Implementation detail for paper "Multi-level colonoscopy malignant tissue detection with adversarial CAC-UNet"

Overview

Multi-level-colonoscopy-malignant-tissue-detection-with-adversarial-CAC-UNet Tweet

Implementation detail for our paper "Multi-level colonoscopy malignant tissue detection with adversarial CAC-UNet"

DigestPath 2019

The proposed scheme in this paper achieves the best results in MICCAI DigestPath2019 challenge (https://digestpath2019.grand-challenge.org/Home/) on colonoscopy tissue segmentation and classification task.

Dataset

Description of dataset can be found here: https://digestpath2019.grand-challenge.org/Dataset/

To download the the DigestPath2019 dataset, please sign the DATABASE USE AGREEMENT first at here: https://digestpath2019.grand-challenge.org/Download/

If you have problems about downing the dataset, please contact Prof. Hongsheng Li:[email protected]

Image sample:

Envs

  • Pytorch 1.0
  • Python 3+
  • cuda 9.0+

install

$ pip install -r  requirements.txt

apex : Tools for easy mixed precision and distributed training in Pytorch

$ git clone https://github.com/NVIDIA/apex
$ cd apex
$ pip install -v --no-cache-dir --global-option="--cpp_ext" --global-option="--cuda_ext" ./

Dataset

├── data/
│   ├── tissue-train-neg/     
│   ├── tissue-train-pos-v1/

Preprocessing

$ cd code/
$ python preprocessing.py

Training

$ cd code/
$ python train.py --config_file='config/cac-unet-r50.yaml'

Citation

Please cite this paper in your publications if it helps your research:

@article{zhu2021multi,
  title={Multi-level colonoscopy malignant tissue detection with adversarial CAC-UNet},
  author={Zhu, Chuang and Mei, Ke and Peng, Ting and Luo, Yihao and Liu, Jun and Wang, Ying and Jin, Mulan},
  journal={Neurocomputing},
  volume={438},
  pages={165--183},
  year={2021},
  publisher={Elsevier}
}

About the multi-level adversarial segmentation part, you can read our ICASSP paper for more details:

@inproceedings{mei2020cross,
  title={Cross-stained segmentation from renal biopsy images using multi-level adversarial learning},
  author={Mei, Ke and Zhu, Chuang and Jiang, Lei and Liu, Jun and Qiao, Yuanyuan},
  booktitle={ICASSP 2020-2020 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)},
  pages={1424--1428},
  year={2020},
  organization={IEEE}
}

Author

Ke Mei, Ting Peng, Chuang Zhu

If you have any questions, you can contact me directly.

Owner
CVSM Group - email: [email protected]
Codes of our papers are released in this GITHUB account.
CVSM Group - email: <a href=[email protected]">
Code for Mining the Benefits of Two-stage and One-stage HOI Detection

Status: Archive (code is provided as-is, no updates expected) PPO-EWMA [Paper] This is code for training agents using PPO-EWMA and PPG-EWMA, introduce

OpenAI 33 Dec 15, 2022
Christmas face app for Decathlon xmas coding party!

Christmas Face Application Use this library to create the perfect picture for your christmas cards! Done by Hasib Zunair, Guillaume Brassard and Samue

Hasib Zunair 4 Dec 20, 2021
Dist2Dec: A Simplicial Neural Network for Homology Localization

Dist2Dec: A Simplicial Neural Network for Homology Localization

Alexandros Keros 6 Jun 12, 2022
pytorchのスライス代入操作をonnxに変換する際にScatterNDならないようにするサンプル

pytorch_remove_ScatterND pytorchのスライス代入操作をonnxに変換する際にScatterNDならないようにするサンプル。 スライスしたtensorにそのまま代入してしまうとScatterNDになるため、計算結果をcatで新しいtensorにする。 python ver

2 Dec 01, 2022
The Unreasonable Effectiveness of Random Pruning: Return of the Most Naive Baseline for Sparse Training

[ICLR 2022] The Unreasonable Effectiveness of Random Pruning: Return of the Most Naive Baseline for Sparse Training The Unreasonable Effectiveness of

