Ilker Hacihaliloglu

Amirhossein Kazerouni, Ehsan Khodapanah Aghdam, Moein Heidari et al.

Denoising diffusion models, a class of generative models, have garnered immense interest lately in various deep-learning problems. A diffusion probabilistic model defines a forward diffusion stage where the input data is gradually perturbed over several steps by adding Gaussian noise and then learns to reverse the diffusion process to retrieve the desired noise-free data from noisy data samples. Diffusion models are widely appreciated for their strong mode coverage and quality of the generated samples despite their known computational burdens. Capitalizing on the advances in computer vision, the field of medical imaging has also observed a growing interest in diffusion models. To help the researcher navigate this profusion, this survey intends to provide a comprehensive overview of diffusion models in the discipline of medical image analysis. Specifically, we introduce the solid theoretical foundation and fundamental concepts behind diffusion models and the three generic diffusion modelling frameworks: diffusion probabilistic models, noise-conditioned score networks, and stochastic differential equations. Then, we provide a systematic taxonomy of diffusion models in the medical domain and propose a multi-perspective categorization based on their application, imaging modality, organ of interest, and algorithms. To this end, we cover extensive applications of diffusion models in the medical domain. Furthermore, we emphasize the practical use case of some selected approaches, and then we discuss the limitations of the diffusion models in the medical domain and propose several directions to fulfill the demands of this field. Finally, we gather the overviewed studies with their available open-source implementations at https://github.com/amirhossein-kz/Awesome-Diffusion-Models-in-Medical-Imaging.

Sina Ghorbani Kolahi, Seyed Kamal Chaharsooghi, Toktam Khatibi et al.

Medical image segmentation involves identifying and separating object instances in a medical image to delineate various tissues and structures, a task complicated by the significant variations in size, shape, and density of these features. Convolutional neural networks (CNNs) have traditionally been used for this task but have limitations in capturing long-range dependencies. Transformers, equipped with self-attention mechanisms, aim to address this problem. However, in medical image segmentation it is beneficial to merge both local and global features to effectively integrate feature maps across various scales, capturing both detailed features and broader semantic elements for dealing with variations in structures. In this paper, we introduce MSA$^2$Net, a new deep segmentation framework featuring an expedient design of skip-connections. These connections facilitate feature fusion by dynamically weighting and combining coarse-grained encoder features with fine-grained decoder feature maps. Specifically, we propose a Multi-Scale Adaptive Spatial Attention Gate (MASAG), which dynamically adjusts the receptive field (Local and Global contextual information) to ensure that spatially relevant features are selectively highlighted while minimizing background distractions. Extensive evaluations involving dermatology, and radiological datasets demonstrate that our MSA$^2$Net outperforms state-of-the-art (SOTA) works or matches their performance. The source code is publicly available at https://github.com/xmindflow/MSA-2Net.

Xiao Qi, David J. Foran, John L. Nosher et al.

The role of chest X-ray (CXR) imaging, due to being more cost-effective, widely available, and having a faster acquisition time compared to CT, has evolved during the COVID-19 pandemic. To improve the diagnostic performance of CXR imaging a growing number of studies have investigated whether supervised deep learning methods can provide additional support. However, supervised methods rely on a large number of labeled radiology images, which is a time-consuming and complex procedure requiring expert clinician input. Due to the relative scarcity of COVID-19 patient data and the costly labeling process, self-supervised learning methods have gained momentum and has been proposed achieving comparable results to fully supervised learning approaches. In this work, we study the effectiveness of self-supervised learning in the context of diagnosing COVID-19 disease from CXR images. We propose a multi-feature Vision Transformer (ViT) guided architecture where we deploy a cross-attention mechanism to learn information from both original CXR images and corresponding enhanced local phase CXR images. We demonstrate the performance of the baseline self-supervised learning models can be further improved by leveraging the local phase-based enhanced CXR images. By using 10\% labeled CXR scans, the proposed model achieves 91.10\% and 96.21\% overall accuracy tested on total 35,483 CXR images of healthy (8,851), regular pneumonia (6,045), and COVID-19 (18,159) scans and shows significant improvement over state-of-the-art techniques. Code is available https://github.com/endiqq/Multi-Feature-ViT

Moein Heidari, Reza Rezaeian, Reza Azad et al.

Implicit Neural Representation (INR), leveraging a neural network to transform coordinate input into corresponding attributes, has recently driven significant advances in several vision-related domains. However, the performance of INR is heavily influenced by the choice of the nonlinear activation function used in its multilayer perceptron (MLP) architecture. To date, multiple nonlinearities have been investigated, but current INRs still face limitations in capturing high-frequency components and diverse signal types. We show that these challenges can be alleviated by introducing a novel approach in INR architecture. Specifically, we propose SL$^{2}$A-INR, a hybrid network that combines a single-layer learnable activation function with an MLP that uses traditional ReLU activations. Our method performs superior across diverse tasks, including image representation, 3D shape reconstruction, and novel view synthesis. Through comprehensive experiments, SL$^{2}$A-INR sets new benchmarks in accuracy, quality, and robustness for INR. Our Code is publicly available on~\href{https://github.com/Iceage7/SL2A-INR}{\textcolor{magenta}{GitHub}}.

Amirhossein Dabiriaghdam, Shayan Vassef, Mohammadreza Bakhtiari et al.

Multimodal large language models are increasingly capable of complex reasoning, yet their performance often degrades when they must externalize a problem through a tool and then reason over the tool's output, specifically when they rely on visual aids. This gap is especially important because real engineering and scientific workflows often rely on visualization tools for analysis, validation, and decision-making. To study this discrepancy, we introduce VAMPS (Visual-Assisted Mathematical Problem Solving), a benchmark for graph-assisted mathematics. VAMPS contains 1,168 multimodal, bilingual multiple-choice question-answer pairs drawn from Iranian University Entrance Exam algebra and calculus problems and expanded with human-reviewed LLM-generated synthetic variants, all selected so that plotting provides a natural solution strategy by revealing intersections, extrema, asymptotes, etc. Designed for both benchmarking and diagnosis, VAMPS goes beyond prior multimodal benchmarks that primarily evaluate reasoning over fixed visual inputs by testing whether a model can benefit from constructing a useful graph and grounding its answer in the resulting visualization. Overall, we found that across a diverse set of models, direct analytical solving surprisingly outperforms tool-enabled visual solving, even on problems where plotting is a natural strategy.

Ali Mehrabian, Parsa Mojarad Adi, Moein Heidari et al.

Implicit neural representations (INRs) use neural networks to provide continuous and resolution-independent representations of complex signals with a small number of parameters. However, existing INR models often fail to capture important frequency components specific to each task. To address this issue, in this paper, we propose a Fourier Kolmogorov Arnold network (FKAN) for INRs. The proposed FKAN utilizes learnable activation functions modeled as Fourier series in the first layer to effectively control and learn the task-specific frequency components. In addition, the activation functions with learnable Fourier coefficients improve the ability of the network to capture complex patterns and details, which is beneficial for high-resolution and high-dimensional data. Experimental results show that our proposed FKAN model outperforms three state-of-the-art baseline schemes, and improves the peak signal-to-noise ratio (PSNR) and structural similarity index measure (SSIM) for the image representation task and intersection over union (IoU) for the 3D occupancy volume representation task, respectively. The code is available at github.com/Ali-Meh619/FKAN.

