Medical Image Representation Learning

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20 papers in the last four weeks, up 233% on the four weeks before. 0.2% of all new papers.

Jul 13Week of Sep 28

Latest papers 168

Apr 16, 2026cs.CV

Beyond Independent Frames: Latent Attention Masked Autoencoders for Multi-View Echocardiography

Echocardiography is a widely used modality for cardiac assessment due to its non-invasive and cost-effective nature, but the sparse and heterogeneous spatiotemporal views of the heart pose distinct challenges. Existing masked autoencoder (MAE) approaches typically process images or short clips independently, failing to capture the inherent multi-view structure required for coherent cardiac representation. We introduce Latent Attention Masked Autoencoder (LAMAE), a foundation model architecture tailored to the multi-view nature of medical imaging. LAMAE augments the standard MAE with a latent attention module that enables information exchange across frames and views directly in latent space. This allows the model to aggregate variable-length sequences and distinct views, reconstructing a holistic representation of cardiac function from partial observations. We pretrain LAMAE on MIMIC-IV-ECHO, a large-scale, uncurated dataset reflecting real-world clinical variability. To the best of our knowledge, we present the first results for predicting ICD-10 codes from MIMIC-IV-ECHO videos. Furthermore, we empirically demonstrate that representations learned from adult data transfer effectively to pediatric cohorts despite substantial anatomical differences. These results provide evidence that incorporating structural priors, such as multi-view attention, yields significantly more robust and transferable representations.

Simon Böhi, Irene Cannistraci, Sergio Muñoz Gonzalez +8

Department of Biomedical Engineering, University of Basel, Switzerland · Department of Computer Science, ETH Zurich, Switzerland

Medical Imaging Foundation Models Masked Autoencoders Multi-View Learning Echocardiography Ultrasound Imaging Medical Image Representation Learning

Apr 16, 2026cs.CV

Co-distilled attention guided masked image modeling with noisy teacher for self-supervised learning on medical images

Masked image modeling (MIM) is a highly effective self-supervised learning (SSL) approach to extract useful feature representations from unannotated data. Predominantly used random masking methods make SSL less effective for medical images due to the contextual similarity of neighboring patches, leading to information leakage and SSL simplification. Hierarchical shifted window (Swin) transformer, a highly effective approach for medical images cannot use advanced masking methods as it lacks a global [CLS] token. Hence, we introduced an attention guided masking mechanism for Swin within a co-distillation learning framework to selectively mask semantically co-occurring and discriminative patches, to reduce information leakage and increase the difficulty of SSL pretraining. However, attention guided masking inevitably reduces the diversity of attention heads, which negatively impacts downstream task performance. To address this, we for the first time, integrate a noisy teacher into the co-distillation framework (termed DAGMaN) that performs attentive masking while preserving high attention head diversity. We demonstrate the capability of DAGMaN on multiple tasks including full- and few-shot lung nodule classification, immunotherapy outcome prediction, tumor segmentation, and unsupervised organs clustering.

Jue Jiang, Aneesh Rangnekar, Harini Veeraraghavan

Memorial Sloan Kettering Cancer Center

Masked Autoencoders Self-Supervised Pre-Training Medical Image Representation Learning Masked Image Modeling

Mar 19, 2026cs.CV

Towards Interpretable Foundation Models for Retinal Fundus Images

Foundation models are used to extract transferable representations from large amounts of unlabeled data, typically via self-supervised learning (SSL). However, many of these models rely on architectures that offer limited interpretability, a critical issue in high-stakes domains such as medical imaging. We propose \model, a foundation model that is interpretable-by-design via a BagNet backbone whose small receptive fields generate class evidence maps that are faithful to the model's decision-making process. Additionally, \model{} incorporates a

2D

projection layer during pretraining that enables direct visualization of the representation space, providing a dataset-level view of the learned structure including meaningful clinical clusters as well as potential spurious correlations. We trained \model{} on over 800,000 color fundus photographs from various sources to learn generalizable representations for different downstream tasks. Our model achieves performance comparable to RETFound, which has

16\times

more parameters, while providing interpretable predictions on out-of-distribution data. These results suggest that large-scale SSL pretraining paired with inherent interpretability can lead to robust representations for retinal imaging. Code and pretrained models are available at www.anonymous.4open.science/dual-IFM.

