arXiv subjects

Sebastien Ourselin

Publications and source records attributed to Sebastien Ourselin.

At least 37 records · Page 2Linked to original sources

arXiv2025

LIHE: Linguistic Instance-Split Hyperbolic-Euclidean Framework for Generalized Weakly-Supervised Referring Expression Comprehension

Existing Weakly-Supervised Referring Expression Comprehension (WREC) methods, while effective, are fundamentally limited by a one-to-one mapping assumption, hindering their ability to handle expressions corresponding to zero or multiple targets in realistic scenarios. To bridge this gap, we introduce the Weakly-Supervised Generalized Referring Expression Comprehension task (WGREC), a more practical paradigm that handles expressions with variable numbers of referents. However, extending WREC to WGREC presents two fundamental challenges: supervisory signal ambiguity, where weak image-level supervision is insufficient for training a model to infer the correct number and identity of referents, and semantic representation collapse, where standard Euclidean similarity forces hierarchically-related concepts into non-discriminative clusters, blurring categorical boundaries. To tackle these challenges, we propose a novel WGREC framework named Linguistic Instance-Split Hyperbolic-Euclidean (LIHE), which operates in two stages. The first stage, Referential Decoupling, predicts the number of target objects and decomposes the complex expression into simpler sub-expressions. The second stage, Referent Grounding, then localizes these sub-expressions using HEMix, our innovative hybrid similarity module that synergistically combines the precise alignment capabilities of Euclidean proximity with the hierarchical modeling strengths of hyperbolic geometry. This hybrid approach effectively prevents semantic collapse while preserving fine-grained distinctions between related concepts. Extensive experiments demonstrate LIHE establishes the first effective weakly supervised WGREC baseline on gRefCOCO and Ref-ZOM, while HEMix achieves consistent improvements on standard REC benchmarks, improving IoU@0.5 by up to 2.5\%. The code is available at https://anonymous.4open.science/r/LIHE.

cs.CV↗

arXiv2025

Light Focusing through Dynamic Media via Real-Valued Intensity Transmission Matrix

Precise light delivery through biological tissue is essential for deep-tissue imaging and phototherapeutic applications. Wavefront shaping enables control over scattered light by modulating the incident wavefront, but its application in living tissue is hindered by tissue-induced temporal decorrelation. This study systematically investigated the real-valued intensity transmission matrix (RVITM), a high-speed wavefront shaping method, for light focusing across a broad range of speckle decorrelation times. The inherent trade-off between static light focusing enhancement and implementation speed is characterized, which provided practical guidelines for implementing RVITM in real-time wavefront shaping under varying dynamic conditions. Effective optical focusing using a RVITM with 33 ms runtime was achieved through porcine liver with decorrelation times as short as 13 ms, demonstrating feasibility for biologically relevant dynamics and supporting the development of adaptive, non-invasive optical control for biomedical applications.

physics.optics↗

arXiv2025

Dynamic causal discovery in Alzheimer's disease through latent pseudotime modelling

The application of causal discovery to diseases like Alzheimer's (AD) is limited by the static graph assumptions of most methods; such models cannot account for an evolving pathophysiology, modulated by a latent disease pseudotime. We propose to apply an existing latent variable model to real-world AD data, inferring a pseudotime that orders patients along a data-driven disease trajectory independent of chronological age, then learning how causal relationships evolve. Pseudotime outperformed age in predicting diagnosis (AUC 0.82 vs 0.59). Incorporating minimal, disease-agnostic background knowledge substantially improved graph accuracy and orientation. Our framework reveals dynamic interactions between novel (NfL, GFAP) and established AD markers, enabling practical causal discovery despite violated assumptions.

stat.AP↗

arXiv2025

Metadata-Aligned 3D MRI Representations for Contrast Understanding and Quality Control

Magnetic Resonance Imaging suffers from substantial data heterogeneity and the absence of standardized contrast labels across scanners, protocols, and institutions, which severely limits large-scale automated analysis. A unified representation of MRI contrast would enable a wide range of downstream utilities, from automatic sequence recognition to harmonization and quality control, without relying on manual annotations. To this end, we introduce MR-CLIP, a metadata-guided framework that learns MRI contrast representations by aligning volumetric images with their DICOM acquisition parameters. The resulting embeddings shows distinct clusters of MRI sequences and outperform supervised 3D baselines under data scarcity in few-shot sequence classification. Moreover, MR-CLIP enables unsupervised data quality control by identifying corrupted or inconsistent metadata through image-metadata embedding distances. By transforming routinely available acquisition metadata into a supervisory signal, MR-CLIP provides a scalable foundation for label-efficient MRI analysis across diverse clinical datasets.

