arXiv subjects

Jorge Cardoso

Publications and source records attributed to Jorge Cardoso.

At least 19 recordsLinked to original sources

arXiv2026

Metadata Supervised MRI Representations for Modelling and Controlling Acquisition Variability

Magnetic resonance imaging exhibits substantial acquisition variability, where identical anatomy can appear markedly different across scanners and imaging protocols. Consequently, learned representations entangle biological structure with acquisition-dependent appearance, limiting interpretability, generalisation, and clinical deployment. We show that these sources of variation can be separated by jointly modelling MRI images and DICOM metadata. Using large-scale clinical brain MRI data, we learn representations that separate anatomical structure from contrast-dependent appearance. Resulting contrast representations organise heterogeneous acquisitions, support sequence understanding, and detect image--metadata inconsistencies, whereas anatomical representations suppress acquisition-specific variation while preserving biologically relevant information. Building on these disentangled representations, we introduce a unified anatomy-preserving harmonisation model for cross-modality and cross-site adaptation, conditioned on image or acquisition metadata. Our findings suggest that acquisition variability is a structured component of the imaging process that can be modelled, audited, and controlled, providing a foundation for acquisition-aware representation learning in large-scale medical imaging.

cs.CV↗

arXiv2026

Understanding Sources of Demographic Predictability in Brain MRI via Disentangling Anatomy and Contrast

Demographic attributes can be predicted from medical images, raising concerns about bias in clinical AI systems. In X-ray imaging, acquisition characteristics have been shown to contribute substantially to this predictability. Whether the same holds in brain MRI remains unclear, as anatomical variation and acquisition-dependent contrast are deeply entangled in the image formation process, obscuring the origins of demographic signal. To address this, we propose a controlled framework based on disentangled representation learning, decomposing brain MRI into anatomy-focused representations that suppress acquisition influence and contrast embeddings that capture acquisition-dependent characteristics. Training predictive models for age, sex, and race on full images, anatomical representations, and contrast embeddings allows us to quantify the relative contributions of structure and acquisition to the demographic signal. Across three datasets and multiple MRI sequences, demographic predictability is found to be driven primarily by anatomical variation, with anatomy-focused representations largely preserving the performance of models trained on raw images. Contrast embeddings retain a weaker signal that is dataset-specific and does not generalize across sites. These findings suggest that effective mitigation must explicitly account for the primarily anatomical and secondarily acquisition-dependent origins of demographic signal, ensuring that any bias reduction generalizes robustly across domains.

cs.CV↗

arXiv2025

DIST-CLIP: Arbitrary Metadata and Image Guided MRI Harmonization via Disentangled Anatomy-Contrast Representations

Deep learning holds immense promise for transforming medical image analysis, yet its clinical generalization remains profoundly limited. A major barrier is data heterogeneity. This is particularly true in Magnetic Resonance Imaging, where scanner hardware differences, diverse acquisition protocols, and varying sequence parameters introduce substantial domain shifts that obscure underlying biological signals. Data harmonization methods aim to reduce these instrumental and acquisition variability, but existing approaches remain insufficient. When applied to imaging data, image-based harmonization approaches are often restricted by the need for target images, while existing text-guided methods rely on simplistic labels that fail to capture complex acquisition details or are typically restricted to datasets with limited variability, failing to capture the heterogeneity of real-world clinical environments. To address these limitations, we propose DIST-CLIP (Disentangled Style Transfer with CLIP Guidance), a unified framework for MRI harmonization that flexibly uses either target images or DICOM metadata for guidance. Our framework explicitly disentangles anatomical content from image contrast, with the contrast representations being extracted using pre-trained CLIP encoders. These contrast embeddings are then integrated into the anatomical content via a novel Adaptive Style Transfer module. We trained and evaluated DIST-CLIP on diverse real-world clinical datasets, and showed significant improvements in performance when compared against state-of-the-art methods in both style translation fidelity and anatomical preservation, offering a flexible solution for style transfer and standardizing MRI data. Our code and weights will be made publicly available upon publication.

cs.CV↗

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

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

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↗

arXiv2024

Data Pruning Can Do More: A Comprehensive Data Pruning Approach for Object Re-identification

