arXiv subjects

Afshin Bozorgpour

Publications and source records attributed to Afshin Bozorgpour.

At least 19 recordsLinked to original sources

arXiv2026

Echo-E$^3$Net: Efficient Endocardial Spatio-Temporal Network for Ejection Fraction Estimation

Left ventricular ejection fraction (LVEF) is a primary marker of cardiac function. However, routine estimation from endocardial measurements requires manual delineation at end-diastole (ED) and end-systole (ES), a process that is time-consuming and subject to inter-observer variability. Reliable automation is especially valuable for point-of-care ultrasound (POCUS), where computational resources are limited and acquisition quality varies. We propose Echo-E$^3$Net, an anatomy-guided spatio-temporal network that explicitly embeds cardiac anatomy into LVEF prediction. A dual-phase Endocardial Border Detector (E$^2$CBD) uses phase-specific cross-attention to localize ED/ES endocardial landmarks and produce phase-aware landmark embeddings, while an Endocardial Feature Aggregator (E$^2$FA) fuses these embeddings with global statistical descriptors of deep feature maps to refine EF regression. Training is guided by a lightweight geometric loss that uses ED and ES endocardial landmarks to regularize EF prediction. On EchoNet-Dynamic and a PSAX subset of EchoNet-Pediatric, Echo-E$^3$Net attains competitive performance using only 1.55M parameters and 8.05 GFLOPs, an order-of-magnitude compute reduction versus recent baselines, supporting real-time deployment. Our code is publicly available at https://github.com/moeinheidari7829/Echo-E3Net.

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arXiv2026

HemaHier: Chain-Conditioned Ordinal Hierarchies for Lineage-Aware Bone-Marrow Cytology

Bone-marrow cytology is inherently structured: each cell belongs to a hematopoietic lineage, and many cell types lie on ordered maturation trajectories. Standard flat classifiers ignore this structure, treating a mild same-lineage confusion the same as a severe cross-lineage mistake and predicting only discrete labels. We propose HemaHier, an ordinal-hierarchical prediction head for a frozen or lightly adapted cytology foundation model. Its central component is a chain-conditioned maturity score that reads a single maturity value under a per-chain query, supervised only on biologically valid healthy chains, while dysplastic and off-chain cell types remain classes but are excluded from maturity supervision. Fine and lineage predictions are coupled through a shared posterior that guarantees hierarchical consistency, and a staged objective first stabilizes recognition, then adds lineage and maturity supervision. On three bone-marrow datasets under a shared ontology, HemaHier achieves competitive recognition while reducing biologically severe errors and adding a within-lineage maturity ordering that flat classifiers lack. Code is available at https://github.com/xmindflow/HemaHier.

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arXiv2026

MaLViL: Multi-axis Low-rank Vision-LSTM for Medical Image Segmentation

Vision-LSTM (ViL) enables efficient global modeling, but its cost still scales with the number of spatial tokens, so existing segmenters confine ViL to a coarse bottleneck and lose fine anatomical detail. Rasterizing 2D features into a 1D sequence further breaks adjacency across the orthogonal scan axis. We propose MaLViL, a Multi-axis Low-rank Vision-LSTM network that extends ViL across decoder resolutions. Bidirectional low-rank ViL (Bi-LRViL) reasons on a compact orthonormal subspace and preserves detail through an orthogonal residual; scale-aware SaLViL restores cross-axis neighbors before serialization; and a Cross-Directional Mixer (CDM) fuses orthogonal horizontal and vertical traversal paths. Statistics-Guided Skip Modulation (SGSM) further retains boundary cues in encoder skips. On skin-lesion, ultrasound, and multi-organ CT benchmarks, MaLViL achieves competitive or state-of-the-art segmentation accuracy, while reducing ViL operator memory by up to $83\times$ at fine decoder resolutions. Code is available at: https://github.com/xmindflow/malvil.

