Fereshteh Yousefirizi

Matthias Eisenmann, Annika Reinke, Vivienn Weru et al. · utoronto

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

Shadab Ahamed, Yixi Xu, Sara Kurkowska et al.

This study addresses critical gaps in automated lymphoma segmentation from PET/CT images, focusing on issues often overlooked in existing literature. While deep learning has been applied for lymphoma lesion segmentation, few studies incorporate out-of-distribution testing, raising concerns about model generalizability across diverse imaging conditions and patient populations. We highlight the need to compare model performance with expert human annotators, including intra- and inter-observer variability, to understand task difficulty better. Most approaches focus on overall segmentation accuracy but overlook lesion-specific measures important for precise lesion detection and disease quantification. To address these gaps, we propose a clinically relevant framework for evaluating deep segmentation networks. Using this lesion measure-specific evaluation, we assess the performance of four deep networks (ResUNet, SegResNet, DynUNet, and SwinUNETR) across 611 cases from multi-institutional datasets, covering various lymphoma subtypes and lesion characteristics. Beyond standard metrics like the Dice similarity coefficient, we evaluate clinical lesion measures and their prediction errors. We also introduce detection criteria for lesion localization and propose a new detection Criterion 3 based on metabolic characteristics. We show that networks perform better on large, intense lesions with higher metabolic activity. Finally, we compare network performance to physicians via intra- and inter-observer variability analyses, demonstrating that network errors closely resemble those made by experts, i.e., the small and faint lesions remain challenging for both humans and networks. This study aims to improve automated lesion segmentation's clinical relevance, supporting better treatment decisions for lymphoma patients. The code is available at: https://github.com/microsoft/lymphoma-segmentation-dnn.

Arman Rahmim, Amirhosein Toosi, Mohammad R. Salmanpour et al.

Radiomics features extract quantitative information from medical images, towards the derivation of biomarkers for clinical tasks, such as diagnosis, prognosis, or treatment response assessment. Different image discretization parameters (e.g. bin number or size), convolutional filters, segmentation perturbation, or multi-modality fusion levels can be used to generate radiomics features and ultimately signatures. Commonly, only one set of parameters is used; resulting in only one value or flavour for a given RF. We propose tensor radiomics (TR) where tensors of features calculated with multiple combinations of parameters (i.e. flavours) are utilized to optimize the construction of radiomics signatures. We present examples of TR as applied to PET/CT, MRI, and CT imaging invoking machine learning or deep learning solutions, and reproducibility analyses: (1) TR via varying bin sizes on CT images of lung cancer and PET-CT images of head & neck cancer (HNC) for overall survival prediction. A hybrid deep neural network, referred to as TR-Net, along with two ML-based flavour fusion methods showed improved accuracy compared to regular rediomics features. (2) TR built from different segmentation perturbations and different bin sizes for classification of late-stage lung cancer response to first-line immunotherapy using CT images. TR improved predicted patient responses. (3) TR via multi-flavour generated radiomics features in MR imaging showed improved reproducibility when compared to many single-flavour features. (4) TR via multiple PET/CT fusions in HNC. Flavours were built from different fusions using methods, such as Laplacian pyramids and wavelet transforms. TR improved overall survival prediction. Our results suggest that the proposed TR paradigm has the potential to improve performance capabilities in different medical imaging tasks.

Maziar Sabouri, Shadab Ahamed, Azin Asadzadeh et al.

