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
๐Ÿฅ‡ LG-AI-Challenge 2022 1์œ„ ์†”๋ฃจ์…˜ ์ž…๋‹ˆ๋‹ค.

LG-AI-Challenge-for-Plant-Classification Dacon์—์„œ ์ง„ํ–‰๋œ ๋†์—… ํ™˜๊ฒฝ ๋ณ€ํ™”์— ๋”ฐ๋ฅธ ์ž‘๋ฌผ ๋ณ‘ํ•ด ์ง„๋‹จ AI ๊ฒฝ์ง„๋Œ€ํšŒ ์— ๋Œ€ํ•œ ์ฝ”๋“œ์ž…๋‹ˆ๋‹ค. (colab directory์— ์ฝ”๋“œ๊ฐ€ ์ž˜ ์ •๋ฆฌ ๋˜์–ด์žˆ์Šต๋‹ˆ๋‹ค.) Requirements python

siwooyong 10 Jun 30, 2022
PyTorch implementation of our paper: Decoupling and Recoupling Spatiotemporal Representation for RGB-D-based Motion Recognition

Decoupling and Recoupling Spatiotemporal Representation for RGB-D-based Motion Recognition, arxiv This is a PyTorch implementation of our paper. 1. Re

DamoCV 11 Nov 19, 2022
Which Style Makes Me Attractive? Interpretable Control Discovery and Counterfactual Explanation on StyleGAN

Interpretable Control Exploration and Counterfactual Explanation (ICE) on StyleGAN Which Style Makes Me Attractive? Interpretable Control Discovery an

Bo Li 11 Dec 01, 2022
Spatial-Location-Constraint-Prototype-Loss-for-Open-Set-Recognition

Spatial Location Constraint Prototype Loss for Open Set Recognition Official PyTorch implementation of "Spatial Location Constraint Prototype Loss for

Xia Ziheng 12 Jun 24, 2022
Implements a fake news detection program using classifiers.

Fake news detection Implements a fake news detection program using classifiers for Data Mining course at UoA. Description The project is the categoriz

Apostolos Karvelas 1 Jan 09, 2022
3rd place solution for the Weather4cast 2021 Stage 1 Challenge

weather4cast2021_Stage1 3rd place solution for the Weather4cast 2021 Stage 1 Challenge Dependencies The code can be executed from a fresh environment

5 Aug 14, 2022
Code for "Adversarial Training for a Hybrid Approach to Aspect-Based Sentiment Analysis

HAABSAStar Code for "Adversarial Training for a Hybrid Approach to Aspect-Based Sentiment Analysis". This project builds on the code from https://gith

1 Sep 14, 2020
From the basics to slightly more interesting applications of Tensorflow

TensorFlow Tutorials You can find python source code under the python directory, and associated notebooks under notebooks. Source code Description 1 b

Parag K Mital 5.6k Jan 09, 2023
Implicit Graph Neural Networks

Implicit Graph Neural Networks This repository is the official PyTorch implementation of "Implicit Graph Neural Networks". Fangda Gu*, Heng Chang*, We

Heng Chang 48 Nov 29, 2022
AirPose: Multi-View Fusion Network for Aerial 3D Human Pose and Shape Estimation

AirPose AirPose: Multi-View Fusion Network for Aerial 3D Human Pose and Shape Estimation Check the teaser video This repository contains the code of A

Robot Perception Group 41 Dec 05, 2022
PyTorch implementation of Trust Region Policy Optimization

PyTorch implementation of TRPO Try my implementation of PPO (aka newer better variant of TRPO), unless you need to you TRPO for some specific reasons.

Ilya Kostrikov 366 Nov 15, 2022
TensorFlow implementation of "Attention is all you need (Transformer)"

[TensorFlow 2] Attention is all you need (Transformer) TensorFlow implementation of "Attention is all you need (Transformer)" Dataset The MNIST datase

YeongHyeon Park 4 Jan 05, 2022
PSPNet in Chainer

PSPNet This is an unofficial implementation of Pyramid Scene Parsing Network (PSPNet) in Chainer. Training Requirement Python 3.4.4+ Chainer 3.0.0b1+

Shunta Saito 76 Dec 12, 2022
AutoDeeplab / auto-deeplab / AutoML for semantic segmentation, implemented in Pytorch

AutoML for Image Semantic Segmentation Currently this repo contains the only working open-source implementation of Auto-Deeplab which, by the way out-

AI Necromancer 299 Dec 17, 2022
MINOS: Multimodal Indoor Simulator

MINOS Simulator MINOS is a simulator designed to support the development of multisensory models for goal-directed navigation in complex indoor environ

194 Dec 27, 2022
Official code for Spoken ObjectNet: A Bias-Controlled Spoken Caption Dataset

Official code for our Interspeech 2021 - Spoken ObjectNet: A Bias-Controlled Spoken Caption Dataset [1]*. Visually-grounded spoken language datasets c

Ian Palmer 3 Jan 26, 2022
Structured Edge Detection Toolbox

################################################################### # # # Structure

Piotr Dollar 779 Jan 02, 2023
Python scripts form performing stereo depth estimation using the HITNET model in ONNX.

ONNX-HITNET-Stereo-Depth-estimation Python scripts form performing stereo depth estimation using the HITNET model in ONNX. Stereo depth estimation on

Ibai Gorordo 30 Nov 08, 2022
a dnn ai project to classify which food people are eating on audio recordings

Deep Learning - EAT Challenge About This project is part of an AI challenge of the DeepLearning course 2021 at the University of Augsburg. The objecti

Marco Trรถster 1 Oct 24, 2021
GPU-Accelerated Deep Learning Library in Python

Hebel GPU-Accelerated Deep Learning Library in Python Hebel is a library for deep learning with neural networks in Python using GPU acceleration with

Hannes Bretschneider 1.2k Dec 21, 2022