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arXiv2026

Gated Differential Linear Attention: A Linear-Time Decoder for High-Fidelity Medical Segmentation

Medical image segmentation requires models that preserve fine anatomical boundaries while remaining practical for clinical deployment. Transformers capture long-range dependencies but incur quadratic attention cost, whereas CNNs are efficient but less effective at global reasoning. Linear attention offers $\mathcal{O}(N)$ scaling, but often produces diffuse feature aggregation that weakens boundary-sensitive prediction. We introduce a gated differential linear-attention mixer for medical image segmentation. Its global path, Gated Differential Linear Attention (GDLA), performs differential subtraction between two kernelized attention branches over complementary query/key subspaces to suppress redundant responses, and employs a data-dependent gate for token refinement. A parallel local token-mixing branch with depthwise convolution strengthens neighborhood interactions for better refinement, and the two branches are fused while preserving $\mathcal{O}(N)$ complexity. When instantiated in a pretrained Pyramid Vision Transformer (PVT)-based encoder--decoder model, \name achieves state-of-the-art results on the evaluated 2D medical segmentation benchmarks spanning CT, MRI, ultrasound, and dermoscopy, with a favorable accuracy--efficiency trade-off over closely related baselines. The code is publicly available at \href{https://github.com/xmindflow/gdla}{https://github.com/xmindflow/gdla}.

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arXiv2026

Footprint-Guided Exemplar-Free Continual Histopathology Report Generation

Rapid progress in vision-language modeling has enabled pathology report generation from gigapixel whole-slide images, but most approaches assume static training with simultaneous access to all data. In clinical deployment, however, new organs, institutions, and reporting conventions emerge over time, and sequential fine-tuning can cause catastrophic forgetting. We introduce an exemplar-free continual learning framework for WSI-to-report generation that avoids storing raw slides or patch exemplars. The core idea is a compact domain footprint built in a frozen patch-embedding space: a small codebook of representative morphology tokens together with slide-level co-occurrence summaries and lightweight patch-count priors. These footprints support generative replay by synthesizing pseudo-WSI representations that reflect domain-specific morphological mixtures, while a teacher snapshot provides pseudo-reports to supervise the updated model without retaining past data. To address shifting reporting conventions, we distill domain-specific linguistic characteristics into a compact style descriptor and use it to steer generation. At inference, the model identifies the most compatible descriptor directly from the slide signal, enabling domain-agnostic setup without requiring explicit domain identifiers. Evaluated across multiple public continual learning benchmarks, our approach outperforms exemplar-free and limited-buffer rehearsal baselines, highlighting footprint-based generative replay as a practical solution for deployment in evolving clinical settings.

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arXiv2025

LHU-Net: a Lean Hybrid U-Net for Cost-efficient, High-performance Volumetric Segmentation

The rise of Transformer architectures has advanced medical image segmentation, leading to hybrid models that combine Convolutional Neural Networks (CNNs) and Transformers. However, these models often suffer from excessive complexity and fail to effectively integrate spatial and channel features, crucial for precise segmentation. To address this, we propose LHU-Net, a Lean Hybrid U-Net for volumetric medical image segmentation. LHU-Net prioritizes spatial feature extraction before refining channel features, optimizing both efficiency and accuracy. Evaluated on four benchmark datasets (Synapse, Left Atrial, BraTS-Decathlon, and Lung-Decathlon), LHU-Net consistently outperforms existing models across diverse modalities (CT/MRI) and output configurations. It achieves state-of-the-art Dice scores while using four times fewer parameters and 20% fewer FLOPs than competing models, without the need for pre-training, additional data, or model ensembles. With an average of 11 million parameters, LHU-Net sets a new benchmark for computational efficiency and segmentation accuracy. Our implementation is available on GitHub: https://github.com/xmindflow/LHUNet

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arXiv2025

CENet: Context Enhancement Network for Medical Image Segmentation

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.

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arXiv2025

Attention-based Generative Latent Replay: A Continual Learning Approach for WSI Analysis

Whole slide image (WSI) classification has emerged as a powerful tool in computational pathology, but remains constrained by domain shifts, e.g., due to different organs, diseases, or institution-specific variations. To address this challenge, we propose an Attention-based Generative Latent Replay Continual Learning framework (AGLR-CL), in a multiple instance learning (MIL) setup for domain incremental WSI classification. Our method employs Gaussian Mixture Models (GMMs) to synthesize WSI representations and patch count distributions, preserving knowledge of past domains without explicitly storing original data. A novel attention-based filtering step focuses on the most salient patch embeddings, ensuring high-quality synthetic samples. This privacy-aware strategy obviates the need for replay buffers and outperforms other buffer-free counterparts while matching the performance of buffer-based solutions. We validate AGLR-CL on clinically relevant biomarker detection and molecular status prediction across multiple public datasets with diverse centers, organs, and patient cohorts. Experimental results confirm its ability to retain prior knowledge and adapt to new domains, offering an effective, privacy-preserving avenue for domain incremental continual learning in WSI classification.

