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.

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Latest papers 168

Oct 7, 2026cs.CV

$Δ$ Representation: Geometry Supervised Representation Learning of Phenotypes via Counterfactual Reasoning for Medical VLMs

Medical vision-language models (VLMs) have shown increasing potential for radiological image interpretation. Medical VLMs encode radiological images into visual representations that capture both anatomical and phenotypic information for diagnosis. Existing approaches improve pathological phenotype representations through semantic-guided representation alignment. However, pathological phenotypes arise as lesion-specific visual changes superimposed on underlying normal anatomy. Such semantic alignment approaches fail to model the phenotype-specific increment relative to the corresponding normal anatomical representation. To address this gap, we propose \textbf{

Δ

Representation}, a visual phenotype representation learning framework based on counterfactual reasoning for medical VLMs. It comprises \textbf{BaseAnatomy}, a geometry-supervised representation learning module, and \textbf{

Δ

Phenotype}, a counterfactual incremental representation learning module. BaseAnatomy provides fine-grained geometric supervision through spatial relationships across and within anatomical structures.

Δ

Phenotype computes the representation increment between lesion representations and their corresponding normal anatomical representations, and supervises increments associated with the same phenotype to cluster in the representation space. Experiments on \textit{ReXGroundingCT} and \textit{LIDC-IDRI} demonstrate that

Δ

Representation effectively structures pathological phenotype representations and improves lesion grounding and phenotype characterization accuracy in medical VLMs. Code is available at https://anonymous.4open.science/r/deltarep-CF6D.

Hao Wang, Qiwei Zeng, Jinghao Lin +6

The University of Sydney · Shanghai Jiao Tong University · Northeastern University +1

Medical Image Representation Learning Medical VLMs Medical Image Grounding Geometric Representation Learning

Oct 7, 2026cs.CV

Geometry-Supervised Visual Representation Learning for Multi-Phenotype Lesion Interpretation in Medical VLMs

Medical vision-language models (VLMs) have shown increasing potential for clinical image interpretation. However, these models still struggle to interpret multi-phenotype lesions whose diagnosis requires the joint assessment of multiple pathological phenotypes. Existing vision-language alignment methods produce visual representations that fail to preserve anatomical hierarchies and relationships among phenotypic subclasses. This stems from their reliance on semantic supervision, which lacks geometric constraints to preserve these relationships in the visual embedding space. Moreover, the sparsity of lesion-related anatomical and phenotypic representations makes it difficult for medical VLMs to capture important diagnostic evidence. To address these limitations, we propose \textbf{PureVision}, a geometry-supervised visual representation learning framework for multi-phenotype lesion interpretation in medical VLMs. It combines a geometry-supervised representation learning module, \textbf{PureEyes}, and an anatomy-guided evidence aggregation module, \textbf{PureNeurons}. PureEyes provides geometric supervision through ideal spatial distributions that encode anatomical hierarchies and phenotypic subclass relationships. PureNeurons projects visual representations into the learned latent space, using their positions to selectively aggregate lesion-specific anatomical and phenotypic evidence. Experiments on \textit{LIDC-IDRI}, \textit{CBIS-DDSM}, and \textit{3DReasonKnee} demonstrate that PureVision improves lesion grounding and phenotype characterization in visual question answering and radiology report generation. Code is available at: https://anonymous.4open.science/r/purevision-06C2.

Hao Wang, Qiwei Zeng, Shuchang Ye +5

The University of Sydney · Shanghai Jiao Tong University · Northeastern University

Visual Representation Learning Medical Image Representation Learning Medical Image Analysis Radiology VLMs

Oct 7, 2026cs.CV

Masked Feature Encoding for Large-Scale Whole Slide Image Representation

Whole slide image (WSI) analysis in computational pathology follows a multiple instance learning (MIL) pipeline where patch embeddings are extracted independently and aggregated for slide-level prediction, but within-slide variance from staining, scanner, and local texture can overwhelm the discriminative signal. We propose Masked Feature Encoding for Multiple Instance Learning (MFE-MIL), a feature-space masking framework that trains a lightweight MLP adapter jointly with a window-based masked reconstruction branch and a MIL classification head. The two objectives are complementary. Classification guides the adapter to suppress within-slide patch variance, while window-based masked reconstruction provides an auxiliary regularizer for the adapted features without using patch coordinates, coordinate graphs, or segmentation preprocessing. The raster patch-extraction order is used only as a weak implicit prior. At inference, the decoder is removed, leaving only the adapter and MIL head. Across CAMELYON16/17, PANDA, and TCGA-BRCA with four diverse encoders, MFE-MIL improves ACC/F1 for nearly all tested aggregator-encoder settings and AUC in most, outperforms coordinate-based spatial methods (CAMIL), and achieves higher AUC than 2DMamba on three of four datasets (UNI). On five TCGA survival cohorts it improves the average concordance index for every aggregator tested, its most consistent gain. Code is available at https://github.com/AtlasAnalyticsLab/MFE-MIL.

Haoyu He, Basile Tessier-Cloutier, Yang Wang +1

Department of Computer Science and Software Engineering (CSSE), Concordia University, Montreal, Canada · McGill University, Montreal, Canada · Mila – Quebec AI Institute, Montreal, Canada

Whole-Slide Image Analysis Medical Image Representation Learning Histopathology Image Classification Multiple Instance Learning Masked Image Modeling

Oct 5, 2026cs.CV

NeuroCBIR: A Fast and Accurate Image Retrieval System for Whole-Brain and Region-Specific MRI

Content-based image retrieval (CBIR) in neuroimaging enables the identification of structurally similar brain scans, supporting diagnosis, prognosis, and treatment planning; however, existing methods are often limited to small datasets, single brain regions, or coarse class labels, thereby restricting their clinical utility and generalizability. Here, we present NeuroCBIR, a framework for fast and flexible retrieval of both whole-brain and region-specific 3D T1w MRI scans. A total of 103 cortical and subcortical regions are extracted to enable both whole-brain and region-level queries. NeuroCBIR leverages latent representations learned by a variational autoencoder (VAE) combined with contrastive learning, producing scan-specific embeddings that capture anatomical patterns. These embeddings were evaluated for subject re-identification, zero-shot age prediction, and zero-shot multi-class pathology stratification. Re-identification performance was high across both whole-brain and brain-region levels (mean average precision across the top-5 retrieved images (mAP@5) >= 98.4%), with robust generalization across datasets and acquisition conditions. While NeuroCBIR is not trained for age prediction or pathology stratification, zero-shot evaluations for these two tasks demonstrate that the embeddings encode meaningful information for downstream tasks. Embedding extraction on a 4-core CPU required approximately 18.7 s per scan, whereas similarity search was effectively instantaneous (less than 0.01 s). NeuroCBIR is publicly available for brain MRI with more than 26,000 precomputed T1w MRI embeddings. It supports reproducible research, region-specific flexibility, and clinically meaningful personalized diagnostic support. The software is available at https://github.com/minnelab/NeuroCBIR.

