Stein thinning is a promising algorithm proposed by (Riabiz et al., 2022) for post-processing outputs of Markov chain Monte Carlo (MCMC). The main principle is to greedily minimize the kernelized Stein discrepancy (KSD), which only requires the gradient of the log-target distribution, and is thus well-suited for Bayesian inference. The main advantages of Stein thinning are the automatic remove of the burn-in period, the correction of the bias introduced by recent MCMC algorithms, and the asymptotic properties of convergence towards the target distribution. Nevertheless, Stein thinning suffers from several empirical pathologies, which may result in poor approximations, as observed in the literature. In this article, we conduct a theoretical analysis of these pathologies, to clearly identify the mechanisms at stake, and suggest improved strategies. Then, we introduce the regularized Stein thinning algorithm to alleviate the identified pathologies. Finally, theoretical guarantees and extensive experiments show the high efficiency of the proposed algorithm. An implementation of regularized Stein thinning as the kernax library in python and JAX is available at https://gitlab.com/drti/kernax.

Recent advances in microscopy have enabled the rapid generation of terabytes of image data in cell biology and biomedical research.

The automation of the medical evidence acquisition and diagnosis process has recently attracted increasing attention in order to reduce the workload of doctors and democratize access to medical care. However, most works proposed in the machine learning literature focus solely on improving the prediction accuracy of a patient's pathology. We argue that this objective is insufficient to ensure doctors' acceptability of such systems. In their initial interaction with patients, doctors do not only focus on identifying the pathology a patient is suffering from; they instead generate a differential diagnosis (in the form of a short list of plausible diseases) because the medical evidence collected from patients is often insufficient to establish a final diagnosis. Moreover, doctors explicitly explore severe pathologies before potentially ruling them out from the differential, especially in acute care settings. Finally, for doctors to trust a system's recommendations, they need to understand how the gathered evidences led to the predicted diseases.

While Bayesian neural networks (BNNs) hold the promise of being flexible, well-calibrated statistical models, inference often requires approximations whose consequences are poorly understood. We study the quality of common variational methods in approximating the Bayesian predictive distribution. For single-hidden layer ReLU BNNs, we prove a fundamental limitation in function-space of two of the most commonly used distributions defined in weight-space: mean-field Gaussian and Monte Carlo dropout. We find there are simple cases where neither method can have substantially increased uncertainty in between well-separated regions of low uncertainty. We provide strong empirical evidence that exact inference does not have this pathology, hence it is due to the approximation and not the model. In contrast, for deep networks, we prove a universality result showing that there exist approximate posteriors in the above classes which provide flexible uncertainty estimates. However, we find empirically that pathologies of a similar form as in the single-hidden layer case can persist when performing variational inference in deeper networks. Our results motivate careful consideration of the implications of approximate inference methods in BNNs.

Few-shot learning (FSL) mitigates data scarcity in cardiac MRI segmentation but typically relies on semi-supervised techniques sensitive to domain shifts and validation bias, restricting zero-shot generalizability. We propose PathCo-LatticE, a fully supervised FSL framework that replaces unlabeled data with pathology-guided synthetic supervision. First, our Virtual Patient Engine models continuous latent disease trajectories from sparse clinical anchors, using generative modeling to synthesize physiologically plausible, fully labeled 3D cohorts. Second, Self-Reinforcing Interleaved Validation (SIV) provides a leakage-free protocol that evaluates models online with progressively challenging synthetic samples, eliminating the need for real validation data. Finally, a dynamic Lattice-of-Experts (LoE) organizes specialized networks within a pathology-aware topology and activates the most relevant experts per input, enabling robust zero-shot generalization to unseen data without target-domain fine-tuning. We evaluated PathCo-LatticE in a strict out-of-distribution (OOD) setting, deriving all anchors and severity statistics from a single-source domain (ACDC) and performing zero-shot testing on the multi-center, multi-vendor M&Ms dataset. PathCo-LatticE outperforms four state-of-the-art FSL methods by 4.2-11% Dice starting from only 7 labeled anchors, and approaches fully supervised performance (within 1% Dice) with only 19 labeled anchors. The method shows superior harmonization across four vendors and generalization to unseen pathologies. [Code will be made publicly available].