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arXiv2025

Domain-incremental White Blood Cell Classification with Privacy-aware Continual Learning

White blood cell (WBC) classification plays a vital role in hematology for diagnosing various medical conditions. However, it faces significant challenges due to domain shifts caused by variations in sample sources (e.g., blood or bone marrow) and differing imaging conditions across hospitals. Traditional deep learning models often suffer from catastrophic forgetting in such dynamic environments, while foundation models, though generally robust, experience performance degradation when the distribution of inference data differs from that of the training data. To address these challenges, we propose a generative replay-based Continual Learning (CL) strategy designed to prevent forgetting in foundation models for WBC classification. Our method employs lightweight generators to mimic past data with a synthetic latent representation to enable privacy-preserving replay. To showcase the effectiveness, we carry out extensive experiments with a total of four datasets with different task ordering and four backbone models including ResNet50, RetCCL, CTransPath, and UNI. Experimental results demonstrate that conventional fine-tuning methods degrade performance on previously learned tasks and struggle with domain shifts. In contrast, our continual learning strategy effectively mitigates catastrophic forgetting, preserving model performance across varying domains. This work presents a practical solution for maintaining reliable WBC classification in real-world clinical settings, where data distributions frequently evolve.

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arXiv2025

Touchstone Benchmark: Are We on the Right Way for Evaluating AI Algorithms for Medical Segmentation?

How can we test AI performance? This question seems trivial, but it isn't. Standard benchmarks often have problems such as in-distribution and small-size test sets, oversimplified metrics, unfair comparisons, and short-term outcome pressure. As a consequence, good performance on standard benchmarks does not guarantee success in real-world scenarios. To address these problems, we present Touchstone, a large-scale collaborative segmentation benchmark of 9 types of abdominal organs. This benchmark is based on 5,195 training CT scans from 76 hospitals around the world and 5,903 testing CT scans from 11 additional hospitals. This diverse test set enhances the statistical significance of benchmark results and rigorously evaluates AI algorithms across various out-of-distribution scenarios. We invited 14 inventors of 19 AI algorithms to train their algorithms, while our team, as a third party, independently evaluated these algorithms on three test sets. In addition, we also evaluated pre-existing AI frameworks--which, differing from algorithms, are more flexible and can support different algorithms--including MONAI from NVIDIA, nnU-Net from DKFZ, and numerous other open-source frameworks. We are committed to expanding this benchmark to encourage more innovation of AI algorithms for the medical domain.

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arXiv2024

MSA$^2$Net: Multi-scale Adaptive Attention-guided Network for Medical Image Segmentation

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.

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arXiv2024

Continual Learning in Medical Image Analysis: A Comprehensive Review of Recent Advancements and Future Prospects

Medical imaging analysis has witnessed remarkable advancements even surpassing human-level performance in recent years, driven by the rapid development of advanced deep-learning algorithms. However, when the inference dataset slightly differs from what the model has seen during one-time training, the model performance is greatly compromised. The situation requires restarting the training process using both the old and the new data which is computationally costly, does not align with the human learning process, and imposes storage constraints and privacy concerns. Alternatively, continual learning has emerged as a crucial approach for developing unified and sustainable deep models to deal with new classes, tasks, and the drifting nature of data in non-stationary environments for various application areas. Continual learning techniques enable models to adapt and accumulate knowledge over time, which is essential for maintaining performance on evolving datasets and novel tasks. This systematic review paper provides a comprehensive overview of the state-of-the-art in continual learning techniques applied to medical imaging analysis. We present an extensive survey of existing research, covering topics including catastrophic forgetting, data drifts, stability, and plasticity requirements. Further, an in-depth discussion of key components of a continual learning framework such as continual learning scenarios, techniques, evaluation schemes, and metrics is provided. Continual learning techniques encompass various categories, including rehearsal, regularization, architectural, and hybrid strategies. We assess the popularity and applicability of continual learning categories in various medical sub-fields like radiology and histopathology...

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arXiv2024

Physics-Inspired Generative Models in Medical Imaging: A Review

Physics-inspired Generative Models (GMs), in particular Diffusion Models (DMs) and Poisson Flow Models (PFMs), enhance Bayesian methods and promise great utility in medical imaging. This review examines the transformative role of such generative methods. First, a variety of physics-inspired GMs, including Denoising Diffusion Probabilistic Models (DDPMs), Score-based Diffusion Models (SDMs), and Poisson Flow Generative Models (PFGMs and PFGM++), are revisited, with an emphasis on their accuracy, robustness as well as acceleration. Then, major applications of physics-inspired GMs in medical imaging are presented, comprising image reconstruction, image generation, and image analysis. Finally, future research directions are brainstormed, including unification of physics-inspired GMs, integration with Vision-Language Models (VLMs), and potential novel applications of GMs. Since the development of generative methods has been rapid, this review will hopefully give peers and learners a timely snapshot of this new family of physics-driven generative models and help capitalize their enormous potential for medical imaging.

