Showing 1–50 of 201 results for author: Cardoso, J

Metadata Supervised MRI Representations for Modelling and Controlling Acquisition Variability

Authors: Mehmet Yigit Avci, Pedro Borges, Virginia Fernandez, Natalia Glazman, Paul Wright, Mehmet Yigitsoy, Sebastien Ourselin, Jorge Cardoso

Abstract: 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… ▽ More 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. △ Less

Submitted 13 July, 2026; originally announced July 2026.

Vision Transformers for Preoperative CT-Based Prediction of Histopathologic Chemotherapy Response Score in High-Grade Serous Ovarian Carcinoma

Authors: Francesca Fati, Felipe Coutinho, Marika Reinius, Marina Rosanu, Gabriel Funingana, Luigi De Vitis, Gabriella Schivardi, Hannah Clayton, Alice Traversa, Zeyu Gao, Guilherme Penteado, Shangqi Gao, Francesco Pastori, Ramona Woitek, Maria Cristina Ghioni, Giovanni Damiano Aletti, Mercedes Jimenez-Linan, Sarah Burge, Nicoletta Colombo, Evis Sala, Maria Francesca Spadea, Timothy L. Kline, James D. Brenton, Jaime Cardoso, Francesco Multinu , et al. (3 additional authors not shown)

Abstract: Purpose. High-grade serous ovarian carcinoma (HGSOC) is characterized by pronounced biological and spatial heterogeneity and is frequently diagnosed at an advanced stage. Neoadjuvant chemotherapy (NACT) followed by delayed primary surgery is commonly employed in patients unsuitable for primary cytoreduction. The Chemotherapy Response Score (CRS) is a validated histopathological biomarker of respon… ▽ More Purpose. High-grade serous ovarian carcinoma (HGSOC) is characterized by pronounced biological and spatial heterogeneity and is frequently diagnosed at an advanced stage. Neoadjuvant chemotherapy (NACT) followed by delayed primary surgery is commonly employed in patients unsuitable for primary cytoreduction. The Chemotherapy Response Score (CRS) is a validated histopathological biomarker of response to NACT, but it is only available postoperatively. In this study, we investigate whether pre-treatment computed tomography (CT) imaging and clinical data can be used to predict CRS as an investigational decision-support adjunct to inform multidisciplinary team (MDT) discussions regarding expected treatment response. Methods. We proposed a 2.5D multimodal deep learning framework that processes lesion-dense omental slices using a pre-trained Vision Transformer encoder and integrates the resulting visual representations with clinical variables through an intermediate fusion module to predict CRS. Results. Our multimodal model, integrating imaging and clinical data, achieved a ROC-AUC of 0.95 alongside 95% accuracy and 80% precision on the internal test cohort (IEO, n=41 patients). On the external test set (OV04, n=70 patients), it achieved a ROC-AUC of 0.68, alongside 67% accuracy and 75% precision. Conclusion. These preliminary results demonstrate the feasibility of transformer-based deep learning for preoperative prediction of CRS in HGSOC using routine clinical data and CT imaging. As an investigational, pre-treatment decision-support tool, this approach may assist MDT discussions by providing early, non-invasive estimates of treatment response. △ Less

Submitted 10 April, 2026; originally announced April 2026.

Ordinal Semantic Segmentation Applied to Medical and Odontological Images

Authors: Mariana Dória Prata Lima, Gilson Antonio Giraldi, Jaime S. Cardoso

Abstract: Semantic segmentation consists of assigning a semantic label to each pixel according to predefined classes. This process facilitates the understanding of object appearance and spatial relationships, playing an important role in the global interpretation of image content. Although modern deep learning approaches achieve high accuracy, they often ignore ordinal relationships among classes, which may… ▽ More Semantic segmentation consists of assigning a semantic label to each pixel according to predefined classes. This process facilitates the understanding of object appearance and spatial relationships, playing an important role in the global interpretation of image content. Although modern deep learning approaches achieve high accuracy, they often ignore ordinal relationships among classes, which may encode important domain knowledge for scene interpretation. In this work, loss functions that incorporate ordinal relationships into deep neural networks are investigated to promote greater semantic consistency in semantic segmentation tasks. These loss functions are categorized as unimodal, quasi-unimodal, and spatial. Unimodal losses constrain the predicted probability distribution according to the class ordering, while quasi-unimodal losses relax this constraint by allowing small variations while preserving ordinal coherence. Spatial losses penalize semantic inconsistencies between neighboring pixels, encouraging smoother transitions in the image space. In particular, this study adapts loss functions originally proposed for ordinal classification to ordinal semantic segmentation. Among them, the Expanded Mean Squared Error (EXP_MSE), the Quasi-Unimodal Loss (QUL), and the spatial Contact Surface Loss using Signal Distance Function (CSSDF) are investigated. These approaches have shown promising results in medical imaging, improving robustness, generalization, and anatomical consistency. △ Less

Submitted 21 March, 2026; originally announced March 2026.