Alvin Kimbowa, Arjun Parmar, Ibrahim Mujtaba et al.

Objective: To develop a robust and compact deep learning model for automated knee cartilage segmentation on point-of-care ultrasound (POCUS) devices. Methods: We propose MonoUNet, an ultra-compact U-Net consisting of (i) an aggressively reduced backbone with an asymmetric decoder, (ii) a trainable monogenic block that extracts multi-scale local phase features, and (iii) a gated feature injection mechanism that integrates these features into the encoder stages to reduce sensitivity to variations in ultrasound image appearance and improve robustness across devices. MonoUNet was evaluated on a multi-site, multi-device knee cartilage ultrasound dataset acquired using cart-based, portable, and handheld POCUS devices. Results: Overall, MonoUNet outperformed existing lightweight segmentation models, with average Dice scores ranging from 92.62% to 94.82% and mean average surface distance (MASD) values between 0.133 mm and 0.254 mm. MonoUNet reduces the number of parameters by 10x--700x and computational cost by 14x--2000x relative to existing lightweight models. MonoUNet cartilage outcomes showed excellent reliability and agreement with the manual outcomes: intraclass correlation coefficients (ICC$_{2,k})$=0.96 and bias=2.00% (0.047 mm) for average thickness, and ICC$_{2,k}$=0.99 and bias=0.80% (0.328 a.u.) for echo intensity. Conclusion: Incorporating trainable local phase features improves the robustness of highly compact neural networks for knee cartilage segmentation across varying acquisition settings and could support scalable ultrasound-based assessment and monitoring of knee osteoarthritis using POCUS devices. The code is publicly available at https://github.com/alvinkimbowa/monounet.

Aimon Rahman, Wele Gedara Chaminda Bandara, Jeya Maria Jose Valanarasu et al.

Due to imaging artifacts and low signal-to-noise ratio in ultrasound images, automatic bone surface segmentation networks often produce fragmented predictions that can hinder the success of ultrasound-guided computer-assisted surgical procedures. Existing pixel-wise predictions often fail to capture the accurate topology of bone tissues due to a lack of supervision to enforce connectivity. In this work, we propose an orientation-guided graph convolutional network to improve connectivity while segmenting the bone surface. We also propose an additional supervision on the orientation of the bone surface to further impose connectivity. We validated our approach on 1042 vivo US scans of femur, knee, spine, and distal radius. Our approach improves over the state-of-the-art methods by 5.01% in connectivity metric.

Aimon Rahman, Jeya Maria Jose Valanarasu, Ilker Hacihaliloglu et al.

Collective insights from a group of experts have always proven to outperform an individual's best diagnostic for clinical tasks. For the task of medical image segmentation, existing research on AI-based alternatives focuses more on developing models that can imitate the best individual rather than harnessing the power of expert groups. In this paper, we introduce a single diffusion model-based approach that produces multiple plausible outputs by learning a distribution over group insights. Our proposed model generates a distribution of segmentation masks by leveraging the inherent stochastic sampling process of diffusion using only minimal additional learning. We demonstrate on three different medical image modalities- CT, ultrasound, and MRI that our model is capable of producing several possible variants while capturing the frequencies of their occurrences. Comprehensive results show that our proposed approach outperforms existing state-of-the-art ambiguous segmentation networks in terms of accuracy while preserving naturally occurring variation. We also propose a new metric to evaluate the diversity as well as the accuracy of segmentation predictions that aligns with the interest of clinical practice of collective insights.

Aimon Rahman, Jeya Maria Jose Valanarasu, Ilker Hacihaliloglu et al.

Segmenting both bone surface and the corresponding acoustic shadow are fundamental tasks in ultrasound (US) guided orthopedic procedures. However, these tasks are challenging due to minimal and blurred bone surface response in US images, cross-machine discrepancy, imaging artifacts, and low signal-to-noise ratio. Notably, bone shadows are caused by a significant acoustic impedance mismatch between the soft tissue and bone surfaces. To leverage this mutual information between these highly related tasks, we propose a single end-to-end network with a shared transformer-based encoder and task independent decoders for simultaneous bone and shadow segmentation. To share complementary features, we propose a cross task feature transfer block which learns to transfer meaningful features from decoder of shadow segmentation to that of bone segmentation and vice-versa. We also introduce a correspondence consistency loss which makes sure that network utilizes the inter-dependency between the bone surface and its corresponding shadow to refine the segmentation. Validation against expert annotations shows that the method outperforms the previous state-of-the-art for both bone surface and shadow segmentation.

Moein Heidari, Ali Mehrabian, Mohammad Amin Roohi et al.

Echocardiography interpretation requires integrating multi-view temporal evidence with quantitative measurements and guideline-grounded reasoning, yet existing foundation-model pipelines largely solve isolated subtasks and fail when tool outputs are noisy or values fall near clinical cutoffs. We propose Echo-CoPilot, an end-to-end agentic framework that combines a multi-perspective workflow with knowledge-graph guided measurement selection. Echo-CoPilot runs three independent ReAct-style agents, structural, pathological, and quantitative, that invoke specialized echocardiography tools to extract parameters while querying EchoKG to determine which measurements are required for the clinical question and which should be avoided. A self-contrast language model then compares the evidence-grounded perspectives, generates a discrepancy checklist, and re-queries EchoKG to apply the appropriate guideline thresholds and resolve conflicts, reducing hallucinated measurement selection and borderline flip-flops. On MIMICEchoQA, Echo-CoPilot provides higher accuracy compared to SOTA baselines and, under a stochasticity stress test, achieves higher reliability through more consistent conclusions and fewer answer changes across repeated runs. Our code is publicly available at~\href{https://github.com/moeinheidari7829/Echo-CoPilot}{\textcolor{magenta}{GitHub}}.

Xiao Qi, David J. Foran, John L. Nosher et al.

Under the global COVID-19 crisis, accurate diagnosis of COVID-19 from Chest X-ray (CXR) images is critical. To reduce intra- and inter-observer variability, during the radiological assessment, computer-aided diagnostic tools have been utilized to supplement medical decision-making and subsequent disease management. Computational methods with high accuracy and robustness are required for rapid triaging of patients and aiding radiologists in the interpretation of the collected data. In this study, we propose a novel multi-feature fusion network using parallel attention blocks to fuse the original CXR images and local-phase feature-enhanced CXR images at multi-scales. We examine our model on various COVID-19 datasets acquired from different organizations to assess the generalization ability. Our experiments demonstrate that our method achieves state-of-art performance and has improved generalization capability, which is crucial for widespread deployment.

Alvin Kimbowa, Moein Heidari, David Liu et al.

