Code to reproduce results and figures in manuscript:
Tiffany M. Tang*, Yuping Zhang*, Ana M. Kenney, Cassie Xie, Lanbo Xiao, Javed Siddiqui, Sudhir Srivastava, Martin G. Sanda, John T. Wei, Ziding Feng, Jeffrey J. Tosoian, Yingye Zheng, Arul M. Chinnaiyan†, and Bin Yu†; for the EDRN-PCA3 Study Group. "A simplified MyProstateScore2.0 for high-grade prostate cancer". Cancer Biomarkers. 2025;42(1). doi:10.1177/18758592241308755
Accompanying supplementary PCS documentation: https://yu-group.github.io/sMPS2/
In this work, we developed and rigorously stress-tested a novel non-invasive biomarker test, the simplified MyProstateScore2.0 (sMPS2), for accurate and early screening of clinically-significant prostate cancer.
- scripts/: contains all scripts to run sMPS model development and evaluation pipeline
- Python scripts:
- 01_train_prediction_methods.py: fits the prediction methods and estimates the feature importances from these learned models
- 02_aggregate_train_results.py: aggregates the training prediction and importance results across the many data splits, methods, and data preprocessing variants
- 03_evaluate_prediction_methods.py: evaluates the prediction methods on the test set given a particular choice of gene rankings and number of gene predictors
- 04_aggregate_eval_results.py: aggregates the test evaluation results across the many data splits, data preprocessing variants, gene ranking modes, and number of gene predictors
- To run the full pipeline, the "driver" scripts should be run in sequential order, i.e., first 01_driver.sh, then 02_driver.sh, then 03_driver.sh, then 04_driver.sh
- Python scripts:
- model_config/: model configuration file, specifying the models, hyperparameters, and feature importances under study
- functions/: contains all functions necessary to reproduce sMPS model development pipeline
- notebooks/: contains files to reproduce supplementary PCS documentation
To cite sMPS2, please use:
@article{tang2025simplified,
author = {Tiffany M Tang and Yuping Zhang and Ana M Kenney and Cassie Xie and Lanbo Xiao and Javed Siddiqui and Sudhir Srivastava and Martin G Sanda and John T Wei and Ziding Feng and Jeffrey J Tosoian and Yingye Zheng and Arul M Chinnaiyan and Bin Yu},
title ={A simplified MyProstateScore2.0 for high-grade prostate cancer},
journal = {Cancer Biomarkers},
volume = {42},
number = {1},
pages = {18758592241308755},
year = {2025},
doi = {10.1177/18758592241308755},
note = {PMID: 40109218},
URL = {https://doi.org/10.1177/18758592241308755}
}