A Self supervised learning framework for imbalanced medical imaging datasets

Two problems often plague medical imaging analysis: 1) Non-availability of large quantities of labeled training data, and 2) Dealing with imbalanced data, i.e., abundant data are available for frequent classes, whereas data are highly limited for the rare class. Self supervised learning (SSL) methods have been proposed to deal with the first problem to a certain extent, but the issue of investigating the robustness of SSL to imbalanced data has rarely been addressed in the domain of medical image classification. In this work, we make the following contributions: 1) The MIMV method proposed by us in an earlier work is extended with a new augmentation strategy to construct asymmetric multi-image, multi-view (AMIMV) pairs to address both data scarcity and dataset imbalance in medical image classification. 2) We carry out a data analysis to evaluate the robustness of AMIMV under varying degrees of class imbalance in medical imaging . 3) We evaluate eight representative SSL methods in 11 medical imaging datasets (MedMNIST) under long-tailed distributions and limited supervision. Our experimental results on the MedMNIST dataset show an improvement of 4.25% on retinaMNIST, 1.88% on tissueMNIST, and 3.1% on DermaMNIST.

Rare-Aware Autoencoding: Reconstructing Spatially Imbalanced Data

Autoencoders can be challenged by spatially non-uniform sampling of image content. This is common in medical imaging, biology, and physics, where informative patterns occur rarely at specific image coordinates, as background dominates these locations in most samples, biasing reconstructions toward the majority appearance. In practice, autoencoders are biased toward dominant patterns resulting in the loss of fine-grained detail and causing blurred reconstructions for rare spatial inputs especially under spatial data imbalance. We address spatial imbalance by two complementary components: (i) self-entropy-based loss that upweights statistically uncommon spatial locations and (ii) Sample Propagation, a replay mechanism that selectively re-exposes the model to hard to reconstruct samples across batches during training. We benchmark existing data balancing strategies, originally developed for supervised classification, in the unsupervised reconstruction setting. Drawing on the limitations of these approaches, our method specifically targets spatial imbalance by encouraging models to focus on statistically rare locations, improving reconstruction consistency compared to existing baselines. We validate in a simulated dataset with controlled spatial imbalance conditions, and in three, uncontrolled, diverse real-world datasets spanning physical, biological, and astronomical domains. Our approach outperforms baselines on various reconstruction metrics, particularly under spatial imbalance distributions. These results highlight the importance of data representation in a batch and emphasize rare samples in unsupervised image reconstruction. We will make all code and related data available.

NEMESIS: Noise-suppressed Efficient MAE with Enhanced Superpatch Integration Strategy

Volumetric CT imaging is essential for clinical diagnosis, yet annotating 3D volumes is expensive and time-consuming, motivating self-supervised learning (SSL) from unlabeled data. However, applying SSL to 3D CT remains challenging due to the high memory cost of full-volume transformers and the anisotropic spatial structure of CT data, which is not well captured by conventional masking strategies. We propose NEMESIS, a masked autoencoder (MAE) framework that operates on local 128x128x128 superpatches, enabling memory-efficient training while preserving anatomical detail. NEMESIS introduces three key components: (i) noise-enhanced reconstruction as a pretext task, (ii) Masked Anatomical Transformer Blocks (MATB) that perform dual-masking through parallel plane-wise and axis-wise token removal, and (iii) NEMESIS Tokens (NT) for cross-scale context aggregation. On the BTCV multi-organ classification benchmark, NEMESIS with a frozen backbone and a linear classifier achieves a mean AUROC of 0.9633, surpassing fully fine-tuned SuPreM (0.9493) and VoCo (0.9387). Under a low-label regime with only 10% of available annotations, it retains an AUROC of 0.9075, demonstrating strong label efficiency. Furthermore, the superpatch-based design reduces computational cost to 31.0 GFLOPs per forward pass, compared to 985.8 GFLOPs for the full-volume baseline, providing a scalable and robust foundation for 3D medical imaging.