Samuel Ofosu Mensah, Camila Roa, Kerol Djoumessi +1

Hertie Institute for AI in Brain Health, University of Tübingen, Germany · Tübingen AI Center, University of Tübingen, Germany

Medical Imaging Medical Imaging Foundation Models Fundus Imaging Explainable Medical Image Analysis Medical Image Representation Learning Self-Supervised Visual Representation Learning

Mar 4, 2026cs.CV

Understanding Sources of Demographic Predictability in Brain MRI via Disentangling Anatomy and Contrast

Demographic attributes can be predicted from medical images, raising concerns about bias in clinical AI systems. In X-ray imaging, acquisition characteristics have been shown to contribute substantially to this predictability. Whether the same holds in brain MRI remains unclear, as anatomical variation and acquisition-dependent contrast are deeply entangled in the image formation process, obscuring the origins of demographic signal. To address this, we propose a controlled framework based on disentangled representation learning, decomposing brain MRI into anatomy-focused representations that suppress acquisition influence and contrast embeddings that capture acquisition-dependent characteristics. Training predictive models for age, sex, and race on full images, anatomical representations, and contrast embeddings allows us to quantify the relative contributions of structure and acquisition to the demographic signal. Across three datasets and multiple MRI sequences, demographic predictability is found to be driven primarily by anatomical variation, with anatomy-focused representations largely preserving the performance of models trained on raw images. Contrast embeddings retain a weaker signal that is dataset-specific and does not generalise across sites. These findings suggest that effective mitigation must explicitly account for the primarily anatomical and secondarily acquisition-dependent origins of demographic signal, ensuring that any bias reduction generalizes robustly across domains.

Mehmet Yigit Avci, Akshit Achara, Andrew King +1

and for the Alzheimer's Disease Neuroimaging Initiative · School of Biomedical Engineering & Imaging Sciences, King’s College London, London, UK

Medical Image Analysis Algorithmic Bias Medical Image Representation Learning Brain MRI

Mar 1, 2026cs.CV

Differential privacy representation geometry for medical image analysis

Differential privacy (DP)'s effect in medical imaging is typically evaluated only through end-to-end performance, leaving the mechanism of privacy-induced utility loss unclear. We introduce Differential Privacy Representation Geometry for Medical Imaging (DP-RGMI), a framework that interprets DP as a structured transformation of representation space and decomposes performance degradation into encoder geometry and task-head utilization. Geometry is quantified by representation displacement from initialization and spectral effective dimension, while utilization is measured as the gap between linear-probe and end-to-end utility. Across over 594,000 images from four chest X-ray datasets and multiple pretrained initializations, we show that DP is consistently associated with a utilization gap even when linear separability is largely preserved. At the same time, displacement and spectral dimension exhibit non-monotonic, initialization- and dataset-dependent reshaping, indicating that DP alters representation anisotropy rather than uniformly collapsing features. Correlation analysis reveals that the association between end-to-end performance and utilization is robust across datasets but can vary by initialization, while geometric quantities capture additional prior- and dataset-conditioned variation. These findings position DP-RGMI as a reproducible framework for diagnosing privacy-induced failure modes and informing privacy model selection.

Soroosh Tayebi Arasteh, Marziyeh Mohammadi, Sven Nebelung +1

Lab for AI in Medicine, RWTH Aachen University, Aachen, Germany · Department of Diagnostic and Interventional Radiology, University Hospital RWTH Aachen, Aachen, Germany · INDA Institute, RWTH Aachen University, Aachen, Germany

Neural Representation Geometry Healthcare Privacy-Preserving ML Differential Privacy Medical Image Representation Learning