While U-Net architectures remain the gold standard for medical image segmentation, their deployment in resource-constrained environments demands aggressive model compression. However, finding an optimally efficient configuration is computationally prohibitive, typically requiring exhaustive train-and-evaluate cycles to find the smallest model that maintains peak performance. In this paper, we introduce a training-free selection framework to automatically identify ultralightweight, dataset-specific U-Net configurations directly at initialization. We observe that systematically scaling down U-Net channel width induces a sharp transition from a stable performance plateau to representational capacity collapse. To pinpoint this boundary without training, we propose a Jacobian-based sensitivity metric that scores discrete, width-capped U-Net variants using a small set of unlabeled images. By analyzing the total variation of this sensitivity curve, we isolate the smallest stable configuration, which we denote as XTinyU-Net. Evaluated across six diverse medical datasets within the nnU-Net framework, XTinyU-Net achieves segmentation accuracy comparable to the heavy nnU-Net baseline with 400x-1600x fewer parameters, and outperforms contemporary lightweight architectures while utilizing 5x-72x fewer parameters. Code is publicly accessible on https://github.com/alvinkimbowa/nntinyunet.git.

Moein Heidari, Reza Azad, Sina Ghorbani Kolahi et al.

Intrigued by the inherent ability of the human visual system to identify salient regions in complex scenes, attention mechanisms have been seamlessly integrated into various Computer Vision (CV) tasks. Building upon this paradigm, Vision Transformer (ViT) networks exploit attention mechanisms for improved efficiency. This review navigates the landscape of redesigned attention mechanisms within ViTs, aiming to enhance their performance. This paper provides a comprehensive exploration of techniques and insights for designing attention mechanisms, systematically reviewing recent literature in the field of CV. This survey begins with an introduction to the theoretical foundations and fundamental concepts underlying attention mechanisms. We then present a systematic taxonomy of various attention mechanisms within ViTs, employing redesigned approaches. A multi-perspective categorization is proposed based on their application, objectives, and the type of attention applied. The analysis includes an exploration of the novelty, strengths, weaknesses, and an in-depth evaluation of the different proposed strategies. This culminates in the development of taxonomies that highlight key properties and contributions. Finally, we gather the reviewed studies along with their available open-source implementations at our \href{https://github.com/mindflow-institue/Awesome-Attention-Mechanism-in-Medical-Imaging}{GitHub}\footnote{\url{https://github.com/xmindflow/Awesome-Attention-Mechanism-in-Medical-Imaging}}. We aim to regularly update it with the most recent relevant papers.

Dina Salama, Mohamed Mahmoud, Nourhan Bayasi et al.

Thyroid ultrasound is the first-line exam for assessing thyroid nodules and determining whether biopsy is warranted. In routine reporting, radiologists produce two coupled outputs: a nodule contour for measurement and a TI-RADS risk category based on sonographic criteria. Yet both contouring style and risk grading vary across readers, creating inconsistent supervision that can degrade standard learning pipelines. In this paper, we address this workflow with a clinically guided multitask framework that jointly predicts the nodule mask and TI-RADS category within a single model. To ground risk prediction in clinically meaningful evidence, we guide the classification embedding using a compact TI-RADS aligned radiomics target during training, while preserving complementary deep features for discriminative performance. However, under annotator variability, naive multitask optimization often fails not because the tasks are unrelated, but because their gradients compete within the shared representation. To make this competition explicit and controllable, we introduce RLAR, a representation-level adversarial gradient regularizer. Rather than performing parameter-level gradient surgery, RLAR uses each task's normalized adversarial direction in latent space as a geometric probe of task sensitivity and penalizes excessive angular alignment between task-specific adversarial directions. On a public TI-RADS dataset, our clinically guided multitask model with RLAR consistently improves risk stratification while maintaining segmentation quality compared to single-task training and conventional multitask baselines. Code and pretrained models will be released.

Yasamin Medghalchi, Milad Yazdani, Amirhossein Dabiriaghdam et al.

Ultrasound is widely used in clinical practice due to its portability, cost-effectiveness, safety, and real-time imaging capabilities. However, image acquisition and interpretation remain highly operator dependent, motivating the development of robust AI-assisted analysis methods. Vision-language models (VLMs) have recently demonstrated strong multimodal reasoning capabilities and competitive performance in medical image analysis, including ultrasound. However, emerging evidence highlights significant concerns about their trustworthiness. In particular, adversarial robustness is critical because Med-VLMs operate via natural-language instructions, rendering prompt formulation a realistic and practically exploitable point of vulnerability. Small variations (typos, shorthand, underspecified requests, or ambiguous wording) can meaningfully shift model outputs. We propose a scalable adversarial evaluation framework that leverages a large language model (LLM) to generate clinically plausible adversarial prompt variants via "humanized" rewrites and minimal edits that mimic routine clinical communication. Using ultrasound multiple-choice question answering benchmarks, we systematically assess the vulnerability of SOTA Med-VLMs to these attacks, examine how attacker LLM capacity influences attack success, analyze the relationship between attack success and model confidence, and identify consistent failure patterns across models. Our results highlight realistic robustness gaps that must be addressed for safe clinical translation. Code will be released publicly following the review process.

Pooria Ashrafian, Milad Yazdani, Moein Heidari et al.

High-quality, large-scale data is essential for robust deep learning models in medical applications, particularly ultrasound image analysis. Diffusion models facilitate high-fidelity medical image generation, reducing the costs associated with acquiring and annotating new images. This paper utilizes recent vision-language models to produce diverse and realistic synthetic echocardiography image data, preserving key features of the original images guided by textual and semantic label maps. Specifically, we investigate three potential avenues: unconditional generation, generation guided by text, and a hybrid approach incorporating both textual and semantic supervision. We show that the rich contextual information present in the synthesized data potentially enhances the accuracy and interpretability of downstream tasks, such as echocardiography segmentation and classification with improved metrics and faster convergence. Our implementation with checkpoints, prompts, and the created synthetic dataset will be publicly available at \href{https://github.com/Pooria90/DiffEcho}{GitHub}.

Yasamin Medghalchi, Moein Heidari, Clayton Allard et al.

Deep neural networks (DNNs) offer significant promise for improving breast cancer diagnosis in medical imaging. However, these models are highly susceptible to adversarial attacks--small, imperceptible changes that can mislead classifiers--raising critical concerns about their reliability and security. Traditional attacks rely on fixed-norm perturbations, misaligning with human perception. In contrast, diffusion-based attacks require pre-trained models, demanding substantial data when these models are unavailable, limiting practical use in data-scarce scenarios. In medical imaging, however, this is often unfeasible due to the limited availability of datasets. Building on recent advancements in learnable prompts, we propose Prompt2Perturb (P2P), a novel language-guided attack method capable of generating meaningful attack examples driven by text instructions. During the prompt learning phase, our approach leverages learnable prompts within the text encoder to create subtle, yet impactful, perturbations that remain imperceptible while guiding the model towards targeted outcomes. In contrast to current prompt learning-based approaches, our P2P stands out by directly updating text embeddings, avoiding the need for retraining diffusion models. Further, we leverage the finding that optimizing only the early reverse diffusion steps boosts efficiency while ensuring that the generated adversarial examples incorporate subtle noise, thus preserving ultrasound image quality without introducing noticeable artifacts. We show that our method outperforms state-of-the-art attack techniques across three breast ultrasound datasets in FID and LPIPS. Moreover, the generated images are both more natural in appearance and more effective compared to existing adversarial attacks. Our code will be publicly available https://github.com/yasamin-med/P2P.