Mine-JEPA: In-Domain Self-Supervised Learning for Mine-Like Object Classification in Side-Scan Sonar

Side-scan sonar (SSS) mine classification is a challenging maritime vision problem characterized by extreme data scarcity and a large domain gap from natural images. While self-supervised learning (SSL) and general-purpose vision foundation models have shown strong performance in general vision and several specialized domains, their use in SSS remains largely unexplored. We present Mine-JEPA, the first in-domain SSL pipeline for SSS mine classification, using SIGReg, a regularization-based SSL loss, to pretrain on only 1,170 unlabeled sonar images. In the binary mine vs. non-mine setting, Mine-JEPA achieves an F1 score of 0.935, outperforming fine-tuned DINOv3 (0.922), a foundation model pretrained on 1.7B images. For 3-class mine-like object classification, Mine-JEPA reaches 0.820 with synthetic data augmentation, again outperforming fine-tuned DINOv3 (0.810). We further observe that applying in-domain SSL to foundation models degrades performance by 10--13 percentage points, suggesting that stronger pretrained models do not always benefit from additional domain adaptation. In addition, Mine-JEPA with a compact ViT-Tiny backbone achieves competitive performance while using 4x fewer parameters than DINOv3. These results suggest that carefully designed in-domain self-supervised learning is a viable alternative to much larger foundation models in data-scarce maritime sonar imagery.

MOOZY: A Patient-First Foundation Model for Computational Pathology

Computational pathology needs whole-slide image (WSI) foundation models that transfer across diverse clinical tasks, yet current approaches remain largely slide-centric, often depend on private data and expensive paired-report supervision, and do not explicitly model relationships among multiple slides from the same patient. We present MOOZY, a patient-first pathology foundation model in which the patient case, not the individual slide, is the core unit of representation. MOOZY explicitly models dependencies across all slides from the same patient via a case transformer during pretraining, combining multi-stage open self-supervision with scaled low-cost task supervision. In Stage 1, we pretrain a vision-only slide encoder on 77,134 public slide feature grids using masked self-distillation. In Stage 2, we align these representations with clinical semantics using a case transformer and multi-task supervision over 333 tasks from 56 public datasets, including 205 classification and 128 survival tasks across four endpoints. Across eight held-out tasks with five-fold frozen-feature probe evaluation, MOOZY achieves best or tied-best performance on most metrics and improves macro averages over TITAN by +7.37%, +5.50%, and +7.83% and over PRISM by +8.83%, +10.70%, and +9.78% for weighted F1, weighted ROC-AUC, and balanced accuracy, respectively. MOOZY is also parameter efficient with 85.77M parameters, 14x smaller than GigaPath. These results demonstrate that open, reproducible patient-level pretraining yields transferable embeddings, providing a practical path toward scalable patient-first histopathology foundation models.

DinoDental: Benchmarking DINOv3 as a Unified Vision Encoder for Dental Image Analysis

The scarcity and high cost of expert annotations in dental imaging present a significant challenge for the development of AI in dentistry. DINOv3, a state-of-the-art, self-supervised vision foundation model pre-trained on 1.7 billion images, offers a promising pathway to mitigate this issue. However, its reliability when transferred to the dental domain, with its unique imaging characteristics and clinical subtleties, remains unclear. To address this, we introduce DinoDental, a unified benchmark designed to systematically evaluate whether DINOv3 can serve as a reliable, off-the-shelf encoder for comprehensive dental image analysis without requiring domain-specific pre-training. Constructed from multiple public datasets, DinoDental covers a wide range of tasks, including classification, detection, and instance segmentation on both panoramic radiographs and intraoral photographs. We further analyze the model's transfer performance by scaling its size and input resolution, and by comparing different adaptation strategies, including frozen features, full fine-tuning, and the parameter-efficient Low-Rank Adaptation (LoRA) method. Our experiments show that DINOv3 can serve as a strong unified encoder for dental image analysis across both panoramic radiographs and intraoral photographs, remaining competitive across tasks while showing particularly clear advantages for intraoral image understanding and boundary-sensitive dense prediction. Collectively, DinoDental provides a systematic framework for comprehensively evaluating DINOv3 in dental analysis, establishing a foundational benchmark to guide efficient and effective model selection and adaptation for the dental AI community.