Feb 22, 2026cs.CV

US-JEPA: A Joint Embedding Predictive Architecture for Ultrasound

Ultrasound (US) imaging poses unique challenges for representation learning due to its inherently noisy acquisition process. The low signal-to-noise ratio and stochastic speckle patterns hinder standard self-supervised learning methods relying on a pixel-level reconstruction objective. Joint-Embedding Predictive Architectures (JEPAs) address this drawback by predicting masked latent representations rather than raw pixels. However, standard approaches depend on hyperparameter-brittle and computationally expensive online teachers updated via exponential moving average. We propose US-JEPA, a self-supervised framework that adopts the Static-teacher Asymmetric Latent Training (SALT) objective. By using a frozen, domain-specific teacher to provide stable latent targets, US-JEPA decouples student-teacher optimization and pushes the student to expand upon the semantic priors of the teacher. In addition, we provide the first rigorous comparison of all publicly available state-of-the-art ultrasound foundation models on UltraBench, a public dataset benchmark spanning multiple organs and pathological conditions. Under linear probing for diverse classification tasks, US-JEPA achieves performance competitive with or superior to domain-specific and universal vision foundation model baselines. Our results demonstrate that masked latent prediction provides a stable and efficient path toward robust ultrasound representations.

Ashwath Radhachandran, Vedrana Ivezić, Shreeram Athreya +2

Biomedical Artificial Intelligence Research Lab, University of California, Los Angeles, Los Angeles, United States of America · Medical Informatics, University of California, Los Angeles, Los Angeles, United States of America · Department of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, United States of America +3

Joint-Embedding Predictive Architecture Ultrasound Imaging Medical Image Representation Learning Self-Supervised Visual Representation Learning

Feb 19, 2026eess.IV

MeDUET: Disentangled Unified Pretraining for 3D Medical Image Synthesis and Analysis

Self-supervised learning (SSL) and diffusion models have respectively advanced representation learning and generative modeling for high-dimensional 3D visual data, yet they are often developed as separate paradigms. Their unification remains challenging under multi-source heterogeneity, as anatomical content must be preserved for analysis while acquisition-related style varies across centers and affects synthesis. In this paper, we propose MeDUET, a 3D Medical image Disentangled UnifiEd PreTraining framework in the variational autoencoder latent space. MeDUET formulates unified pretraining as an empirical factor identifiability problem, aiming to learn domain-invariant content factors for anatomy and domain-specific style factors for appearance. To improve factor separation, MeDUET first uses token demixing with a standard adversarial domain regularizer to establish basic content-style specialization, and further introduces Mixed Factor Token Distillation and Swap-invariance Quadruplet Contrast to reduce mixed-region factor leakage and organize factor spaces with factor-wise invariance and discriminability. With these learned factors, MeDUET transfers effectively to both synthesis and analysis, yielding higher fidelity, faster convergence, and better controllability for synthesis, while achieving competitive or superior domain generalization and label efficiency on diverse datasets, tasks, and modalities. Overall, MeDUET shows that multi-source heterogeneity can serve as useful supervision, with disentanglement providing an effective interface for unifying 3D medical image synthesis and analysis. Our code is available at https://github.com/JK-Liu7/MeDUET.

Junkai Liu, Ling Shao, Le Zhang

School of Engineering, College of Engineering and Physical Sciences, University of Birmingham, Birmingham, England, United Kingdom · UCAS-Terminus AI Laboratory, University of Chinese Academy of Sciences, Beijing 100049, China

Disentangled Representation Learning Self-Supervised Pre-Training 3D Medical Imaging Domain Generalization Medical Image Synthesis Medical Image Representation Learning

Jan 22, 2026cs.CV

RadJEPA: Radiology Encoder for Chest X-Rays via Joint Embedding Predictive Architecture

Vision-language pretraining has driven progress in medical image representation learning, but it depends on paired image-text data and can inherit reporting bias from clinical narratives. We study whether language-free predictive pretraining can produce an image encoder that transfers effectively to radiology report generation. RadJEPA is a chest-X-ray adaptation of I-JEPA, pretrained on approximately 840K unlabeled radiographs using latent context-to-target prediction. Our primary contribution is an extensive empirical evaluation of this language-free encoder for report generation: the frozen image encoder is coupled to a trainable two-layer projector and language decoder, and is also substituted into four established vision-language backbones. Across MIMIC-CXR and IU-Xray, RadJEPA matches or exceeds the evaluated image-only and image-text baselines on lexical, entity-relation, and clinical-label metrics. Controlled MIMIC-only comparisons provide evidence that the predictive objective contributes beyond domain-specific pretraining, while broader comparisons also reflect differences in pretraining data, model capacity, and input resolution. Complementary classification and segmentation experiments assess transfer beyond report generation.

