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Development and validation of an improved volumetric breast density estimation model using the ResNet technique.

Asai Y, Yamamuro M, Yamada T, Kimura Y, Ishii K, Nakamura Y, Otsuka Y, Kondo Y

pubmed logo•papers•Jul 7 2025

Temporal changes in volumetric breast density (VBD) may serve as prognostic biomarkers for predicting the risk of future breast cancer development. However, accurately measuring VBD from archived X-ray mammograms remains challenging. In a previous study, we proposed a method to estimate volumetric breast density using imaging parameters (tube voltage, tube current, and exposure time) and patient age. This approach, based on a multiple regression model, achieved a determination coefficient (R²) of 0.868. 
Approach:
In this study, we developed and applied machine learning models-Random Forest, XG-Boost-and the deep learning model Residual Network (ResNet) to the same dataset. Model performance was assessed using several metrics: determination coefficient, correlation coefficient, root mean square error, mean absolute error, root mean square percentage error, and mean absolute percentage error. A five-fold cross-validation was conducted to ensure robust validation. 
Main results:
The best-performing fold resulted in R² values of 0.895, 0.907, and 0.918 for Random Forest, XG-Boost, and ResNet, respectively, all surpassing the previous study's results. ResNet consistently achieved the lowest error values across all metrics. 
Significance:
These findings suggest that ResNet successfully achieved the task of accurately determining VBD from past mammography-a task that has not been realised to date. We are confident that this achievement contributes to advancing research aimed at predicting future risks of breast cancer development by enabling high-accuracy time-series analyses of retrospective VBD.&#xD.
MammographyRegistrationBreastRetrospective ClinicalIn SilicoAcademic LabBenchmark SOTA

Self-supervised Deep Learning for Denoising in Ultrasound Microvascular Imaging

Lijie Huang, Jingyi Yin, Jingke Zhang, U-Wai Lok, Ryan M. DeRuiter, Jieyang Jin, Kate M. Knoll, Kendra E. Petersen, James D. Krier, Xiang-yang Zhu, Gina K. Hesley, Kathryn A. Robinson, Andrew J. Bentall, Thomas D. Atwell, Andrew D. Rule, Lilach O. Lerman, Shigao Chen, Chengwu Huang

arxiv logo•preprint•Jul 7 2025
Ultrasound microvascular imaging (UMI) is often hindered by low signal-to-noise ratio (SNR), especially in contrast-free or deep tissue scenarios, which impairs subsequent vascular quantification and reliable disease diagnosis. To address this challenge, we propose Half-Angle-to-Half-Angle (HA2HA), a self-supervised denoising framework specifically designed for UMI. HA2HA constructs training pairs from complementary angular subsets of beamformed radio-frequency (RF) blood flow data, across which vascular signals remain consistent while noise varies. HA2HA was trained using in-vivo contrast-free pig kidney data and validated across diverse datasets, including contrast-free and contrast-enhanced data from pig kidneys, as well as human liver and kidney. An improvement exceeding 15 dB in both contrast-to-noise ratio (CNR) and SNR was observed, indicating a substantial enhancement in image quality. In addition to power Doppler imaging, denoising directly in the RF domain is also beneficial for other downstream processing such as color Doppler imaging (CDI). CDI results of human liver derived from the HA2HA-denoised signals exhibited improved microvascular flow visualization, with a suppressed noisy background. HA2HA offers a label-free, generalizable, and clinically applicable solution for robust vascular imaging in both contrast-free and contrast-enhanced UMI.
UltrasoundReconstructionAbdominalMethodologyIn SilicoAcademic LabReproducibility

MedGemma Technical Report

Andrew Sellergren, Sahar Kazemzadeh, Tiam Jaroensri, Atilla Kiraly, Madeleine Traverse, Timo Kohlberger, Shawn Xu, Fayaz Jamil, Cían Hughes, Charles Lau, Justin Chen, Fereshteh Mahvar, Liron Yatziv, Tiffany Chen, Bram Sterling, Stefanie Anna Baby, Susanna Maria Baby, Jeremy Lai, Samuel Schmidgall, Lu Yang, Kejia Chen, Per Bjornsson, Shashir Reddy, Ryan Brush, Kenneth Philbrick, Howard Hu, Howard Yang, Richa Tiwari, Sunny Jansen, Preeti Singh, Yun Liu, Shekoofeh Azizi, Aishwarya Kamath, Johan Ferret, Shreya Pathak, Nino Vieillard, Ramona Merhej, Sarah Perrin, Tatiana Matejovicova, Alexandre Ramé, Morgane Riviere, Louis Rouillard, Thomas Mesnard, Geoffrey Cideron, Jean-bastien Grill, Sabela Ramos, Edouard Yvinec, Michelle Casbon, Elena Buchatskaya, Jean-Baptiste Alayrac, Dmitry Lepikhin, Vlad Feinberg, Sebastian Borgeaud, Alek Andreev, Cassidy Hardin, Robert Dadashi, Léonard Hussenot, Armand Joulin, Olivier Bachem, Yossi Matias, Katherine Chou, Avinatan Hassidim, Kavi Goel, Clement Farabet, Joelle Barral, Tris Warkentin, Jonathon Shlens, David Fleet, Victor Cotruta, Omar Sanseviero, Gus Martins, Phoebe Kirk, Anand Rao, Shravya Shetty, David F. Steiner, Can Kirmizibayrak, Rory Pilgrim, Daniel Golden, Lin Yang

