Subgroup performance analysis of adaptation strategies for chest X-ray foundation models

Foundation models are increasingly adapted for downstream medical imaging tasks, yet the influence of the chosen adaptation strategy on subgroup fairness remains poorly understood. We investigate how three parameter-efficient adaptation techniques, including linear heads on the raw CLS token, an MLP, and an attention-pooling module over multi-layer patch features, affect both pathology classification performance and subgroup disparities when applied to the frozen Rad-DINO chest X-ray encoder. Using MIMIC-CXR, we evaluate eight pathologies across race, sex, and imaging-view subgroups on a prevalence-preserving, demographically balanced test set, and additionally probe how strongly each adapter encodes protected attributes. We find that attention pooling achieves the strongest overall discriminative performance and encodes attributes, particularly race, most strongly, but that improved overall performance does not consistently reduce subgroup disparities. Notably, stronger attribute encoding did not correspond to larger disparities: early network layers encoded race most weakly yet produced the largest subgroup performance gaps. Exploring different attention-pooling layer combinations further revealed no consistent relationship between the layers pooled, attribute encoding strength, and subgroup fairness. Our results indicate that richer, more expressive representations can improve accuracy while leaving fairness implications task-dependent and unpredictable, which must be assessed directly and per-task rather than inferred from encoding strength or overall performance alone.

Benchmarking the Robustness of Foundation Models for Mammography under Domain Shift

Foundation models are increasingly used as image feature extractors for mammography, but their robustness under external domain shift remains unclear. We benchmark 15 foundation-model backbones across breast density, BI-RADS severity, and cancer status using a unified frozen-backbone linear-probe protocol, training on 3 source datasets and evaluating on 12 task-compatible out-of-distribution (OOD) datasets after label harmonization. Mammography-specific vision-language models (Mammo-FM and MaMA) provide the strongest mean OOD performance, but robustness is not explained by mammography exposure alone. DINOv3 remains a competitive vision-only baseline, and mammography-adapted pretraining does not consistently improve generalization. Dataset-level analysis further shows that even leading models show heterogeneous performance across datasets. Feature-space inspection reveals that useful representations can preserve clinical signal while retaining dataset and acquisition structure. These findings highlight dataset-level OOD evaluation as a central criterion for assessing mammography representations. Our code is publicly available: https://github.com/biomedia-mira/mammo-ood.

GRC-ProbNet: Uncertainty-aware Feature Extraction for Cardiovascular Disease Classification

The automatic detection and classification of cardiovascular disease (CVD) from computed tomography (CT) images plays an important role in clinical practice. Recently, a hybrid pipeline (GRC-Net) for CVD classification was proposed, which leverages a deep-learning-based segmentation and registration method to extract radiomic and geometric features. However, GRC-Net relies on a deterministic segmentation mask, without considering the inherent ambiguity associated with cardiac anatomy. In this paper, we propose GRC-ProbNet, which takes advantage of a deep ensemble to produce multiple segmentation masks for a given input. From these masks, we extract multiple uncertainty features. We analyze these uncertainty features for both their correlation with segmentation error and their propagation effects on downstream CVD classification performance. Our experiments on the publicly available MM-WHS and ASOCA datasets show that the uncertainty measure that best reflects segmentation quality is not necessarily the one that provides the strongest signal for downstream CVD classification. Overall, our results demonstrate that GRC-ProbNet utilizing uncertainty features substantially improves CVD classification AUROC (92.92\) compared to the baseline GRC-Net model (91.25%). Our code is publicly available: https://github.com/biomedia-mira/GRC-ProbNet.

Steering Optimisation Trajectories in Diffusion Representation Learning

We study why diffusion autoencoders can achieve similar image quality while learning substantially different latent structures. We trace this behaviour to optimisation dynamics; we analyse curves of image reconstruction against latent representation quality, revealing trajectories that organise around two distinct regimes early in training. Models in the reconstruction regime prioritise image fidelity early, whereas those in the disentanglement regime improve reconstruction and disentanglement more gradually. We hypothesise that this behaviour can be influenced by targeting shortcut pathways in the diffusion U-Net and controlling early noise-level exposure, thereby shaping the reconstruction-disentanglement trade-off during training. To steer optimisation toward stronger representations, we introduce SteeringDRL, combining gated residual U-Nets with a simple noise-level exposure curriculum for training. Across disentanglement benchmarks, SteeringDRL improves representation quality and reduces seed sensitivity. Our method further extends to spatial disentanglement in object-centric learning, improving segmentation quality on synthetic and real-world datasets.

