This code is for our paper "VTGAN: Semi-supervised Retinal Image Synthesis and Disease Prediction using Vision Transformers"

Overview

ICCV Workshop 2021 VTGAN

PWC

This code is for our paper "VTGAN: Semi-supervised Retinal Image Synthesis and Disease Prediction using Vision Transformers" which is part of the supplementary materials for ICCV 2021 Workshop on Computer Vision for Automated Medical Diagnosis. The paper has since been accpeted and presented at ICCV 2021 Workshop.

Arxiv Pre-print

https://arxiv.org/abs/2104.06757

CVF ICCVW 2021

https://openaccess.thecvf.com/content/ICCV2021W/CVAMD/html/Kamran_VTGAN_Semi-Supervised_Retinal_Image_Synthesis_and_Disease_Prediction_Using_Vision_ICCVW_2021_paper.html

IEE Xplore ICCVW 2021

https://ieeexplore.ieee.org/document/9607858

Citation

@INPROCEEDINGS{9607858,
  author={Kamran, Sharif Amit and Hossain, Khondker Fariha and Tavakkoli, Alireza and Zuckerbrod, Stewart Lee and Baker, Salah A.},
  booktitle={2021 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW)}, 
  title={VTGAN: Semi-supervised Retinal Image Synthesis and Disease Prediction using Vision Transformers}, 
  year={2021},
  volume={},
  number={},
  pages={3228-3238},
  doi={10.1109/ICCVW54120.2021.00362}
}

Pre-requisite

  • Ubuntu 18.04 / Windows 7 or later
  • NVIDIA Graphics card

Installation Instruction for Ubuntu

sudo add-apt-repository ppa:deadsnakes/ppa
sudo apt install python3.7
  • Install Tensorflow-Gpu version-2.5.0 and Keras version-2.5.0
sudo pip3 install tensorflow-gpu
sudo pip3 install keras
  • Install packages from requirements.txt
sudo pip3 install -r requirements.txt

Dataset download link for Hajeb et al.

https://sites.google.com/site/hosseinrabbanikhorasgani/datasets-1/fundus-fluorescein-angiogram-photographs--colour-fundus-images-of-diabetic-patients
  • Please cite the paper if you use their data
@article{hajeb2012diabetic,
  title={Diabetic retinopathy grading by digital curvelet transform},
  author={Hajeb Mohammad Alipour, Shirin and Rabbani, Hossein and Akhlaghi, Mohammad Reza},
  journal={Computational and mathematical methods in medicine},
  volume={2012},
  year={2012},
  publisher={Hindawi}
}
  • Folder structure for data-preprocessing given below. Please make sure it matches with your local repository.
├── Dataset
|   ├──ABNORMAL
|   ├──NORMAL

Dataset Pre-processing

  • Type this in terminal to run the random_crop.py file
python3 random_crop.py --output_dir=data --input_dim=512 --datadir=Dataset
  • There are different flags to choose from. Not all of them are mandatory.
    '--input_dim', type=int, default=512
    '--n_crops', type=int, default=50
    '--datadir', type=str, required=True, help='path/to/data_directory',default='Dataset'
    '--output_dir', type=str, default='data'   

NPZ file conversion

  • Convert all the images to npz format
python3 convert_npz.py --outfile_name=vtgan --input_dim=512 --datadir=data --n_crops=50
  • There are different flags to choose from. Not all of them are mandatory.
    '--input_dim', type=int, default=512
    '--n_crops', type=int, default=50
    '--datadir', type=str, required=True, help='path/to/data_directory',default='data'
    '--outfile_name', type=str, default='vtgan'
    '--n_images', type=int, default=17

Training

  • Type this in terminal to run the train.py file
python3 train.py --npz_file=vtgan --batch=2 --epochs=100 --savedir=VTGAN
  • There are different flags to choose from. Not all of them are mandatory
    '--epochs', type=int, default=100
    '--batch_size', type=int, default=2
    '--npz_file', type=str, default='vtgan', help='path/to/npz/file'
    '--input_dim', type=int, default=512
    '--n_patch', type=int, default=64
    '--savedir', type=str, required=False, help='path/to/save_directory',default='VTGAN'
    '--resume_training', type=str, required=False,  default='no', choices=['yes','no']

License

The code is released under the BSD 3-Clause License, you can read the license file included in the repository for details.