The objective of this study was to develop an automated pipeline that enhances thyroid disease classification using thyroid scintigraphy images, aiming to decrease assessment time and increase diagnostic accuracy. Anterior thyroid scintigraphy images from 2,643 patients were collected and categorized into diffuse goiter (DG), multinodal goiter (MNG), and thyroiditis (TH) based on clinical reports, and then segmented by an expert. A ResUNet model was trained to perform auto-segmentation. Radiomic features were extracted from both physician (scenario 1) and ResUNet segmentations (scenario 2), followed by omitting highly correlated features using Spearman's correlation, and feature selection using Recursive Feature Elimination (RFE) with XGBoost as the core. All models were trained under leave-one-center-out cross-validation (LOCOCV) scheme, where nine instances of algorithms were iteratively trained and validated on data from eight centers and tested on the ninth for both scenarios separately. Segmentation performance was assessed using the Dice similarity coefficient (DSC), while classification performance was assessed using metrics, such as precision, recall, F1-score, accuracy, area under the Receiver Operating Characteristic (ROC AUC), and area under the precision-recall curve (PRC AUC). ResUNet achieved DSC values of 0.84$\pm$0.03, 0.71$\pm$0.06, and 0.86$\pm$0.02 for MNG, TH, and DG, respectively. Classification in scenario 1 achieved an accuracy of 0.76$\pm$0.04 and a ROC AUC of 0.92$\pm$0.02 while in scenario 2, classification yielded an accuracy of 0.74$\pm$0.05 and a ROC AUC of 0.90$\pm$0.02. The automated pipeline demonstrated comparable performance to physician segmentations on several classification metrics across different classes, effectively reducing assessment time while maintaining high diagnostic accuracy. Code available at: https://github.com/ahxmeds/thyroidiomics.git.

Robert V. Bergen, Jean-Francois Rajotte, Fereshteh Yousefirizi et al.

Training computer-vision related algorithms on medical images for disease diagnosis or image segmentation is difficult in large part due to privacy concerns. For this reason, generative image models are highly sought after to facilitate data sharing. However, 3-D generative models are understudied, and investigation of their privacy leakage is needed. We introduce our 3-D generative model, Transversal GAN (TrGAN), using head & neck PET images which are conditioned on tumour masks as a case study. We define quantitative measures of image fidelity, utility and privacy for our model. These metrics are evaluated in the course of training to identify ideal fidelity, utility and privacy trade-offs and establish the relationships between these parameters. We show that the discriminator of the TrGAN is vulnerable to attack, and that an attacker can identify which samples were used in training with almost perfect accuracy (AUC = 0.99). We also show that an attacker with access to only the generator cannot reliably classify whether a sample had been used for training (AUC = 0.51). This suggests that TrGAN generators, but not discriminators, may be used for sharing synthetic 3-D PET data with minimal privacy risk while maintaining good utility and fidelity.

Shadab Ahamed, Natalia Dubljevic, Ingrid Bloise et al.

Accurate detection and segmentation of diffuse large B-cell lymphoma (DLBCL) from PET images has important implications for estimation of total metabolic tumor volume, radiomics analysis, surgical intervention and radiotherapy. Manual segmentation of tumors in whole-body PET images is time-consuming, labor-intensive and operator-dependent. In this work, we develop and validate a fast and efficient three-step cascaded deep learning model for automated detection and segmentation of DLBCL tumors from PET images. As compared to a single end-to-end network for segmentation of tumors in whole-body PET images, our three-step model is more effective (improves 3D Dice score from 58.9% to 78.1%) since each of its specialized modules, namely the slice classifier, the tumor detector and the tumor segmentor, can be trained independently to a high degree of skill to carry out a specific task, rather than a single network with suboptimal performance on overall segmentation.

Alejandro Lopez-Montes, Fereshteh Yousefirizi, Yizhou Chen et al.

KEY WORDS: Artificial Intelligence (AI), Theranostics, Dosimetry, Radiopharmaceutical Therapy (RPT), Patient-friendly dosimetry KEY POINTS - The rapid evolution of radiopharmaceutical therapy (RPT) highlights the growing need for personalized and patient-centered dosimetry. - Artificial Intelligence (AI) offers solutions to the key limitations in current dosimetry calculations. - The main advances on AI for simplified dosimetry toward patient-friendly RPT are reviewed. - Future directions on the role of AI in RPT dosimetry are discussed.