Yasamin Medghalchi, Niloufar Zakariaei, Arman Rahmim et al.

The effectiveness of Deep Neural Networks (DNNs) heavily relies on the abundance and accuracy of available training data. However, collecting and annotating data on a large scale is often both costly and time-intensive, particularly in medical cases where practitioners are already occupied with their duties. Moreover, ensuring that the model remains robust across various scenarios of image capture is crucial in medical domains, especially when dealing with ultrasound images that vary based on the settings of different devices and the manual operation of the transducer. To address this challenge, we introduce a novel pipeline called MEDDAP, which leverages Stable Diffusion (SD) models to augment existing small datasets by automatically generating new informative labeled samples. Pretrained checkpoints for SD are typically based on natural images, and training them for medical images requires significant GPU resources due to their heavy parameters. To overcome this challenge, we introduce USLoRA (Ultrasound Low-Rank Adaptation), a novel fine-tuning method tailored specifically for ultrasound applications. USLoRA allows for selective fine-tuning of weights within SD, requiring fewer than 0.1\% of parameters compared to fully fine-tuning only the UNet portion of SD. To enhance dataset diversity, we incorporate different adjectives into the generation process prompts, thereby desensitizing the classifiers to intensity changes across different images. This approach is inspired by clinicians' decision-making processes regarding breast tumors, where tumor shape often plays a more crucial role than intensity. In conclusion, our pipeline not only outperforms classifiers trained on the original dataset but also demonstrates superior performance when encountering unseen datasets. The source code is available at https://github.com/yasamin-med/MEDDAP.

Milad Yazdani, Yasamin Medghalchi, Pooria Ashrafian et al.

Deep learning models have emerged as a powerful tool for various medical applications. However, their success depends on large, high-quality datasets that are challenging to obtain due to privacy concerns and costly annotation. Generative models, such as diffusion models, offer a potential solution by synthesizing medical images, but their practical adoption is hindered by long inference times. In this paper, we propose the use of an optimal transport flow matching approach to accelerate image generation. By introducing a straighter mapping between the source and target distribution, our method significantly reduces inference time while preserving and further enhancing the quality of the outputs. Furthermore, this approach is highly adaptable, supporting various medical imaging modalities, conditioning mechanisms (such as class labels and masks), and different spatial dimensions, including 2D and 3D. Beyond image generation, it can also be applied to related tasks such as image enhancement. Our results demonstrate the efficiency and versatility of this framework, making it a promising advancement for medical imaging applications. Code with checkpoints and a synthetic dataset (beneficial for classification and segmentation) is now available on: https://github.com/milad1378yz/MOTFM.

Morteza Alizadeh, Mehrdad Oveisi, Sonya Falahati et al.

Machine learning (ML) models rely heavily on consistent and accurate performance metrics to evaluate and compare their effectiveness. However, existing libraries often suffer from fragmentation, inconsistent implementations, and insufficient data validation protocols, leading to unreliable results. Existing libraries have often been developed independently and without adherence to a unified standard, particularly concerning the specific tasks they aim to support. As a result, each library tends to adopt its conventions for metric computation, input/output formatting, error handling, and data validation protocols. This lack of standardization leads to both implementation differences (ID) and reporting differences (RD), making it difficult to compare results across frameworks or ensure reliable evaluations. To address these issues, we introduce AllMetrics, an open-source unified Python library designed to standardize metric evaluation across diverse ML tasks, including regression, classification, clustering, segmentation, and image-to-image translation. The library implements class-specific reporting for multi-class tasks through configurable parameters to cover all use cases, while incorporating task-specific parameters to resolve metric computation discrepancies across implementations. Various datasets from domains like healthcare, finance, and real estate were applied to our library and compared with Python, Matlab, and R components to identify which yield similar results. AllMetrics combines a modular Application Programming Interface (API) with robust input validation mechanisms to ensure reproducibility and reliability in model evaluation. This paper presents the design principles, architectural components, and empirical analyses demonstrating the ability to mitigate evaluation errors and to enhance the trustworthiness of ML workflows.

Moein Heidari, Afshin Bozorgpour, AmirHossein Zarif-Fakharnia et al.

Left ventricular ejection fraction (LVEF) is a critical metric for assessing cardiac function, widely used in diagnosing heart failure and guiding clinical decisions. Despite its importance, conventional LVEF estimation remains time-consuming and operator-dependent. Recent deep learning advancements have enhanced automation, yet many existing models are computationally demanding, hindering their feasibility for real-time clinical applications. Additionally, the interplay between spatial and temporal features is crucial for accurate estimation but is often overlooked. In this work, we propose Echo-E$^3$Net, an efficient Endo-Epi spatio-temporal network tailored for LVEF estimation. Our method introduces the Endo-Epi Cardial Border Detector (E$^2$CBD) module, which enhances feature extraction by leveraging spatial and temporal landmark cues. Complementing this, the Endo-Epi Feature Aggregator (E$^2$FA) distills statistical descriptors from backbone feature maps, refining the final EF prediction. These modules, along with a multi-component loss function tailored to align with the clinical definition of EF, collectively enhance spatial-temporal representation learning, ensuring robust and efficient EF estimation. We evaluate Echo-E$^3$Net on the EchoNet-Dynamic dataset, achieving a RMSE of 5.15 and an R$^2$ score of 0.82, setting a new benchmark in efficiency with 6.8 million parameters and only 8.49G Flops. Our model operates without pre-training, data augmentation, or ensemble methods, making it well-suited for real-time point-of-care ultrasound (PoCUS) applications. Our Code is publicly available on~\href{https://github.com/moeinheidari7829/Echo-E3Net}{\textcolor{magenta}{GitHub}}.

Moein Heidari, Yasamin Medghalchi, Mahdi Khoursha et al.

Parameter-efficient fine-tuning (PEFT) has gained widespread adoption across various applications. Among PEFT techniques, Low-Rank Adaptation (LoRA) and its extensions have emerged as particularly effective, allowing efficient model adaptation while significantly reducing computational overhead. However, existing approaches typically rely on global low-rank factorizations, which overlook local or multi-scale structure, failing to capture complex patterns in the weight updates. To address this, we propose WaRA, a novel PEFT method that leverages wavelet transforms to decompose the weight update matrix into a multi-resolution representation. By performing low-rank factorization in the wavelet domain and reconstructing updates through an inverse transform, WaRA obtains compressed adaptation parameters that harness multi-resolution analysis, enabling it to capture both coarse and fine-grained features while providing greater flexibility and sparser representations than standard LoRA. Through comprehensive experiments and analysis, we demonstrate that WaRA performs superior on diverse vision tasks, including image generation, classification, and semantic segmentation, significantly enhancing generated image quality while reducing computational complexity. Although WaRA was primarily designed for vision tasks, we further showcase its effectiveness in language tasks, highlighting its broader applicability and generalizability. The code is publicly available at \href{GitHub}{https://github.com/moeinheidari7829/WaRA}.

