Reza Forghani

Md Mahfuz Al Hasan, Mahdi Zaman, Abdul Jawad et al.

Transformer-based architectures have advanced medical image analysis by effectively modeling long-range dependencies, yet they often struggle in 3D settings due to substantial memory overhead and insufficient capture of fine-grained local features. We address these limitations with WaveFormer, a novel 3D-transformer that: i) leverages the fundamental frequency-domain properties of features for contextual representation, and ii) is inspired by the top-down mechanism of the human visual recognition system, making it a biologically motivated architecture. By employing discrete wavelet transformations (DWT) at multiple scales, WaveFormer preserves both global context and high-frequency details while replacing heavy upsampling layers with efficient wavelet-based summarization and reconstruction. This significantly reduces the number of parameters, which is critical for real-world deployment where computational resources and training times are constrained. Furthermore, the model is generic and easily adaptable to diverse applications. Evaluations on BraTS2023, FLARE2021, and KiTS2023 demonstrate performance on par with state-of-the-art methods while offering substantially lower computational complexity.

Farhad Maleki, Linda Moy, Reza Forghani et al.

Deep learning techniques hold immense promise for advancing medical image analysis, particularly in tasks like image segmentation, where precise annotation of regions or volumes of interest within medical images is crucial but manually laborious and prone to interobserver and intraobserver biases. As such, deep learning approaches could provide automated solutions for such applications. However, the potential of these techniques is often undermined by challenges in reproducibility and generalizability, which are key barriers to their clinical adoption. This paper introduces the RIDGE checklist, a comprehensive framework designed to assess the Reproducibility, Integrity, Dependability, Generalizability, and Efficiency of deep learning-based medical image segmentation models. The RIDGE checklist is not just a tool for evaluation but also a guideline for researchers striving to improve the quality and transparency of their work. By adhering to the principles outlined in the RIDGE checklist, researchers can ensure that their developed segmentation models are robust, scientifically valid, and applicable in a clinical setting.

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.

Segolene Brivet, Faicel Chamroukhi, Mark Coates et al.

Dual-energy computed tomography (DECT) is an advanced CT scanning technique enabling material characterization not possible with conventional CT scans. It allows the reconstruction of energy decay curves at each 3D image voxel, representing varying image attenuation at different effective scanning energy levels. In this paper, we develop novel functional data analysis (FDA) techniques and adapt them to the analysis of DECT decay curves. More specifically, we construct functional mixture models that integrate spatial context in mixture weights, with mixture component densities being constructed upon the energy decay curves as functional observations. We design unsupervised clustering algorithms by developing dedicated expectation maximization (EM) algorithms for the maximum likelihood estimation of the model parameters. To our knowledge, this is the first article to adapt statistical FDA tools and model-based clustering to take advantage of the full spectral information provided by DECT. We evaluate our methods on 91 head and neck cancer DECT scans. We compare our unsupervised clustering results to tumor contours traced manually by radiologists, as well as to several baseline algorithms. Given the inter-rater variability even among experts at delineating head and neck tumors, and given the potential importance of tissue reactions surrounding the tumor itself, our proposed methodology has the potential to add value in downstream machine learning applications for clinical outcome prediction based on DECT data in head and neck cancer.

Andreas Maier, Seung Hee Yang, Farhad Maleki et al.

In the domain of medical image processing, medical device manufacturers protect their intellectual property in many cases by shipping only compiled software, i.e. binary code which can be executed but is difficult to be understood by a potential attacker. In this paper, we investigate how well this procedure is able to protect image processing algorithms. In particular, we investigate whether the computation of mono-energetic images and iodine maps from dual energy CT data can be reverse-engineered by machine learning methods. Our results indicate that both can be approximated using only one single slice image as training data at a very high accuracy with structural similarity greater than 0.98 in all investigated cases.