VITA 44 Dec 23, 2022
Annotate datasets with a semi-trained or fully trained YOLOv5 model

YOLOv5 Auto Annotator Annotate datasets with a semi-trained or fully trained YOLOv5 model Prerequisites Ubuntu =20.04 Python =3.7 System dependencie

Akash James 3 May 14, 2022
This repo contains the code and data used in the paper "Wizard of Search Engine: Access to Information Through Conversations with Search Engines"

Wizard of Search Engine: Access to Information Through Conversations with Search Engines by Pengjie Ren, Zhongkun Liu, Xiaomeng Song, Hongtao Tian, Zh

19 Oct 27, 2022
Adaout is a practical and flexible regularization method with high generalization and interpretability

Adaout Adaout is a practical and flexible regularization method with high generalization and interpretability. Requirements python 3.6 (Anaconda versi

lambett 1 Feb 09, 2022
Asterisk is a framework to generate high-quality training datasets at scale

Asterisk is a framework to generate high-quality training datasets at scale

Mona Nashaat 44 Apr 25, 2022
Predictive Modeling on Electronic Health Records(EHR) using Pytorch

Predictive Modeling on Electronic Health Records(EHR) using Pytorch Overview Although there are plenty of repos on vision and NLP models, there are ve

81 Jan 01, 2023
Official implementation for paper Render In-between: Motion Guided Video Synthesis for Action Interpolation

Render In-between: Motion Guided Video Synthesis for Action Interpolation [Paper] [Supp] [arXiv] [4min Video] This is the official Pytorch implementat

8 Oct 27, 2022
Sinkformers: Transformers with Doubly Stochastic Attention

Code for the paper : "Sinkformers: Transformers with Doubly Stochastic Attention" Paper You will find our paper here. Compat This package has been dev

Michael E. Sander 31 Dec 29, 2022
MazeRL is an application oriented Deep Reinforcement Learning (RL) framework

MazeRL is an application oriented Deep Reinforcement Learning (RL) framework, addressing real-world decision problems. Our vision is to cover the complete development life cycle of RL applications ra

EnliteAI GmbH 222 Dec 24, 2022
NEO: Non Equilibrium Sampling on the orbit of a deterministic transform

NEO: Non Equilibrium Sampling on the orbit of a deterministic transform Description of the code This repo describes the NEO estimator described in the

0 Dec 01, 2021
Source code of article "Towards Toxic and Narcotic Medication Detection with Rotated Object Detector"

Towards Toxic and Narcotic Medication Detection with Rotated Object Detector Introduction This is the source code of article: Towards Toxic and Narcot

Woody. Wang 3 Oct 29, 2022
[CVPR 2021] "Multimodal Motion Prediction with Stacked Transformers": official code implementation and project page.

mmTransformer Introduction This repo is official implementation for mmTransformer in pytorch. Currently, the core code of mmTransformer is implemented

DeciForce: Crossroads of Machine Perception and Autonomy 232 Dec 31, 2022
Dynamical movement primitives (DMPs), probabilistic movement primitives (ProMPs), spatially coupled bimanual DMPs.

Movement Primitives Movement primitives are a common group of policy representations in robotics. There are many different types and variations. This

DFKI Robotics Innovation Center 63 Jan 06, 2023
Zsseg.baseline - Zero-Shot Semantic Segmentation

This repo is for our paper A Simple Baseline for Zero-shot Semantic Segmentation

98 Dec 20, 2022
VISSL is FAIR's library of extensible, modular and scalable components for SOTA Self-Supervised Learning with images.

What's New Below we share, in reverse chronological order, the updates and new releases in VISSL. All VISSL releases are available here. [Oct 2021]: V

Meta Research 2.9k Jan 07, 2023
Single Red Blood Cell Hydrodynamic Traps Via the Generative Design

Rbc-traps-generative-design - The generative design for single red clood cell hydrodynamic traps using GEFEST framework

Natural Systems Simulation Lab 4 Jun 16, 2022