Anas Anwarul Haq Khan, Mariam Husain, Pratik Jalan +1

Department of Computer Science (CSE), Indian Institute of Technology Bombay, India · Mohamed bin Zayed University of Artificial Intelligence, Abu Dhabi, UAE · Department of Biomedical Engineering, Johns Hopkins University, USA +1

Radiology Report Generation Medical Imaging Self-Supervised Pre-Training Joint-Embedding Predictive Architecture Medical Image Representation Learning

Jan 18, 2026cs.CV

CytoCLIP: Learning Cytoarchitectural Characteristics in Developing Human Brain Using Contrastive Language Image Pre-Training

The functions of different regions of the human brain are closely linked to their distinct cytoarchitecture, which is defined by the spatial arrangement and morphology of the cells. Identifying brain regions by their cytoarchitecture enables various scientific analyses of the brain. However, delineating these areas manually in brain histological sections is time-consuming and requires specialized knowledge. An automated approach is necessary to minimize the effort needed from human experts. To address this, we propose CytoCLIP, a suite of vision-language models derived from pre-trained Contrastive Language-Image Pre-Training (CLIP) frameworks to learn joint visual-text representations of brain cytoarchitecture. CytoCLIP comprises two model variants: one is trained using low-resolution whole-region images to understand the overall cytoarchitectural pattern of an area, and the other is trained on high-resolution image tiles for detailed cellular-level representation. The training dataset is created from NISSL-stained histological sections of developing fetal brains of different gestational weeks. It includes 86 distinct regions for low-resolution images and 379 brain regions for high-resolution tiles. We evaluate the model's understanding of the cytoarchitecture and generalization ability using region classification and cross-modal retrieval tasks. Multiple experiments are performed under various data setups, including data from samples of different ages and sectioning planes. Experimental results demonstrate that CytoCLIP outperforms existing methods. It achieves a weighted F1 score of 0.87 for whole-region classification and 0.91 for high-resolution image tile classification.

Pralaypati Ta, Sriram Venkatesaperumal, Keerthi Ram +1

Sudha Gopalakrishnan Brain Centre, Indian Institute of Technology, Madras, Chennai, India. · Department of Electrical Engineering, Indian Institute of Technology, Madras, Chennai, India.

Medical VLMs Histopathology Image Classification Medical Image Representation Learning

Dec 29, 2025cs.LG

Stochastic Siamese MAE Pretraining for Longitudinal Medical Images

Temporally aware image representations are crucial for capturing disease progression in 3D volumes of longitudinal medical datasets. However, recent state-of-the-art self-supervised learning approaches like Masked Autoencoding (MAE), despite their strong representation learning capabilities, lack temporal awareness. In this paper, we propose STAMP (Stochastic Temporal Autoencoder with Masked Pretraining), a Siamese MAE framework that encodes temporal information through a stochastic process by conditioning on the time difference between the 2 input volumes. Unlike deterministic Siamese approaches, which compare scans from different time points but fail to account for the inherent uncertainty in disease evolution, STAMP learns temporal dynamics stochastically by reframing the MAE reconstruction loss as a conditional variational inference objective. We evaluated STAMP on two OCT and one MRI datasets with multiple visits per patient. STAMP pretrained ViT models outperformed both existing temporal MAE methods and foundation models on different late stage Age-Related Macular Degeneration and Alzheimer's Disease progression prediction which require models to learn the underlying non-deterministic temporal dynamics of the diseases.