Comments: 23 pages, 1 figure

WeNLEX: Weakly Supervised Natural Language Explanations for Multilabel Chest X-ray Classification

Authors: Isabel Rio-Torto, Jaime S. Cardoso, Luís F. Teixeira

Abstract: Natural language explanations provide an inherently human-understandable way to explain black-box models, closely reflecting how radiologists convey their diagnoses in textual reports. Most works explicitly supervise the explanation generation process using datasets annotated with explanations. Thus, though plausible, the generated explanations are not faithful to the model's reasoning. In this wo… ▽ More Natural language explanations provide an inherently human-understandable way to explain black-box models, closely reflecting how radiologists convey their diagnoses in textual reports. Most works explicitly supervise the explanation generation process using datasets annotated with explanations. Thus, though plausible, the generated explanations are not faithful to the model's reasoning. In this work, we propose WeNLEX, a weakly supervised model for the generation of natural language explanations for multilabel chest X-ray classification. Faithfulness is ensured by matching images generated from their corresponding natural language explanations with original images, in the black-box model's feature space. Plausibility is maintained via distribution alignment with a small database of clinician-annotated explanations. We empirically demonstrate, through extensive validation on multiple metrics to assess faithfulness, simulatability, diversity, and plausibility, that WeNLEX is able to produce faithful and plausible explanations, using as little as 5 ground-truth explanations per diagnosis. Furthermore, WeNLEX can operate in both post-hoc and in-model settings. In the latter, i.e., when the multilabel classifier is trained together with the rest of the network, WeNLEX improves the classification AUC of the standalone classifier by 2.21%, thus showing that adding interpretability to the training process can actually increase the downstream task performance. Additionally, simply by changing the database, WeNLEX explanations are adaptable to any target audience, and we showcase this flexibility by training a layman version of WeNLEX, where explanations are simplified for non-medical users. △ Less

Submitted 19 March, 2026; originally announced March 2026.

Personalized Cell Segmentation: Benchmark and Framework for Reference-Guided Cell Type Segmentation

Authors: Bisheng Wang, Jaime S. Cardoso, Lin Wu

Abstract: Accurate cell segmentation is critical for biological and medical imaging studies. Although recent deep learning models have advanced this task, most methods are limited to generic cell segmentation, lacking the ability to differentiate specific cell types. In this work, we introduce the Personalized Cell Segmentation (PerCS) task, which aims to segment all cells of a specific type given a referen… ▽ More Accurate cell segmentation is critical for biological and medical imaging studies. Although recent deep learning models have advanced this task, most methods are limited to generic cell segmentation, lacking the ability to differentiate specific cell types. In this work, we introduce the Personalized Cell Segmentation (PerCS) task, which aims to segment all cells of a specific type given a reference cell. To support this task, we establish a benchmark by reorganizing publicly available datasets, yielding 1,372 images and over 110,000 annotated cells. As a pioneering solution, we propose PerCS-DINO, a framework built on the DINOv2 backbone. By integrating image features and reference embeddings via a cross-attention transformer and contrastive learning, PerCS-DINO effectively segments cells matching the reference. Extensive experiments demonstrate the effectiveness of the proposed PerCS-DINO and highlight the challenges of this new task. We expect PerCS to serve as a useful testbed for advancing research in cell-based applications. △ Less

Submitted 15 March, 2026; originally announced March 2026.

Comments: Accepted by IEEE ICASSP 2026. 5 pages, 3 figures. (C) 2026 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising/promotional purposes, creating new collective works, for resale or redistribution, or reuse of any copyrighted component

CLoPA: Continual Low Parameter Adaptation of Interactive Segmentation for Medical Image Annotation

Authors: Parhom Esmaeili, Chayanin Tangwiriyasakul, Eli Gibson, Sebastien Ourselin, M. Jorge Cardoso

Abstract: Interactive segmentation enables clinicians to guide annotation, but existing zero-shot models like nnInteractive fail to consistently reach expert-level performance across diverse medical imaging tasks. Because annotation campaigns produce a growing stream of task-specific labelled data, online adaptation of the segmentation model is a natural complement to zero-shot inference. We propose CLoPA,… ▽ More Interactive segmentation enables clinicians to guide annotation, but existing zero-shot models like nnInteractive fail to consistently reach expert-level performance across diverse medical imaging tasks. Because annotation campaigns produce a growing stream of task-specific labelled data, online adaptation of the segmentation model is a natural complement to zero-shot inference. We propose CLoPA, a continual adaptation strategy that tunes a small fraction of nnInteractive's parameters on the annotation cache, triggered by lightweight episode scheduling. CLoPA requires no new parameters or changes to the inference pipeline, and operates entirely within the existing annotation workflow. Across eight Medical Segmentation Decathlon tasks spanning diverse anatomical targets and imaging characteristics, CLoPA rapidly elevates performance to expert-level, even for tasks where nnInteractive previously failed, with the majority of gains realised after a single training episode. We show that the benefits of tuning different parameter groups depends on task characteristics and data regimes. Also, that for targets with complex geometries (e.g., hepatic vessels), instance normalisation and low-level feature tuning saturates, suggesting a need for deeper feature-representation alignment in the most challenging scenarios. △ Less

Submitted 6 March, 2026; originally announced March 2026.