Felix Nieto-del-Amor, Jingru Fu, J. -Sebastian Muehlboeck +3

Medical Image Representation Learning Brain MRI

Oct 4, 2026cs.CV

EchoDino: A pediatric foundation model for transferable echocardiographic analysis across the lifespan

Echocardiography is the most widely used cardiac imaging modality, yet interpretation demands integrating visual evidence across global anatomy, localized structures and dynamic cardiac motion. Machine-learning models have automated individual tasks, but they are typically built for a single purpose and depend on expensively labeled datasets - a barrier particularly acute in pediatric care, where data are scarce and anatomy changes with age. Here we present EchoDino, a self-supervised foundation model for echocardiography, created by adapting the DINOv3 framework to 3.7 million frames from 1.7 million unlabeled pediatric echocardiography videos. With its encoder frozen, EchoDino produces representations that capture global context, local anatomy, and dense spatial detail. We introduce Motion-biased Entropy Maximization Sampling (MEMS) to select the most informative frames for video-level analysis. Across nine pediatric and adult datasets, EchoDino outperformed strong baseline models, raising view-classification accuracy from 0.609 to 0.889 and the area under the receiver operating characteristic curve for structural-heart-disease detection from 0.811 to 0.872, while also cutting age-estimation error from 3.857 to 1.389 years, achieving the best segmentation accuracy and lowering ejection-fraction errors. By generalizing from label-free pediatric data to adult echocardiography, EchoDino offers a versatile foundation for cardiac image analysis across the lifespan.

Sheng Cheng, Donnchadh M. O'Sullivan, Daniel J. Penny +3

Department of Computer Science, Rice University, Houston, TX, USA · Division of Pediatric Cardiology, Baylor College of Medicine, Houston, TX, USA · Texas Children’s Hospital, Houston, TX, USA

Medical Imaging Foundation Models Self-Supervised Learning Echocardiography Medical Image Representation Learning

Oct 1, 2026cs.CV

Surface-volume self-supervised representation learning of brain MRI for genetic discovery

Existing genome-wide association studies (GWAS) of brain imaging provide predefined or deep-learning-derived imaging phenotypes, yet these phenotypes come from either volumetric scans or cortical surface meshes, so each captures only part of the heritable variation in brain anatomy. Here we introduce MEVA (Mesh-Enhanced Volumetric Autoencoder), a self-supervised framework that encodes voxel-level image intensity together with cortical mesh geometry, including curvature and cortical thickness at each surface vertex, into one shared set of imaging features. Combining the mesh and volumetric inputs in MEVA yields modest performance gains in age and sex prediction over models that use either input alone. When these features serve as phenotypes for GWAS in the UK Biobank, they reveal more genome-wide significant loci than features learned from volumes alone or from meshes alone. These results suggest that adding cortical surface geometry to volumetric self-supervised learning captures additional heritable variation and so increases the number of loci detected.

Tian Xia, Nuo Chen, Zihao Zhu +4

D. Bradley McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, US. · Department of Biomedical Informatics and Data Science, Yale School of Medicine, New Haven, US. · Department of Electrical and Computer Engineering, Texas A&M University, College Station, US. +1

Self-Supervised Learning Medical Image Representation Learning Brain MRI Multimodal Learning

Sep 30, 2026cs.CV

PLRS-IC: A Dual-Calibration Framework for Chest X-Ray Vision-Language Alignment

Fine-grained vision-language alignment in chest radiography enables zero-shot classification, grounding, and segmentation without task-specific annotations. However, this alignment is fundamentally hindered by two intertwined sources of ambiguity: projection-induced visual mismatch and patient-agnostic semantic overlap. First, at the local feature level, frontal and lateral radiographs exhibit distinct appearances for the same clinical finding, rendering a shared patch-text similarity geometry inherently suboptimal. Compounding this visual ambiguity is a semantic mismatch during global contrastive optimization, where instance-level objectives penalize cross-patient pairs as strict negatives even when they share identical positive clinical concepts. To address this dual ambiguity, we propose PLRS-IC, a unified dual-calibration framework for chest X-ray representation learning. At the local alignment stage, Projection-Conditioned Low-Rank Residual Similarity (PLRS) dynamically adapts patch-text matching to projection-specific manifolds using a bounded, parameter-efficient low-rank residual. At the global optimization stage, Information-Content-Calibrated Soft False-Negative Suppression (IC-SFNS) leverages a corpus-derived information-theoretic prior to soften the penalty of semantically overlapping negatives without altering original contrastive assignments. Extensive experiments across nine public zero-shot benchmark settings demonstrate that our framework yields consistent improvements in classification, grounding, and segmentation, validating the necessity of dual-calibration in medical vision-language pre-training.

Qixing Zhao, Jinpeng Li

South China University of Technology

Radiology VLMs Vision-Language Alignment Multimodal Contrastive Learning Medical Image Representation Learning

Sep 29, 2026cs.CV

Med-RADIO: Reducing All Medical Domains Into One via Multi-Teacher Distillation

The rapid expansion of large-scale medical datasets and computational resources has driven significant progress in medical foundation models. Given the inherent heterogeneity of medical imaging modalities, current research mainly follows two paths: specialized models optimized for specific modalities, and generalist models designed to handle multiple modalities. However, medical generalist models suffer from both insufficient training data scale relative to natural image generalists and inadequate domain-specific depth relative to medical specialists. Empirically, generalist models establish a cross-modality performance baseline, while specialists define the performance ceiling within their respective domains. To elevate this baseline toward these ceilings, we propose Med-RADIO, a medical multi-teacher distillation framework that Reduces All Domains Into One by compressing complementary expertise from multiple domain-specific teachers into a unified medical vision foundation model. Our method curates both generalist and specialist teachers, allocates modality-aligned distillation streams to reorganize generalist pretraining data so it matches specialist domains, and uses a balanced loss to prevent any single teacher from dominating the distillation process. On internal and external classification benchmarks spanning five modalities, Med-RADIO improves over strong medical generalists under linear probing and remains competitive with representative specialists on most evaluated modalities. Code is available at https://github.com/CAIR-HKISI/Med-RADIO.