Taha Emre, Arunava Chakravarty, Thomas Pinetz +9

Institute of Artificial Intelligence, Center for Medical Data Science, Medical University of Vienna, Austria · Department of Ophthalmology and Optometry, Medical University of Vienna, Austria · BioMedIA, Department of Computing, Imperial College London, London, United Kingdom +8

Masked Autoencoders Self-Supervised Pre-Training Longitudinal Medical Image Analysis Clinical Outcome Prediction Medical Image Representation Learning

Aug 27, 2025cs.CV

Diverse Normal Prototypes-Guided Contrastive Reconstruction for Medical Anomaly Detection

Anomaly detection in medical images is challenging due to limited annotations and the domain gap. Existing reconstruction-based methods often rely on frozen pre-trained encoders, restricting adaptation to domain-specific patterns and degrading localization accuracy. Meanwhile, prototype-based learning offers interpretable representations but commonly suffers from prototype collapse, where a few prototypes dominate training and reduce diversity. To address these issues, we propose DNP-ConFormer, a unified framework that integrates a trainable encoder with prototype-guided reconstruction and a Diversity-Aware Alignment Loss. A momentum encoder enables stable domain-adaptive representation learning, while a lightweight Prototype Extractor discovers informative normal prototypes and injects them into the decoder via attention to guide reconstruction. The proposed alignment objective further encourages balanced feature-to-prototype assignments, effectively mitigating prototype collapse. Extensive experiments on multiple medical imaging benchmarks demonstrate improved representation quality and anomaly localization compared with prior methods. Visualization and prototype assignment analyses further validate the effectiveness and interpretability of our approach. The code is available at https://github.com/liluhu0/DNP-ConFormer.

Luhu Li, Bin Liu, Bowen Lin +3

School of Mathematics, Shandong University, Jinan 250100, China · Department of Interventional Medicine and Minimally Invasive Oncology, The Second Qilu Hospital of Shandong University, Jinan 250033, China · Department of Neurosurgery, The Second Qilu Hospital of Shandong University,2026 Jinan 250033, China

Prototype Learning Medical Image Anomaly Detection Anomaly Localization Reconstruction-Based Anomaly Detection Medical Image Representation Learning

Jun 23, 2025cs.CV

Latent Space Analysis for Interpretable Uncertainty in Melanoma Classification

Melanoma is a highly aggressive skin cancer, making early and accurate diagnosis critical. While deep learning excels in skin lesion classification, standard ``black-box" models struggle to explain diagnostic uncertainty, limiting clinical trust. This work introduces a hybrid framework combining a class-aware adversarial Variational Autoencoder and an XGBoost classifier, transcending simple binary classification by leveraging a generative latent space for interpretable decision support. Guided by adversarial training, the model learns the visual characteristics of skin lesions and projects them into a continuous latent space, ensuring that similar images are grouped closely together. Trained on this latent space, the XGBoost classifier achieves a robust AUC of 0.868, competing closely with state-of-the-art models. For borderline cases, the framework enables clinicians to leverage the latent topology through Content-Based Image Retrieval. This provides a dual benefit: it allows the clinician to visually compare an ambiguous lesion against biopsy-confirmed precedents and acts as an early warning sign since a borderline classification can indicate that a lesion shares features of both nevi and melanomas, potentially requiring close monitoring. Our approach translates algorithmic hesitation into transparent, evidence-based visual support, bridging the gap between predictive performance and clinical trust.

Ciro Listone, Aniello Murano

University of Naples Federico II, Naples, Italy.

Variational Autoencoders Skin Lesion Classification Uncertainty Quantification Medical Image Classification Explainable Medical Image Analysis Medical Image Representation Learning

May 27, 2025cs.CV

Good Enough? An Investigation on the Impact of Label Quality in Large-Scale Medical Datasets

Manually refining radiological segmentation masks is highly resource-intensive. To determine when this expert commitment is truly justified for the training of segmentation models, we investigate the relationship between label quality and model performance. Expanding beyond models trained directly for inference, we conduct the first study isolating the impact of label quality in pre-training datasets. While high-quality labels remain essential for models proceeding directly to deployment, we find no evidence that strict label quality is crucial for pre-training efficacy. These results question the necessity of exhaustive human-in-the-loop refinement for massive corpora intended for pretraining and suggest that expert effort is more effectively invested in well-curated downstream target datasets.