Afshin Bozorgpour, Sina Ghorbani Kolahi, Reza Azad et al.

Medical image segmentation, particularly in multi-domain scenarios, requires precise preservation of anatomical structures across diverse representations. While deep learning has advanced this field, existing models often struggle with accurate boundary representation, variability in organ morphology, and information loss during downsampling, limiting their accuracy and robustness. To address these challenges, we propose the Context Enhancement Network (CENet), a novel segmentation framework featuring two key innovations. First, the Dual Selective Enhancement Block (DSEB) integrated into skip connections enhances boundary details and improves the detection of smaller organs in a context-aware manner. Second, the Context Feature Attention Module (CFAM) in the decoder employs a multi-scale design to maintain spatial integrity, reduce feature redundancy, and mitigate overly enhanced representations. Extensive evaluations on both radiology and dermoscopic datasets demonstrate that CENet outperforms state-of-the-art (SOTA) methods in multi-organ segmentation and boundary detail preservation, offering a robust and accurate solution for complex medical image analysis tasks. The code is publicly available at https://github.com/xmindflow/cenet.

Moein Heidari, Sina Ghorbani Kolahi, Sanaz Karimijafarbigloo et al.

Sequence modeling plays a vital role across various domains, with recurrent neural networks being historically the predominant method of performing these tasks. However, the emergence of transformers has altered this paradigm due to their superior performance. Built upon these advances, transformers have conjoined CNNs as two leading foundational models for learning visual representations. However, transformers are hindered by the $\mathcal{O}(N^2)$ complexity of their attention mechanisms, while CNNs lack global receptive fields and dynamic weight allocation. State Space Models (SSMs), specifically the \textit{\textbf{Mamba}} model with selection mechanisms and hardware-aware architecture, have garnered immense interest lately in sequential modeling and visual representation learning, challenging the dominance of transformers by providing infinite context lengths and offering substantial efficiency maintaining linear complexity in the input sequence. Capitalizing on the advances in computer vision, medical imaging has heralded a new epoch with Mamba models. Intending to help researchers navigate the surge, this survey seeks to offer an encyclopedic review of Mamba models in medical imaging. Specifically, we start with a comprehensive theoretical review forming the basis of SSMs, including Mamba architecture and its alternatives for sequence modeling paradigms in this context. Next, we offer a structured classification of Mamba models in the medical field and introduce a diverse categorization scheme based on their application, imaging modalities, and targeted organs. Finally, we summarize key challenges, discuss different future research directions of the SSMs in the medical domain, and propose several directions to fulfill the demands of this field. In addition, we have compiled the studies discussed in this paper along with their open-source implementations on our GitHub repository.

Jeya Maria Jose Valanarasu, Poojan Oza, Ilker Hacihaliloglu et al.

Over the past decade, Deep Convolutional Neural Networks have been widely adopted for medical image segmentation and shown to achieve adequate performance. However, due to the inherent inductive biases present in the convolutional architectures, they lack understanding of long-range dependencies in the image. Recently proposed Transformer-based architectures that leverage self-attention mechanism encode long-range dependencies and learn representations that are highly expressive. This motivates us to explore Transformer-based solutions and study the feasibility of using Transformer-based network architectures for medical image segmentation tasks. Majority of existing Transformer-based network architectures proposed for vision applications require large-scale datasets to train properly. However, compared to the datasets for vision applications, for medical imaging the number of data samples is relatively low, making it difficult to efficiently train transformers for medical applications. To this end, we propose a Gated Axial-Attention model which extends the existing architectures by introducing an additional control mechanism in the self-attention module. Furthermore, to train the model effectively on medical images, we propose a Local-Global training strategy (LoGo) which further improves the performance. Specifically, we operate on the whole image and patches to learn global and local features, respectively. The proposed Medical Transformer (MedT) is evaluated on three different medical image segmentation datasets and it is shown that it achieves better performance than the convolutional and other related transformer-based architectures. Code: https://github.com/jeya-maria-jose/Medical-Transformer

Xiao Qi, Lloyd Brown, David J. Foran et al.

Recently, the outbreak of the novel Coronavirus disease 2019 (COVID-19) pandemic has seriously endangered human health and life. Due to limited availability of test kits, the need for auxiliary diagnostic approach has increased. Recent research has shown radiography of COVID-19 patient, such as CT and X-ray, contains salient information about the COVID-19 virus and could be used as an alternative diagnosis method. Chest X-ray (CXR) due to its faster imaging time, wide availability, low cost and portability gains much attention and becomes very promising. Computational methods with high accuracy and robustness are required for rapid triaging of patients and aiding radiologist in the interpretation of the collected data. In this study, we design a novel multi-feature convolutional neural network (CNN) architecture for multi-class improved classification of COVID-19 from CXR images. CXR images are enhanced using a local phase-based image enhancement method. The enhanced images, together with the original CXR data, are used as an input to our proposed CNN architecture. Using ablation studies, we show the effectiveness of the enhanced images in improving the diagnostic accuracy. We provide quantitative evaluation on two datasets and qualitative results for visual inspection. Quantitative evaluation is performed on data consisting of 8,851 normal (healthy), 6,045 pneumonia, and 3,323 Covid-19 CXR scans. In Dataset-1, our model achieves 95.57\% average accuracy for a three classes classification, 99\% precision, recall, and F1-scores for COVID-19 cases. For Dataset-2, we have obtained 94.44\% average accuracy, and 95\% precision, recall, and F1-scores for detection of COVID-19. Our proposed multi-feature guided CNN achieves improved results compared to single-feature CNN proving the importance of the local phase-based CXR image enhancement (https://github.com/endiqq/Fus-CNNs_COVID-19).

Jeya Maria Jose Valanarasu, Vishwanath A. Sindagi, Ilker Hacihaliloglu et al.

Most methods for medical image segmentation use U-Net or its variants as they have been successful in most of the applications. After a detailed analysis of these "traditional" encoder-decoder based approaches, we observed that they perform poorly in detecting smaller structures and are unable to segment boundary regions precisely. This issue can be attributed to the increase in receptive field size as we go deeper into the encoder. The extra focus on learning high level features causes the U-Net based approaches to learn less information about low-level features which are crucial for detecting small structures. To overcome this issue, we propose using an overcomplete convolutional architecture where we project our input image into a higher dimension such that we constrain the receptive field from increasing in the deep layers of the network. We design a new architecture for image segmentation- KiU-Net which has two branches: (1) an overcomplete convolutional network Kite-Net which learns to capture fine details and accurate edges of the input, and (2) U-Net which learns high level features. Furthermore, we also propose KiU-Net 3D which is a 3D convolutional architecture for volumetric segmentation. We perform a detailed study of KiU-Net by performing experiments on five different datasets covering various image modalities like ultrasound (US), magnetic resonance imaging (MRI), computed tomography (CT), microscopic and fundus images. The proposed method achieves a better performance as compared to all the recent methods with an additional benefit of fewer parameters and faster convergence. Additionally, we also demonstrate that the extensions of KiU-Net based on residual blocks and dense blocks result in further performance improvements. The implementation of KiU-Net can be found here: https://github.com/jeya-maria-jose/KiU-Net-pytorch

Jeya Maria Jose, Vishwanath Sindagi, Ilker Hacihaliloglu et al.