Scaling Generative Foundation Models for Chest Radiography with Rectified Flow Transformers

We introduce the first generative foundation model for chest radiograph synthesis trained from scratch at the billion-parameter scale. Existing radiographic AI models often suffer from poor generalisation across patient subpopulations, institutions, and acquisition settings, resulting in limited real-world clinical utility. Controlled, high-fidelity synthesis of chest radiographs is a promising path toward diversifying clinical datasets and evaluating the robustness of diagnostic models. Therefore, we present the largest specialist generative foundation model for chest radiographs to date, with over 1.3B parameters, trained for 1.6T tokens on a curated, heterogeneous dataset comprising 1.2M radiographs and clinical expert-guided metadata. Our model supports controllable radiograph generation and editing across multiple demographic subgroups, acquisition views, and a dozen pathologies. Moreover, we significantly advance the state of the art in radiograph synthesis fidelity, producing images that are indistinguishable from real radiographs to clinical experts.

Counterfactual Stress Testing for Image Classification Models

Deep learning models in medical imaging often fail when deployed in new clinical environments due to distribution shifts in demographics, scanner hardware, or acquisition protocols. A central challenge is underspecification, where models with similar validation performance exhibit divergent real-world failure modes. Although stress testing has emerged as a tool to assess this, current methods typically rely on simple, uninformed perturbations (e.g., brightness or contrast changes), which fail to capture clinically realistic variation and can overestimate robustness. In this work, we introduce a counterfactual stress testing framework based on causal generative models that create realistic "what if" images by intervening on attributes such as scanner type and patient sex while preserving anatomical identity, enabling controlled and semantically meaningful evaluation under targeted distribution shifts. Across two imaging modalities (chest X-ray and mammography), three model architectures, and multiple shift scenarios, we show that counterfactual stress tests provide a substantially more accurate proxy for real out-of-distribution performance than classical perturbations, capturing the direction and relative magnitude of performance changes as well as model ranking. These results suggest that causal generative models can serve as practical simulators for robustness assessment, offering a more reliable basis for evaluating medical AI systems prior to deployment.

Positional Segmentor-Guided Counterfactual Fine-Tuning for Spatially Localized Image Synthesis

Counterfactual image generation enables controlled data augmentation, bias mitigation, and disease modeling. However, existing methods guided by external classifiers or regressors are limited to subject-level factors (e.g., age) and fail to produce localized structural changes, often resulting in global artifacts. Pixel-level guidance using segmentation masks has been explored, but requires user-defined counterfactual masks, which are tedious and impractical. Segmentor-guided Counterfactual Fine-Tuning (Seg-CFT) addressed this by using segmentation-derived measurements to supervise structure-specific variables, yet it remains restricted to global interventions. We propose Positional Seg-CFT, which subdivides each structure into regional segments and derives independent measurements per region, enabling spatially localized and anatomically coherent counterfactuals. Experiments on coronary CT angiography show that Pos-Seg-CFT generates realistic, region-specific modifications, providing finer spatial control for modeling disease progression.

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.

A Causal Framework for Mitigating Data Shifts in Healthcare

Developing predictive models that perform reliably across diverse patient populations and heterogeneous environments is a core aim of medical research. However, generalization is only possible if the learned model is robust to statistical differences between data used for training and data seen at the time and place of deployment. Domain generalization methods provide strategies to address data shifts, but each method comes with its own set of assumptions and trade-offs. To apply these methods in healthcare, we must understand how domain shifts arise, what assumptions we prefer to make, and what our design constraints are. This article proposes a causal framework for the design of predictive models to improve generalization. Causality provides a powerful language to characterize and understand diverse domain shifts, regardless of data modality. This allows us to pinpoint why models fail to generalize, leading to more principled strategies to prepare for and adapt to shifts. We recommend general mitigation strategies, discussing trade-offs and highlighting existing work. Our causality-based perspective offers a critical foundation for developing robust, interpretable, and clinically relevant AI solutions in healthcare, paving the way for reliable real-world deployment.

A Primer on Causal and Statistical Dataset Biases for Fair and Robust Image Analysis

Machine learning methods often fail when deployed in the real world. Worse still, they fail in high-stakes situations and across socially sensitive lines. These issues have a chilling effect on the adoption of machine learning methods in settings such as medical diagnosis, where they are arguably best-placed to provide benefits if safely deployed. In this primer, we introduce the causal and statistical structures which induce failure in machine learning methods for image analysis. We highlight two previously overlooked problems, which we call the \textit{no fair lunch} problem and the \textit{subgroup separability} problem. We elucidate why today's fair representation learning methods fail to adequately solve them and propose potential paths forward for the field.