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Prognostic AI-monitoring

This repository contains the code of our research on prognostic AI-monitoring: a prototype for automatic response evaluation to treatment of cancer patients with advanced disease based on deep learning image-to-image registration.

🚧 This research is still in its preliminary phase, further development and validation is warrant before clinical use.

Graphical Abstract

pam

Requirements

  • Python 3.6
  • Tensorflow 1.15.0
  • Keras
  • Scikit-Learn
  • Pandas
  • SimpleITK

VoxelMorph, Neuron and Frida are already included in the libs folder.

Parts of Keras-Group-Normalization and Recursive-Cascaded-Networks are reused in the main code.

Installing requirements using Anaconda

  • Virtual environment

        $ conda create --name tf-1.15
    $ conda activate tf-1.15

  • Installing packages inside the virtual environment

        $ conda install -c anaconda tensorflow-gpu==1.15
    $ conda install -c anaconda scikit-learn
    $ conda install -c anaconda pandas
    $ conda install -c simpleitk simpleitk
    $ conda install -c conda-forge keras
    $ conda install -c conda-forge nibabel
    $ conda install -c conda-forge tqdm
    $ conda install -c anaconda pillow
    $ conda install -c conda-forge matplotlib

Publications

Stefano Trebeschi, Zuhir Bodalal, Thierry N. Boellaard, Teresa M. Tareco Bucho, Silvia G. Drago, Ieva Kurilova, Adriana M. Calin-Vainak, Andrea Delli Pizzi, Mirte Muller, Karlijn Hummelink, Koen J. Hartemink, Thi Dan Linh Nguyen-Kim, Egbert F. Smit, Hugo J. Aerts and Regina G. Beets-Tan; Prognostic value of deep learning mediated treatment monitoring in lung cancer patients receiving immunotherapy, Frontiers in Oncology, Cancer Imaging and Imaging directed Interventions, 2021 doi: 10.3389/fonc.2021.609054 (it's open access!)

Stefano Trebeschi, Zuhir Bodalal, Nick van Dijk, Thierry N. Boellaard, Paul Apfaltrer, Teresa M. Tareco Bucho, Thi Dan Linh Nguyen-Kim, Michiel S. van der Heijden, Hugo J. W. L. Aerts and Regina G. H. Beets-Tan; Development of a Prognostic AI-Monitor for Metastatic Urothelial Cancer Patients Receiving Immunotherapy, Frontiers in Oncology, Genitourinary Oncology, 2021 doi: 10.3389/fonc.2021.637804 (it's also open access!)