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
这是一个yolox-pytorch的源码，可以用于训练自己的模型。

YOLOX：You Only Look Once目标检测模型在Pytorch当中的实现 目录 性能情况 Performance 实现的内容 Achievement 所需环境 Environment 小技巧的设置 TricksSet 文件下载 Download 训练步骤 How2train 预测步骤

Bubbliiiing 613 Jan 05, 2023
Raster Vision is an open source Python framework for building computer vision models on satellite, aerial, and other large imagery sets

Raster Vision is an open source Python framework for building computer vision models on satellite, aerial, and other large imagery sets (including obl

Azavea 1.7k Dec 22, 2022
An Inverse Kinematics library aiming performance and modularity

IKPy Demo Live demos of what IKPy can do (click on the image below to see the video): Also, a presentation of IKPy: Presentation. Features With IKPy,

Pierre Manceron 481 Jan 02, 2023
For encoding a text longer than 512 tokens, for example 800. Set max_pos to 800 during both preprocessing and training.

LongScientificFormer For encoding a text longer than 512 tokens, for example 800. Set max_pos to 800 during both preprocessing and training. Some code

Athar Sefid 6 Nov 02, 2022
CTRL-C: Camera calibration TRansformer with Line-Classification

CTRL-C: Camera calibration TRansformer with Line-Classification This repository contains the official code and pretrained models for CTRL-C (Camera ca

57 Nov 14, 2022
Reference implementation of code generation projects from Facebook AI Research. General toolkit to apply machine learning to code, from dataset creation to model training and evaluation. Comes with pretrained models.

This repository is a toolkit to do machine learning for programming languages. It implements tokenization, dataset preprocessing, model training and m

Facebook Research 408 Jan 01, 2023
Tensorflow implementation of "BEGAN: Boundary Equilibrium Generative Adversarial Networks"

BEGAN in Tensorflow Tensorflow implementation of BEGAN: Boundary Equilibrium Generative Adversarial Networks. Requirements Python 2.7 or 3.x Pillow tq

Taehoon Kim 922 Dec 21, 2022
Public repository created to store my custom-made tools for Just Dance (UbiArt Engine)

Woody's Just Dance Tools Public repository created to store my custom-made tools for Just Dance (UbiArt Engine) Development and updates Almost all of

Wodson de Andrade 8 Dec 24, 2022
PyTorch implementation of MulMON

MulMON This repository contains a PyTorch implementation of the paper: Learning Object-Centric Representations of Multi-object Scenes from Multiple Vi

NanboLi 16 Nov 03, 2022
PatchMatch-RL: Deep MVS with Pixelwise Depth, Normal, and Visibility

PatchMatch-RL: Deep MVS with Pixelwise Depth, Normal, and Visibility Jae Yong Lee, Joseph DeGol, Chuhang Zou, Derek Hoiem Installation To install nece

31 Apr 19, 2022
The VeriNet toolkit for verification of neural networks

VeriNet The VeriNet toolkit is a state-of-the-art sound and complete symbolic interval propagation based toolkit for verification of neural networks.

9 Dec 21, 2022
Source codes for the paper "Local Additivity Based Data Augmentation for Semi-supervised NER"

LADA This repo contains codes for the following paper: Jiaao Chen*, Zhenghui Wang*, Ran Tian, Zichao Yang, Diyi Yang: Local Additivity Based Data Augm

GT-SALT 36 Dec 02, 2022
DeLiGAN - This project is an implementation of the Generative Adversarial Network

This project is an implementation of the Generative Adversarial Network proposed in our CVPR 2017 paper - DeLiGAN : Generative Adversarial Net

Video Analytics Lab -- IISc 110 Sep 13, 2022
Styled Augmented Translation

SAT Style Augmented Translation Introduction By collecting high-quality data, we were able to train a model that outperforms Google Translate on 6 dif

139 Dec 29, 2022
Integrated Semantic and Phonetic Post-correction for Chinese Speech Recognition

Integrated Semantic and Phonetic Post-correction for Chinese Speech Recognition | paper | dataset | pretrained detection model | Authors: Yi-Chang Che

Yi-Chang Chen 1 Aug 23, 2022
A demo of how to use JAX to create a simple gravity simulation

JAX Gravity This repo contains a demo of how to use JAX to create a simple gravity simulation. It uses JAX's experimental ode package to solve the dif

Cristian Garcia 16 Sep 22, 2022
BisQue is a web-based platform designed to provide researchers with organizational and quantitative analysis tools for 5D image data. Users can extend BisQue by implementing containerized ML workflows.

Overview BisQue is a web-based platform specifically designed to provide researchers with organizational and quantitative analysis tools for up to 5D

Vision Research Lab @ UCSB 26 Nov 29, 2022
Deep Learning and Logical Reasoning from Data and Knowledge

Logic Tensor Networks (LTN) Logic Tensor Network (LTN) is a neurosymbolic framework that supports querying, learning and reasoning with both rich data

171 Dec 29, 2022
JupyterLite demo deployed to GitHub Pages 🚀

JupyterLite Demo JupyterLite deployed as a static site to GitHub Pages, for demo purposes. ✨ Try it in your browser ✨ ➡️ https://jupyterlite.github.io

JupyterLite 223 Jan 04, 2023
Scale-aware Automatic Augmentation for Object Detection (CVPR 2021)

SA-AutoAug Scale-aware Automatic Augmentation for Object Detection Yukang Chen, Yanwei Li, Tao Kong, Lu Qi, Ruihang Chu, Lei Li, Jiaya Jia [Paper] [Bi

DV Lab 182 Dec 29, 2022