Due to its excellent performance, U-Net is the most widely used backbone architecture for biomedical image segmentation in the recent years. However, in our studies, we observe that there is a considerable performance drop in the case of detecting smaller anatomical landmarks with blurred noisy boundaries. We analyze this issue in detail, and address it by proposing an over-complete architecture (Ki-Net) which involves projecting the data onto higher dimensions (in the spatial sense). This network, when augmented with U-Net, results in significant improvements in the case of segmenting small anatomical landmarks and blurred noisy boundaries while obtaining better overall performance. Furthermore, the proposed network has additional benefits like faster convergence and fewer number of parameters. We evaluate the proposed method on the task of brain anatomy segmentation from 2D Ultrasound (US) of preterm neonates, and achieve an improvement of around 4% in terms of the DICE accuracy and Jaccard index as compared to the standard-U-Net, while outperforming the recent best methods by 2%. Code: https://github.com/jeya-maria-jose/KiU-Net-pytorch .

Mohammad R. Salmanpour, Amin Mousavi, Yixi Xu et al.

Purpose: This study examines the core traits of image-to-image translation (I2I) networks, focusing on their effectiveness and adaptability in everyday clinical settings. Methods: We have analyzed data from 794 patients diagnosed with prostate cancer (PCa), using ten prominent 2D/3D I2I networks to convert ultrasound (US) images into MRI scans. We also introduced a new analysis of Radiomic features (RF) via the Spearman correlation coefficient to explore whether networks with high performance (SSIM>85%) could detect subtle RFs. Our study further examined synthetic images by 7 invited physicians. As a final evaluation study, we have investigated the improvement that are achieved using the synthetic MRI data on two traditional machine learning and one deep learning method. Results: In quantitative assessment, 2D-Pix2Pix network substantially outperformed the other 7 networks, with an average SSIM~0.855. The RF analysis revealed that 76 out of 186 RFs were identified using the 2D-Pix2Pix algorithm alone, although half of the RFs were lost during the translation process. A detailed qualitative review by 7 medical doctors noted a deficiency in low-level feature recognition in I2I tasks. Furthermore, the study found that synthesized image-based classification outperformed US image-based classification with an average accuracy and AUC~0.93. Conclusion: This study showed that while 2D-Pix2Pix outperformed cutting-edge networks in low-level feature discovery and overall error and similarity metrics, it still requires improvement in low-level feature performance, as highlighted by Group 3. Further, the study found using synthetic image-based classification outperformed original US image-based methods.

Mohammad R. Salmanpour, Sajad Amiri, Sara Gharibi et al.

We investigate the connection between visual semantic features defined in PI-RADS and associated risk factors, moving beyond abnormal imaging findings, establishing a shared framework between medical and AI professionals by creating a standardized dictionary of biological/radiological RFs. Subsequently, 6 interpretable and seven complex classifiers, linked with nine interpretable feature selection algorithms (FSA) applied to risk factors, were extracted from segmented lesions in T2-weighted imaging (T2WI), diffusion-weighted imaging (DWI), and apparent diffusion coefficient (ADC) multiparametric-prostate MRI sequences to predict the UCLA scores. We then utilized the created dictionary to interpret the best-predictive models. Combining T2WI, DWI, and ADC with FSAs including ANOVA F-test, Correlation Coefficient, and Fisher Score, and utilizing logistic regression, identified key features: The 90th percentile from T2WI, which captures hypo-intensity related to prostate cancer risk; Variance from T2WI, indicating lesion heterogeneity; shape metrics including Least Axis Length and Surface Area to Volume ratio from ADC, describing lesion shape and compactness; and Run Entropy from ADC, reflecting texture consistency. This approach achieved the highest average accuracy of 0.78, significantly outperforming single-sequence methods (p-value<0.05). The developed dictionary for Prostate-MRI (PM1.0) serves as a common language, fosters collaboration between clinical professionals and AI developers to advance trustworthy AI solutions that support reliable/interpretable clinical decisions.

Mohammad R. Salmanpour, Somayeh Sadat Mehrnia, Sajad Jabarzadeh Ghandilu et al.

Machine learning (ML), including deep learning (DL) and radiomics-based methods, is increasingly used for cancer outcome prediction with PET and SPECT imaging. However, the comparative performance of handcrafted radiomics features (HRF), deep radiomics features (DRF), DL models, and hybrid fusion approaches remains inconsistent across clinical applications. This systematic review analyzed 226 studies published from 2020 to 2025 that applied ML to PET or SPECT imaging for outcome prediction. Each study was evaluated using a 59-item framework covering dataset construction, feature extraction, validation methods, interpretability, and risk of bias. We extracted key details including model type, cancer site, imaging modality, and performance metrics such as accuracy and area under the curve (AUC). PET-based studies (95%) generally outperformed those using SPECT, likely due to higher spatial resolution and sensitivity. DRF models achieved the highest mean accuracy (0.862), while fusion models yielded the highest AUC (0.861). ANOVA confirmed significant differences in performance (accuracy: p=0.0006, AUC: p=0.0027). Common limitations included inadequate handling of class imbalance (59%), missing data (29%), and low population diversity (19%). Only 48% of studies adhered to IBSI standards. These findings highlight the need for standardized pipelines, improved data quality, and explainable AI to support clinical integration.

Mohammad R. Salmanpour, Amir Hossein Pouria, Sonia Falahati et al.

Background: CT imaging is vital for lung cancer management, offering detailed visualization for AI-based prognosis. However, supervised learning SL models require large labeled datasets, limiting their real-world application in settings with scarce annotations. Methods: We analyzed CT scans from 977 patients across 12 datasets extracting 1218 radiomics features using Laplacian of Gaussian and wavelet filters via PyRadiomics Dimensionality reduction was applied with 56 feature selection and extraction algorithms and 27 classifiers were benchmarked A semi supervised learning SSL framework with pseudo labeling utilized 478 unlabeled and 499 labeled cases Model sensitivity was tested in three scenarios varying labeled data in SL increasing unlabeled data in SSL and scaling both from 10 percent to 100 percent SHAP analysis was used to interpret predictions Cross validation and external testing in two cohorts were performed. Results: SSL outperformed SL, improving overall survival prediction by up to 17 percent. The top SSL model, Random Forest plus XGBoost classifier, achieved 0.90 accuracy in cross-validation and 0.88 externally. SHAP analysis revealed enhanced feature discriminability in both SSL and SL, especially for Class 1 survival greater than 4 years. SSL showed strong performance with only 10 percent labeled data, with more stable results compared to SL and lower variance across external testing, highlighting SSL's robustness and cost effectiveness. Conclusion: We introduced a cost-effective, stable, and interpretable SSL framework for CT-based survival prediction in lung cancer, improving performance, generalizability, and clinical readiness by integrating SHAP explainability and leveraging unlabeled data.