cs.CV↗

arXiv2025

DARIL: When Imitation Learning outperforms Reinforcement Learning in Surgical Action Planning

Surgical action planning requires predicting future instrument-verb-target triplets for real-time assistance. While teleoperated robotic surgery provides natural expert demonstrations for imitation learning (IL), reinforcement learning (RL) could potentially discover superior strategies through self-exploration. We present the first comprehensive comparison of IL versus RL for surgical action planning on CholecT50. Our Dual-task Autoregressive Imitation Learning (DARIL) baseline achieves 34.6% action triplet recognition mAP and 33.6% next frame prediction mAP with smooth planning degradation to 29.2% at 10-second horizons. We evaluated three RL variants: world model-based RL, direct video RL, and inverse RL enhancement. Surprisingly, all RL approaches underperformed DARIL--world model RL dropped to 3.1% mAP at 10s while direct video RL achieved only 15.9%. Our analysis reveals that distribution matching on expert-annotated test sets systematically favors IL over potentially valid RL policies that differ from training demonstrations. This challenges assumptions about RL superiority in sequential decision making and provides crucial insights for surgical AI development.

cs.AI↗

arXiv2025

A methodology for clinically driven interactive segmentation evaluation

Interactive segmentation is a promising strategy for building robust, generalisable algorithms for volumetric medical image segmentation. However, inconsistent and clinically unrealistic evaluation hinders fair comparison and misrepresents real-world performance. We propose a clinically grounded methodology for defining evaluation tasks and metrics, and built a software framework for constructing standardised evaluation pipelines. We evaluate state-of-the-art algorithms across heterogeneous and complex tasks and observe that (i) minimising information loss when processing user interactions is critical for model robustness, (ii) adaptive-zooming mechanisms boost robustness and speed convergence, (iii) performance drops if validation prompting behaviour/budgets differ from training, (iv) 2D methods perform well with slab-like images and coarse targets, but 3D context helps with large or irregularly shaped targets, (v) performance of non-medical-domain models (e.g. SAM2) degrades with poor contrast and complex shapes.

cs.CV↗

arXiv2025

Individualized prescriptive inference in ischaemic stroke

The gold standard in the treatment of ischaemic stroke is set by evidence from randomized controlled trials, based on simple descriptions of presumptively homogeneous populations. Yet the manifest complexity of the brain's functional, connective, and vascular architectures introduces heterogeneities that violate the underlying statistical premisses, potentially leading to substantial errors at both individual and population levels. The counterfactual nature of interventional inference renders quantifying the impact of this defect difficult. Here we conduct a comprehensive series of semi-synthetic, biologically plausible, virtual interventional trials across 100M+ distinct simulations. We generate empirically grounded virtual trial data from large-scale meta-analytic connective, functional, genetic expression, and receptor distribution data, with high-resolution maps of 4K+ acute ischaemic lesions. Within each trial, we estimate treatment effects using models varying in complexity, in the presence of increasingly confounded outcomes and noisy treatment responses. Individualized prescriptions inferred from simple models, fitted to unconfounded data, were less accurate than those from complex models, fitted to confounded data. Our results indicate that complex modelling with richly represented lesion data is critical to individualized prescriptive inference in ischaemic stroke.

q-bio.QM↗

arXiv2025

A Fully Open and Generalizable Foundation Model for Ultrasound Clinical Applications

Artificial intelligence (AI) that can effectively learn ultrasound representations by integrating multi-source data holds significant promise for advancing clinical care. However, the scarcity of large labeled datasets in real-world clinical environments and the limited generalizability of task-specific models have hindered the development of generalizable clinical AI models for ultrasound applications. In this study, we present EchoCare, a novel ultrasound foundation model for generalist clinical use, developed via self-supervised learning on our curated, publicly available, large-scale dataset EchoCareData. EchoCareData comprises 4.5 million ultrasound images, sourced from over 23 countries across 5 continents and acquired via a diverse range of distinct imaging devices, thus encompassing global cohorts that are multi-center, multi-device, and multi-ethnic. Unlike prior studies that adopt off-the-shelf vision foundation model architectures, we introduce a hierarchical classifier into EchoCare to enable joint learning of pixel-level and representation-level features, capturing both global anatomical contexts and local ultrasound characteristics. With minimal training, EchoCare outperforms state-of-the-art comparison models across 10 representative ultrasound benchmarks of varying diagnostic difficulties, spanning disease diagnosis, lesion segmentation, organ detection, landmark prediction, quantitative regression, imaging enhancement and report generation. The code and pretrained model are publicly released, rendering EchoCare accessible for fine-tuning and local adaptation, supporting extensibility to additional applications. EchoCare provides a fully open and generalizable foundation model to boost the development of AI technologies for diverse clinical ultrasound applications.

