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Introducing Image-Space Preconditioning in the Variational Formulation of MRI Reconstructions

Bastien Milani, Jean-Baptist Ledoux, Berk Can Acikgoz, Xavier Richard

arxiv logopreprintJul 7 2025
The aim of the present article is to enrich the comprehension of iterative magnetic resonance imaging (MRI) reconstructions, including compressed sensing (CS) and iterative deep learning (DL) reconstructions, by describing them in the general framework of finite-dimensional inner-product spaces. In particular, we show that image-space preconditioning (ISP) and data-space preconditioning (DSP) can be formulated as non-conventional inner-products. The main gain of our reformulation is an embedding of ISP in the variational formulation of the MRI reconstruction problem (in an algorithm-independent way) which allows in principle to naturally and systematically propagate ISP in all iterative reconstructions, including many iterative DL and CS reconstructions where preconditioning is lacking. The way in which we apply linear algebraic tools to MRI reconstructions as presented in this article is a novelty. A secondary aim of our article is to offer a certain didactic material to scientists who are new in the field of MRI reconstruction. Since we explore here some mathematical concepts of reconstruction, we take that opportunity to recall some principles that may be understood for experts, but which may be hard to find in the literature for beginners. In fact, the description of many mathematical tools of MRI reconstruction is fragmented in the literature or sometimes missing because considered as a general knowledge. Further, some of those concepts can be found in mathematic manuals, but not in a form that is oriented toward MRI. For example, we think of the conjugate gradient descent, the notion of derivative with respect to non-conventional inner products, or simply the notion of adjoint. The authors believe therefore that it is beneficial for their field of research to dedicate some space to such a didactic material.

SV-DRR: High-Fidelity Novel View X-Ray Synthesis Using Diffusion Model

Chun Xie, Yuichi Yoshii, Itaru Kitahara

arxiv logopreprintJul 7 2025
X-ray imaging is a rapid and cost-effective tool for visualizing internal human anatomy. While multi-view X-ray imaging provides complementary information that enhances diagnosis, intervention, and education, acquiring images from multiple angles increases radiation exposure and complicates clinical workflows. To address these challenges, we propose a novel view-conditioned diffusion model for synthesizing multi-view X-ray images from a single view. Unlike prior methods, which are limited in angular range, resolution, and image quality, our approach leverages the Diffusion Transformer to preserve fine details and employs a weak-to-strong training strategy for stable high-resolution image generation. Experimental results demonstrate that our method generates higher-resolution outputs with improved control over viewing angles. This capability has significant implications not only for clinical applications but also for medical education and data extension, enabling the creation of diverse, high-quality datasets for training and analysis. Our code is available at GitHub.

Introducing Image-Space Preconditioning in the Variational Formulation of MRI Reconstructions

Bastien Milani, Jean-Baptist Ledoux, Berk Can Acikgoz, Xavier Richard

arxiv logopreprintJul 7 2025
The aim of the present article is to enrich the comprehension of iterative magnetic resonance imaging (MRI) reconstructions, including compressed sensing (CS) and iterative deep learning (DL) reconstructions, by describing them in the general framework of finite-dimensional inner-product spaces. In particular, we show that image-space preconditioning (ISP) and data-space preconditioning (DSP) can be formulated as non-conventional inner-products. The main gain of our reformulation is an embedding of ISP in the variational formulation of the MRI reconstruction problem (in an algorithm-independent way) which allows in principle to naturally and systematically propagate ISP in all iterative reconstructions, including many iterative DL and CS reconstructions where preconditioning is lacking. The way in which we apply linear algebraic tools to MRI reconstructions as presented in this article is a novelty. A secondary aim of our article is to offer a certain didactic material to scientists who are new in the field of MRI reconstruction. Since we explore here some mathematical concepts of reconstruction, we take that opportunity to recall some principles that may be understood for experts, but which may be hard to find in the literature for beginners. In fact, the description of many mathematical tools of MRI reconstruction is fragmented in the literature or sometimes missing because considered as a general knowledge. Further, some of those concepts can be found in mathematic manuals, but not in a form that is oriented toward MRI. For example, we think of the conjugate gradient descent, the notion of derivative with respect to non-conventional inner products, or simply the notion of adjoint. The authors believe therefore that it is beneficial for their field of research to dedicate some space to such a didactic material.

Towards Reliable Healthcare Imaging: A Multifaceted Approach in Class Imbalance Handling for Medical Image Segmentation.

