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
Attendance Monitoring with Face Recognition using Python

Attendance Monitoring with Face Recognition using Python A python GUI integrated attendance system using face recognition to take attendance. In this

Vaibhav Rajput 2 Jun 21, 2022
Pytorch implementation of forward and inverse Haar Wavelets 2D

Pytorch implementation of forward and inverse Haar Wavelets 2D

Sergei Belousov 9 Oct 30, 2022
An OpenAI-Gym Package for Training and Testing Reinforcement Learning algorithms with OpenSim Models

Authors: Utkarsh A. Mishra and Dr. Dimitar Stanev Advisors: Dr. Dimitar Stanev and Prof. Auke Ijspeert, Biorobotics Laboratory (BioRob), EPFL Video Pl

Utkarsh Mishra 16 Dec 13, 2022
FastyAPI is a Stack boilerplate optimised for heavy loads.

FastyAPI A FastAPI based Stack boilerplate for heavy loads. Explore the docs » View Demo · Report Bug · Request Feature Table of Contents About The Pr

Ali Chaayb 47 Dec 27, 2022
Pop-Out Motion: 3D-Aware Image Deformation via Learning the Shape Laplacian (CVPR 2022)

Pop-Out Motion Pop-Out Motion: 3D-Aware Image Deformation via Learning the Shape Laplacian (CVPR 2022) Jihyun Lee*, Minhyuk Sung*, Hyunjin Kim, Tae-Ky

Jihyun Lee 88 Nov 22, 2022
Knowledgeable Prompt-tuning: Incorporating Knowledge into Prompt Verbalizer for Text Classification

Knowledgeable Prompt-tuning: Incorporating Knowledge into Prompt Verbalizer for Text Classification

DingDing 143 Jan 01, 2023
Official code for "End-to-End Optimization of Scene Layout" -- including VAE, Diff Render, SPADE for colorization (CVPR 2020 Oral)

End-to-End Optimization of Scene Layout Code release for: End-to-End Optimization of Scene Layout CVPR 2020 (Oral) Project site, Bibtex For help conta

Andrew Luo 41 Dec 09, 2022
A scikit-learn compatible neural network library that wraps PyTorch

A scikit-learn compatible neural network library that wraps PyTorch. Resources Documentation Source Code Examples To see more elaborate examples, look

4.9k Jan 03, 2023
This is an official implementation for "DeciWatch: A Simple Baseline for 10x Efficient 2D and 3D Pose Estimation"

DeciWatch: A Simple Baseline for 10× Efficient 2D and 3D Pose Estimation This repo is the official implementation of "DeciWatch: A Simple Baseline for

117 Dec 24, 2022
Training RNNs as Fast as CNNs

News SRU++, a new SRU variant, is released. [tech report] [blog] The experimental code and SRU++ implementation are available on the dev branch which

ASAPP Research 2.1k Jan 01, 2023
Official PyTorch implementation of the paper "Deep Constrained Least Squares for Blind Image Super-Resolution", CVPR 2022.

Deep Constrained Least Squares for Blind Image Super-Resolution [Paper] This is the official implementation of 'Deep Constrained Least Squares for Bli

MEGVII Research 141 Dec 30, 2022
A PoC Corporation Relationship Knowledge Graph System on top of Nebula Graph.

Corp-Rel is a PoC of Corpartion Relationship Knowledge Graph System. It's built on top of the Open Source Graph Database: Nebula Graph with a dataset

Wey Gu 20 Dec 11, 2022
Large-scale Hyperspectral Image Clustering Using Contrastive Learning, CIKM 21 Workshop

Spectral-spatial contrastive clustering (SSCC) Yaoming Cai, Yan Liu, Zijia Zhang, Zhihua Cai, and Xiaobo Liu, Large-scale Hyperspectral Image Clusteri

Yaoming Cai 4 Nov 02, 2022
Code for paper: "Spinning Language Models for Propaganda-As-A-Service"

Spinning Language Models for Propaganda-As-A-Service This is the source code for the Arxiv version of the paper. You can use this Google Colab to expl

Eugene Bagdasaryan 16 Jan 03, 2023
Quadruped-command-tracking-controller - Quadruped command tracking controller (flat terrain)

Quadruped command tracking controller (flat terrain) Prepare Install RAISIM link

Yunho Kim 4 Oct 20, 2022
A tight inclusion function for continuous collision detection

Tight-Inclusion Continuous Collision Detection A conservative Continuous Collision Detection (CCD) method with support for minimum separation. You can

Continuous Collision Detection 89 Jan 01, 2023
ContourletNet: A Generalized Rain Removal Architecture Using Multi-Direction Hierarchical Representation

ContourletNet: A Generalized Rain Removal Architecture Using Multi-Direction Hierarchical Representation (Accepted by BMVC'21) Abstract: Images acquir

10 Dec 08, 2022
Official Pytorch implementation of C3-GAN

Official pytorch implemenation of C3-GAN Contrastive Fine-grained Class Clustering via Generative Adversarial Networks [Paper] Authors: Yunji Kim, Jun

NAVER AI 114 Dec 02, 2022
[SDM 2022] Towards Similarity-Aware Time-Series Classification

SimTSC This is the PyTorch implementation of SDM2022 paper Towards Similarity-Aware Time-Series Classification. We propose Similarity-Aware Time-Serie

Daochen Zha 49 Dec 27, 2022
Deep Semisupervised Multiview Learning With Increasing Views (IEEE TCYB 2021, PyTorch Code)

Deep Semisupervised Multiview Learning With Increasing Views (ISVN, IEEE TCYB) Peng Hu, Xi Peng, Hongyuan Zhu, Liangli Zhen, Jie Lin, Huaibai Yan, Dez

3 Nov 19, 2022