Chu Zhang, Haoyu Jiang, Hongyuan Zhang +2

Center for Artificial Intelligence and Robotics, Hong Kong Institute of Science and Innovation, Chinese Academy of Sciences, Hong Kong, China

Medical Imaging Foundation Models Medical Image Classification Multi-Teacher Knowledge Distillation Medical Image Representation Learning

Sep 28, 2026cs.CV

HERO: Histology Encoder for Robust Representation in Oncology

Foundation models trained on large pathology image corpora now provide strong, transferable representations for computational pathology. Over the past few years a series of such models has been released, each trained on more slides than the last; on standard classification and segmentation benchmarks, the leading models are now separated by small margins. In clinical use, however, the foundation model is applied to images from hospitals, scanners, and staining protocols outside its training data. Encoders generally embed these acquisition factors alongside biological information, which may introduce downstream errors and hinder safe clinical adoption. A pathology foundation model should therefore be robust to acquisition shift without giving up representation quality, yet robustness is seldom the axis along which models are compared. In this report, we introduce HERO (Histology Encoder for Robust Representation in Oncology), a ViT-G/14 pathology foundation model trained with the DINO and iBOT objectives and refined with high-resolution Gram anchoring on a morphology-balanced corpus of 500 million tiles from approximately 575,000 clinical whole-slide images. Across the evaluated public benchmarks, HERO shows the strongest robustness to center, scanner, and stain variation among the compared state-of-the-art foundation models, performs comparably on tile-level classification, segmentation, and gene-expression prediction, ranks first on average across 39 evaluated slide-level clinical tasks, and, under an equal-weighted framework-level analysis, has the best average rank across the six benchmark frameworks.

Zhi Li, Eghbal Amidi, Yating Cheng +12

Caris Life Sciences, Irving, TX, United States

Computational Pathology Domain Generalization Pathology Foundation Models Medical Image Representation Learning Whole-Slide Image Analysis

Sep 28, 2026cs.CV

Role-Guided MOE for Encoder-Level Pathology Representation Learning in WSI Classification

Whole slide image classification is a fundamental task in computational pathology, where patch representation quality directly affects downstream aggregation and slide-level discriminability. Pathology foundation models are widely adopted as frozen feature extractors for WSI classification; however, their fixed encoders may produce representations insufficiently adapted to target-specific tissue patterns and discriminative cues. Fine-tuning can improve target adaptation, but introduces a trade-off between pathology-specific representation capacity and adaptation efficiency, particularly in data-scarce settings. To address this, we propose a pathology role-guided mixture-of-experts feed-forward network (MoE-FFN) framework for efficient encoder-level representation learning. We design a two-stage training paradigm to establish and adapt pathology-aware expert specialization. In source-domain expert initialization, pathology-specific priors are distilled from a frozen Virchow2 teacher into a lightweight DINOv2-small student, while role prototypes serve as weak pathological anchors to encourage distinct expert functions. MoE-FFN blocks are introduced into selected high-level transformer layers to provide transformation diversity for heterogeneous pathological patterns. In target-domain adaptation, the initialized experts are refined through asymmetric prototype-guided optimization, enhancing task-relevant positive evidence and separating confusable hard negatives. The resulting encoder extracts offline patch representations that can be directly integrated with standard MIL aggregators. Experiments on the public BRACS dataset and a private PAROTID WSI dataset across five representative backbones demonstrate consistent improvements over the strongest baseline.

Xinyu Ma, Xing Yang, Hongtao Jin +4

Artificial Intelligence Research Institute, Shenzhen MSU-BIT University, Shenzhen 518172, China · Shenzhen People’s Hospital, Shenzhen 518020, China

Pathology Foundation Models Mixture-of-Experts Models Medical Image Representation Learning Whole-Slide Image Analysis

Sep 28, 2026cs.CV

Natural Image Autoencoder-Based fMRI Representations for Trait and State Prediction

Foundation models pre-trained on large-scale fMRI datasets have shown strong downstream performance, but at substantial data and computation cost. To investigate how much fMRI-specific pre-training is actually needed for such performance, we introduce FReD, which derives fMRI representations from a frozen Deep Compression AutoEncoder (DCAE) pre-trained exclusively on natural images and pairs them with a task specific readout. For trait prediction, FReD summarizes frame-wise representations by their temporal mean and log-standard deviation and applies linear probing, with late fusion across two normalization schemes. For state prediction, it represents each frame as a single token and models temporal dependencies with a shallow Transformer. Across four resting-state datasets spanning six trait-prediction targets, linear probes on frozen DCAE features generally outperform those on fMRI foundation model representations and remain competitive with fully fine-tuned fMRI foundation models. On three task-fMRI state-prediction tasks, a temporal readout on DCAE features performs comparably to the strongest foundation models evaluated. A Gaussian injection analysis further shows that localized signal changes are recovered more accurately from the frozen DCAE features than from the evaluated foundation-model representations. Together, these results show that strong performance on current fMRI benchmarks is possible without fMRI-specific representation pre-training, making frozen natural-image features as a useful baseline for assessing its added value.

Juhyeon Park, Yeonwoo Kim, Peter Yongho Kim +5

IPAI, Seoul National University · Microsoft Research · ECE, Seoul National University +1

Medical Imaging Foundation Models fMRI Foundation Models Neuroimaging Medical Image Representation Learning

Sep 24, 2026cs.CV

ConPro: Contrast Projection Pretraining for Label-Efficient Vessel Segmentation in DSA Sequences

Dense vessel annotation in digital subtraction angiography (DSA) is labor-intensive, yet every unlabeled sequence records how contrast passes through the vessels. Semi-supervised methods take their targets from the current model, and generic self-supervised pretexts reconstruct static appearance, so this signal goes unused. We propose ConPro, a self-supervised pretraining scheme whose target is a contrast projection, the normalized drop of every pixel below its temporal median over the sequence. On DIAS and DSCA, with 10%, 20% and 50% of the training cases labeled, ConPro improves on training from scratch at every label fraction and is the best of the compared methods on DSCA at 20% and 50% labels. Controlled comparisons show that the gain comes from the target. A temporal-median target with the same input, loss and budget stays at scratch level, and using the projection directly instead of learning it, as an input channel or a pseudo-label, helps little or hurts. ConPro provides pretrained weights without changing the segmentation architecture, so it combines with semi-supervised training, and UniMatch, the strongest baseline, gains 0.5 to 2.0 Dice and 0.9 to 2.3 clDice at every label fraction when started from ConPro weights, reaching 75.4 Dice on DIAS and 81.3 on DSCA.

