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
Official repository of the paper "GPR1200: A Benchmark for General-PurposeContent-Based Image Retrieval"

GPR1200 Dataset GPR1200: A Benchmark for General-Purpose Content-Based Image Retrieval (ArXiv) Konstantin Schall, Kai Uwe Barthel, Nico Hezel, Klaus J

Visual Computing Group 16 Nov 21, 2022
Instance-conditional Knowledge Distillation for Object Detection

Instance-conditional Knowledge Distillation for Object Detection This is a MegEngine implementation of the paper "Instance-conditional Knowledge Disti

MEGVII Research 47 Nov 17, 2022
YOLTv5 rapidly detects objects in arbitrarily large aerial or satellite images that far exceed the ~600×600 pixel size typically ingested by deep learning object detection frameworks

YOLTv5 rapidly detects objects in arbitrarily large aerial or satellite images that far exceed the ~600×600 pixel size typically ingested by deep learning object detection frameworks.

Adam Van Etten 145 Jan 01, 2023
[ICCV 2021] Encoder-decoder with Multi-level Attention for 3D Human Shape and Pose Estimation

MAED: Encoder-decoder with Multi-level Attention for 3D Human Shape and Pose Estimation Getting Started Our codes are implemented and tested with pyth

ZiNiU WaN 176 Dec 15, 2022
PyTorch implementation of an end-to-end Handwritten Text Recognition (HTR) system based on attention encoder-decoder networks

AttentionHTR PyTorch implementation of an end-to-end Handwritten Text Recognition (HTR) system based on attention encoder-decoder networks. Scene Text

Dmitrijs Kass 31 Dec 22, 2022
Python scripts using the Mediapipe models for Halloween.

Mediapipe-Halloween-Examples Python scripts using the Mediapipe models for Halloween. WHY Mainly for fun. But this repository also includes useful exa

Ibai Gorordo 23 Jan 06, 2023
PyTorch Implementation for "ForkGAN with SIngle Rainy NIght Images: Leveraging the RumiGAN to See into the Rainy Night"

ForkGAN with Single Rainy Night Images: Leveraging the RumiGAN to See into the Rainy Night By Seri Lee, Department of Engineering, Seoul National Univ

Seri Lee 52 Oct 12, 2022
Autonomous racing with the Anki Overdrive

Anki Autonomous Racing Autonomous racing with the Anki Overdrive. Using the Overdrive-Python API (https://github.com/xerodotc/overdrive-python) develo

3 Dec 11, 2022
Ranger deep learning optimizer rewrite to use newest components

Ranger21 - integrating the latest deep learning components into a single optimizer Ranger deep learning optimizer rewrite to use newest components Ran

Less Wright 266 Dec 28, 2022
PyTorch Implement of Context Encoders: Feature Learning by Inpainting

Context Encoders: Feature Learning by Inpainting This is the Pytorch implement of CVPR 2016 paper on Context Encoders 1) Semantic Inpainting Demo Inst

321 Dec 25, 2022
Unleashing Transformers: Parallel Token Prediction with Discrete Absorbing Diffusion for Fast High-Resolution Image Generation from Vector-Quantized Codes

Unleashing Transformers: Parallel Token Prediction with Discrete Absorbing Diffusion for Fast High-Resolution Image Generation from Vector-Quantized C

Sam Bond-Taylor 139 Jan 04, 2023
공공장소에서 눈만 돌리면 CCTV가 보인다는 말이 과언이 아닐 정도로 CCTV가 우리 생활에 깊숙이 자리 잡았습니다.

ObsCare_Main 소개 공공장소에서 눈만 돌리면 CCTV가 보인다는 말이 과언이 아닐 정도로 CCTV가 우리 생활에 깊숙이 자리 잡았습니다. CCTV의 대수가 급격히 늘어나면서 관리와 효율성 문제와 더불어, 곳곳에 설치된 CCTV를 개별 관제하는 것으로는 응급 상

5 Jul 07, 2022
Experiment about Deep Person Re-identification with EfficientNet-v2

We evaluated the baseline with Resnet50 and Efficienet-v2 without using pretrained models. Also Resnet50-IBN-A and Efficientnet-v2 using pretrained on ImageNet. We used two datasets: Market-1501 and

lan.nguyen2k 77 Jan 03, 2023
Streamlit tool to explore coco datasets

What is this This tool given a COCO annotations file and COCO predictions file will let you explore your dataset, visualize results and calculate impo

Jakub Cieslik 75 Dec 16, 2022
Official Keras Implementation for UNet++ in IEEE Transactions on Medical Imaging and DLMIA 2018

UNet++: A Nested U-Net Architecture for Medical Image Segmentation UNet++ is a new general purpose image segmentation architecture for more accurate i

Zongwei Zhou 1.8k Dec 27, 2022
Machine Learning Model deployment for Container (TensorFlow Serving)

try_tf_serving ├───dataset │ ├───testing │ │ ├───paper │ │ ├───rock │ │ └───scissors │ └───training │ ├───paper │ ├───rock

Azhar Rizki Zulma 5 Jan 07, 2022
'Aligned mixture of latent dynamical systems' (amLDS) for stimulus decoding probabilistic manifold alignment across animals. P. Herrero-Vidal et al. NeurIPS 2021 code.

Across-animal odor decoding by probabilistic manifold alignment (NeurIPS 2021) This repository is the official implementation of aligned mixture of la

Pedro Herrero-Vidal 3 Jul 12, 2022
[NeurIPS 2021] A weak-shot object detection approach by transferring semantic similarity and mask prior.

TransMaS This repository is the official pytorch implementation of the following paper: NIPS2021 Mixed Supervised Object Detection by TransferringMask

BCMI 49 Jul 27, 2022
The Unsupervised Reinforcement Learning Benchmark (URLB)

The Unsupervised Reinforcement Learning Benchmark (URLB) URLB provides a set of leading algorithms for unsupervised reinforcement learning where agent

259 Dec 26, 2022
A Pytorch implementation of MoveNet from Google. Include training code and pre-train model.

Movenet.Pytorch Intro MoveNet is an ultra fast and accurate model that detects 17 keypoints of a body. This is A Pytorch implementation of MoveNet fro

Mr.Fire 241 Dec 26, 2022