Volumetric CT vision-language pretraining learns 3D representations from scan-report pairs, but global and anatomy-aware objectives supervise only correspondence: they establish what is present and leave how much unconstrained. Nothing separates a mild from an extensive case of the same finding along a consistent direction, so the graded burden language in reports collapses into a present/absent signal. Longitudinal supervision would supply this order, but patient-matched CT pairs are scarce at scale; cross-sectional cohorts already encode weak burden cues across different patients. We introduce Spectrum, an anatomy-conditioned framework that represents each study at whole-study and organ scopes. For each organ-mapped pathology, a rule-based scorer mines confidence-filtered lower-to-higher pairs of different patients, and Burden-Direction Alignment (BDA) aligns the pathology-conditioned image delta with the report delta at each scope, separating that direction from its reverse. Because the endpoints are different people, a target-conditioned aligner first makes them comparable, so the delta reflects burden rather than between-patient variation. BDA further separates the selected direction from its reverse, anchors it to the observed higher-burden endpoint, and enforces consistency across ordered triplets. Since every pair is drawn within a single pathology, BDA is designed to constrain intra-class structure that image-report contrast alone never touches. Spectrum attains 85.6 zero-shot AUROC on CT-RATE and 72.7 on external RAD-ChestCT, with consistent gains in linear probing and retrieval. Weak cross-patient order is thus a scalable complement to anatomy-aware correspondence, yielding burden-aware CT representations without longitudinal data.
Computed tomography (CT) vision-language pretraining from paired volumes and radiology reports is a scalable yet challenging task. Existing methods commonly adopt global scan-report contrast, which is scalable but obscures heterogeneous organ evidence. Meanwhile, direct organ-level alignment remains coarse, since the same anatomy can exhibit multiple distinct radiological appearances. Therefore, pretraining requires a finer alignment unit: the organ-conditioned radiological pattern. In this work, we propose OCP-CT, an organ-conditioned pattern-token alignment framework for CT vision-language pretraining. Specifically, OCP-CT preserves a stable global CT-report contrastive branch and introduces an organ pattern interface: sparse Mixture-of-Experts (MoE) routes image and text tokens according to latent radiological patterns, learnable slots query the routed tokens into continuous pattern tokens, and paired token contrast aligns image-text pattern tokens with structured soft targets built from report-derived clinical similarity. On the publicly available CT-RATE and RAD-ChestCT benchmarks, OCP-CT achieves average AUROCs of 84.5% and 69.9% for zero-shot abnormality diagnosis, respectively. Compared with the strongest prior reported results, these results yield absolute AUROC gains of 6.7 and 0.8 percentage points.
Medical vision-language pretraining (VLP) from paired CT images and radiology reports enables scalable representation learning, but most existing methods align either whole scans with entire reports or local image regions with text fragments. These formulations underuse a key property of radiology reports: findings are organized around anatomical structures, with abnormalities described by organs, disease concepts, locations, and severity-related attributes. We propose OKA-CT, an organ-hierarchical knowledge-augmented framework for CT-report VLP. OKA-CT first converts free-text reports into organ-conditioned knowledge using radiology report parsing and LLM-assisted semantic structuring. The extracted hierarchy is used across two learning stages. Stage~1 injects anatomy-grounded evidence into the CT visual representation through fine-grained organ-conditioned supervision, while Stage~2 uses organ-specific report evidence to guide structured report-CT contrastive learning, where hierarchy-derived semantic soft targets treat non-paired cases with shared organ-level findings as weak semantic positives rather than uniform negatives. A lightweight query-based global branch further aggregates disease-relevant volumetric evidence for whole-scan representation. On CT-RATE and RAD-ChestCT datasets, OKA-CT achieves zero-shot abnormality diagnosis AUROCs of 84.9 and 72.2, outperforming prior CT VLP baselines. Retrieval and patch-occlusion analyses further show improved report-image alignment and stronger sensitivity to disease-associated anatomical regions.
Vision-language foundation models have shown strong potential in medical image analysis. Although foundation models for ultrasound imaging have recently emerged, the domain remains particularly challenging due to severe speckle noise, acquisition variability, and subtle anatomical boundaries, leading to high inter-observer variability. Existing CLIP-based models rely primarily on global image-text alignment, limiting their sensitivity to clinically decisive local structures. We propose SonoCLIP, the first million-scale region-controllable fetal ultrasound vision-language foundation model that integrates segmentation masks as mask-channel visual prompts within the vision encoder, enabling joint global-local contrastive representation learning. To support scalable region-text alignment, we introduce a sigmoid-based pairwise contrastive loss that improves stability under large-scale supervision. We further curate a 1.44M-image multimodal fetal ultrasound dataset spanning 24 standard planes for large-scale pretraining. Extensive cross-center evaluations demonstrate that SonoCLIP achieves superior zero-shot transfer performance under both global and mask-guided inference, establishing a controllable and clinically oriented foundation model for fetal ultrasound analysis. Our code and data are available at https://github.com/Harrison-one/SonoCLIP.