Xinge Guo, Yuanhao Wang, Liqi Shu +2

Duke University, Durham, NC, USA · Carnegie Mellon University, Pittsburgh, PA, USA · University of Pittsburgh Medical Center, Pittsburgh, PA, USA

Medical Imaging Semi-Supervised Medical Image Segmentation Medical Image Segmentation Medical Image Representation Learning

Sep 23, 2026cs.CV

From ECG Signals to Representative-Morphology Heatmaps for Biometric Recognition

Electrocardiography (ECG) contains subject-specific morphology that supports biometric recognition, yet image-based performance depends on how the waveform is rendered. We introduce representative-morphology heatmaps, a deterministic ECG-to-image representation adapted from ECGXtractor. Within each block of ten aligned beats, the five beats closest to the block mean are averaged into a 400 by L matrix and rendered either as a conventional trace or as a dense cardiac-time-by-lead heatmap. Since both representations contain identical physiological samples, their comparison isolates the effect of rendering. We evaluate verification and closed-set identification on PTB, ECG-ID, and MIMIC-IV-ECG-DEMO. Five compact models, including ZACH-ViT, are trained from scratch, while six ImageNet-pretrained CNN and transformer backbones assess model scale and visual transfer. Heatmaps improve both FNMR operating points and both identification ranks in all 15 compact model-dataset comparisons, while EER improves in 14. Across the matched experiments, EER decreases by 9.59 percentage points and Rank-1 increases by 24.69 points on average. ConvNeXt-Tiny reaches 2.43% EER on PTB and 5.79% on ECG-ID, whereas DeiT-Base reaches 14.92% on MIMIC-DEMO. ImageNet initialization clearly benefits the two multilead datasets but has a mixed effect on ECG-ID, and performance does not increase monotonically with model size. The best heatmap systems approach the strongest signal-domain EER on PTB and ECG-ID, while DeiT-Base provides the strongest evaluated performance on MIMIC-DEMO. Lead-channel ablation further shows that useful channel combinations depend on the cohort and biometric task. Overall, representative-morphology heatmaps provide an effective image representation for ECG verification and identification.

Athanasios Angelakis, Marta Gomez-Barrero

BioML, Research Institute CODE, University of the Bundeswehr Munich, Munich, Germany · Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands

Biometric Identification Electrocardiography Medical Image Representation Learning

Sep 22, 2026cs.CV

nnFoundation: 3D Foundation Models for Radiology

Radiological artificial intelligence has advanced rapidly, yet most systems remain narrowly task-specific, data-intensive, and fragile under domain shift. Foundation models promise more transferable and data-efficient solutions, but existing approaches are limited in scale, evaluated narrowly, and often assume that a single pretrained model can support diverse downstream tasks. Here we present nnFoundation, complementary convolutional and transformer-based 3D radiological foundation models. Developed within the Human Radiome Project (THRP), nnFoundation is trained on 2.1 million CT, MRI, and PET image volumes from 125 institutional and public datasets. We evaluate them across 108 tasks spanning segmentation, detection, classification, report generation, and image retrieval, including evaluations under domain shift, by external partners and in low-data and low-compute regimes. Across all task types, our convolution- and transformer-based nnFoundation models consistently outperform both prior 3D foundation models and training from scratch, establishing state-of-the-art performance for radiological imaging. However, performance follows a consistent task-dependent structure: the convolutional nnFoundation model dominates spatially localized tasks, whereas the transformer-based nnFoundation model excels in tasks requiring global semantic reasoning and in frozen-feature settings. Dynamically aligning the foundation model topology with the dataset characteristics post-hoc further improves transfer across heterogeneous 3D settings. These results show that transferable 3D radiological performance is governed not by a single universal model, but by the interplay of scalable pretraining, complementary architectures, and dataset-aware adaptation. We release nnFoundation models integrated into nnU-Net and nnDetection, enabling immediate application across established radiology workflows.

Constantin Ulrich Harsy, Tassilo Wald, Karol Gotkowski +80

3D Foundation Models Medical Imaging Foundation Models Vision Foundation Model Adaptation Medical Image Representation Learning

Sep 22, 2026cs.CV

Foundation model embeddings capture pre-diagnostic changes on screening mammograms

Foundation model embeddings of screening mammograms may encode pre-diagnostic tissue change without task-specific adaptation. We tested whether embeddings move faster along a data-derived "cancer direction" in women later biopsied for cancer than in matched screen-negative controls, and whether this depends on pretraining domain. We studied 1,773 biopsied women (785 malignant, 988 biopsy-negative) and 1,773 matched controls, each with at least two annual screening exams before their index exam. An identical pipeline was applied to four 2D models: Mammo-CLIP (MC, out-of-distribution mammography), HOPPR (in-distribution mammography), MedImageInsight (MII, general medical imaging), and BiomedCLIP (biomedical vision-language pretraining on literature figures). Breast-level embeddings quantified longitudinal movement along the cancer direction. We compared cases and controls using a between-patient design with complementary mixed-effects analysis, and biopsied versus healthy contralateral breasts within patients. Under matched modality in MII embedding space, malignant cases drifted significantly faster than controls in the first two screening intervals preceding the index exam; biopsy-negative cases showed significance only in the first. MC differences were significant in the first interval for both biopsy groups. Within-patient comparisons showed a broadly similar pattern, with MC significance extending to the second interval in both groups and HOPPR showing significance at interval 1. BiomedCLIP showed no significant differences in either design or biopsy group. Overall, directional embedding velocity emerges as a property of clinically grounded rather than general biomedical pretraining, showing that foundation model embeddings can encode pre-diagnostic mammographic change without task-specific adaptation.

