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Project: 4Dsurvival (GitHub Link)

• 4Dsurvival-master
  • environment.yml
  • demo
    • demo_modelcomp_pvalue.ipynb
    • demo_modelcomp_pvalue.py
    • demo_validate.ipynb
    • demo_hypersearchDL.py
    • demo_validate.py
    • demo_KMplot.py
    • demo_KMplot.ipynb
    • demo_hypersearchDL.ipynb
    • demo_validateDL.py
  • code
    • hypersearch.py
    • CoxReg_Single_Run.ipynb
    • CoxReg_Single_run.py
    • trainDL.py
    • trainDL.ipynb
  • inputdata_setup.py
  • LICENSE
  • data
    • inputdata_conv.pkl
    • modelCstats_conv.pkl
    • modelCstats_DL.pkl
  • README.md

Deep learning cardiac motion analysis for human survival prediction (4Dsurvival)

The code in this repository implements 4Dsurvival, a deep neural network for carrying out classification/prediction using 3D motion input data. The present implementation was trained using MRI-derived heart motion data and survival outcomes on pulmonary hypertension patients.

Overview

The files in this repository are organized into 3 directories:

• code : contains base functions for fitting the 2 types of statistical models used in our paper: 4Dsurvival (supervised denoising autoencoder for survival outcomes) and a penalized Cox Proportional Hazards regression model.
• demo : contains functions for the statistical analyses carried out in our paper:
  • Training of DL model - demo/demo_hypersearchDL.py
  • Generation of Kaplan-Meier plots - demo/demo_KMplot.py
  • statistical comparison of model performance - demo/demo_modelcomp_pvalue.py
  • Bootstrap internal validation - demo/demo_validate.py
• data : contains simulated data on which functions from the demo directory can be run.

To run the code in the demo directory, we provide a Binder interface (for the Jupyter notebooks) and a Docker container (for the corresponding Python scripts). Below are usage instructions:

1. Running Jupyter notebooks via Binder or Code Ocean

The Jupyter notebooks in the demo directory are hosted on Binder, which provides an interactive user interface for executing Jupyter notebooks. Click the link provided below for access:

You can also edit code, change parameters, and re-run the analysis interactively in Code Ocean.

2. Installation/Usage instructions for Docker Image

A Docker image is available for running the code available in the demo directory. This image contains a base Ubuntu Linux operating system image set up with all the libraries required to run the code (e.g. Tensorflow, Keras, Optunity, etc.). The image contains all the code, as well as simulated cardiac data on which the code can be run.

Install Docker

Running our 4Dsurvival Docker image requires installation of the Docker software, instructions are available at https://docs.docker.com/install/

Download 4Dsurvival Docker image

Once the Docker software has been installed, our 4Dsurvival Docker image can be pulled from the Docker hub using the following command:

docker pull ghalibbello/4dsurvival:latest

Once the image download is complete, open up a command-line terminal. On Windows operating systems, this would be the Command Prompt (cmd.exe), accessible by opening the Run Command utility using the shortcut key Win+R and then typing cmd. On Mac OS, the terminal is accessible via (Finder > Applications > Utilities > Terminal). On Linux systems, any terminal can be used. Once a terminal is open, running the following command:

docker images

should show ghalibbello/4dsurvival on the list of Docker images on your local system

Run 4Dsurvival Docker image

docker run -it ghalibbello/4dsurvival:latest /bin/bash

launches an interactive linux shell terminal that gives users access to the image's internal file system. This file system contains all the code in this repository, along with the simulated data on which the code can be run. Typing

ls -l

will list all the folders in the working directory of the Docker image (/4DSurv). You should see the 3 main folders code, data and demo, which contain the same files as the corresponding folders with the same name in this github repository.

Below we will demonstrate how to perform (within the Docker image) the following analyses:

• [x] Train deep learning network
• [x] Train and validate conventional parameter model

Train deep learning network

From the 4dSurv directory, navigate to the demo directory by typing:

cd demo
ls -l

The demo_hypersearchDL.py file should be visible. This executes a hyperparameter search (see Methods section in paper) for training of the 4Dsurvival deep learning network. A demo of this code (which uses simulated input data) can now be run (WARNING: on most machines, this will take several hours to complete):

python3 demo_hypersearchDL.py

Also under the demo folder, the demo_validate.py file should be visible. This executes the bootstrap-based approach for training and internal validation of the Cox Proportional Hazards model for conventional (volumetric) parameters. A demo of this code (which uses simulated input data) can now be run :

python3 demo_validate.py

Citations

Bello GA, Dawes TJW, Duan J, Biffi C, de Marvao A, Howard LSGE, Gibbs JSR, Wilkins MR, Cook SA, Rueckert D, O'Regan DP. Deep-learning cardiac motion analysis for human survival prediction. Nature Machine Intelligence 1, 95–104 (2019).

Duan J, Bello G, Schlemper J, Bai W, Dawes TJ, Biffi C, de Marvao A, Doumou G, O’Regan DP, Rueckert D. Automatic 3D bi-ventricular segmentation of cardiac images by a shape-refined multi-task deep learning approach. IEEE Transactions on Medical Imaging 38(9), 2151-2164 (2019).