Previous studies have demonstrated that not each sample in a dataset is of equal importance during training. Data pruning aims to remove less important or informative samples while still achieving comparable results as training on the original (untruncated) dataset, thereby reducing storage and training costs. However, the majority of data pruning methods are applied to image classification tasks. To our knowledge, this work is the first to explore the feasibility of these pruning methods applied to object re-identification (ReID) tasks, while also presenting a more comprehensive data pruning approach. By fully leveraging the logit history during training, our approach offers a more accurate and comprehensive metric for quantifying sample importance, as well as correcting mislabeled samples and recognizing outliers. Furthermore, our approach is highly efficient, reducing the cost of importance score estimation by 10 times compared to existing methods. Our approach is a plug-and-play, architecture-agnostic framework that can eliminate/reduce 35%, 30%, and 5% of samples/training time on the VeRi, MSMT17 and Market1501 datasets, respectively, with negligible loss in accuracy (< 0.1%). The lists of important, mislabeled, and outlier samples from these ReID datasets are available at https://github.com/Zi-Y/data-pruning-reid.

cs.CV↗

arXiv2024

Command-line Risk Classification using Transformer-based Neural Architectures

To protect large-scale computing environments necessary to meet increasing computing demand, cloud providers have implemented security measures to monitor Operations and Maintenance (O&M) activities and therefore prevent data loss and service interruption. Command interception systems are used to intercept, assess, and block dangerous Command-line Interface (CLI) commands before they can cause damage. Traditional solutions for command risk assessment include rule-based systems, which require expert knowledge and constant human revision to account for unseen commands. To overcome these limitations, several end-to-end learning systems have been proposed to classify CLI commands. These systems, however, have several other limitations, including the adoption of general-purpose text classifiers, which may not adapt to the language characteristics of scripting languages such as Bash or PowerShell, and may not recognize dangerous commands in the presence of an unbalanced class distribution. In this paper, we propose a transformer-based command risk classification system, which leverages the generalization power of Large Language Models (LLM) to provide accurate classification and the ability to identify rare dangerous commands effectively, by exploiting the power of transfer learning. We verify the effectiveness of our approach on a realistic dataset of production commands and show how to apply our model for other security-related tasks, such as dangerous command interception and auditing of existing rule-based systems.

cs.AI↗

arXiv2024

Investigating Memory Failure Prediction Across CPU Architectures

Large-scale datacenters often experience memory failures, where Uncorrectable Errors (UEs) highlight critical malfunction in Dual Inline Memory Modules (DIMMs). Existing approaches primarily utilize Correctable Errors (CEs) to predict UEs, yet they typically neglect how these errors vary between different CPU architectures, especially in terms of Error Correction Code (ECC) applicability. In this paper, we investigate the correlation between CEs and UEs across different CPU architectures, including X86 and ARM. Our analysis identifies unique patterns of memory failure associated with each processor platform. Leveraging Machine Learning (ML) techniques on production datasets, we conduct the memory failure prediction in different processors' platforms, achieving up to 15% improvements in F1-score compared to the existing algorithm. Finally, an MLOps (Machine Learning Operations) framework is provided to consistently improve the failure prediction in the production environment.

cs.AR↗

arXiv2024

AutoNet: Automatic Reachability Policy Management in Public Cloud Networks

Virtual Private Cloud (VPC) is the main network abstraction technology used in public cloud systems. VPCs are composed of a set of network services that permit the definition of complex network reachability properties among internal and external cloud entities such as tenants' VMs or some generic internet nodes. Although hiding the underlying complexity through a comprehensible abstraction layer, manually enforcing particular reachability intents in VPC networks is still notably error-prone and complex. In this paper, we propose AutoNet, a new model for assisting cloud tenants in managing reachability-based policies in VPC networks. AutoNet is capable of safely generating incremental VPC configurations while satisfying some metric-based high-level intent defined by the tenants. To achieve this goal, we leverage a MaxSAT-based encoding of the network configuration combined with several optimizations to scale to topologies with thousands of nodes. Our results show that the developed system is capable of achieving a sub-second response time for production VPC deployments while still providing fine-grained control over the generated configurations.

