FAE

FeAture Explorer (FAE), a radiomics (or medical analysis) tool that helps radiologists extract features, preprocess feature matrix, develop machine learning models (Binary Classification & Survival Analysis) with one-click, and evaluate models qualitatively and quantitatively. This project was inspired on the Radiomics, and provides a GUI with convenient process. FAE was initially developed by East China Normal University and Siemens Healthineers Ltd.

If FAE could help in your project, We appreciate that you could cite this work:

Y. Song, J. Zhang, Y. Zhang, Y. Hou, X. Yan, Y. Wang, M. Zhou, Y. Yao, G. Yang. FeAture Explorer (FAE): A tool for developing and comparing radiomics models. PLoS One. 2020. DOI: https://doi.org/10.1371/journal.pone.0237587

Welcome any issues and PR.

Release

The Windows64 version and the Ubuntut 20.04 release could be found Google Drive or Baidu Drive. A short tutorial video with Chinese version may help.

Pre-install

The below modules must be installed first to make the FAE work.

- imbalanced-learn=0.6.2
- lifelines=0.26.0
- matplotlib=3.2.0
- numpy=1.18.1
- pandas=1.0.1
- pdfdocument=3.3
- pillow=7.0.0
- pycox=0.2.2
- PyQt5=5.14.1
- PyQtGraph=0.10.0
- pyradiomics=3.0
- reportlab=3.5.34
- scikit-learn=0.22.2
- scikit-image=0.18.3
- scipy=1.4.1
- seaborn=0.10.0
- statsmodels=0.11.1
- trimesh=3.9.29

Installing

Just clone it by typing in:

git clone https://github.com/salan668/FAE.git

The .ui file has to be transferred to the .py file by pyuic manually. For example, GUI/HomePage.ui should be transferred to GUI/HomePage.py file.

Main Architecture of Project

• BC: Binary Classification Pipeline
  • DataContainer. The data structure including feature array, label, cases ID, and feature names.
  • Description. The PDF generator to describe the developed BC model.
  • FeatureAnalysis. The module of the feature pipeline, including Data Balance, Normalization, Dimension Reduction, Feature Selector, Classifier, and Cross Validation.
  • Visualization. The common visualized plots, like ROC curve and the plot of AUC against different parameters.
• Image2Feature
  • RadiomicsFeatureExtractor. An Extractor to get features from self-config multi-aligned images with defined ROI.
• SA: Survival Analysis Pipeline

License

This project is licensed under the GPL 3.0 License

Contributor and Acknowledge List

• Yang Song
• Jing Zhang
• Guang Yang
• Chengxiu Zhang
• Xue-xiang Cao
• Xu Yan
• Tian-jing Zhang
• Yi-lai Pei
• jmtaysom
• Zhiyong Zhao
• Yu-dong Zhang