Owner
Sharif Amit Kamran
Interested in Deep learning for Medical Imaging and Computer Vision. Designing robust generative architectures for Ophthalmology and Calcium Imaging.
Sharif Amit Kamran
DeepMind's software stack for physics-based simulation and Reinforcement Learning environments, using MuJoCo.

dm_control: DeepMind Infrastructure for Physics-Based Simulation. DeepMind's software stack for physics-based simulation and Reinforcement Learning en

DeepMind 3k Dec 31, 2022
A Model for Natural Language Attack on Text Classification and Inference

TextFooler A Model for Natural Language Attack on Text Classification and Inference This is the source code for the paper: Jin, Di, et al. "Is BERT Re

Di Jin 418 Dec 16, 2022
Binary Stochastic Neurons in PyTorch

Binary Stochastic Neurons in PyTorch http://r2rt.com/binary-stochastic-neurons-in-tensorflow.html https://github.com/pytorch/examples/tree/master/mnis

Onur Kaplan 54 Nov 21, 2022
Reproduction process of AlexNet

PaddlePaddle论文复现杂谈 背景 注:该repo基于PaddlePaddle,对AlexNet进行复现。时间仓促,难免有所疏漏,如果问题或者想法,欢迎随时提issue一块交流。 飞桨论文复现赛地址:https://aistudio.baidu.com/aistudio/competitio

19 Nov 29, 2022
TART - A PyTorch implementation for Transition Matrix Representation of Trees with Transposed Convolutions

TART This project is a PyTorch implementation for Transition Matrix Representati

Lee Sael 2 Jan 19, 2022
"Projelerle Yapay Zeka Ve Bilgisayarlı Görü" Kitabımın projeleri

"Projelerle Yapay Zeka Ve Bilgisayarlı Görü" Kitabımın projeleri Bu Github Reposundaki tüm projeler; kaleme almış olduğum "Projelerle Yapay Zekâ ve Bi

Ümit Aksoylu 4 Aug 03, 2022
OOD Dataset Curator and Benchmark for AI-aided Drug Discovery

🔥 DrugOOD 🔥 : OOD Dataset Curator and Benchmark for AI Aided Drug Discovery This is the official implementation of the DrugOOD project, this is the

108 Dec 17, 2022
Predicting Student Attentiveness using OpenCV

Predicting-Student-Attentiveness-using-OpenCV The model will predict if a student is attentive or not through facial parameter received through the st

Johann Pinto 2 Aug 20, 2022
A simple rest api serving a deep learning model that classifies human gender based on their faces. (vgg16 transfare learning)

this is a simple rest api serving a deep learning model that classifies human gender based on their faces. (vgg16 transfare learning)

crispengari 5 Dec 09, 2021
Implementation for "Exploiting Aliasing for Manga Restoration" (CVPR 2021)

[CVPR Paper](To appear) | [Project Website](To appear) | BibTex Introduction As a popular entertainment art form, manga enriches the line drawings det

133 Dec 15, 2022
DatasetGAN: Efficient Labeled Data Factory with Minimal Human Effort

DatasetGAN This is the official code and data release for: DatasetGAN: Efficient Labeled Data Factory with Minimal Human Effort Yuxuan Zhang*, Huan Li

302 Jan 05, 2023
Open source code for Paper "A Co-Interactive Transformer for Joint Slot Filling and Intent Detection"

A Co-Interactive Transformer for Joint Slot Filling and Intent Detection This repository contains the PyTorch implementation of the paper: A Co-Intera

67 Dec 05, 2022
[CVPRW 2021] Code for Region-Adaptive Deformable Network for Image Quality Assessment

RADN [CVPRW 2021] Code for Region-Adaptive Deformable Network for Image Quality Assessment [Paper on arXiv] Overview Update [2021/5/7] add codes for W

IIGROUP 53 Dec 28, 2022
Data for "Driving the Herd: Search Engines as Content Influencers" paper

herding_data Data for "Driving the Herd: Search Engines as Content Influencers" paper Dataset description The collection contains 2250 documents, 30 i

0 Aug 17, 2021
Official Pytorch implementation of "CLIPstyler:Image Style Transfer with a Single Text Condition"

CLIPstyler Official Pytorch implementation of "CLIPstyler:Image Style Transfer with a Single Text Condition" Environment Pytorch 1.7.1, Python 3.6 $ c

203 Dec 30, 2022
Ipython notebook presentations for getting starting with basic programming, statistics and machine learning techniques

Data Science 45-min Intros Every week*, our data science team @Gnip (aka @TwitterBoulder) gets together for about 50 minutes to learn something. While

Scott Hendrickson 1.6k Dec 31, 2022
Cross-modal Deep Face Normals with Deactivable Skip Connections

Cross-modal Deep Face Normals with Deactivable Skip Connections Victoria Fernández Abrevaya*, Adnane Boukhayma*, Philip H. S. Torr, Edmond Boyer (*Equ

72 Nov 27, 2022
A Lightweight Experiment & Resource Monitoring Tool 📺

Lightweight Experiment & Resource Monitoring 📺 "Did I already run this experiment before? How many resources are currently available on my cluster?"

170 Dec 28, 2022
COCO Style Dataset Generator GUI

A simple GUI-based COCO-style JSON Polygon masks' annotation tool to facilitate quick and efficient crowd-sourced generation of annotation masks and bounding boxes. Optionally, one could choose to us

Hans Krupakar 142 Dec 09, 2022
An implementation of shampoo

shampoo.pytorch An implementation of shampoo, proposed in Shampoo : Preconditioned Stochastic Tensor Optimization by Vineet Gupta, Tomer Koren and Yor

Ryuichiro Hataya 69 Sep 10, 2022