Kalina P. Slavkova, Eric Brattain, Aditya Gowd +6

HOPPR, Chicago, IL, USA · University of Utah School of Medicine, Salt Lake City, UT, USA · 4DMedical, Woodland Hills, CA, USA +1

Breast Cancer Medical Imaging Foundation Models Longitudinal Medical Image Analysis Mammography Medical Image Representation Learning

Sep 21, 2026cs.CV

MiTHras: Task-specific Hierarchical Semi-supervised Contrastive Masked Autoencoder for Mitotic Figure Analysis

Mitotic figure (MF) analysis supports tumor grading and prognostic assessment, but automated models remain sensitive to differences in tissue type and image acquisition. We present MiTHras, a task-specific pretraining framework that combines pseudo-label-guided image- and token-level contrastive learning with masked reconstruction. We construct TCGA-MF-Pseudo, a corpus of 1.8 million cell-centered images from 14 TCGA cohorts spanning 11 organ sites. Comprehensive evaluation on MF classification, detection, count-based survival prediction, and subtype classification demonstrates the efficacy of MiTHras. It achieves the highest mean F1 on all three MF classification benchmarks and both subtype benchmarks. MiTHras also outperforms general-purpose and pathology foundation encoders by a larger margin under frozen-encoder linear probing than under full fine-tuning. Although detection gains are modest due to a shared candidate-detection stage, ablations confirm that token-level supervision improves typical-versus-atypical classification and linear probing. These findings establish that MiTHras yields robust, transferable representations for automated mitotic activity assessment.

Trinh T. L. Vuong, Simon Graham, Quoc Dang Vu +5

Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, USA · Histofy Ltd, Coventry, United Kingdom · Department of Pathology, University Medical Center Ho Chi Minh City, Ho Chi Minh City, Vietnam +1

Contrastive Learning Masked Autoencoders Histopathology Image Classification Medical Image Representation Learning Microscopy Image Analysis

Sep 21, 2026cs.CV

What Makes a Good Medical Image Tokenizer? Rethinking Reconstruction and Generation in Medical Image Tokenization

Latent diffusion models now dominate medical image generation, and every such pipeline rests on a \emph{tokenizer} that compresses images into the latent codes for image generation to operate on. Thereby, the tokenizer choice bounds every downstream task from reconstruction fidelity and generation quality to the representations available for downstream analysis. Yet, medical imaging pipelines routinely utilize tokenizers from natural imaging on the hypothesis that their behavior carries over. However, this is an assumption never tested in the medical imaging regime, where datasets are orders of magnitude smaller and images exhibit far lower inter-sample variance. We present a systematic evaluation of medical image tokenizers evaluating thirty configurations across ten model families on twelve datasets at three compression factors, spanning reconstruction, generation, latent geometry, downstream classification, and memorization. We find that (1) performance on image reconstruction and generation strongly correlate, unlike prior reports on natural images; (2) modern tokenizers use nearly all of their codebook entries, but still leave most of the latent space unused; (3) training-set memorization is mild and is further suppressed by stronger latent space compression; and (4) discrete quantization can largely preserve downstream classification, with lookup-free schemes being the main exception.

Niklas Bubeck, Yundi Zhang, Vasiliki Sideri-Lampretsa +4

School of Computation, Information and Technology, Technical University of Munich, Germany · Munich Center for Machine Learning, Technical University of Munich, Germany · School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Germany +3

Image Tokenization Medical Image Synthesis Image Generation Evaluation Medical Image Representation Learning

Sep 16, 2026cs.CV

Seeing Abnormal from Normal: Glomerular Abnormality in Representations of Normal Renal Morphology

Fine-grained evaluation of glomerular pathology must distinguish normal glomeruli from abnormalities such as global and segmental glomerulosclerosis, obsolescent, ischemic, solidified, disappearing, and atubular glomeruli. Supervised classification requires labeled examples of every category, which is impractical when subtypes are rare or absent from the training cohort. One-class anomaly detection offers an alternative by modeling normal data and scoring deviations, allowing previously unseen abnormalities to be detected. We use the frozen residual U-Net backbone of Omni-Seg, pretrained to segment structurally normal renal primitives without abnormal-subtype labels. We propose NoRDeC (Normal-Reference Detection and Characterization), a framework combining Mahalanobis normal-reference scoring with layer-wise representation analysis to determine whether and where glomerular pathology is encoded, how spatial aggregation affects detection, and whether abnormalities alter inter-layer relationships differently. Using glomerular images from two institutions, we evaluate backbone layers and aggregation strategies, compare NoRDeC with PaDiM and PatchCore, and analyze representations using centered kernel alignment (CKA). Layer 4 with Center-70 aggregation achieved a pooled AUROC of

0.926\pm0.013

. NoRDeC achieved the highest AUROC in six of seven abnormality categories and in the pooled analysis, while CKA suggested subtype-dependent changes in inter-layer relationships not captured by anomaly scores alone. The normal-reference model is fitted using only normal glomeruli; abnormality labels are used for configuration selection, evaluation, and grouping in the representation analysis. These results show that a frozen renal feature extractor can support both detection and representation-level characterization of glomerular abnormalities without using abnormal examples to fit the detector.

Greta Hasko, Rachit Saluja, Tianyu Shi +11

Cornell University, Ithaca, NY 14853, USA · Cornell Tech, New York, NY 10044, USA · Sichuan University, Chengdu, 610207, CN +6

Medical Image Anomaly Detection Unsupervised Anomaly Detection Medical Image Representation Learning

Sep 15, 2026cs.CV

Which Pretext Task Transfers? Self-Supervised Pretraining Objectives for Lung Ultrasound

Self-supervised learning (SSL) can reduce the need for labelled medical images, but the choice of pretext objective remains unclear for lung ultrasound (LUS). Contrastive learning, masked reconstruction, and joint-embedding predictive architectures (JEPA) differ in the space in which their targets are defined, yet existing ultrasound studies compare them under different corpora, backbones, and evaluation protocols. We compare these three objective families using the same encoder backbone, pretraining corpus, optimisation schedule, and frozen-evaluation protocol. Encoders are pretrained on COVID-BLUeS LUS videos and evaluated with linear,

k

NN, and attentive probes at 5%, 10%, 50%, and 100% label budgets. Evaluation is performed on POCUS using patient-level five-fold cross-validation and on the independently acquired Mendeley-Uganda dataset, which is excluded from both pretraining and probe fitting. At the full label budget under linear probing, VideoMAE and V-JEPA achieve

66.5 \pm 13.1

and

65.4 \pm 11.7

balanced accuracy on POCUS, while MoCo achieves

42.1 \pm 1.2

. On Mendeley-Uganda, the ranking reverses: MoCo performs best at

62.7 \pm 1.0

, followed by VideoMAE at

53.8 \pm 2.8

, while V-JEPA falls near chance at

35.1 \pm 4.9

. These results show that POCUS probe accuracy alone does not identify the objective that transfers best across datasets. We also outline planned representation-level analyses to examine this reversal. Code is publicly available at https://github.com/moeinheidari7829/LUSVideoSSL.