Cui L, Xu M, Liu C, Liu T, Yan X, Zhang Y, Yang X

pubmed logopapersJul 7 2025
Class imbalance is a dominant challenge in medical image segmentation when dealing with MRI images from highly imbalanced datasets. This study introduces a comprehensive, multifaceted approach to enhance the accuracy and reliability of segmentation models under such conditions. Our model integrates advanced data augmentation, innovative algorithmic adjustments, and novel architectural features to address class label distribution effectively. To ensure the multiple aspects of training process, we have customized the data augmentation technique for medical imaging with multi-dimensional angles. The multi-dimensional augmentation technique helps to reduce the bias towards majority classes. We have implemented novel attention mechanisms, i.e., Enhanced Attention Module (EAM) and spatial attention. These attention mechanisms enhance the focus of the model on the most relevant features. Further, our architecture incorporates a dual decoder system and Pooling Integration Layer (PIL) to capture accurate foreground and background details. We also introduce a hybrid loss function, which is designed to handle the class imbalance by guiding the training process. For experimental purposes, we have used multiple datasets such as Digital Database Thyroid Image (DDTI), Breast Ultrasound Images Dataset (BUSI) and LiTS MICCAI 2017 to demonstrate the prowess of the proposed network using key evaluation metrics, i.e., IoU, Dice coefficient, precision, and recall.

An enhanced fusion of transfer learning models with optimization based clinical diagnosis of lung and colon cancer using biomedical imaging.

Vinoth NAS, Kalaivani J, Arieth RM, Sivasakthiselvan S, Park GC, Joshi GP, Cho W

pubmed logopapersJul 7 2025
Lung and colon cancers (LCC) are among the foremost reasons for human death and disease. Early analysis of this disorder contains various tests, namely ultrasound (US), magnetic resonance imaging (MRI), and computed tomography (CT). Despite analytical imaging, histopathology is one of the effective methods that delivers cell-level imaging of tissue under inspection. These are mainly due to a restricted number of patients receiving final analysis and early healing. Furthermore, there are probabilities of inter-observer faults. Clinical informatics is an interdisciplinary field that integrates healthcare, information technology, and data analytics to improve patient care, clinical decision-making, and medical research. Recently, deep learning (DL) proved to be effective in the medical sector, and cancer diagnosis can be made automatically by utilizing the capabilities of artificial intelligence (AI), enabling faster analysis of more cases cost-effectively. On the other hand, with extensive technical developments, DL has arisen as an effective device in medical settings, mainly in medical imaging. This study presents an Enhanced Fusion of Transfer Learning Models and Optimization-Based Clinical Biomedical Imaging for Accurate Lung and Colon Cancer Diagnosis (FTLMO-BILCCD) model. The main objective of the FTLMO-BILCCD technique is to develop an efficient method for LCC detection using clinical biomedical imaging. Initially, the image pre-processing stage applies the median filter (MF) model to eliminate the unwanted noise from the input image data. Furthermore, fusion models such as CapsNet, EffcientNetV2, and MobileNet-V3 Large are employed for the feature extraction. The FTLMO-BILCCD technique implements a hybrid of temporal pattern attention and bidirectional gated recurrent unit (TPA-BiGRU) for classification. Finally, the beluga whale optimization (BWO) technique alters the hyperparameter range of the TPA-BiGRU model optimally and results in greater classification performance. The FTLMO-BILCCD approach is experimented with under the LCC-HI dataset. The performance validation of the FTLMO-BILCCD approach portrayed a superior accuracy value of 99.16% over existing models.

Sequential Attention-based Sampling for Histopathological Analysis

Tarun G, Naman Malpani, Gugan Thoppe, Sridharan Devarajan

arxiv logopreprintJul 7 2025
Deep neural networks are increasingly applied for automated histopathology. Yet, whole-slide images (WSIs) are often acquired at gigapixel sizes, rendering it computationally infeasible to analyze them entirely at high resolution. Diagnostic labels are largely available only at the slide-level, because expert annotation of images at a finer (patch) level is both laborious and expensive. Moreover, regions with diagnostic information typically occupy only a small fraction of the WSI, making it inefficient to examine the entire slide at full resolution. Here, we propose SASHA -- {\it S}equential {\it A}ttention-based {\it S}ampling for {\it H}istopathological {\it A}nalysis -- a deep reinforcement learning approach for efficient analysis of histopathological images. First, SASHA learns informative features with a lightweight hierarchical, attention-based multiple instance learning (MIL) model. Second, SASHA samples intelligently and zooms selectively into a small fraction (10-20\%) of high-resolution patches, to achieve reliable diagnosis. We show that SASHA matches state-of-the-art methods that analyze the WSI fully at high-resolution, albeit at a fraction of their computational and memory costs. In addition, it significantly outperforms competing, sparse sampling methods. We propose SASHA as an intelligent sampling model for medical imaging challenges that involve automated diagnosis with exceptionally large images containing sparsely informative features.

X-ray transferable polyrepresentation learning

Weronika Hryniewska-Guzik, Przemyslaw Biecek

arxiv logopreprintJul 7 2025
The success of machine learning algorithms is inherently related to the extraction of meaningful features, as they play a pivotal role in the performance of these algorithms. Central to this challenge is the quality of data representation. However, the ability to generalize and extract these features effectively from unseen datasets is also crucial. In light of this, we introduce a novel concept: the polyrepresentation. Polyrepresentation integrates multiple representations of the same modality extracted from distinct sources, for example, vector embeddings from the Siamese Network, self-supervised models, and interpretable radiomic features. This approach yields better performance metrics compared to relying on a single representation. Additionally, in the context of X-ray images, we demonstrate the transferability of the created polyrepresentation to a smaller dataset, underscoring its potential as a pragmatic and resource-efficient approach in various image-related solutions. It is worth noting that the concept of polyprepresentation on the example of medical data can also be applied to other domains, showcasing its versatility and broad potential impact.