Alexander Jaus, Zdravko Marinov, Constantin Seibold +4

Image Segmentation Medical Imaging Foundation Models Healthcare Medical Image Segmentation Learning with Noisy Labels Medical Image Representation Learning

Feb 7, 2025cs.LG

Stochastic Optimal Control for Continuous-Time fMRI Representation Learning

Learning robust representations from functional magnetic resonance imaging (fMRI) is fundamentally challenged by the temporal irregularity and noise inherent in data from heterogeneous sources. Existing self-supervised learning (SSL) methods often discard critical temporal information by discretizing or averaging fMRI signals. To address this, we introduce a novel framework that reframes SSL as a Stochastic Optimal Control (SOC) problem. Our approach models brain activity as continuous-time latent dynamics, learning a robust representation of brain dynamics by optimizing a control policy that is agnostic to the temporal irregularity. This SOC framework naturally unifies masked autoencoding (MAE) and joint-embedding prediction (JEPA) to extract compact, control-derived representations. Furthermore, a simulation-free inference strategy ensures computational efficiency and scalability for large-scale fMRI datasets. Our model demonstrates state-of-the-art performance across diverse downstream applications, highlighting the potential of the SOC-based continuous-time representation learning framework.

Joonhyeong Park, Byoungwoo Park, Chang-Bae Bang +4

KAIST · Yonsei University · EverEx +1

Latent Dynamics Modeling Self-Supervised Time Series Representation Learning Predictive Representation Learning Medical Image Representation Learning

Nov 28, 2023eess.IV

Full-resolution MLPs Empower Medical Dense Prediction

Dense prediction is a fundamental requirement for many medical vision tasks such as medical image restoration, registration, and segmentation. The most popular vision model, Convolutional Neural Networks (CNNs), has reached bottlenecks due to the intrinsic locality of convolution operations. Recently, transformers have been widely adopted for dense prediction for their capability to capture long-range visual dependence. However, due to the high computational complexity and large memory consumption of self-attention operations, transformers are usually used at downsampled feature resolutions. Such usage cannot effectively leverage the tissue-level textural information available only at the full image resolution. This textural information is crucial for medical dense prediction as it can differentiate the subtle human anatomy in medical images. In this study, we hypothesize that Multi-layer Perceptrons (MLPs) are superior alternatives to transformers in medical dense prediction where tissue-level details dominate the performance, as MLPs enable long-range dependence at the full image resolution. To validate our hypothesis, we develop a full-resolution hierarchical MLP framework that uses MLPs beginning from the full image resolution. We evaluate this framework with various MLP blocks on a wide range of medical dense prediction tasks including restoration, registration, and segmentation. Extensive experiments on six public well-benchmarked datasets show that, by simply using MLPs at full resolution, our framework outperforms its CNN and transformer counterparts and achieves state-of-the-art performance on various medical dense prediction tasks.

Mingyuan Meng, Yuxin Xue, Dagan Feng +2

School of Computer Science, The University of Sydney, Australia. · Institute of Translational Medicine, Shanghai Jiao Tong University, China.

Medical Image Registration Medical Image Segmentation Medical Image Representation Learning

Mar 3, 2022cs.CV

Structure-Guided Self-Supervised Matching for One-Shot Medical Landmark Detection

Medical landmark detection usually requires accurate expert annotations, which are laborious and difficult to scale across anatomical regions. In this work, we study an extreme annotation-efficient setting where only a single annotated template image is available. We propose SGB-Match, a structure-guided coarse-to-fine self-supervised matching framework for one-shot medical landmark detection. The framework first learns dense anatomical correspondence from unlabeled augmented image pairs, and then transfers the landmark definition from the annotated template to each target image through feature matching. Different from standard contrastive correspondence learning, where negative candidates are penalized by a structure-agnostic rule, we introduce a structure-guided bias into the contrastive objective. The bias is constructed from relative distance and edge-aware anatomical cues, and explicitly reweights the negative gradients: nearby structure-relevant candidates are weakly repelled, while distant or structure-irrelevant negatives are strongly suppressed. As a result, the learned feature space better preserves local anatomical structures around template landmarks and reduces confusing responses from repeated textures. We further adopt a global-to-local design, where a global encoder provides coarse landmark localization and a local encoder refines the prediction in a cropped region. Extensive experiments on four 2D radiological landmark datasets demonstrate that SGB-Match achieves strong one-shot performance across both public and newly collected datasets and consistently benefits from both structure-guided bias and two-stage refinement.