Moein Heidari, Junbo Rao, Jai Choraria +3

University of British Columbia, Vancouver, BC, Canada · Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA

Contrastive Learning Masked Autoencoders Self-Supervised Pre-Training Joint-Embedding Predictive Architecture Ultrasound Imaging Medical Image Representation Learning

Sep 14, 2026cs.CV

AlignUS: MRI-Guided Ultrasound Representation Learning for ALS Classification from Tongue Images

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease in which early assessment remains challenging, particularly in low-resource settings where MRI is often unavailable. High-resolution ultrasound (HRUS) of the tongue offers a portable and low-cost alternative for evaluating bulbar involvement, but learning reliable diagnostic models is limited by small datasets and the difficulty of extracting robust representations from ultrasound alone. We propose AlignUS, a cross-modal knowledge distillation framework that transfers anatomical knowledge from MRI to a HRUS-based classifier while requiring only HRUS at inference time. The model combines classification loss, supervised contrastive learning, and feature-level distillation to align HRUS representations with MRI embeddings. AlignUS achieves a patient-level balanced accuracy of 0.958, macro-F1 of 0.963, and ROC-AUC of 0.990, aggregated across four patient-level cross-validation folds, with consistent improvements over HRUS baselines and cross-modal alternatives. These results demonstrate that MRI-derived supervision can substantially improve ultrasound-based ALS assessment while preserving low-cost, inference-time independence from MRI.

Kadija Abdel Ghader, Emani Babe, Lorenzo Pettinari +2

Unité de Recherche en Systèmes Intelligents Avancés (URSIA), Institut Supérieur du Numérique (SupNum), Nouakchott, Mauritanie · University of Basel, Basel, Switzerland

Cross-Modal Knowledge Distillation Ultrasound Imaging Medical Image Representation Learning

Sep 14, 2026cs.LG

Geometric-to-Semantic Spherical Transfer Learning for Cortical Sulci Labeling

Deep learning on cortical surfaces faces a dilemma: capturing the complex topology of over 60 nomenclature-dependent sulci per hemisphere requires high-capacity models, yet the extreme scarcity of expert annotations (

N=62

subjects) inevitably causes overfitting. Standard supervised approaches fail to generalize in this data-scarce regime, particularly for variable and small sulci where topological ambiguity is high. To overcome this limitation, we introduce a Geometric-to-Semantic Spherical Transfer Learning framework. First, we leverage massive unlabeled data (UK Biobank,

\approx

30,000 subjects) to pre-train a spherical encoder using a locally-optimized strategy. By relying solely on continuous surface features (curvature and depth), the relevance of this pre-training is confirmed by the model's ability to detect localized and rare topological traits, such as sulcal interruptions. The downstream labeling task, however, introduces extracted sulcal fundi (lines) as an explicit semantic input. To bridge this dimensional domain gap (from purely geometric to semantic) without causing catastrophic forgetting, these anatomical lines are integrated into the pre-trained backbone via a soft-initialized Topological Prior Injector. Our experiments demonstrate that this approach outperforms fully supervised baselines trained from scratch, achieving a mean Dice of 0.77. Crucially, a local analysis reveals that the self-supervised geometric priors yield the largest performance gains on variable and tertiary sulci (up to 14.8%), confirming that learning the cortex shape is highly beneficial for identifying its rarest parts.

Saeb Tounsi, Joël Chavas, Pietro Gori +3

Paris-Saclay University, CEA, NeuroSpin, Baobab, Saclay, France · LTCI, Télécom Paris, Institut Polytechnique de Paris, France

Self-Supervised Pre-Training Geometric Representation Learning Cross-Domain Transfer Learning Neuroimaging Medical Image Representation Learning

Sep 14, 2026cs.CV

Self-supervised Pre-training Helps Retinal Disease Progression Modelling Most When Data Is Scarce

Modelling how a disease progresses over time requires longitudinal imaging cohorts, which are scarce and small, whereas cross-sectional data -- one image per participant -- is abundant. Self-supervised pre-training on such data offers a way to bridge this gap, but it is unclear which strategy best supports progression modelling, or how that answer depends on the amount of labelled longitudinal data. We study this for age-related macular degeneration (AMD), pre-training encoders on the large cross-sectional NAKO cohort and predicting time to late AMD on the longitudinal AREDS dataset. We compare in-house self-supervised encoders against a general-purpose (DINOv2) and a domain-specific (RETFound) foundation model, across contrastive, masked-autoencoding, and self-distillation objectives, under frozen and fine-tuned protocols, and across labelled training sets from 100 to 32,250 examples. Which model performs best depends on how the encoder is used. When the encoder is frozen and labels are few -- the regime typical of longitudinal cohorts -- pre-trained representations reach clinically reasonable discrimination from a few hundred labelled samples, while models trained from scratch do not; this advantage fades under fine-tuning. Transfer is governed by the self-supervision objective rather than corpus scale or domain match, so that an encoder pre-trained on a modest cross-sectional cohort matches or exceeds a far larger in-domain foundation model. Together, these results offer a practical recipe for building progression models where longitudinal data is scarce: a frozen self-supervised encoder with a lightweight survival head.

Ifeoma Veronica Nwabufo, Julius Gervelmeyer, Sarah Müller +1

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

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

Sep 11, 2026cs.CV

SCDM: Spatial-Contextual Disentanglement Mamba via Differential Inference for Efficient Image Classification

State Space Models (SSMs), particularly VMamba, have emerged as efficient alternatives for modeling long-range dependencies in medical image analysis. However, distinguishing subtle pathological features from visually similar anatomical backgrounds remains a significant challenge. Existing SSM architectures often learn entangled representations, lacking explicit mechanisms to separate disease-specific signals from normal anatomy. To address this limitation, we propose Spatial-Contextual Differential Mamba (SCDM), an asymmetric dual-branch architecture designed for selective representational disentanglement. SCDM introduces a Positive Branch for extracting discriminative features and a Negative Branch that actively models and suppresses normal anatomical context. This separation is achieved through a similarity-driven repulsion gate and a differential inference rule, which promote competitive feature learning without requiring additional branch labels or increasing model capacity. Evaluated on the RSNA Pneumonia dataset, SCDM achieves competitive classification performance (AUC of 0.858) while requiring significantly fewer parameters (29.4M) and FLOPs (1.44G) compared to standard VMamba and vision transformer baselines. Furthermore, activation analyses demonstrate that our differential mechanism yields highly precise localization, effectively isolating lesions by inhibiting irrelevant anatomical distractors.