Deep Learning Model Based on Dual-energy CT for Assessing Cervical Lymph Node Metastasis in Oral Squamous Cell Carcinoma.

Qi YM, Zhang LJ, Wang Y, Duan XH, Li YJ, Xiao EH, Luo YH

pubmed logopapersJul 7 2025
Accurate detection of lymph node metastasis (LNM) in oral squamous cell carcinoma (OSCC) is crucial for treatment planning. This study developed a deep learning model using dual-energy CT to improve LNM detection. Preoperative dual-energy CT images (Iodine Map, Fat Map, monoenergetic 70 keV, and RHO/Z Map) and clinical data were collected from two centers. From the first center, 248 patients were divided into training (n=198) and internal validation (n=50) cohorts (8:2 ratio), while 106 patients from the second center comprised the external validation cohort. Region-of-interest images from all four sequences were stacked along the channel dimension to generate fused four-channel composite images. 16 deep learning models were developed as follows: three architectures (Crossformer, Densenet169, Squeezenet1_0) applied to each single-sequence/fused image, followed by MLP integration. Additionally, a Crossformer_Transformer model was constructed based on fused image. The top-performing model was compared against radiologists' assessments. Among the 16 deep learning models trained in this study, the Crossformer_Transformer model demonstrated the best diagnostic performance in predicting LNM in OSCC patients, with an AUC of 0.960 (95% CI: 0.9355-0.9842) on the training dataset, and 0.881 (95% CI: 0.7396-1.0000) and 0.881 (95% CI: 0.8033-0.9590) on the internal and external validation sets, respectively. The average AUC for radiologists across both validation cohorts (0.723-0.819) was lower than that of the model. The Crossformer_Transformer model, validated on multicenter data, shows strong potential for improving preoperative risk assessment and clinical decision-making in cervical LNM for OSCC patients.

Automated Deep Learning-Based 3D-to-2D Segmentation of Geographic Atrophy in Optical Coherence Tomography Data

Al-khersan, H., Oakley, J. D., Russakoff, D. B., Cao, J. A., Saju, S. M., Zhou, A., Sodhi, S. K., Pattathil, N., Choudhry, N., Boyer, D. S., Wykoff, C. C.

medrxiv logopreprintJul 7 2025
PurposeWe report on a deep learning-based approach to the segmentation of geographic atrophy (GA) in patients with advanced age-related macular degeneration (AMD). MethodThree-dimensional (3D) optical coherence tomography (OCT) data was collected from two instruments at two different retina practices. This totaled 367 and 348 volumes, respectively, of routinely collected clinical data. For all data, the accuracy of a 3D-to-2D segmentation model was assessed relative to ground-truth manual labeling. ResultsDice Similarity Scores (DSC) averaged 0.824 and 0.826 for each data set. Correlations (r2) between manual and automated areas were 0.883 and 0.906, respectively. The inclusion of near Infra-red imagery as an additional information channel to the algorithm did not notably improve performance. ConclusionAccurate assessment of GA in real-world clinical OCT data can be achieved using deep learning. In the advent of therapeutics to slow the rate of GA progression, reliable, automated assessment is a clinical objective and this work validates one such method.

Geometric-Guided Few-Shot Dental Landmark Detection with Human-Centric Foundation Model

Anbang Wang, Marawan Elbatel, Keyuan Liu, Lizhuo Lin, Meng Lan, Yanqi Yang, Xiaomeng Li

arxiv logopreprintJul 7 2025
Accurate detection of anatomic landmarks is essential for assessing alveolar bone and root conditions, thereby optimizing clinical outcomes in orthodontics, periodontics, and implant dentistry. Manual annotation of landmarks on cone-beam computed tomography (CBCT) by dentists is time-consuming, labor-intensive, and subject to inter-observer variability. Deep learning-based automated methods present a promising approach to streamline this process efficiently. However, the scarcity of training data and the high cost of expert annotations hinder the adoption of conventional deep learning techniques. To overcome these challenges, we introduce GeoSapiens, a novel few-shot learning framework designed for robust dental landmark detection using limited annotated CBCT of anterior teeth. Our GeoSapiens framework comprises two key components: (1) a robust baseline adapted from Sapiens, a foundational model that has achieved state-of-the-art performance in human-centric vision tasks, and (2) a novel geometric loss function that improves the model's capacity to capture critical geometric relationships among anatomical structures. Experiments conducted on our collected dataset of anterior teeth landmarks revealed that GeoSapiens surpassed existing landmark detection methods, outperforming the leading approach by an 8.18% higher success detection rate at a strict 0.5 mm threshold-a standard widely recognized in dental diagnostics. Code is available at: https://github.com/xmed-lab/GeoSapiens.
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