Daily Papers

The integration of neural-network-based systems into clinical practice is limited by challenges related to domain generalization and robustness. The computer vision community established benchmarks such as ImageNet-C as a fundamental prerequisite to measure progress towards those challenges. Similar datasets are largely absent in the medical imaging community which lacks a comprehensive benchmark that spans across imaging modalities and applications. To address this gap, we create and open-source MedMNIST-C, a benchmark dataset based on the MedMNIST+ collection covering 12 datasets and 9 imaging modalities. We simulate task and modality-specific image corruptions of varying severity to comprehensively evaluate the robustness of established algorithms against real-world artifacts and distribution shifts. We further provide quantitative evidence that our simple-to-use artificial corruptions allow for highly performant, lightweight data augmentation to enhance model robustness. Unlike traditional, generic augmentation strategies, our approach leverages domain knowledge, exhibiting significantly higher robustness when compared to widely adopted methods. By introducing MedMNIST-C and open-sourcing the corresponding library allowing for targeted data augmentations, we contribute to the development of increasingly robust methods tailored to the challenges of medical imaging. The code is available at https://github.com/francescodisalvo05/medmnistc-api .

Convolutional networks, transformers, hybrid models, and Mamba-based architectures have demonstrated strong performance across various medical image classification tasks. However, these methods were primarily designed to classify clean images using labeled data. In contrast, real-world clinical data often involve image corruptions that are unique to multi-center studies and stem from variations in imaging equipment across manufacturers. In this paper, we introduce the Medical Vision Transformer (MedViTV2), a novel architecture incorporating Kolmogorov-Arnold Network (KAN) layers into the transformer architecture for the first time, aiming for generalized medical image classification. We have developed an efficient KAN block to reduce computational load while enhancing the accuracy of the original MedViT. Additionally, to counteract the fragility of our MedViT when scaled up, we propose an enhanced Dilated Neighborhood Attention (DiNA), an adaptation of the efficient fused dot-product attention kernel capable of capturing global context and expanding receptive fields to scale the model effectively and addressing feature collapse issues. Moreover, a hierarchical hybrid strategy is introduced to stack our Local Feature Perception and Global Feature Perception blocks in an efficient manner, which balances local and global feature perceptions to boost performance. Extensive experiments on 17 medical image classification datasets and 12 corrupted medical image datasets demonstrate that MedViTV2 achieved state-of-the-art results in 27 out of 29 experiments with reduced computational complexity. MedViTV2 is 44\% more computationally efficient than the previous version and significantly enhances accuracy, achieving improvements of 4.6\% on MedMNIST, 5.8\% on NonMNIST, and 13.4\% on the MedMNIST-C benchmark.

Medical Vision-Language Models (MVLMs) have achieved par excellence generalization in medical image analysis, yet their performance under noisy, corrupted conditions remains largely untested. Clinical imaging is inherently susceptible to acquisition artifacts and noise; however, existing evaluations predominantly assess generally clean datasets, overlooking robustness -- i.e., the model's ability to perform under real-world distortions. To address this gap, we first introduce MediMeta-C, a corruption benchmark that systematically applies several perturbations across multiple medical imaging datasets. Combined with MedMNIST-C, this establishes a comprehensive robustness evaluation framework for MVLMs. We further propose RobustMedCLIP, a visual encoder adaptation of a pretrained MVLM that incorporates few-shot tuning to enhance resilience against corruptions. Through extensive experiments, we benchmark 5 major MVLMs across 5 medical imaging modalities, revealing that existing models exhibit severe degradation under corruption and struggle with domain-modality tradeoffs. Our findings highlight the necessity of diverse training and robust adaptation strategies, demonstrating that efficient low-rank adaptation when paired with few-shot tuning, improves robustness while preserving generalization across modalities.

Foundation models trained on large-scale dataset gain a recent surge in CV and NLP. In contrast, development in biomedical domain lags far behind due to data scarcity. To address this issue, we build and release PMC-OA, a biomedical dataset with 1.6M image-caption pairs collected from PubMedCentral's OpenAccess subset, which is 8 times larger than before. PMC-OA covers diverse modalities or diseases, with majority of the image-caption samples aligned at finer-grained level, i.e., subfigure and subcaption. While pretraining a CLIP-style model on PMC-OA, our model named PMC-CLIP achieves state-of-the-art results on various downstream tasks, including image-text retrieval on ROCO, MedMNIST image classification, Medical VQA, i.e. +8.1% R@10 on image-text retrieval, +3.9% accuracy on image classification.