Mustafa Bora Çelik, Hayriye Aktaş Dinçer, Ayse Keles

Department of Computer Engineering, Faculty of Engineering and Natural Sciences, Ankara Medipol University, Ankara, Turkiye · School of Computer Science, University of Galway, Galway, Ireland

Visual SSMs Medical Image Classification Medical Image Representation Learning

Sep 7, 2026cs.AI

A radiographic world model for clinical reasoning and evidence generation

Medical imaging artificial intelligence (AI) is commonly developed as separate mappings from radiographs to diagnostic outputs or from clinical descriptions to generated images, although both arise from the same underlying radiographic state. A world-model formulation instead seeks to learn an internal representation of this state that can support both clinical readout and conditional simulation of radiographic observations. Here we introduce MedDream, a radiographic world model that learns a shared continuous latent state from paired chest radiograph-text observations for diagnostic reasoning and report-conditioned evidence generation. MedDream was pretrained on 2.65 million leakage-controlled chest radiograph-text pairs curated from 4.40 million candidates. Across eight clinical datasets and two independent reader cohorts, MedDream outperformed leading diagnostic and generative comparators. For diagnostic reasoning, MedDream showed strong generalization across disease recognition, label-scarce adaptation, severity assessment, and localization, while MedDream-supported review increased mean resident concordance with independent radiologist consensus from 56.3% to 63.0%. For evidence generation, MedDream produced radiographs that preserved clinically relevant pathology and improved downstream performance on held-out real data, with synthetic augmentation increasing external VinDr-CXR macro-AUROC from 76.4% to 81.4%. More importantly, conditioning generation on prespecified subgroup performance gaps enabled targeted evidence construction, increasing weighted F1 by 3.1 percentage points in Asian patients, whereas matched-volume unguided augmentation decreased it by 2.3 points. These findings establish radiographic world models as a path toward medical AI that learns clinically meaningful internal states for interpreting, simulating, and constructing evidence for clinical use.

Suyang Xi, Songtao Hu, Shansong Wang +8

Department of Computer Science and Informatics, Emory University, Atlanta, GA, USA. · Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, USA. · Department of Radiation Oncology and Winship Cancer Institute, Emory University, Atlanta, GA, USA. +2

Chest X-Ray Classification Radiology VLMs World Models Medical Image Synthesis Medical Image Representation Learning

Sep 2, 2026cs.CV

Synergistic Information Disentanglement for Omni-modal Slide Representation Learning in Computational Pathology

In computational pathology (CPath), developing omni-modal self-supervised learning (SSL) models that integrate histology, genomics, and clinical reports enables transferable representation learning for whole slide images (WSIs). Existing approaches implicitly force heterogeneous modalities into a uniform latent space by contrastive alignment, causing modality collapse where unique, synergistic diagnostic signals (termed as

\mathrmΦ

) are discarded in favor of trivial redundancy. We hypothesize that the strongest task-agnostic SSL training signal stems from distilling the synergistic interactions over merely aligning shared redundancy. To this end, we introduce \textsc{

\mathrmΦ

-Omni}, a synergistic information disentanglement framework grounded in Partial Information Decomposition (PID) theory for slide representation learning. Unlike standard contrastive approaches, \textsc{

\mathrmΦ

-Omni} employs a Synergistic Information Bottleneck (SIB) regulated by the proposed

\mathrmΦ\text{ID}

objective, which explicitly suppresses marginal redundancy while maximizing irreducible synergy, thereby distilling high-order cross-modal interactions. Following pretraining on breast (

n

=1031) and lung (

n

=919) cohorts, \textsc{

\mathrmΦ

-Omni} demonstrates superior few-shot performance across five independent external datasets spanning eight tasks compared to supervised and SSL baselines. Source code is available here.

Mingxin Liu, Chengfei Cai, Anwen Lu +5

Jiangsu Key Laboratory of Intelligent Medical Image Computing, School of Artificial Intelligence, Nanjing University of Information Science and Technology, Nanjing, China · Jiangsu Key Laboratory of Intelligent Drug Screening and Repositioning, College of Information Engineering, Taizhou University, Taizhou, China · College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China

Medical Image Representation Learning Computational Pathology Multimodal Learning Information Bottleneck

Sep 1, 2026cs.CV

Pix2Rep-v2: Data-Efficient Representation Learning for Dense Medical Imaging Applications

Dense self-supervised learning (SSL) is a powerful paradigm for learning without annotations the local descriptors required to solve dense medical imaging tasks. We present Pix2Rep-v2, a framework for SSL of pixel- and voxel-level representations suitable for few-shot downstream applications. Pix2Rep-v2 addresses the main challenges of dense SSL by leveraging a redundancy reduction objective at the pixel-level with a principle of equivariance of dense representations, that scales efficiently to 3D or wide field-of-view applications. We evaluate our method on four datasets, across multiple tasks, multiple modalities and anatomical structures using multiple backbones in 2D and 3D, and under various data regimes. As an alternative to linear probing or full fine-tuning on the downstream task, we also propose an in-context variant, without downstream training, based on a dense prototype approach. Pix2Rep-v2 shows substantially higher data-efficiency in few-shot scenarios compared to fully supervised baselines, and is competitive with the state-of-the-art e.g., +9.3 Dice points in one-shot segmentation on the M&Ms-2 dataset. Our code and pre-trained models are publicly available at https://github.com/BioMedTP/pix2rep-v2.

S. Sifaoui, E. Angelini, S. Toupin +2

LTCI, Télécom Paris, Institut Polytechnique de Paris, Palaiseau, France · MIRACL.ai Laboratory, Hôpital Universitaire Lariboisière (AP-HP), Paris, France · Université Paris Cité, Inserm MASCOT, Paris, France

Representation Learning Visual Representation Learning Equivariant Representation Learning Few-Shot Medical Image Segmentation Medical Image Representation Learning Self-Supervised Visual Representation Learning

Aug 12, 2026cs.CV

GenFAR: A generalized representation of brain structure, derived from 49,246 multi-cohort MRIs via deep learning

Deep learning models for neuroimaging have largely been developed for individual tasks, limiting knowledge transfer across applications. Here we introduce GenFAR, a modular deep learning framework that learns general, clinically informed features from brain MRIs. We trained this modular architecture on 49,246 individuals across 11 cohorts, using 17 diverse classification and regression tasks spanning cognition, clinical, diagnosis, demographics, and biomarkers. This yields aggregated, focused feature sets that capture rich, clinically- and biologically-relevant brain representations. We developed a sequential learning approach where tasks progressively build on previously learned representations. Through an analysis of 5,000 task sequences, we identified an optimal sequence length of six tasks and introduced a Donor Score metric to quantify each task's contribution to downstream performance. This analysis revealed five consistently strong donor tasks (Age, AD/MCI, MMSE, Hypertension, Hyperlipidemia) that formed the base of our sequential model. We demonstrated the utility of our learned representation, in various tasks beyond those included in the training set, to serve as the foundation for specialized secondary predictors. We further showed that using the learned feature representation can substantially increase the sample efficiency of secondary deep learning training tasks and models, as well as improve their accuracy.

