Head and Neck Tumour Segmentation and Prediction of Patient Survival Project

Overview

Head-and-Neck-Tumour-Segmentation-and-Prediction-of-Patient-Survival

Welcome to the Head and Neck Tumour Segmentation and Prediction of Patient Survival Project!

This project aims to provide methods to automatically segment the primary gross target volume on fluoro-deoxyglucose (FDG)-PET and Computed Tomography (CT) images and prediction of progression-free survival in H&N oropharyngeal cancer. We participated to the HEad and neCK TumOR Segmentation and Prediction of Patient Outcome Challenge 2021 (HECKTOR 2021) which creates a platform for comparing segmentation methods and predictions of patient survival.

For the segmentation task, we proposed a new network based on an encoder/decoder architecture with attention mechanisms and full inter- and intra-skip connections and attention mechanisms inspired from UNet3+ to take advantage of low-level and high-level semantics at full scales. Additionally, we used Conditional Random Fields (CRF) as a post-processing step to refine the predicted segmentation maps.

For prediction of patient progression free survival, we extracted relevant clinical, radiomic, and deep learning features using Lasso regression. Our best performing model was a Cox proportional hazard regression.

Installation

  1. Clone the repo
    git clone https://github.com/EmmanuelleB985/Head-and-Neck-Tumour-Segmentation-and-Prediction-of-Patient-Survival.git
  2. Install the packages
    pip install requirements.txt

Usage

  • For segmentation task
   cd src/Segmentation_Task

To train the model

   python main.py
  • For Survival task
   cd src/Survival_Task

To train and evaluate the models, run the notebook Survival.ipynb

License

Distributed under the MIT License. See LICENSE for more information.

PyTorch implementation of Histogram Layers from DeepHist: Differentiable Joint and Color Histogram Layers for Image-to-Image Translation

deep-hist PyTorch implementation of Histogram Layers from DeepHist: Differentiable Joint and Color Histogram Layers for Image-to-Image Translation PyT

Winfried Lötzsch 10 Dec 06, 2022
[CVPR2021] Invertible Image Signal Processing

Invertible Image Signal Processing This repository includes official codes for "Invertible Image Signal Processing (CVPR2021)". Figure: Our framework

Yazhou XING 281 Dec 31, 2022
This is the official code for the paper "Ad2Attack: Adaptive Adversarial Attack for Real-Time UAV Tracking".

Ad^2Attack:Adaptive Adversarial Attack on Real-Time UAV Tracking Demo video 📹 Our video on bilibili demonstrates the test results of Ad^2Attack on se

Intelligent Vision for Robotics in Complex Environment 10 Nov 07, 2022
DenseCLIP: Language-Guided Dense Prediction with Context-Aware Prompting

DenseCLIP: Language-Guided Dense Prediction with Context-Aware Prompting Created by Yongming Rao*, Wenliang Zhao*, Guangyi Chen, Yansong Tang, Zheng Z

Yongming Rao 322 Dec 31, 2022
Library for fast text representation and classification.

fastText fastText is a library for efficient learning of word representations and sentence classification. Table of contents Resources Models Suppleme

Facebook Research 24.1k Jan 01, 2023
This is the official implementation of "One Question Answering Model for Many Languages with Cross-lingual Dense Passage Retrieval".

CORA This is the official implementation of the following paper: Akari Asai, Xinyan Yu, Jungo Kasai and Hannaneh Hajishirzi. One Question Answering Mo

Akari Asai 59 Dec 28, 2022
Code for ICE-BeeM paper - NeurIPS 2020

ICE-BeeM: Identifiable Conditional Energy-Based Deep Models Based on Nonlinear ICA This repository contains code to run and reproduce the experiments

Ilyes Khemakhem 65 Dec 22, 2022
DeepI2I: Enabling Deep Hierarchical Image-to-Image Translation by Transferring from GANs

DeepI2I: Enabling Deep Hierarchical Image-to-Image Translation by Transferring from GANs Abstract: Image-to-image translation has recently achieved re

yaxingwang 23 Apr 14, 2022
minimizer-space de Bruijn graphs (mdBG) for whole genome assembly

rust-mdbg: Minimizer-space de Bruijn graphs (mdBG) for whole-genome assembly rust-mdbg is an ultra-fast minimizer-space de Bruijn graph (mdBG) impleme

Barış Ekim 148 Dec 01, 2022
[ICCV2021] IICNet: A Generic Framework for Reversible Image Conversion

IICNet - Invertible Image Conversion Net Official PyTorch Implementation for IICNet: A Generic Framework for Reversible Image Conversion (ICCV2021). D

felixcheng97 55 Dec 06, 2022
Multiview 3D object detection on MultiviewC dataset through moft3d.

Voxelized 3D Feature Aggregation for Multiview Detection [arXiv] Multiview 3D object detection on MultiviewC dataset through VFA. Introduction We prop

Jiahao Ma 20 Dec 21, 2022
CLEAR algorithm for multi-view data association

CLEAR: Consistent Lifting, Embedding, and Alignment Rectification Algorithm The Matlab, Python, and C++ implementation of the CLEAR algorithm, as desc

MIT Aerospace Controls Laboratory 30 Jan 02, 2023
VIMPAC: Video Pre-Training via Masked Token Prediction and Contrastive Learning

This is a release of our VIMPAC paper to illustrate the implementations. The pretrained checkpoints and scripts will be soon open-sourced in HuggingFace transformers.

Hao Tan 74 Dec 03, 2022
Scripts and a shader to get you started on setting up an exported Koikatsu character in Blender.

KK Blender Shader Pack A plugin and a shader to get you started with setting up an exported Koikatsu character in Blender. The plugin is a Blender add

166 Jan 01, 2023
CAR-API: Cityscapes Attributes Recognition API

CAR-API: Cityscapes Attributes Recognition API This is the official api to download and fetch attributes annotations for Cityscapes Dataset. Content I

Kareem Metwaly 5 Dec 22, 2022
📚 Papermill is a tool for parameterizing, executing, and analyzing Jupyter Notebooks.

papermill is a tool for parameterizing, executing, and analyzing Jupyter Notebooks. Papermill lets you: parameterize notebooks execute notebooks This

nteract 5.1k Jan 03, 2023
Implementation of "Distribution Alignment: A Unified Framework for Long-tail Visual Recognition"(CVPR 2021)

Implementation of "Distribution Alignment: A Unified Framework for Long-tail Visual Recognition"(CVPR 2021)

105 Nov 07, 2022
PyTorch-lightning implementation of the ESFW module proposed in our paper Edge-Selective Feature Weaving for Point Cloud Matching

Edge-Selective Feature Weaving for Point Cloud Matching This repository contains a PyTorch-lightning implementation of the ESFW module proposed in our

5 Feb 14, 2022
"Learning and Analyzing Generation Order for Undirected Sequence Models" in Findings of EMNLP, 2021

undirected-generation-dev This repo contains the source code of the models described in the following paper "Learning and Analyzing Generation Order f

Yichen Jiang 0 Mar 25, 2022
Source code for "OmniPhotos: Casual 360° VR Photography"

OmniPhotos: Casual 360° VR Photography Project Page | Video | Paper | Demo | Data This repository contains the source code for creating and viewing Om

Christian Richardt 144 Dec 30, 2022