FDIF: Formula-Driven supervised Learning with Implicit Functions for 3D Medical Image Segmentation

Deep learning-based 3D medical image segmentation methods relies on large-scale labeled datasets, yet acquiring such data is difficult due to privacy constraints and the high cost of expert annotation. Formula-Driven Supervised Learning (FDSL) offers an appealing alternative by generating training data and labels directly from mathematical formulas. However, existing voxel-based approaches are limited in geometric expressiveness and cannot synthesize realistic textures. We introduce Formula-Driven supervised learning with Implicit Functions (FDIF), a framework that enables scalable pre-training without using any real data and medical expert annotations. FDIF introduces an implicit-function representation based on signed distance functions (SDFs), enabling compact modeling of complex geometries while exploiting the surface representation of SDFs to support controllable synthesis of both geometric and intensity textures. Across three medical image segmentation benchmarks (AMOS, ACDC, and KiTS) and three architectures (SwinUNETR, nnUNet ResEnc-L, and nnUNet Primus-M), FDIF consistently improves over a formula-driven method, and achieves performance comparable to self-supervised approaches pre-trained on large-scale real datasets. We further show that FDIF pre-training also benefits 3D classification tasks, highlighting implicit-function-based formula supervision as a promising paradigm for data-free representation learning. Code is available at https://github.com/yamanoko/FDIF.

Revisiting Autoregressive Models for Generative Image Classification

Class-conditional generative models have emerged as accurate and robust classifiers, with diffusion models demonstrating clear advantages over other visual generative paradigms, including autoregressive (AR) models. In this work, we revisit visual AR-based generative classifiers and identify an important limitation of prior approaches: their reliance on a fixed token order, which imposes a restrictive inductive bias for image understanding. We observe that single-order predictions rely more on partial discriminative cues, while averaging over multiple token orders provides a more comprehensive signal. Based on this insight, we leverage recent any-order AR models to estimate order-marginalized predictions, unlocking the high classification potential of AR models. Our approach consistently outperforms diffusion-based classifiers across diverse image classification benchmarks, while being up to 25x more efficient. Compared to state-of-the-art self-supervised discriminative models, our method delivers competitive classification performance - a notable achievement for generative classifiers.

Pixel-level Counterfactual Contrastive Learning for Medical Image Segmentation

Image segmentation relies on large annotated datasets, which are expensive and slow to produce. Silver-standard (AI-generated) labels are easier to obtain, but they risk introducing bias. Self-supervised learning, needing only images, has become key for pre-training. Recent work combining contrastive learning with counterfactual generation improves representation learning for classification but does not readily extend to pixel-level tasks. We propose a pipeline combining counterfactual generation with dense contrastive learning via Dual-View (DVD-CL) and Multi-View (MVD-CL) methods, along with supervised variants that utilize available silver-standard annotations. A new visualisation algorithm, the Color-coded High Resolution Overlay map (CHRO-map) is also introduced. Experiments show annotation-free DVD-CL outperforms other dense contrastive learning methods, while supervised variants using silver-standard labels outperform training on the silver-standard labeled data directly, achieving $\sim$94% DSC on challenging data. These results highlight that pixel-level contrastive learning, enhanced by counterfactuals and silver-standard annotations, improves robustness to acquisition and pathological variations.

Automated Diabetic Screening via Anterior Segment Ocular Imaging: A Deep Learning and Explainable AI Approach

Diabetic retinopathy screening traditionally relies on fundus photography, requiring specialized equipment and expertise often unavailable in primary care and resource limited settings. We developed and validated a deep learning (DL) system for automated diabetic classification using anterior segment ocular imaging a readily accessible alternative utilizing standard photography equipment. The system leverages visible biomarkers in the iris, sclera, and conjunctiva that correlate with systemic diabetic status. We systematically evaluated five contemporary architectures (EfficientNet-V2-S with self-supervised learning (SSL), Vision Transformer, Swin Transformer, ConvNeXt-Base, and ResNet-50) on 2,640 clinically annotated anterior segment images spanning Normal, Controlled Diabetic, and Uncontrolled Diabetic categories. A tailored preprocessing pipeline combining specular reflection mitigation and contrast limited adaptive histogram equalization (CLAHE) was implemented to enhance subtle vascular and textural patterns critical for classification. SSL using SimCLR on domain specific ocular images substantially improved model performance.EfficientNet-V2-S with SSL achieved optimal performance with an F1-score of 98.21%, precision of 97.90%, and recall of 98.55% a substantial improvement over ImageNet only initialization (94.63% F1). Notably, the model attained near perfect precision (100%) for Normal classification, critical for minimizing unnecessary clinical referrals.