Self-supervised learning (SSL) has emerged as a promising paradigm in medical imaging, addressing the chronic challenge of limited labeled data in healthcare settings. While SSL has shown impressive results, existing studies in the medical domain are often limited in scope, focusing on specific datasets or modalities, or evaluating only isolated aspects of model performance. This fragmented evaluation approach poses a significant challenge, as models deployed in critical medical settings must not only achieve high accuracy but also demonstrate robust performance and generalizability across diverse datasets and varying conditions. To address this gap, we present a comprehensive evaluation of SSL methods within the medical domain, with a particular focus on robustness and generalizability. Using the MedMNIST dataset collection as a standardized benchmark, we evaluate 8 major SSL methods across 11 different medical datasets. Our study provides an in-depth analysis of model performance in both in-domain scenarios and the detection of out-of-distribution (OOD) samples, while exploring the effect of various initialization strategies, model architectures, and multi-domain pre-training. We further assess the generalizability of SSL methods through cross-dataset evaluations and the in-domain performance with varying label proportions (1%, 10%, and 100%) to simulate real-world scenarios with limited supervision. We hope this comprehensive benchmark helps practitioners and researchers make more informed decisions when applying SSL methods to medical applications.

We introduce MedMNIST v2, a large-scale MNIST-like dataset collection of standardized biomedical images, including 12 datasets for 2D and 6 datasets for 3D. All images are pre-processed into a small size of 28x28 (2D) or 28x28x28 (3D) with the corresponding classification labels so that no background knowledge is required for users. Covering primary data modalities in biomedical images, MedMNIST v2 is designed to perform classification on lightweight 2D and 3D images with various dataset scales (from 100 to 100,000) and diverse tasks (binary/multi-class, ordinal regression, and multi-label). The resulting dataset, consisting of 708,069 2D images and 10,214 3D images in total, could support numerous research / educational purposes in biomedical image analysis, computer vision, and machine learning. We benchmark several baseline methods on MedMNIST v2, including 2D / 3D neural networks and open-source / commercial AutoML tools. The data and code are publicly available at https://medmnist.com/.

Deep learning has revolutionized medical imaging, but its effectiveness is severely limited by insufficient labeled training data. This paper introduces a novel GAN-based semi-supervised learning framework specifically designed for low labeled-data regimes, evaluated across settings with 5 to 50 labeled samples per class. Our approach integrates three specialized neural networks -- a generator for class-conditioned image translation, a discriminator for authenticity assessment and classification, and a dedicated classifier -- within a three-phase training framework. The method alternates between supervised training on limited labeled data and unsupervised learning that leverages abundant unlabeled images through image-to-image translation rather than generation from noise. We employ ensemble-based pseudo-labeling that combines confidence-weighted predictions from the discriminator and classifier with temporal consistency through exponential moving averaging, enabling reliable label estimation for unlabeled data. Comprehensive evaluation across eleven MedMNIST datasets demonstrates that our approach achieves statistically significant improvements over six state-of-the-art GAN-based semi-supervised methods, with particularly strong performance in the extreme 5-shot setting where the scarcity of labeled data is most challenging. The framework maintains its superiority across all evaluated settings (5, 10, 20, and 50 shots per class). Our approach offers a practical solution for medical imaging applications where annotation costs are prohibitive, enabling robust classification performance even with minimal labeled data. Code is available at https://github.com/GuidoManni/SPARSE.

Reliable medical image classification requires accurate predictions and well-calibrated uncertainty estimates, especially in high-stakes clinical settings. This work presents MedSymmFlow, a generative-discriminative hybrid model built on Symmetrical Flow Matching, designed to unify classification, generation, and uncertainty quantification in medical imaging. MedSymmFlow leverages a latent-space formulation that scales to high-resolution inputs and introduces a semantic mask conditioning mechanism to enhance diagnostic relevance. Unlike standard discriminative models, it naturally estimates uncertainty through its generative sampling process. The model is evaluated on four MedMNIST datasets, covering a range of modalities and pathologies. The results show that MedSymmFlow matches or exceeds the performance of established baselines in classification accuracy and AUC, while also delivering reliable uncertainty estimates validated by performance improvements under selective prediction.

