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Background: The number of survivors of cancer is growing, and they often experience negative long-term behavioral outcomes due to cancer treatments. There is a need for better computational methods to handle and predict these outcomes so that physicians and health care providers can implement preventive treatments. Objective: This study aimed to create a new feature selection algorithm to improve the performance of machine learning classifiers to predict negative long-term behavioral outcomes in survivors of cancer. Methods: We devised a hybrid deep learning–based feature selection approach to support early detection of negative long-term behavioral outcomes in survivors of cancer. Within a data-driven, clinical domain–guided framework to select the best set of features among cancer treatments, chronic health conditions, and socioenvironmental factors, we developed a 2-stage feature selection algorithm, that is, a multimetric, majority-voting filter and a deep dropout neural network, to dynamically and automatically select the best set of features for each behavioral outcome. We also conducted an experimental case study on existing study data with 102 survivors of acute lymphoblastic leukemia (aged 15-39 years at evaluation and >5 years postcancer diagnosis) who were treated in a public hospital in Hong Kong. Finally, we designed and implemented radial charts to illustrate the significance of the selected features on each behavioral outcome to support clinical professionals’ future treatment and diagnoses. Results: In this pilot study, we demonstrated that our approach outperforms the traditional statistical and computation methods, including linear and nonlinear feature selectors, for the addressed top-priority behavioral outcomes. Our approach holistically has higher F1, precision, and recall scores compared to existing feature selection methods. The models in this study select several significant clinical and socioenvironmental variables as risk factors associated with the development of behavioral problems in young survivors of acute lymphoblastic leukemia. Conclusions: Our novel feature selection algorithm has the potential to improve machine learning classifiers’ capability to predict adverse long-term behavioral outcomes in survivors of cancer.
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A robust ensemble feature selection approach to prioritize genes associated with survival outcome in high-dimensional gene expression data
Exploring features associated with the clinical outcome of interest is a rapidly advancing area of research. However, with contemporary sequencing technologies capable of identifying over thousands of genes per sample, there is a challenge in constructing efficient prediction models that balance accuracy and resource utilization. To address this challenge, researchers have developed feature selection methods to enhance performance, reduce overfitting, and ensure resource efficiency. However, applying feature selection models to survival analysis, particularly in clinical datasets characterized by substantial censoring and limited sample sizes, introduces unique challenges. We propose a robust ensemble feature selection approach integrated with group Lasso to identify compelling features and evaluate its performance in predicting survival outcomes. Our approach consistently outperforms established models across various criteria through extensive simulations, demonstrating low false discovery rates, high sensitivity, and high stability. Furthermore, we applied the approach to a colorectal cancer dataset from The Cancer Genome Atlas, showcasing its effectiveness by generating a composite score based on the selected genes to correctly distinguish different subtypes of the patients. In summary, our proposed approach excels in selecting impactful features from high-dimensional data, yielding better outcomes compared to contemporary state-of-the-art models.
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- Award ID(s):
- 2137983
- PAR ID:
- 10659498
- Publisher / Repository:
- Frontiers
- Date Published:
- Journal Name:
- Frontiers in Systems Biology
- Volume:
- 4
- ISSN:
- 2674-0702
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.3389/fsysb.2024.1355595