cs.CV↗

arXiv2025

MR-CLIP: Efficient Metadata-Guided Learning of MRI Contrast Representations

Accurate interpretation of Magnetic Resonance Imaging scans in clinical systems is based on a precise understanding of image contrast. This contrast is primarily governed by acquisition parameters, such as echo time and repetition time, which are stored in the DICOM metadata. To simplify contrast identification, broad labels such as T1-weighted or T2-weighted are commonly used, but these offer only a coarse approximation of the underlying acquisition settings. In many real-world datasets, such labels are entirely missing, leaving raw acquisition parameters as the only indicators of contrast. Adding to this challenge, the available metadata is often incomplete, noisy, or inconsistent. The lack of reliable and standardized metadata complicates tasks such as image interpretation, retrieval, and integration into clinical workflows. Furthermore, robust contrast-aware representations are essential to enable more advanced clinical applications, such as achieving modality-invariant representations and data harmonization. To address these challenges, we propose MR-CLIP, a multimodal contrastive learning framework that aligns MR images with their DICOM metadata to learn contrast-aware representations, without relying on manual labels. Trained on a diverse clinical dataset that spans various scanners and protocols, MR-CLIP captures contrast variations across acquisitions and within scans, enabling anatomy-invariant representations. We demonstrate its effectiveness in cross-modal retrieval and contrast classification, highlighting its scalability and potential for further clinical applications. The code and weights are publicly available at https://github.com/myigitavci/MR-CLIP.

cs.CV↗

arXiv2025

ReCAP: Recursive Cross Attention Network for Pseudo-Label Generation in Robotic Surgical Skill Assessment

In surgical skill assessment, the Objective Structured Assessments of Technical Skills (OSATS) and Global Rating Scale (GRS) are well-established tools for evaluating surgeons during training. These metrics, along with performance feedback, help surgeons improve and reach practice standards. Recent research on the open-source JIGSAWS dataset, which includes both GRS and OSATS labels, has focused on regressing GRS scores from kinematic data, video, or their combination. However, we argue that regressing GRS alone is limiting, as it aggregates OSATS scores and overlooks clinically meaningful variations during a surgical trial. To address this, we developed a weakly-supervised recurrent transformer model that tracks a surgeon's performance throughout a session by mapping hidden states to six OSATS, derived from kinematic data. These OSATS scores are averaged to predict GRS, allowing us to compare our model's performance against state-of-the-art (SOTA) methods. We report Spearman's Correlation Coefficients (SCC) demonstrating that our model outperforms SOTA using kinematic data (SCC 0.83-0.88), and matches performance with video-based models. Our model also surpasses SOTA in most tasks for average OSATS predictions (SCC 0.46-0.70) and specific OSATS (SCC 0.56-0.95). The generation of pseudo-labels at the segment level translates quantitative predictions into qualitative feedback, vital for automated surgical skill assessment pipelines. A senior surgeon validated our model's outputs, agreeing with 77\% of the weakly-supervised predictions \(p=0.006\).

cs.CV↗

arXiv2025

SWAG: Long-term Surgical Workflow Prediction with Generative-based Anticipation

While existing approaches excel at recognising current surgical phases, they provide limited foresight and intraoperative guidance into future procedural steps. Similarly, current anticipation methods are constrained to predicting short-term and single events, neglecting the dense, repetitive, and long sequential nature of surgical workflows. To address these needs and limitations, we propose SWAG (Surgical Workflow Anticipative Generation), a framework that combines phase recognition and anticipation using a generative approach. This paper investigates two distinct decoding methods - single-pass (SP) and auto-regressive (AR) - to generate sequences of future surgical phases at minute intervals over long horizons. We propose a novel embedding approach using class transition probabilities to enhance the accuracy of phase anticipation. Additionally, we propose a generative framework using remaining time regression to classification (R2C). SWAG was evaluated on two publicly available datasets, Cholec80 and AutoLaparo21. Our single-pass model with class transition probability embeddings (SP*) achieves 32.1% and 41.3% F1 scores over 20 and 30 minutes on Cholec80 and AutoLaparo21, respectively. Moreover, our approach competes with existing methods on phase remaining time regression, achieving weighted mean absolute errors of 0.32 and 0.48 minutes for 2- and 3-minute horizons. SWAG demonstrates versatility across generative decoding frame works and classification and regression tasks to create temporal continuity between surgical workflow recognition and anticipation. Our method provides steps towards intraoperative surgical workflow generation for anticipation. Project: https://maxboels.com/research/swag.

