Caroline Reinhold

Mahdi Ait Lhaj Loutfi, Teodora Boblea Podasca, Alex Zwanenburg et al.

Background: The high dimensionality of radiomic feature sets, the variability in radiomic feature types and potentially high computational requirements all underscore the need for an effective method to identify the smallest set of predictive features for a given clinical problem. Purpose: Develop a methodology and tools to identify and explain the smallest set of predictive radiomic features. Materials and Methods: 89,714 radiomic features were extracted from five cancer datasets: low-grade glioma, meningioma, non-small cell lung cancer (NSCLC), and two renal cell carcinoma cohorts (n=2104). Features were categorized by computational complexity into morphological, intensity, texture, linear filters, and nonlinear filters. Models were trained and evaluated on each complexity level using the area under the curve (AUC). The most informative features were identified, and their importance was explained. The optimal complexity level and associated most informative features were identified using systematic statistical significance analyses and a false discovery avoidance procedure, respectively. Their predictive importance was explained using a novel tree-based method. Results: MEDimage, a new open-source tool, was developed to facilitate radiomic studies. Morphological features were optimal for MRI-based meningioma (AUC: 0.65) and low-grade glioma (AUC: 0.68). Intensity features were optimal for CECT-based renal cell carcinoma (AUC: 0.82) and CT-based NSCLC (AUC: 0.76). Texture features were optimal for MRI-based renal cell carcinoma (AUC: 0.72). Tuning the Hounsfield unit range improved results for CECT-based renal cell carcinoma (AUC: 0.86). Conclusion: Our proposed methodology and software can estimate the optimal radiomics complexity level for specific medical outcomes, potentially simplifying the use of radiomics in predictive modeling across various contexts.

Farhad Maleki, Katie Ovens, Rajiv Gupta et al.

Purpose: Despite the potential of machine learning models, the lack of generalizability has hindered their widespread adoption in clinical practice. We investigate three methodological pitfalls: (1) violation of independence assumption, (2) model evaluation with an inappropriate performance indicator or baseline for comparison, and (3) batch effect. Materials and Methods: Using several retrospective datasets, we implement machine learning models with and without the pitfalls to quantitatively illustrate these pitfalls' effect on model generalizability. Results: Violation of independence assumption, more specifically, applying oversampling, feature selection, and data augmentation before splitting data into train, validation, and test sets, respectively, led to misleading and superficial gains in F1 scores of 71.2% in predicting local recurrence and 5.0% in predicting 3-year overall survival in head and neck cancer as well as 46.0% in distinguishing histopathological patterns in lung cancer. Further, randomly distributing data points for a subject across training, validation, and test sets led to a 21.8% superficial increase in F1 score. Also, we showed the importance of the choice of performance measures and baseline for comparison. In the presence of batch effect, a model built for pneumonia detection led to F1 score of 98.7%. However, when the same model was applied to a new dataset of normal patients, it only correctly classified 3.86% of the samples. Conclusions: These methodological pitfalls cannot be captured using internal model evaluation, and the inaccurate predictions made by such models may lead to wrong conclusions and interpretations. Therefore, understanding and avoiding these pitfalls is necessary for developing generalizable models.