Moein Heidari, Ehsan Khodapanah Aghdam, Alexander Manzella et al.

The retroperitoneum hosts a variety of tumors, including rare benign and malignant types, which pose diagnostic and treatment challenges due to their infrequency and proximity to vital structures. Estimating tumor volume is difficult due to their irregular shapes, and manual segmentation is time-consuming. Automatic segmentation using U-Net and its variants, incorporating Vision Transformer (ViT) elements, has shown promising results but struggles with high computational demands. To address this, architectures like the Mamba State Space Model (SSM) and Extended Long-Short Term Memory (xLSTM) offer efficient solutions by handling long-range dependencies with lower resource consumption. This study evaluates U-Net enhancements, including CNN, ViT, Mamba, and xLSTM, on a new in-house CT dataset and a public organ segmentation dataset. The proposed ViLU-Net model integrates Vi-blocks for improved segmentation. Results highlight xLSTM's efficiency in the U-Net framework. The code is publicly accessible on GitHub.

Mohammad R. Salmanpour, Morteza Alizadeh, Ghazal Mousavi et al.

This study evaluates metrics for tasks such as classification, regression, clustering, correlation analysis, statistical tests, segmentation, and image-to-image (I2I) translation. Metrics were compared across Python libraries, R packages, and Matlab functions to assess their consistency and highlight discrepancies. The findings underscore the need for a unified roadmap to standardize metrics, ensuring reliable and reproducible ML evaluations across platforms. This study examined a wide range of evaluation metrics across various tasks and found only some to be consistent across platforms, such as (i) Accuracy, Balanced Accuracy, Cohens Kappa, F-beta Score, MCC, Geometric Mean, AUC, and Log Loss in binary classification; (ii) Accuracy, Cohens Kappa, and F-beta Score in multi-class classification; (iii) MAE, MSE, RMSE, MAPE, Explained Variance, Median AE, MSLE, and Huber in regression; (iv) Davies-Bouldin Index and Calinski-Harabasz Index in clustering; (v) Pearson, Spearman, Kendall's Tau, Mutual Information, Distance Correlation, Percbend, Shepherd, and Partial Correlation in correlation analysis; (vi) Paired t-test, Chi-Square Test, ANOVA, Kruskal-Wallis Test, Shapiro-Wilk Test, Welchs t-test, and Bartlett's test in statistical tests; (vii) Accuracy, Precision, and Recall in 2D segmentation; (viii) Accuracy in 3D segmentation; (ix) MAE, MSE, RMSE, and R-Squared in 2D-I2I translation; and (x) MAE, MSE, and RMSE in 3D-I2I translation. Given observation of discrepancies in a number of metrics (e.g. precision, recall and F1 score in binary classification, WCSS in clustering, multiple statistical tests, and IoU in segmentation, amongst multiple metrics), this study concludes that ML evaluation metrics require standardization and recommends that future research use consistent metrics for different tasks to effectively compare ML techniques and solutions.

Sajad Amiri, Shahram Taeb, Sara Gharibi et al.

Gadolinium-based contrast agents (GBCAs) are central to glioma imaging but raise safety, cost, and accessibility concerns. Predicting contrast enhancement from non-contrast MRI using machine learning (ML) offers a safer alternative, as enhancement reflects tumor aggressiveness and informs treatment planning. Yet scanner and cohort variability hinder robust model selection. We propose a stability-aware framework to identify reproducible ML pipelines for multicenter prediction of glioma MRI contrast enhancement. We analyzed 1,446 glioma cases from four TCIA datasets (UCSF-PDGM, UPENN-GB, BRATS-Africa, BRATS-TCGA-LGG). Non-contrast T1WI served as input, with enhancement derived from paired post-contrast T1WI. Using PyRadiomics under IBSI standards, 108 features were extracted and combined with 48 dimensionality reduction methods and 25 classifiers, yielding 1,200 pipelines. Rotational validation was trained on three datasets and tested on the fourth. Cross-validation prediction accuracies ranged from 0.91 to 0.96, with external testing achieving 0.87 (UCSF-PDGM), 0.98 (UPENN-GB), and 0.95 (BRATS-Africa), with an average of 0.93. F1, precision, and recall were stable (0.87 to 0.96), while ROC-AUC varied more widely (0.50 to 0.82), reflecting cohort heterogeneity. The MI linked with ETr pipeline consistently ranked highest, balancing accuracy and stability. This framework demonstrates that stability-aware model selection enables reliable prediction of contrast enhancement from non-contrast glioma MRI, reducing reliance on GBCAs and improving generalizability across centers. It provides a scalable template for reproducible ML in neuro-oncology and beyond.

Arman Gorji, Nima Sanati, Amir Hossein Pouria et al.

Radiomics-based AI models show promise for breast cancer diagnosis but often lack interpretability, limiting clinical adoption. This study addresses the gap between radiomic features (RF) and the standardized BI-RADS lexicon by proposing a dual-dictionary framework. First, a Clinically-Informed Feature Interpretation Dictionary (CIFID) was created by mapping 56 RFs to BI-RADS descriptors (shape, margin, internal enhancement) through literature and expert review. The framework was applied to classify triple-negative breast cancer (TNBC) versus non-TNBC using dynamic contrast-enhanced MRI from a multi-institutional cohort of 1,549 patients. We trained 27 machine learning classifiers with 27 feature selection methods. SHapley Additive exPlanations (SHAP) were used to interpret predictions and generate a complementary Data-Driven Feature Interpretation Dictionary (DDFID) for 52 additional RFs. The best model, combining Variance Inflation Factor (VIF) selection with Extra Trees Classifier, achieved an average cross-validation accuracy of 0.83. Key predictive RFs aligned with clinical knowledge: higher Sphericity (round/oval shape) and lower Busyness (more homogeneous enhancement) were associated with TNBC. The framework confirmed known imaging biomarkers and uncovered novel, interpretable associations. This dual-dictionary approach (BM1.0) enhances AI model transparency and supports the integration of RFs into routine breast cancer diagnosis and personalized care.

Mohammad R. Salmanpour, Seyed Mohammad Piri, Somayeh Sadat Mehrnia et al.

Artificial intelligence (AI) holds strong potential for medical diagnostics, yet its clinical adoption is limited by a lack of interpretability and generalizability. This study introduces the Pathobiological Dictionary for Liver Cancer (LCP1.0), a practical framework designed to translate complex Pathomics and Radiomics Features (PF and RF) into clinically meaningful insights aligned with existing diagnostic workflows. QuPath and PyRadiomics, standardized according to IBSI guidelines, were used to extract 333 imaging features from hepatocellular carcinoma (HCC) tissue samples, including 240 PF-based-cell detection/intensity, 74 RF-based texture, and 19 RF-based first-order features. Expert-defined ROIs from the public dataset excluded artifact-prone areas, and features were aggregated at the case level. Their relevance to the WHO grading system was assessed using multiple classifiers linked with feature selectors. The resulting dictionary was validated by 8 experts in oncology and pathology. In collaboration with 10 domain experts, we developed a Pathobiological dictionary of imaging features such as PFs and RF. In our study, the Variable Threshold feature selection algorithm combined with the SVM model achieved the highest accuracy (0.80, P-value less than 0.05), selecting 20 key features, primarily clinical and pathomics traits such as Centroid, Cell Nucleus, and Cytoplasmic characteristics. These features, particularly nuclear and cytoplasmic, were strongly associated with tumor grading and prognosis, reflecting atypia indicators like pleomorphism, hyperchromasia, and cellular orientation.The LCP1.0 provides a clinically validated bridge between AI outputs and expert interpretation, enhancing model transparency and usability. Aligning AI-derived features with clinical semantics supports the development of interpretable, trustworthy diagnostic tools for liver cancer pathology.