Foundation models have transformed computational pathology by providing generalizable representations from large-scale histology datasets. However, existing models are predominantly trained on surgical pathology data, which is enriched for non-nervous tissue and overrepresents neoplastic, inflammatory, metabolic, and other non-neurological diseases. Neuropathology represents a markedly different domain of histopathology, characterized by unique cell types (neurons, glia, etc.), distinct cytoarchitecture, and disease-specific pathological features including neurofibrillary tangles, amyloid plaques, Lewy bodies, and pattern-specific neurodegeneration. This domain mismatch may limit the ability of general-purpose foundation models to capture the morphological patterns critical for interpreting neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and cerebellar ataxias. To address this gap, we developed NeuroFM, a foundation model trained specifically on whole-slide images of brain tissue spanning diverse neurodegenerative pathologies. NeuroFM demonstrates superior performance compared to general-purpose models across multiple neuropathology-specific downstream tasks, including mixed dementia disease classification, hippocampal region segmentation, and neurodegenerative ataxia identification encompassing cerebellar essential tremor and spinocerebellar ataxia subtypes. This work establishes that domain-specialized foundation models trained on brain tissue can better capture neuropathology-specific features than models trained on general surgical pathology datasets. By tailoring foundation models to the unique morphological landscape of neurodegenerative diseases, NeuroFM enables more accurate and reliable AI-based analysis for brain disease diagnosis and research, setting a precedent for domain-specific model development in specialized areas of digital pathology.

The limited availability of annotated data presents a major challenge for applying deep learning methods to medical image analysis. Few-shot learning methods aim to recognize new classes from only a small number of labeled examples. These methods are typically studied under the standard few-shot learning setting, where all classes in a task are new. However, medical applications such as pathology classification from chest X-rays often require learning new classes while simultaneously leveraging knowledge of previously known ones, a scenario more closely aligned with generalized few-shot classification. Despite its practical relevance, few-shot learning has been scarcely studied in this context. In this work, we present MetaChest, a large-scale dataset of 479,215 chest X-rays collected from four public databases. MetaChest includes a meta-set partition specifically designed for standard few-shot classification, as well as an algorithm for generating multi-label episodes. We conduct extensive experiments evaluating both a standard transfer learning approach and an extension of ProtoNet across a wide range of few-shot multi-label classification tasks. Our results demonstrate that increasing the number of classes per episode and the number of training examples per class improves classification performance. Notably, the transfer learning approach consistently outperforms the ProtoNet extension, despite not being tailored for few-shot learning. We also show that higher-resolution images improve accuracy at the cost of additional computation, while efficient model architectures achieve comparable performance to larger models with significantly reduced resource requirements.

Chronic diseases often progress differently across patients. Rather than randomly varying, there are typically a small number of subtypes for how a disease progresses across patients. To capture this structured heterogeneity, the Subtype and Stage Inference Event-Based Model (SuStaIn) estimates the number of subtypes, the order of disease progression for each subtype, and assigns each patient to a subtype from primarily cross-sectional data. It has been widely applied to uncover the subtypes of many diseases and inform our understanding of them. But how robust is its performance? In this paper, we develop a principled Bayesian subtype variant of the event-based model (BEBMS) and compare its performance to SuStaIn in a variety of synthetic data experiments with varied levels of model misspecification. BEBMS substantially outperforms SuStaIn across ordering, staging, and subtype assignment tasks. Further, we apply BEBMS and SuStaIn to a real-world Alzheimer's data set. We find BEBMS has results that are more consistent with the scientific consensus of Alzheimer's disease progression than SuStaIn.

Deep learning has shown strong performance in musculoskeletal imaging, but prior work has largely targeted conditions where diagnosis is relatively straightforward. More challenging problems remain underexplored, such as detecting Bankart lesions (anterior-inferior glenoid labral tears) on standard MRIs. These lesions are difficult to diagnose due to subtle imaging features, often necessitating invasive MRI arthrograms (MRAs). We introduce ScopeMRI, the first publicly available, expert-annotated dataset for shoulder pathologies, and present a deep learning framework for Bankart lesion detection on both standard MRIs and MRAs. ScopeMRI contains shoulder MRIs from patients who underwent arthroscopy, providing ground-truth labels from intraoperative findings, the diagnostic gold standard. Separate models were trained for MRIs and MRAs using CNN- and transformer-based architectures, with predictions ensembled across multiple imaging planes. Our models achieved radiologist-level performance, with accuracy on standard MRIs surpassing radiologists interpreting MRAs. External validation on independent hospital data demonstrated initial generalizability across imaging protocols. By releasing ScopeMRI and a modular codebase for training and evaluation, we aim to accelerate research in musculoskeletal imaging and foster development of datasets and models that address clinically challenging diagnostic tasks.