Driven by advancements in deep learning, computer-aided diagnoses have made remarkable progress. However, outside controlled laboratory settings, algorithms may encounter several challenges. In the medical domain, these difficulties often stem from limited data availability due to ethical and legal restrictions, as well as the high cost and time required for expert annotations-especially in the face of emerging or rare diseases. In this context, open-set recognition plays a vital role by identifying whether a sample belongs to one of the known classes seen during training or should be rejected as an unknown. Recent studies have shown that features learned in the later stages of deep neural networks are observed to cluster around their class means, which themselves are arranged as individual vertices of a regular simplex [32]. The proposed method introduces a loss function designed to reject samples of unknown classes effectively by penalizing open space regions using auxiliary datasets. This approach achieves significant performance gain across four MedMNIST datasets-BloodMNIST, OCTMNIST, DermaMNIST, TissueMNIST and a publicly available skin dataset [29] outperforming state-of-the-art techniques.

Convolutional Neural Networks (CNNs) have advanced existing medical systems for automatic disease diagnosis. However, there are still concerns about the reliability of deep medical diagnosis systems against the potential threats of adversarial attacks since inaccurate diagnosis could lead to disastrous consequences in the safety realm. In this study, we propose a highly robust yet efficient CNN-Transformer hybrid model which is equipped with the locality of CNNs as well as the global connectivity of vision Transformers. To mitigate the high quadratic complexity of the self-attention mechanism while jointly attending to information in various representation subspaces, we construct our attention mechanism by means of an efficient convolution operation. Moreover, to alleviate the fragility of our Transformer model against adversarial attacks, we attempt to learn smoother decision boundaries. To this end, we augment the shape information of an image in the high-level feature space by permuting the feature mean and variance within mini-batches. With less computational complexity, our proposed hybrid model demonstrates its high robustness and generalization ability compared to the state-of-the-art studies on a large-scale collection of standardized MedMNIST-2D datasets.

In this paper we introduce the SCoRe (Submodular Combinatorial Representation Learning) framework, a novel approach in representation learning that addresses inter-class bias and intra-class variance. SCoRe provides a new combinatorial viewpoint to representation learning, by introducing a family of loss functions based on set-based submodular information measures. We develop two novel combinatorial formulations for loss functions, using the Total Information and Total Correlation, that naturally minimize intra-class variance and inter-class bias. Several commonly used metric/contrastive learning loss functions like supervised contrastive loss, orthogonal projection loss, and N-pairs loss, are all instances of SCoRe, thereby underlining the versatility and applicability of SCoRe in a broad spectrum of learning scenarios. Novel objectives in SCoRe naturally model class-imbalance with up to 7.6\% improvement in classification on CIFAR-10-LT, CIFAR-100-LT, MedMNIST, 2.1% on ImageNet-LT, and 19.4% in object detection on IDD and LVIS (v1.0), demonstrating its effectiveness over existing approaches.

Medical image classification requires not only high predictive performance but also interpretability to ensure clinical trust and adoption. Graph Neural Networks (GNNs) offer a powerful framework for modeling relational structures within datasets; however, standard GNNs often operate as black boxes, limiting transparency and usability, particularly in clinical settings. In this work, we present an interpretable graph-based learning framework named FireGNN that integrates trainable fuzzy rules into GNNs for medical image classification. These rules embed topological descriptors - node degree, clustering coefficient, and label agreement - using learnable thresholds and sharpness parameters to enable intrinsic symbolic reasoning. Additionally, we explore auxiliary self-supervised tasks (e.g., homophily prediction, similarity entropy) as a benchmark to evaluate the contribution of topological learning. Our fuzzy-rule-enhanced model achieves strong performance across five MedMNIST benchmarks and the synthetic dataset MorphoMNIST, while also generating interpretable rule-based explanations. To our knowledge, this is the first integration of trainable fuzzy rules within a GNN. Source Code: https://github.com/basiralab/FireGNN