Yuetong Yu, Ruiyang Ge, Ilker Hacihaliloglu et al.

Background: Data driven stratification of patients into biologically informed subtypes holds promise for precision neuropsychiatry, yet neuroimaging-based clustering methods often fail to generalize across cohorts. While algorithmic innovations have focused on model complexity, the role of underlying dataset characteristics remains underexplored. We hypothesized that cluster separation, size imbalance, noise, and the direction and magnitude of disease-related effects in the input data critically determine both within-algorithm accuracy and reproducibility. Methods: We evaluated 4 widely used stratification algorithms, HYDRA, SuStaIn, SmileGAN, and SurrealGAN, on a suite of synthetic brain-morphometry cohorts derived from the Human Connectome Project Young Adult dataset. Three global transformation patterns were applied to 600 pseudo-patients against 508 controls, followed by 4 within-dataset variations varying cluster count (k=2-6), overlap, and effect magnitude. Algorithm performance was quantified by accuracy in recovering the known ground-truth clusters. Results: Across 122 synthetic scenarios, data complexity consistently outweighed algorithm choice in predicting stratification success. Well-separated clusters yielded high accuracy for all methods, whereas overlapping, unequal-sized, or subtle effects reduced accuracy by up to 50%. SuStaIn could not scale beyond 17 features, HYDRA's accuracy varied unpredictably with data heterogeneity. SmileGAN and SurrealGAN maintained robust pattern detection but did not assign discrete cluster labels to individuals. Conclusions: The study results demonstrate the impact of statistical properties of input data across algorithms and highlight the need for using realistic dataset distributions when new algorithms are being developed and suggest greater focus on data-centric strategies that actively shape and standardize the input distributions.

Alvin Kimbowa, Arjun Parmar, Maziar Badii et al.

Automated knee cartilage segmentation using point-of-care ultrasound devices and deep-learning networks has the potential to enhance the management of knee osteoarthritis. However, segmentation algorithms often struggle with domain shifts caused by variations in ultrasound devices and acquisition parameters, limiting their generalizability. In this paper, we propose Mono2D, a monogenic layer that extracts multi-scale, contrast- and intensity-invariant local phase features using trainable bandpass quadrature filters. This layer mitigates domain shifts, improving generalization to out-of-distribution domains. Mono2D is integrated before the first layer of a segmentation network, and its parameters jointly trained alongside the network's parameters. We evaluated Mono2D on a multi-domain 2D ultrasound knee cartilage dataset for single-source domain generalization (SSDG). Our results demonstrate that Mono2D outperforms other SSDG methods in terms of Dice score and mean average surface distance. To further assess its generalizability, we evaluate Mono2D on a multi-site prostate MRI dataset, where it continues to outperform other SSDG methods, highlighting its potential to improve domain generalization in medical imaging. Nevertheless, further evaluation on diverse datasets is still necessary to assess its clinical utility.

Hui Che, Sumana Ramanathan, David Foran et al.

With the success of deep learning-based methods applied in medical image analysis, convolutional neural networks (CNNs) have been investigated for classifying liver disease from ultrasound (US) data. However, the scarcity of available large-scale labeled US data has hindered the success of CNNs for classifying liver disease from US data. In this work, we propose a novel generative adversarial network (GAN) architecture for realistic diseased and healthy liver US image synthesis. We adopt the concept of stacking to synthesize realistic liver US data. Quantitative and qualitative evaluation is performed on 550 in-vivo B-mode liver US images collected from 55 subjects. We also show that the synthesized images, together with real in vivo data, can be used to significantly improve the performance of traditional CNN architectures for Nonalcoholic fatty liver disease (NAFLD) classification.

Jeya Maria Jose V., Rajeev Yasarla, Puyang Wang et al.

Automatic segmentation of anatomical landmarks from ultrasound (US) plays an important role in the management of preterm neonates with a very low birth weight due to the increased risk of developing intraventricular hemorrhage (IVH) or other complications. One major problem in developing an automatic segmentation method for this task is the limited availability of annotated data. To tackle this issue, we propose a novel image synthesis method using multi-scale self attention generator to synthesize US images from various segmentation masks. We show that our method can synthesize high-quality US images for every manipulated segmentation label with qualitative and quantitative improvements over the recent state-of-the-art synthesis methods. Furthermore, for the segmentation task, we propose a novel method, called Confidence-guided Brain Anatomy Segmentation (CBAS) network, where segmentation and corresponding confidence maps are estimated at different scales. In addition, we introduce a technique which guides CBAS to learn the weights based on the confidence measure about the estimate. Extensive experiments demonstrate that the proposed method for both synthesis and segmentation tasks achieve significant improvements over the recent state-of-the-art methods. In particular, we show that the new synthesis framework can be used to generate realistic US images which can be used to improve the performance of a segmentation algorithm.

Puyang Wang, Vishal M. Patel, Ilker Hacihaliloglu

Various imaging artifacts, low signal-to-noise ratio, and bone surfaces appearing several millimeters in thickness have hindered the success of ultrasound (US) guided computer assisted orthopedic surgery procedures. In this work, a multi-feature guided convolutional neural network (CNN) architecture is proposed for simultaneous enhancement, segmentation, and classification of bone surfaces from US data. The proposed CNN consists of two main parts: a pre-enhancing net, that takes the concatenation of B-mode US scan and three filtered image features for the enhancement of bone surfaces, and a modified U-net with a classification layer. The proposed method was validated on 650 in vivo US scans collected using two US machines, by scanning knee, femur, distal radius and tibia bones. Validation, against expert annotation, achieved statistically significant improvements in segmentation of bone surfaces compared to state-of-the-art.

Jian Ren, Ilker Hacihaliloglu, Eric A. Singer et al.

Automatic and accurate Gleason grading of histopathology tissue slides is crucial for prostate cancer diagnosis, treatment, and prognosis. Usually, histopathology tissue slides from different institutions show heterogeneous appearances because of different tissue preparation and staining procedures, thus the predictable model learned from one domain may not be applicable to a new domain directly. Here we propose to adopt unsupervised domain adaptation to transfer the discriminative knowledge obtained from the source domain to the target domain without requiring labeling of images at the target domain. The adaptation is achieved through adversarial training to find an invariant feature space along with the proposed Siamese architecture on the target domain to add a regularization that is appropriate for the whole-slide images. We validate the method on two prostate cancer datasets and obtain significant classification improvement of Gleason scores as compared with the baseline models.