiotempor

Michael A. Alcorn 56 Nov 15, 2022
Hyperbolic Procrustes Analysis Using Riemannian Geometry

Hyperbolic Procrustes Analysis Using Riemannian Geometry The code in this repository creates the figures presented in this article: Please notice that

Ronen Talmon's Lab 2 Jan 08, 2023
Informer: Beyond Efficient Transformer for Long Sequence Time-Series Forecasting

Informer: Beyond Efficient Transformer for Long Sequence Time-Series Forecasting This is the origin Pytorch implementation of Informer in the followin

Haoyi 3.1k Dec 29, 2022
Let's Git - Versionsverwaltung & Open Source Hausaufgabe

Let's Git - Versionsverwaltung & Open Source Hausaufgabe Herzlich Willkommen zu dieser Hausaufgabe für unseren MOOC: Let's Git! Wir hoffen, dass Du vi

1 Dec 13, 2021
Image segmentation with private İstanbul Dataset

Image Segmentation This repo was created for academic research and test result. Repo will update after academic article online. This repo contains wei

İrem KÖMÜRCÜ 9 Dec 11, 2022
Distance Encoding for GNN Design

Distance-encoding for GNN design This repository is the official PyTorch implementation of the DEGNN and DEAGNN framework reported in the paper: Dista

172 Nov 08, 2022
Model Agnostic Interpretability for Multiple Instance Learning

MIL Model Agnostic Interpretability This repo contains the code for "Model Agnostic Interpretability for Multiple Instance Learning". Overview Executa

Joe Early 10 Dec 17, 2022
Beyond imagenet attack (accepted by ICLR 2022) towards crafting adversarial examples for black-box domains.

Beyond ImageNet Attack: Towards Crafting Adversarial Examples for Black-box Domains (ICLR'2022) This is the Pytorch code for our paper Beyond ImageNet

Alibaba-AAIG 37 Nov 23, 2022
Neural Surface Maps

Neural Surface Maps Official implementation of Neural Surface Maps - Luca Morreale, Noam Aigerman, Vladimir Kim, Niloy J. Mitra [Paper] [Project Page]

Luca Morreale 49 Dec 13, 2022