Qingsong Yao, Zhen Huang, Ao Wang +4

Soochow School of Artificial Intelligence Renmin University of China · Department of Computer Science University of Science and Technology of China · School of Biomedical Engineering University of Science and Technology of China +3

Self-Supervised Learning Image Matching Few-Shot Learning Medical Image Representation Learning Medical Image Localization Local Feature Matching

Date pendingeess.IV

PathoHR: Breast Cancer Survival Prediction on High-Resolution Pathological Images

Breast cancer survival prediction in computational pathology presents a remarkable challenge due to tumor heterogeneity. For instance, different regions of the same tumor in the pathology image can show distinct morphological and molecular characteristics. This makes it difficult to extract representative features from whole slide images (WSIs) that truly reflect the tumor's aggressive potential and likely survival outcomes. In this paper, we present PathoHR, a novel pipeline for accurate breast cancer survival prediction that enhances any size of pathological images to enable more effective feature learning. Our approach entails (1) the incorporation of a plug-and-play high-resolution Vision Transformer (ViT) to enhance patch-wise WSI representation, enabling more detailed and comprehensive feature extraction, (2) the systematic evaluation of multiple advanced similarity metrics for comparing WSI-extracted features, optimizing the representation learning process to better capture tumor characteristics, (3) the demonstration that smaller image patches enhanced follow the proposed pipeline can achieve equivalent or superior prediction accuracy compared to raw larger patches, while significantly reducing computational overhead. Experimental findings valid that PathoHR provides the potential way of integrating enhanced image resolution with optimized feature learning to advance computational pathology, offering a promising direction for more accurate and efficient breast cancer survival prediction. Code will be available at https://github.com/AIGeeksGroup/PathoHR.

Yang Luo, Shiru Wang, Jun Liu +7

XJLTU · Dartmouth · NUP +7

Computational Pathology Cancer Survival Prediction Medical Image Representation Learning Whole-Slide Image Analysis

Date pendingq-bio.QM

Representation learning of human cortical folding to reveal long lasting neurodevelopmental signatures

The human brain folds in utero, primarily during late gestation. Shortly after birth, cortical folding patterns are established and remain stable thereafter, making them promising early neurodevelopmental markers. Yet it is unclear whether the representations given by current neuroimaging foundation models capture cortical folding variability. Here, we introduce Champollion, a self-supervised learning framework that learns interpretable local representations of cortical folding from structural MRI. Optimized on representative folding-related tasks, Champollion accurately captures known folding patterns across cortical regions and external datasets. In a comprehensive benchmark, it consistently outperforms neuroimaging and general-purpose foundation models. Furthermore, Champollion reveals richer genetic associations than conventional morphometric descriptors and identifies localized folding signatures associated with incomplete hippocampal inversion, prematurity, and maternal smoking. These results establish cortical folding as a rich and largely untapped source of neurodevelopmental information, and Champollion provides a unified framework for discovering, localizing and interpreting long lasting cortical folding signatures.

Julien Laval, Robin Guiavarch, Antoine Dufournet +24

Universit´e Paris-Saclay, CEA, CNRS, Neurospin, UMR 9027 BAOBAB, GAIA Laboratory, Gif-sur-Yvette, France · LTCI, Institut Polytechnique de Paris, T´el´ecom Paris, Palaiseau, France · Maison de la simulation, Universit´e Paris-Saclay, CEA, Gif-sur-Yvette, France +10

Representation Learning Self-Supervised Learning Neuroimaging Medical Image Representation Learning