arxiv logo•preprint•Jul 7 2025
Artificial intelligence (AI) has significant potential in healthcare applications, but its training and deployment faces challenges due to healthcare's diverse data, complex tasks, and the need to preserve privacy. Foundation models that perform well on medical tasks and require less task-specific tuning data are critical to accelerate the development of healthcare AI applications. We introduce MedGemma, a collection of medical vision-language foundation models based on Gemma 3 4B and 27B. MedGemma demonstrates advanced medical understanding and reasoning on images and text, significantly exceeding the performance of similar-sized generative models and approaching the performance of task-specific models, while maintaining the general capabilities of the Gemma 3 base models. For out-of-distribution tasks, MedGemma achieves 2.6-10% improvement on medical multimodal question answering, 15.5-18.1% improvement on chest X-ray finding classification, and 10.8% improvement on agentic evaluations compared to the base models. Fine-tuning MedGemma further improves performance in subdomains, reducing errors in electronic health record information retrieval by 50% and reaching comparable performance to existing specialized state-of-the-art methods for pneumothorax classification and histopathology patch classification. We additionally introduce MedSigLIP, a medically-tuned vision encoder derived from SigLIP. MedSigLIP powers the visual understanding capabilities of MedGemma and as an encoder achieves comparable or better performance than specialized medical image encoders. Taken together, the MedGemma collection provides a strong foundation of medical image and text capabilities, with potential to significantly accelerate medical research and development of downstream applications. The MedGemma collection, including tutorials and model weights, can be found at https://goo.gle/medgemma.
X-RayClassificationChestMethodologyIn SilicoBig TechBenchmark SOTAOpen Code

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

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

arxiv logo•preprint•Jul 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.
MRIReconstructionMethodologyConceptReproducibility

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 logo•papers•Jul 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.
CTClassificationRetrospective ClinicalIn SilicoAcademic Lab

Efficient Ultrasound Breast Cancer Detection with DMFormer: A Dynamic Multiscale Fusion Transformer.

Guo L, Zhang H, Ma C

pubmed logo•papers•Jul 7 2025
To develop an advanced deep learning model for accurate differentiation between benign and malignant masses in ultrasound breast cancer screening, addressing the challenges of noise, blur, and complex tissue structures in ultrasound imaging. We propose Dynamic Multiscale Fusion Transformer (DMFormer), a novel Transformer-based architecture featuring a dynamic multiscale feature fusion mechanism. The model integrates window attention for local feature interaction with grid attention for global context mixing, enabling comprehensive capture of both fine-grained tissue details and broader anatomical contexts. DMFormer was evaluated on two independent datasets and compared against state-of-the-art approaches, including convolutional neural networks, Transformer-based architectures, and hybrid models. The model achieved areas under the curve of 90.48% and 86.57% on the respective datasets, consistently outperforming all comparison models. DMFormer demonstrates superior performance in ultrasound breast cancer detection through its innovative dual-attention approach. The model's ability to effectively balance local and global feature processing while maintaining computational efficiency represents a significant advancement in medical image analysis. These results validate DMFormer's potential for enhancing the accuracy and reliability of breast cancer screening in clinical settings.
UltrasoundClassificationBreastRetrospective ClinicalIn Silico

Dynamic abdominal MRI image generation using cGANs: A generalized model for various breathing patterns with extensive evaluation.

Cordón-Avila A, Ballı ÖF, Damme K, Abayazid M

pubmed logo•papers•Jul 7 2025
Organ motion is a limiting factor during the treatment of abdominal tumors. During abdominal interventions, medical images are acquired to provide guidance, however, this increases operative time and radiation exposure. In this paper, conditional generative adversarial networks are implemented to generate dynamic magnetic resonance images using external abdominal motion as a surrogate signal. The generator was trained to account for breathing variability, and different models were investigated to improve motion quality. Additionally, an objective and subjective study were conducted to assess image and motion quality. The objective study included different metrics, such as structural similarity index measure (SSIM) and mean absolute error (MAE). In the subjective study, 32 clinical experts participated in evaluating the generated images by completing different tasks. The tasks involved identifying images and videos as real or fake, via a questionnaire allowing experts to assess the realism in static images and dynamic sequences. The results of the best-performing model displayed an SSIM of 0.73 ± 0.13, and the MAE was below 4.5 and 1.8 mm for the superior-inferior and anterior-posterior directions of motion. The proposed framework was compared to a related method that utilized a set of convolutional neural networks combined with recurrent layers. In the subjective study, more than 50% of the generated images and dynamic sequences were classified as real, except for one task. Synthetic images have the potential to reduce the need for acquiring intraoperative images, decreasing time and radiation exposure. A video summary can be found in the supplementary material.
MRIImage SynthesisAbdominalMethodologyIn Silico

X-ray transferable polyrepresentation learning

Weronika Hryniewska-Guzik, Przemyslaw Biecek

arxiv logo•preprint•Jul 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.
X-RayClassificationMethodologyIn SilicoAcademic LabBenchmark SOTA

Sequential Attention-based Sampling for Histopathological Analysis

Tarun G, Naman Malpani, Gugan Thoppe, Sridharan Devarajan

arxiv logo•preprint•Jul 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.
OCTClassificationMethodologyIn SilicoAcademic LabBenchmark SOTA

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 logo•preprint•Jul 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.
OCTSegmentationRetrospective ClinicalIn Silico
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