cs.CV↗

arXiv2025

EndoMamba: An Efficient Foundation Model for Endoscopic Videos via Hierarchical Pre-training

Endoscopic video-based tasks, such as visual navigation and surgical phase recognition, play a crucial role in minimally invasive surgeries by providing real-time assistance. While recent video foundation models have shown promise, their applications are hindered by (1) computational inefficiencies and (2) suboptimal performance caused by limited data for pre-training in endoscopy. To address these issues, we present EndoMamba, a foundation model designed for real-time inference while learning generalized spatiotemporal representations. First, to mitigate computational inefficiencies, we propose the EndoMamba backbone, optimized for real-time inference. Inspired by recent advancements in state space models, EndoMamba integrates Bidirectional Mamba blocks for spatial modeling within individual frames and vanilla Mamba blocks for past-to-present reasoning across the temporal domain. This design enables both strong spatiotemporal modeling and efficient inference in online video streams. Second, we propose a self-supervised hierarchical pre-training diagram to enhance EndoMamba's representation learning using endoscopic videos and incorporating general video domain knowledge. Specifically, our approach combines masked reconstruction with auxiliary supervision, leveraging low-level reconstruction to capture spatial-temporal structures and high-level alignment to transfer broader knowledge from a pretrained general-video domain foundation model. Extensive experiments on four downstream tasks--classification, segmentation, surgical phase recognition, and localization--demonstrate that EndoMamba outperforms existing foundation models and task-specific methods while maintaining real-time inference speed. The source code is available at https://github.com/TianCuteQY/EndoMamba.

cs.CV↗

arXiv2025

Motion-Boundary-Driven Unsupervised Surgical Instrument Segmentation in Low-Quality Optical Flow

Unsupervised video-based surgical instrument segmentation has the potential to accelerate the adoption of robot-assisted procedures by reducing the reliance on manual annotations. However, the generally low quality of optical flow in endoscopic footage poses a great challenge for unsupervised methods that rely heavily on motion cues. To overcome this limitation, we propose a novel approach that pinpoints motion boundaries, regions with abrupt flow changes, while selectively discarding frames with globally low-quality flow and adapting to varying motion patterns. Experiments on the EndoVis2017 VOS and EndoVis2017 Challenge datasets show that our method achieves mean Intersection-over-Union (mIoU) scores of 0.75 and 0.72, respectively, effectively alleviating the constraints imposed by suboptimal optical flow. This enables a more scalable and robust surgical instrument segmentation solution in clinical settings. The code will be publicly released.

cs.CV↗

arXiv2025

Resolution Invariant Autoencoder

Deep learning has significantly advanced medical imaging analysis, yet variations in image resolution remain an overlooked challenge. Most methods address this by resampling images, leading to either information loss or computational inefficiencies. While solutions exist for specific tasks, no unified approach has been proposed. We introduce a resolution-invariant autoencoder that adapts spatial resizing at each layer in the network via a learned variable resizing process, replacing fixed spatial down/upsampling at the traditional factor of 2. This ensures a consistent latent space resolution, regardless of input or output resolution. Our model enables various downstream tasks to be performed on an image latent whilst maintaining performance across different resolutions, overcoming the shortfalls of traditional methods. We demonstrate its effectiveness in uncertainty-aware super-resolution, classification, and generative modelling tasks and show how our method outperforms conventional baselines with minimal performance loss across resolutions.

cs.CV↗

arXiv2025

SurgPLAN++: Universal Surgical Phase Localization Network for Online and Offline Inference