cs.NI↗

arXiv2024

On Software Ageing Indicators in OpenStack

Distributed systems in general and cloud systems in particular, are susceptible to failures that can lead to substantial economic and data losses, security breaches, and even potential threats to human safety. Software ageing is an example of one such vulnerability. It emerges due to routine re-usage of computational systems units which induce fatigue within the components, resulting in an increased failure rate and potential system breakdown. Due to its stochastic nature, ageing cannot be directly measured, instead ageing indicators as proxies are used. While there are dozens of studies on different ageing indicators, their comprehensive comparison in different settings remains underexplored. In this paper, we compare two ageing indicators in OpenStack as a use case. Specifically, our evaluation compares memory usage (including swap memory) and request response time, as readily available indicators. By executing multiple OpenStack deployments with varying configurations, we conduct a series of experiments and analyze the ageing indicators. Comparative analysis through statistical tests provides valuable insights into the strengths and weaknesses of the utilised ageing indicators. Finally, through an in-depth analysis of other OpenStack failures, we identify underlying failure patterns and their impact on the studied ageing indicators.

cs.DC↗

arXiv2023

Exploring Error Bits for Memory Failure Prediction: An In-Depth Correlative Study

In large-scale datacenters, memory failure is a common cause of server crashes, with Uncorrectable Errors (UEs) being a major indicator of Dual Inline Memory Module (DIMM) defects. Existing approaches primarily focus on predicting UEs using Correctable Errors (CEs), without fully considering the information provided by error bits. However, error bit patterns have a strong correlation with the occurrence of UEs. In this paper, we present a comprehensive study on the correlation between CEs and UEs, specifically emphasizing the importance of spatio-temporal error bit information. Our analysis reveals a strong correlation between spatio-temporal error bits and UE occurrence. Through evaluations using real-world datasets, we demonstrate that our approach significantly improves prediction performance by 15% in F1-score compared to the state-of-the-art algorithms. Overall, our approach effectively reduces the number of virtual machine interruptions caused by UEs by approximately 59%.

cs.AR↗

arXiv2023

Privacy Distillation: Reducing Re-identification Risk of Multimodal Diffusion Models

Knowledge distillation in neural networks refers to compressing a large model or dataset into a smaller version of itself. We introduce Privacy Distillation, a framework that allows a text-to-image generative model to teach another model without exposing it to identifiable data. Here, we are interested in the privacy issue faced by a data provider who wishes to share their data via a multimodal generative model. A question that immediately arises is ``How can a data provider ensure that the generative model is not leaking identifiable information about a patient?''. Our solution consists of (1) training a first diffusion model on real data (2) generating a synthetic dataset using this model and filtering it to exclude images with a re-identifiability risk (3) training a second diffusion model on the filtered synthetic data only. We showcase that datasets sampled from models trained with privacy distillation can effectively reduce re-identification risk whilst maintaining downstream performance.

cs.LG↗

arXiv2023

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↗

arXiv2022

CrossMoDA 2021 challenge: Benchmark of Cross-Modality Domain Adaptation techniques for Vestibular Schwannoma and Cochlea Segmentation

Domain Adaptation (DA) has recently raised strong interests in the medical imaging community. While a large variety of DA techniques has been proposed for image segmentation, most of these techniques have been validated either on private datasets or on small publicly available datasets. Moreover, these datasets mostly addressed single-class problems. To tackle these limitations, the Cross-Modality Domain Adaptation (crossMoDA) challenge was organised in conjunction with the 24th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2021). CrossMoDA is the first large and multi-class benchmark for unsupervised cross-modality DA. The challenge's goal is to segment two key brain structures involved in the follow-up and treatment planning of vestibular schwannoma (VS): the VS and the cochleas. Currently, the diagnosis and surveillance in patients with VS are performed using contrast-enhanced T1 (ceT1) MRI. However, there is growing interest in using non-contrast sequences such as high-resolution T2 (hrT2) MRI. Therefore, we created an unsupervised cross-modality segmentation benchmark. The training set provides annotated ceT1 (N=105) and unpaired non-annotated hrT2 (N=105). The aim was to automatically perform unilateral VS and bilateral cochlea segmentation on hrT2 as provided in the testing set (N=137). A total of 16 teams submitted their algorithm for the evaluation phase. The level of performance reached by the top-performing teams is strikingly high (best median Dice - VS:88.4%; Cochleas:85.7%) and close to full supervision (median Dice - VS:92.5%; Cochleas:87.7%). All top-performing methods made use of an image-to-image translation approach to transform the source-domain images into pseudo-target-domain images. A segmentation network was then trained using these generated images and the manual annotations provided for the source image.

