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Add to EdgeLHU-Net: A Light Hybrid U-Net for Cost-Efficient, High-Performance Volumetric Medical Image Segmentation
Apr 07, 2024
As a result of the rise of Transformer architectures in medical image analysis, specifically in the domain of medical image segmentation, a multitude of hybrid models have been created that merge the advantages of Convolutional Neural Networks (CNNs) and Transformers. These hybrid models have achieved notable success by significantly improving segmentation accuracy. Yet, this progress often comes at the cost of increased model complexity, both in terms of parameters and computational demand. Moreover, many of these models fail to consider the crucial interplay between spatial and channel features, which could further refine and improve segmentation outcomes. To address this, we introduce LHU-Net, a Light Hybrid U-Net architecture optimized for volumetric medical image segmentation. LHU-Net is meticulously designed to prioritize spatial feature analysis in its initial layers before shifting focus to channel-based features in its deeper layers, ensuring a comprehensive feature extraction process. Rigorous evaluation across five benchmark datasets - Synapse, LA, Pancreas, ACDC, and BRaTS 2018 - underscores LHU-Net's superior performance, showcasing its dual capacity for efficiency and accuracy. Notably, LHU-Net sets new performance benchmarks, such as attaining a Dice score of 92.66 on the ACDC dataset, while simultaneously reducing parameters by 85% and quartering the computational load compared to existing state-of-the-art models. Achieved without any reliance on pre-training, additional data, or model ensemble, LHU-Net's effectiveness is further evidenced by its state-of-the-art performance across all evaluated datasets, utilizing fewer than 11 million parameters. This achievement highlights that balancing computational efficiency with high accuracy in medical image segmentation is feasible. Our implementation of LHU-Net is freely accessible to the research community on GitHub.
Enhancing Efficiency in Vision Transformer Networks: Design Techniques and Insights
Mar 28, 2024
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.
Continual Learning in Medical Imaging Analysis: A Comprehensive Review of Recent Advancements and Future Prospects
Dec 28, 2023Medical 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...
HCA-Net: Hierarchical Context Attention Network for Intervertebral Disc Semantic Labeling
Nov 21, 2023Accurate 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}.
Foundational Models in Medical Imaging: A Comprehensive Survey and Future Vision
Oct 28, 2023Foundation 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.
Unlocking Fine-Grained Details with Wavelet-based High-Frequency Enhancement in Transformers
Sep 12, 2023
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}.
* Accepted in MICCAI 2023 workshop MLMI
DermoSegDiff: A Boundary-aware Segmentation Diffusion Model for Skin Lesion Delineation
Aug 05, 2023
Skin lesion segmentation plays a critical role in the early detection and accurate diagnosis of dermatological conditions. Denoising Diffusion Probabilistic Models (DDPMs) have recently gained attention for their exceptional image-generation capabilities. Building on these advancements, we propose DermoSegDiff, a novel framework for skin lesion segmentation that incorporates boundary information during the learning process. Our approach introduces a novel loss function that prioritizes the boundaries during training, gradually reducing the significance of other regions. We also introduce a novel U-Net-based denoising network that proficiently integrates noise and semantic information inside the network. Experimental results on multiple skin segmentation datasets demonstrate the superiority of DermoSegDiff over existing CNN, transformer, and diffusion-based approaches, showcasing its effectiveness and generalization in various scenarios. The implementation is publicly accessible on \href{https://github.com/mindflow-institue/dermosegdiff}{GitHub}
Medical Image Segmentation Review: The success of U-Net
Nov 27, 2022Automatic medical image segmentation is a crucial topic in the medical domain and successively a critical counterpart in the computer-aided diagnosis paradigm. U-Net is the most widespread image segmentation architecture due to its flexibility, optimized modular design, and success in all medical image modalities. Over the years, the U-Net model achieved tremendous attention from academic and industrial researchers. Several extensions of this network have been proposed to address the scale and complexity created by medical tasks. Addressing the deficiency of the naive U-Net model is the foremost step for vendors to utilize the proper U-Net variant model for their business. Having a compendium of different variants in one place makes it easier for builders to identify the relevant research. Also, for ML researchers it will help them understand the challenges of the biological tasks that challenge the model. To address this, we discuss the practical aspects of the U-Net model and suggest a taxonomy to categorize each network variant. Moreover, to measure the performance of these strategies in a clinical application, we propose fair evaluations of some unique and famous designs on well-known datasets. We provide a comprehensive implementation library with trained models for future research. In addition, for ease of future studies, we created an online list of U-Net papers with their possible official implementation. All information is gathered in https://github.com/NITR098/Awesome-U-Net repository.
Multi-scale Regional Attention Deeplab3+: Multiple Myeloma Plasma Cells Segmentation in Microscopic Images
May 13, 2021
Multiple myeloma cancer is a type of blood cancer that happens when the growth of abnormal plasma cells becomes out of control in the bone marrow. There are various ways to diagnose multiple myeloma in bone marrow such as complete blood count test (CBC) or counting myeloma plasma cell in aspirate slide images using manual visualization or through image processing technique. In this work, an automatic deep learning method for the detection and segmentation of multiple myeloma plasma cell have been explored. To this end, a two-stage deep learning method is designed. In the first stage, the nucleus detection network is utilized to extract each instance of a cell of interest. The extracted instance is then fed to the multi-scale function to generate a multi-scale representation. The objective of the multi-scale function is to capture the shape variation and reduce the effect of object scale on the cytoplasm segmentation network. The generated scales are then fed into a pyramid of cytoplasm networks to learn the segmentation map in various scales. On top of the cytoplasm segmentation network, we included a scale aggregation function to refine and generate a final prediction. The proposed approach has been evaluated on the SegPC2021 grand-challenge and ranked second on the final test phase among all teams.