Vishnu M. Bashyam, Guray Erus, Junhao Wen +29

Artificial Intelligence in Biomedical Imaging Lab, University of Pennsylvania · Department of Electrical and Systems Engineering, University of Pennsylvania · Florey Institute of Neuroscience and Mental Health, University of Melbourne +16

Medical Imaging Foundation Models Multi-Task Learning Medical Image Representation Learning

Aug 10, 2026cs.CV

Frozen Brain-MRI Foundation Models Are Site Fingerprints

Frozen foundation-model (FM) embeddings are increasingly used as off-the-shelf brain-MRI representations, on the assumption that they capture anatomy. We audit what they actually encode and find that acquisition site is a large, intrinsic component of the representation. Across two independent cohorts (ABIDE-I, ABIDE-II), three frozen 3-D encoders (brain-pretrained, CT-pretrained, and randomly initialized), and every network depth, site is linearly decodable at roughly 0.9 balanced accuracy at deep layers, exceeding the decodability of every clinical or demographic variable (sex, age, autism diagnosis) at every layer. The effect is intrinsic rather than learned: a randomly initialized encoder is already a ~0.9 site classifier on both cohorts and across three architecture families (Swin, ViT, ResNet), and site is decodable at ~0.95 directly from the raw downsampled image with no encoder, so the fingerprint reflects low-level image statistics that any encoder preserves rather than a product of pretraining. Residualizing measured population covariates leaves site decodability essentially unchanged, indicating an acquisition- rather than population-driven effect. A nonlinear probe matches the linear one, so the fingerprint is fully linearly accessible. The site subspace is removable post hoc by iterative null-space projection or ComBat (site decodability 0.94 -> 0.07/0.00), and is a site-attribution concern for shared or federated embeddings; but for dense segmentation this removal is not free, because site and anatomy occupy an entangled linear subspace (a matched-rank random-direction projection is Dice-neutral, whereas removing the site subspace is destructive). We recommend site-audited use of frozen brain-MRI FMs and release an open audit toolkit.

Saman Rahbar

University of British Columbia, Vancouver, Canada

Medical Imaging Medical Imaging Foundation Models Medical Image Analysis Medical Image Representation Learning Brain MRI

Aug 10, 2026cs.CV

Motion Artifact-Aware Self-Supervised Representation Learning for 3D Brain MRI Motion Artifact Reduction

Patient motion remains a source of image degradation in brain MRI, leading to signal loss, blurring, and geometric distortion that compromise quantitative analysis. Existing deep learning methods for motion correction typically rely on paired clean-corrupted data or k-space acquisitions, which are rarely available in clinical settings. We propose SSRL-MAR, a motion artifact-aware unpaired representation learning framework for motion artifact reduction that requires neither paired training data nor explicit motion labels. SSRL-MAR employed a three-stage training strategy: (1) contrastive learning on 3D patches to extract motion representations by contrasting clean and synthetically corrupted images, (2) a motion artifact-aware synthesis network to generate motion artifacts from clean scans, and (3) a motion artifact-aware generator to restore clean volumes using the learned degrader for self-supervised supervision. On in-silico dataset, SSRL-MAR achieved PSNR 23.81dB, SSIM 91.55%, and NMSE 0.79%. On in-vivo MR-ART dataset, the pretrained model reduced motion distortion, and unsupervised domain adaptation further improved anatomical fidelity. Against a source-only supervised model trained on the same simulated pairs, SSRL-MAR improved PSNR by up to 2.0 dB on MR-ART after unsupervised domain adaptation, and remained within 0.25-0.47 dB of an oracle supervised model that requires real paired data unavailable in practice. At the milder motion level, volumetric error in structures such as the corpus callosum and ventricular system decreased by more than 50%, confirming improved neuroanatomical consistency. These results indicate that SSRL-MAR provides a robust and scalable image-domain solution for 3D brain MRI motion correction, enabling reliable structural quantification in large-scale neuroimaging studies without requiring prospectively acquired pairs or acquisition-specific calibration.

Mojtaba Safari, Shansong Wang, Zach Eidex +4

Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, USA · Radiation Oncology and Winship Cancer Institute, Emory University, Atlanta, GA, USA · Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY, USA +1

Magnetic Resonance Imaging Medical Image Representation Learning Brain MRI

Aug 10, 2026cs.CV

P3CA: Encoder-Agnostic Interpretation of Vision Foundation Model Embeddings via Spatial Probing

Vision foundation models are increasingly used as reusable encoders in medical image computing, yet their high-dimensional spatial embeddings are difficult to inspect beyond downstream task performance or global dimensionality reduction. We propose position-prompted PCA (P3CA), an encoder-agnostic method for local probing of channel-rich spatial tensors. Given a user-selected spatial prompt, P3CA estimates the feature normalization and dominant covariance directions within that region, then applies the resulting projection to the full tensor to visualize where locally informative directions are expressed. This produces a region-conditioned representation lens without modifying the encoder, retraining, or requiring task-specific labels. We implement P3CA in EmbedVision, an interactive 3D Slicer-based workflow, and evaluate it across natural images, colorectal pathology foundation-model embeddings, and spatial transcriptomic tensors. Across these settings, prompted projections reveal local structure suppressed by global PCA, improve prompt-matched pathology discrimination from frozen three-dimensional projections, and support comparison between learned and measured spatial representations.

Amoon Jamzad, Dilakshan Srikanthan, Faranak Akbarifar +2

School of Computing, Queen’s University, Kingston, Ontario, K7L 2N8, Canada

Vision Foundation Models Representation Probing Explainable Medical Image Analysis Medical Image Representation Learning