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arXiv2024

Computation-Efficient Era: A Comprehensive Survey of State Space Models in Medical Image Analysis

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.

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arXiv2024

Enhancing Efficiency in Vision Transformer Networks: Design Techniques and Insights

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.

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arXiv2023

HCA-Net: Hierarchical Context Attention Network for Intervertebral Disc Semantic Labeling

Accurate and automated segmentation of intervertebral discs (IVDs) in medical images is crucial for assessing spine-related disorders, such as osteoporosis, vertebral fractures, or IVD herniation. We present HCA-Net, a novel contextual attention network architecture for semantic labeling of IVDs, with a special focus on exploiting prior geometric information. Our approach excels at processing features across different scales and effectively consolidating them to capture the intricate spatial relationships within the spinal cord. To achieve this, HCA-Net models IVD labeling as a pose estimation problem, aiming to minimize the discrepancy between each predicted IVD location and its corresponding actual joint location. In addition, we introduce a skeletal loss term to reinforce the model's geometric dependence on the spine. This loss function is designed to constrain the model's predictions to a range that matches the general structure of the human vertebral skeleton. As a result, the network learns to reduce the occurrence of false predictions and adaptively improves the accuracy of IVD location estimation. Through extensive experimental evaluation on multi-center spine datasets, our approach consistently outperforms previous state-of-the-art methods on both MRI T1w and T2w modalities. The codebase is accessible to the public on \href{https://github.com/xmindflow/HCA-Net}{GitHub}.

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arXiv2023

Foundational Models in Medical Imaging: A Comprehensive Survey and Future Vision

Foundation models, large-scale, pre-trained deep-learning models adapted to a wide range of downstream tasks have gained significant interest lately in various deep-learning problems undergoing a paradigm shift with the rise of these models. Trained on large-scale dataset to bridge the gap between different modalities, foundation models facilitate contextual reasoning, generalization, and prompt capabilities at test time. The predictions of these models can be adjusted for new tasks by augmenting the model input with task-specific hints called prompts without requiring extensive labeled data and retraining. Capitalizing on the advances in computer vision, medical imaging has also marked a growing interest in these models. To assist researchers in navigating this direction, this survey intends to provide a comprehensive overview of foundation models in the domain of medical imaging. Specifically, we initiate our exploration by providing an exposition of the fundamental concepts forming the basis of foundation models. Subsequently, we offer a methodical taxonomy of foundation models within the medical domain, proposing a classification system primarily structured around training strategies, while also incorporating additional facets such as application domains, imaging modalities, specific organs of interest, and the algorithms integral to these models. Furthermore, we emphasize the practical use case of some selected approaches and then discuss the opportunities, applications, and future directions of these large-scale pre-trained models, for analyzing medical images. In the same vein, we address the prevailing challenges and research pathways associated with foundational models in medical imaging. These encompass the areas of interpretability, data management, computational requirements, and the nuanced issue of contextual comprehension.

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arXiv2023

Unlocking Fine-Grained Details with Wavelet-based High-Frequency Enhancement in Transformers

Medical image segmentation is a critical task that plays a vital role in diagnosis, treatment planning, and disease monitoring. Accurate segmentation of anatomical structures and abnormalities from medical images can aid in the early detection and treatment of various diseases. In this paper, we address the local feature deficiency of the Transformer model by carefully re-designing the self-attention map to produce accurate dense prediction in medical images. To this end, we first apply the wavelet transformation to decompose the input feature map into low-frequency (LF) and high-frequency (HF) subbands. The LF segment is associated with coarse-grained features while the HF components preserve fine-grained features such as texture and edge information. Next, we reformulate the self-attention operation using the efficient Transformer to perform both spatial and context attention on top of the frequency representation. Furthermore, to intensify the importance of the boundary information, we impose an additional attention map by creating a Gaussian pyramid on top of the HF components. Moreover, we propose a multi-scale context enhancement block within skip connections to adaptively model inter-scale dependencies to overcome the semantic gap among stages of the encoder and decoder modules. Throughout comprehensive experiments, we demonstrate the effectiveness of our strategy on multi-organ and skin lesion segmentation benchmarks. The implementation code will be available upon acceptance. \href{https://github.com/mindflow-institue/WaveFormer}{GitHub}.

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