eess.IV↗

arXiv2022

The Liver Tumor Segmentation Benchmark (LiTS)

In this work, we report the set-up and results of the Liver Tumor Segmentation Benchmark (LiTS), which was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI) 2017 and the International Conferences on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2017 and 2018. The image dataset is diverse and contains primary and secondary tumors with varied sizes and appearances with various lesion-to-background levels (hyper-/hypo-dense), created in collaboration with seven hospitals and research institutions. Seventy-five submitted liver and liver tumor segmentation algorithms were trained on a set of 131 computed tomography (CT) volumes and were tested on 70 unseen test images acquired from different patients. We found that not a single algorithm performed best for both liver and liver tumors in the three events. The best liver segmentation algorithm achieved a Dice score of 0.963, whereas, for tumor segmentation, the best algorithms achieved Dices scores of 0.674 (ISBI 2017), 0.702 (MICCAI 2017), and 0.739 (MICCAI 2018). Retrospectively, we performed additional analysis on liver tumor detection and revealed that not all top-performing segmentation algorithms worked well for tumor detection. The best liver tumor detection method achieved a lesion-wise recall of 0.458 (ISBI 2017), 0.515 (MICCAI 2017), and 0.554 (MICCAI 2018), indicating the need for further research. LiTS remains an active benchmark and resource for research, e.g., contributing the liver-related segmentation tasks in \url{http://medicaldecathlon.com/}. In addition, both data and online evaluation are accessible via \url{www.lits-challenge.com}.

cs.CV↗

arXiv2022

First CE Matters: On the Importance of Long Term Properties on Memory Failure Prediction

Dynamic random access memory failures are a threat to the reliability of data centres as they lead to data loss and system crashes. Timely predictions of memory failures allow for taking preventive measures such as server migration and memory replacement. Thereby, memory failure prediction prevents failures from externalizing, and it is a vital task to improve system reliability. In this paper, we revisited the problem of memory failure prediction. We analyzed the correctable errors (CEs) from hardware logs as indicators for a degraded memory state. As memories do not always work with full occupancy, access to faulty memory parts is time distributed. Following this intuition, we observed that important properties for memory failure prediction are distributed through long time intervals. In contrast, related studies, to fit practical constraints, frequently only analyze the CEs from the last fixed-size time interval while ignoring the predating information. Motivated by the observed discrepancy, we study the impact of including the overall (long-range) CE evolution and propose novel features that are calculated incrementally to preserve long-range properties. By coupling the extracted features with machine learning methods, we learn a predictive model to anticipate upcoming failures three hours in advance while improving the average relative precision and recall for 21% and 19% accordingly. We evaluated our methodology on real-world memory failures from the server fleet of a large cloud provider, justifying its validity and practicality.

cs.DC↗

arXiv2022

Morphology-preserving Autoregressive 3D Generative Modelling of the Brain

Human anatomy, morphology, and associated diseases can be studied using medical imaging data. However, access to medical imaging data is restricted by governance and privacy concerns, data ownership, and the cost of acquisition, thus limiting our ability to understand the human body. A possible solution to this issue is the creation of a model able to learn and then generate synthetic images of the human body conditioned on specific characteristics of relevance (e.g., age, sex, and disease status). Deep generative models, in the form of neural networks, have been recently used to create synthetic 2D images of natural scenes. Still, the ability to produce high-resolution 3D volumetric imaging data with correct anatomical morphology has been hampered by data scarcity and algorithmic and computational limitations. This work proposes a generative model that can be scaled to produce anatomically correct, high-resolution, and realistic images of the human brain, with the necessary quality to allow further downstream analyses. The ability to generate a potentially unlimited amount of data not only enables large-scale studies of human anatomy and pathology without jeopardizing patient privacy, but also significantly advances research in the field of anomaly detection, modality synthesis, learning under limited data, and fair and ethical AI. Code and trained models are available at: https://github.com/AmigoLab/SynthAnatomy.

eess.IV↗