This is the winning solution of the Endocv-2021 grand challange.

Related tags

Deep Learningdivergent-nets
Overview

Endocv2021-winner

[Paper]

This is the winning solution of the Endocv-2021 grand challange.

Dependencies

pytorch # tested with 1.7 and 1.8
torchvision 
tqdm
pandas
numpy
albumentations # for augmentations
torchsummary
segmentation_models_pytorch # for basic segmentaion models
pyra_pytorch # pyra_pytorch.PYRADatasetFromDF is used. But this can be replaced with normal pytorch dataset.

Tri-Unet

Block diagram of Tri-Unet

TriUnet

How to train Tri-Unet and other basic models to DivergentNet?

# To train Tri-unet

python tri_unet.py train \
    --num_epochs 2 \
    --device_id 0  \
    --train_CSVs sample_CSV_files/C1.csv sample_CSV_files/C1.csv \
    --val_CSVs sample_CSV_files/C2.csv sample_CSV_files/C3.csv \
    --test_CSVs sample_CSV_files/C3.csv \
    --out_dir ../temp_data \
    --tensorboard_dir ../temp_data  

# To train other models, you have to replace tri_unet.py with one of the follwings:
unet_plusplus.py
deeplabv3.py
deeplabv3_plusplus.py

Pretrained checkpoint paths

DivergentNet

DivergentNet

Merging and predicting from divergent networks

Set following parameters in inference_from_divergentNets.sh

--input_dir <directory to input images>
--output_dir <directory to save predicted mask>
--chk_paths <path to pretrained checkpoints. You can provide single checkpoint path or multiple checkpoint paths. Use a space to seperate multiple checkpoint paths or '\' as the given example paths.>

Then run it:

bash inference_from_divergentNets.sh

For Windows users we provide an inference script that supports windows. You can run it without the bash. For example:

python inference_from_divergentNets.py --input_dir C:\Users\xxx\GitHub\divergent-nets\input --output_dir C:\Users\xxx\GitHub\divergent-nets\output --chk_paths C:\Users\xxx\OneDrive\Dokumente\GitHub\divergent-nets\checkpoints\best_checkpoint_Deeplabv3.pth

Sample predictions from different models used in DivergentNets and it's own output.

predictions

Citation

@inproceedings{divergentNets,
  title={DivergentNets: Medical Image Segmentation by Network Ensemble},
  author={Thambawita, Vajira and Hicks, Steven A. and Halvorsen, P{\aa}l and Riegler, Michael A.},
  booktitle={Proceedings of the 3rd International Workshop and Challenge on Computer Vision in Endoscopy (EndoCV 2021)
co-located with with the 17th IEEE International Symposium on Biomedical Imaging (ISBI 2021)},
  year={2021}
}

Contact us:

[email protected], [email protected], [email protected]

You might also like...
2nd solution of ICDAR 2021 Competition on Scientific Literature Parsing, Task B.
2nd solution of ICDAR 2021 Competition on Scientific Literature Parsing, Task B.

TableMASTER-mmocr Contents About The Project Method Description Dependency Getting Started Prerequisites Installation Usage Data preprocess Train Infe

Jianquan Ye 298 Dec 21, 2022
1st Solution For ICDAR 2021 Competition on Mathematical Formula Detection
1st Solution For ICDAR 2021 Competition on Mathematical Formula Detection

This project releases our 1st place solution on ICDAR 2021 Competition on Mathematical Formula Detection. We implement our solution based on MMDetection, which is an open source object detection toolbox based on PyTorch.

yuxzho 94 Dec 25, 2022
4th place solution for the SIGIR 2021 challenge.

SIGIR-2021 (Tinkoff.AI) How to start Download train and test data: https://sigir-ecom.github.io/data-task.html Place it under sigir-2021/data/. Run py

Tinkoff.AI 4 Jul 1, 2022
Meli Data Challenge 2021 - First Place Solution
Meli Data Challenge 2021 - First Place Solution

My solution for the Meli Data Challenge 2021

Matias Moreyra 23 Mar 9, 2022
Codebase for the solution that won first place and was awarded the most human-like agent in the 2021 NeurIPS Competition MineRL BASALT Challenge.

KAIROS MineRL BASALT Codebase for the solution that won first place and was awarded the most human-like agent in the 2021 NeurIPS Competition MineRL B

Vinicius G. Goecks 37 Oct 30, 2022
1st Solution For NeurIPS 2021 Competition on ML4CO Dual Task

KIDA: Knowledge Inheritance in Data Aggregation This project releases our 1st place solution on NeurIPS2021 ML4CO Dual Task. Slide and model weights a

MEGVII Research 24 Sep 8, 2022
NeuroFind - A solution to the to the Task given by the Oberseminar of Messtechnik Institute of TU Dresden in 2021

NeuroFind A solution to the to the Task given by the Oberseminar of Messtechnik

null 1 Jan 20, 2022
1st place solution in CCF BDCI 2021 ULSEG 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 (

Chenxu Peng 30 Nov 22, 2022
Kaggle Lyft Motion Prediction for Autonomous Vehicles 4th place solution