Surgical phase recognition is critical for assisting surgeons in understanding surgical videos. Existing studies focused more on online surgical phase recognition, by leveraging preceding frames to predict the current frame. Despite great progress, they formulated the task as a series of frame-wise classification, which resulted in a lack of global context of the entire procedure and incoherent predictions. Moreover, besides online analysis, accurate offline surgical phase recognition is also in significant clinical need for retrospective analysis, and existing online algorithms do not fully analyze the entire video, thereby limiting accuracy in offline analysis. To overcome these challenges and enhance both online and offline inference capabilities, we propose a universal Surgical Phase Localization Network, named SurgPLAN++, with the principle of temporal detection. To ensure a global understanding of the surgical procedure, we devise a phase localization strategy for SurgPLAN++ to predict phase segments across the entire video through phase proposals. For online analysis, to generate high-quality phase proposals, SurgPLAN++ incorporates a data augmentation strategy to extend the streaming video into a pseudo-complete video through mirroring, center-duplication, and down-sampling. For offline analysis, SurgPLAN++ capitalizes on its global phase prediction framework to continuously refine preceding predictions during each online inference step, thereby significantly improving the accuracy of phase recognition. We perform extensive experiments to validate the effectiveness, and our SurgPLAN++ achieves remarkable performance in both online and offline modes, which outperforms state-of-the-art methods. The source code is available at https://github.com/franciszchen/SurgPLAN-Plus.

cs.CV↗

arXiv2025

Generalizable automated ischaemic stroke lesion segmentation with vision transformers

Ischaemic stroke, a leading cause of death and disability, critically relies on neuroimaging for characterising the anatomical pattern of injury. Diffusion-weighted imaging (DWI) provides the highest expressivity in ischemic stroke but poses substantial challenges for automated lesion segmentation: susceptibility artefacts, morphological heterogeneity, age-related comorbidities, time-dependent signal dynamics, instrumental variability, and limited labelled data. Current U-Net-based models therefore underperform, a problem accentuated by inadequate evaluation metrics that focus on mean performance, neglecting anatomical, subpopulation, and acquisition-dependent variability. Here, we present a high-performance DWI lesion segmentation tool addressing these challenges through optimized vision transformer-based architectures, integration of 3563 annotated lesions from multi-site data, and algorithmic enhancements, achieving state-of-the-art results. We further propose a novel evaluative framework assessing model fidelity, equity (across demographics and lesion subtypes), anatomical precision, and robustness to instrumental variability, promoting clinical and research utility. This work advances stroke imaging by reconciling model expressivity with domain-specific challenges and redefining performance benchmarks to prioritize equity and generalizability, critical for personalized medicine and mechanistic research.

eess.IV↗

arXiv2025

Neuradicon: operational representation learning of neuroimaging reports

Radiological reports typically summarize the content and interpretation of imaging studies in unstructured form that precludes quantitative analysis. This limits the monitoring of radiological services to throughput undifferentiated by content, impeding specific, targeted operational optimization. Here we present Neuradicon, a natural language processing (NLP) framework for quantitative analysis of neuroradiological reports. Our framework is a hybrid of rule-based and artificial intelligence models to represent neurological reports in succinct, quantitative form optimally suited to operational guidance. We demonstrate the application of Neuradicon to operational phenotyping of a corpus of 336,569 reports, and report excellent generalizability across time and two independent healthcare institutions.

cs.CL↗

arXiv2025

EndoOmni: Zero-Shot Cross-Dataset Depth Estimation in Endoscopy by Robust Self-Learning from Noisy Labels

Single-image depth estimation is essential for endoscopy tasks such as localization, reconstruction, and augmented reality. Most existing methods in surgical scenes focus on in-domain depth estimation, limiting their real-world applicability. This constraint stems from the scarcity and inferior labeling quality of medical data for training. In this work, we present EndoOmni, the first foundation model for zero-shot cross-domain depth estimation for endoscopy. To harness the potential of diverse training data, we refine the advanced self-learning paradigm that employs a teacher model to generate pseudo-labels, guiding a student model trained on large-scale labeled and unlabeled data. To address training disturbance caused by inherent noise in depth labels, we propose a robust training framework that leverages both depth labels and estimated confidence from the teacher model to jointly guide the student model training. Moreover, we propose a weighted scale-and-shift invariant loss to adaptively adjust learning weights based on label confidence, thus imposing learning bias towards cleaner label pixels while reducing the influence of highly noisy pixels. Experiments on zero-shot relative depth estimation show that our EndoOmni improves state-of-the-art methods in medical imaging for 33\% and existing foundation models for 34\% in terms of absolute relative error on specific datasets. Furthermore, our model provides strong initialization for fine-tuning metric depth estimation, maintaining superior performance in both in-domain and out-of-domain scenarios. The source code is publicly available at https://github.com/TianCuteQY/EndoOmni.

cs.CV↗