Alireza Jafari, Fereshteh Yousefirizi, Vahid Seydi

Atrial fibrillation (AF) is a prevalent cardiac arrhythmia associated with elevated health risks, where timely detection is pivotal for mitigating stroke-related morbidity. This study introduces an innovative hybrid methodology integrating unsupervised deep learning and gradient boosting models to improve AF detection. A 19-layer deep convolutional autoencoder (DCAE) is coupled with three boosting classifiers-AdaBoost, XGBoost, and LightGBM (LGBM)-to harness their complementary advantages while addressing individual limitations. The proposed framework uniquely combines DCAE with gradient boosting, enabling end-to-end AF identification devoid of manual feature extraction. The DCAE-LGBM model attains an F1-score of 95.20%, sensitivity of 99.99%, and inference latency of four seconds, outperforming existing methods and aligning with clinical deployment requirements. The DCAE integration significantly enhances boosting models, positioning this hybrid system as a reliable tool for automated AF detection in clinical settings.

Fereshteh Yousefirizi, Ian Janzen, Natalia Dubljevic et al.

We utilized a 3D nnU-Net model with residual layers supplemented by squeeze and excitation (SE) normalization for tumor segmentation from PET/CT images provided by the Head and Neck Tumor segmentation chal-lenge (HECKTOR). Our proposed loss function incorporates the Unified Fo-cal and Mumford-Shah losses to take the advantage of distribution, region, and boundary-based loss functions. The results of leave-one-out-center-cross-validation performed on different centers showed a segmentation performance of 0.82 average Dice score (DSC) and 3.16 median Hausdorff Distance (HD), and our results on the test set achieved 0.77 DSC and 3.01 HD. Following lesion segmentation, we proposed training a case-control proportional hazard Cox model with an MLP neural net backbone to predict the hazard risk score for each discrete lesion. This hazard risk prediction model (CoxCC) was to be trained on a number of PET/CT radiomic features extracted from the segmented lesions, patient and lesion demographics, and encoder features provided from the penultimate layer of a multi-input 2D PET/CT convolutional neural network tasked with predicting time-to-event for each lesion. A 10-fold cross-validated CoxCC model resulted in a c-index validation score of 0.89, and a c-index score of 0.61 on the HECKTOR challenge test dataset.

Robert V Bergen, Jean-Francois Rajotte, Fereshteh Yousefirizi et al.

Training computer-vision related algorithms on medical images for disease diagnosis or image segmentation is difficult due to the lack of training data, labeled samples, and privacy concerns. For this reason, a robust generative method to create synthetic data is highly sought after. However, most three-dimensional image generators require additional image input or are extremely memory intensive. To address these issues we propose adapting video generation techniques for 3-D image generation. Using the temporal GAN (TGAN) architecture, we show we are able to generate realistic head and neck PET images. We also show that by conditioning the generator on tumour masks, we are able to control the geometry and location of the tumour in the generated images. To test the utility of the synthetic images, we train a segmentation model using the synthetic images. Synthetic images conditioned on real tumour masks are automatically segmented, and the corresponding real images are also segmented. We evaluate the segmentations using the Dice score and find the segmentation algorithm performs similarly on both datasets (0.65 synthetic data, 0.70 real data). Various radionomic features are then calculated over the segmented tumour volumes for each data set. A comparison of the real and synthetic feature distributions show that seven of eight feature distributions had statistically insignificant differences (p>0.05). Correlation coefficients were also calculated between all radionomic features and it is shown that all of the strong statistical correlations in the real data set are preserved in the synthetic data set.

Fereshteh Yousefirizi, Pierre Decazes, Amine Amyar et al.

Artificial intelligence (AI) techniques have significant potential to enable effective, robust and automated image phenotyping including identification of subtle patterns. AI-based detection searches the image space to find the regions of interest based on patterns and features. There is a spectrum of tumor histologies from benign to malignant that can be identified by AI-based classification approaches using image features. The extraction of minable information from images gives way to the field of radiomics and can be explored via explicit (handcrafted/engineered) and deep radiomics frameworks. Radiomics analysis has the potential to be utilized as a noninvasive technique for the accurate characterization of tumors to improve diagnosis and treatment monitoring. This work reviews AI-based techniques, with a special focus on oncological PET and PET/CT imaging, for different detection, classification, and prediction/prognosis tasks. We also discuss needed efforts to enable the translation of AI techniques to routine clinical workflows, and potential improvements and complementary techniques such as the use of natural language processing on electronic health records and neuro-symbolic AI techniques.