Lyft Motion Prediction for Autonomous Vehicles Code for the 4th place solution of Lyft Motion Prediction for Autonomous Vehicles on Kaggle. Discussion

null 44 Jun 27, 2022
Owner
Vajira Thambawita
I am a Ph.D. candidate at SimulaMet, Oslo, Norway, researching machine learning in medicine.
Vajira Thambawita
GitHub Repository
This was initially the repo for the project of [email protected] of Asaf Mazar, Millad Kassaie and Georgios Chochlakis named "Powered by the Will? Exploring Lay Theories of Behavior Change through Social Media"

Subreddit Analysis This repo includes tools for Subreddit analysis, originally developed for our class project of PSYC 626 in USC, titled "Powered by

Georgios Chochlakis 1 Dec 17, 2021
MiraiML: asynchronous, autonomous and continuous Machine Learning in Python

MiraiML Mirai: future in japanese. MiraiML is an asynchronous engine for continuous & autonomous machine learning, built for real-time usage. Usage In

Arthur Paulino 25 Jul 27, 2022
Api for getting bin info and getting encrypted card details for adyen.

Bin Info And Adyen Cse Enc Python api for getting bin info and getting encrypted

Roldex Stark 8 Dec 30, 2022
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

Optimization for AI 176 Jan 07, 2023
Parameterized Explainer for Graph Neural Network

PGExplainer This is a Tensorflow implementation of the paper: Parameterized Explainer for Graph Neural Network https://arxiv.org/abs/2011.04573 NeurIP

Dongsheng Luo 89 Dec 12, 2022
Gesture Volume Control Using OpenCV and MediaPipe

This Project Uses OpenCV and MediaPipe Hand solutions to identify hands and Change system volume by taking thumb and index finger positions

Pratham Bhatnagar 6 Sep 12, 2022
basic tutorial on pytorch

Quick Tutorial on PyTorch PyTorch Basics Linear Regression Logistic Regression Artificial Neural Networks Convolutional Neural Networks Recurrent Neur

7 Sep 15, 2022
Cobalt Strike teamserver detection.

Cobalt-Strike-det Cobalt Strike teamserver detection. usage: cobaltstrike_verify.py [-l TARGETS] [-t THREADS] optional arguments: -h, --help show this

TimWhite 17 Sep 27, 2022
Posterior predictive distributions quantify uncertainties ignored by point estimates.

Posterior predictive distributions quantify uncertainties ignored by point estimates.

DeepMind 177 Dec 06, 2022
TorchIO is a Medical image preprocessing and augmentation toolkit for deep learning. Part of the PyTorch Ecosystem.

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

Fernando Pérez-García 1.6k Jan 06, 2023
This is a repository with the code for the ACL 2019 paper

The Story of Heads This is the official repo for the following papers: (ACL 2019) Analyzing Multi-Head Self-Attention: Specialized Heads Do the Heavy

231 Nov 15, 2022
[ICCV2021] Safety-aware Motion Prediction with Unseen Vehicles for Autonomous Driving

Safety-aware Motion Prediction with Unseen Vehicles for Autonomous Driving Safety-aware Motion Prediction with Unseen Vehicles for Autonomous Driving

Xuanchi Ren 44 Dec 03, 2022
PyTorch implementation of Barlow Twins.

Barlow Twins: Self-Supervised Learning via Redundancy Reduction PyTorch implementation of Barlow Twins. @article{zbontar2021barlow, title={Barlow Tw

Facebook Research 839 Dec 29, 2022
PyTorch code for our paper "Image Super-Resolution with Non-Local Sparse Attention" (CVPR2021).

Image Super-Resolution with Non-Local Sparse Attention This repository is for NLSN introduced in the following paper "Image Super-Resolution with Non-

143 Dec 28, 2022
Our CIKM21 Paper "Incorporating Query Reformulating Behavior into Web Search Evaluation"

Reformulation-Aware-Metrics Introduction This codebase contains source-code of the Python-based implementation of our CIKM 2021 paper. Chen, Jia, et a

xuanyuan14 5 Mar 05, 2022
Kaggle-titanic - A tutorial for Kaggle's Titanic: Machine Learning from Disaster competition. Demonstrates basic data munging, analysis, and visualization techniques. Shows examples of supervised machine learning techniques.

Kaggle-titanic This is a tutorial in an IPython Notebook for the Kaggle competition, Titanic Machine Learning From Disaster. The goal of this reposito

Andrew Conti 800 Dec 15, 2022
Hitters Linear Regression - Hitters Linear Regression With Python

Hitters_Linear_Regression Kullanacağımız veri seti Carnegie Mellon Üniversitesi'

AyseBuyukcelik 2 Jan 26, 2022
Awesome Graph Classification - A collection of important graph embedding, classification and representation learning papers with implementations.

A collection of graph classification methods, covering embedding, deep learning, graph kernel and factorization papers

Benedek Rozemberczki 4.5k Jan 01, 2023
SiT: Self-supervised vIsion Transformer

This repository contains the official PyTorch self-supervised pretraining, finetuning, and evaluation codes for SiT (Self-supervised image Transformer).

Sara Ahmed 275 Dec 28, 2022
Official code release for ICCV 2021 paper SNARF: Differentiable Forward Skinning for Animating Non-rigid Neural Implicit Shapes.

Official code release for ICCV 2021 paper SNARF: Differentiable Forward Skinning for Animating Non-rigid Neural Implicit Shapes.

235 Dec 26, 2022