Vision-language pre-training (VLP) holds great promise for general-purpose medical AI by leveraging radiology reports as rich textual supervision, yet existing methods struggle with 3D CT imaging due to inefficient visual backbones and coarse semantic alignment. To address these issues, we propose a tailored VLP framework featuring three key components: (1) a CNN-ViT hybrid encoder that replaces ViT's patch embedding with a 3D CNN backbone to efficiently capture local anatomical details while preserving global attention and compatibility with pre-trained cross-modal priors; (2) a disease-level contrastive learning mechanism using learnable query tokens to dynamically extract disease-specific semantics from full reports and align them with corresponding visual features, thereby disentangling distinct diseases within the same anatomical region; and (3) a diagnosis-aware prompt strategy that employs real clinical phrases and aggregated disease prototypes to bridge the pre-training-inference gap and enhance zero-shot diagnostic reliability. Our model achieves state-of-the-art performance on CT-RATE (84.4% AUC, +5.1%) and Rad-ChestCT (75.4% AUC, +5.4%), with even larger gains (+9.8% AUC) on a challenging 60-disease benchmark, and demonstrates strong transferability to radiology report generation, underscoring the generality and clinical utility of our approach.
Julien Khlaut, Charles Corbière, Baptiste Callard +9cs.CV
Vision-language contrastive pretraining has become the dominant recipe for 3D medical foundation models, leveraging the large volumes of paired scans and reports produced in clinical practice. However, medical images usually span dozens of organs, and radiological reports are much longer than typical natural image captions and are composed of multiple structured sections. CLIP-style pretraining compresses this structure by encoding each modality into a single global token, at the risk of losing important details. We introduce ConQuer (Concept Queries), an image-text pretraining method that augments CLIP's global alignment with a set of localized alignments, one per concept. ConQuer splits the report into concept-specific sections and learns cross-attention queries that pool the matching image features without using any segmentation mask or spatial supervision. Contrastive learning is then applied independently for each concept. Concepts can be any unit of semantic localization; here, they are anatomical regions, one query per organ or gross body region. As a byproduct, each query learns attention maps focused on its concept, providing built-in spatial interpretability. We use ConQuer to train Jolia, a 3D CT foundation model on chest and abdominal CT. Jolia consistently outperforms a CLIP baseline on findings classification, report generation, and cross-center transfer, and sets a new state of the art across multiple public benchmarks. Jolia's weights will be released upon acceptance.
Chest X-ray (CXR) interpretation often requires longitudinal comparison to assess disease progression. Existing approaches typically rely on temporal feature fusion or inter-study discrepancy modeling, yet remain limited in capturing subtle progression semantics and overlook the inherently directional nature of disease trajectories. In this paper, we propose ProTrans, a novel vision-language pretraining framework that formulates disease progression as a directional semantic transition between paired CXR studies. ProTrans leverages radiology reports to anchor individual CXR representations within interpretable disease states, and introduces a learnable progression feature map to explicitly encode semantic shifts between states, aligned with report-derived progression descriptions. To enforce direction-aware perception, ProTrans incorporates a reversed temporal modeling process and imposes bidirectional reconstruction consistency across states and transitions, thereby disentangling directional semantics and promoting coherent trajectory modeling. Extensive experiments on longitudinal downstream tasks, including disease progression classification and progression captioning, demonstrate that ProTrans consistently outperforms existing methods, establishing a unified pretraining framework for longitudinal CXR understanding. https://github.com/RPIDIAL/ProTrans
Chest computed tomography (CT) is central to the detection and management of thoracic disease, yet the growing scale and complexity of volumetric imaging increasingly exceed what can be addressed by scan-level prediction alone. Clinically useful AI for CT must not only recognize disease across the whole volume, but also localize abnormalities and provide interpretable visual evidence. Existing vision-language foundation models typically compress scans and reports into global image-text representations, limiting their ability to preserve spatial evidence and support clinically meaningful interpretation. Here we developed EXACT, an explainable anomaly-aware foundation model for three-dimensional chest CT that learns spatially resolved representations from paired clinical scans and radiology reports. EXACT was pre-trained on 25,692 CT-reports pairs using anatomy-aware weak supervision, jointly learning organ segmentation and multi-instance anomaly localization without manual voxel-level annotations. The resulting organ-specific anomaly-aware maps assign each voxel a disease-specific anomaly score confined to its corresponding anatomy, jointly encoding lesion extent and organ-level context. In retrospective multinational and multi-center evaluations, EXACT showed broad and consistent improvements across clinically relevant CT tasks, spanning multi-disease diagnosis, zero-shot anomaly localization, downstream adaptation, and visually grounded report generation, outperforming existing three-dimensional medical foundation models. By transforming routine clinical CT scans and free-text reports into explainable voxel-level representations, EXACT establishes a scalable paradigm for trustworthy volumetric medical AI.