Comments: 10 pages, 2 figures

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

Authors: Mehmet Yigit Avci, Akshit Achara, Andrew King, Jorge Cardoso

Abstract: 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, obscurin… ▽ More 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. △ Less

Submitted 17 August, 2026; v1 submitted 4 March, 2026; originally announced March 2026.

ADAPT: Hybrid Prompt Optimization for LLM Feature Visualization

Authors: João N. Cardoso, Arlindo L. Oliveira, Bruno Martins

Abstract: Understanding what features are encoded by learned directions in LLM activation space requires identifying inputs that strongly activate them. Feature visualization, which optimizes inputs to maximally activate a target direction, offers an alternative to costly dataset search approaches, but remains underexplored for LLMs due to the discrete nature of text. Furthermore, existing prompt optimizati… ▽ More Understanding what features are encoded by learned directions in LLM activation space requires identifying inputs that strongly activate them. Feature visualization, which optimizes inputs to maximally activate a target direction, offers an alternative to costly dataset search approaches, but remains underexplored for LLMs due to the discrete nature of text. Furthermore, existing prompt optimization techniques are poorly suited to this domain, which is highly prone to local minima. To overcome these limitations, we introduce ADAPT, a hybrid method combining beam search initialization with adaptive gradient-guided mutation, designed around these failure modes. We evaluate on Sparse Autoencoder latents from Gemma 2 2B, proposing metrics grounded in dataset activation statistics to enable rigorous comparison, and show that ADAPT consistently outperforms prior methods across layers and latent types. Our results establish that feature visualization for LLMs is tractable, but requires design assumptions tailored to the domain. △ Less

Submitted 19 February, 2026; originally announced February 2026.

Performance uncertainty in medical image analysis: a large-scale investigation of confidence intervals

Authors: Pascaline André, Charles Heitz, Evangelia Christodoulou, Annika Reinke, Carole H. Sudre, Michela Antonelli, Patrick Godau, M. Jorge Cardoso, Antoine Gilson, Sophie Tezenas du Montcel, Gaël Varoquaux, Lena Maier-Hein, Olivier Colliot

Abstract: Performance uncertainty quantification is essential for reliable validation and eventual clinical translation of medical imaging artificial intelligence (AI). Confidence intervals (CIs) play a central role in this process by indicating how precise a reported performance estimate is. Yet, due to the limited amount of work examining CI behavior in medical imaging, the community remains largely unawa… ▽ More Performance uncertainty quantification is essential for reliable validation and eventual clinical translation of medical imaging artificial intelligence (AI). Confidence intervals (CIs) play a central role in this process by indicating how precise a reported performance estimate is. Yet, due to the limited amount of work examining CI behavior in medical imaging, the community remains largely unaware of how many diverse CI methods exist and how they behave in specific settings. The purpose of this study is to close this gap. To this end, we conducted a large-scale empirical analysis across a total of 24 segmentation and classification tasks, using 19 trained models per task group, a broad spectrum of commonly used performance metrics, multiple aggregation strategies, and several widely adopted CI methods. Reliability (coverage) and precision (width) of each CI method were estimated across all settings to characterize their dependence on study characteristics. Our analysis revealed five principal findings: 1) the sample size required for reliable CIs varies from a few dozens to several thousands of cases depending on study parameters; 2) CI behavior is strongly affected by the choice of performance metric; 3) aggregation strategy substantially influences the reliability of CIs, e.g. they require more observations for macro than for micro; 4) the machine learning problem (segmentation versus classification) modulates these effects; 5) different CI methods are not equally reliable and precise depending on the use case. These results form key components for the development of future guidelines on reporting performance uncertainty in medical imaging AI. △ Less

Submitted 23 January, 2026; originally announced January 2026.

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

Authors: Mehmet Yigit Avci, Pedro Borges, Virginia Fernandez, Paul Wright, Mehmet Yigitsoy, Sebastien Ourselin, Jorge Cardoso

Abstract: 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 biologic… ▽ More 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. △ Less

Submitted 8 December, 2025; originally announced December 2025.

Leveraging Adversarial Learning for Pathological Fidelity in Virtual Staining

Authors: José Teixeira, Pascal Klöckner, Diana Montezuma, Melis Erdal Cesur, João Fraga, Hugo M. Horlings, Jaime S. Cardoso, Sara P. Oliveira

Abstract: In addition to evaluating tumor morphology using H&E staining, immunohistochemistry is used to assess the presence of specific proteins within the tissue. However, this is a costly and labor-intensive technique, for which virtual staining, as an image-to-image translation task, offers a promising alternative. Although recent, this is an emerging field of research with 64% of published studies just… ▽ More In addition to evaluating tumor morphology using H&E staining, immunohistochemistry is used to assess the presence of specific proteins within the tissue. However, this is a costly and labor-intensive technique, for which virtual staining, as an image-to-image translation task, offers a promising alternative. Although recent, this is an emerging field of research with 64% of published studies just in 2024. Most studies use publicly available datasets of H&E-IHC pairs from consecutive tissue sections. Recognizing the training challenges, many authors develop complex virtual staining models based on conditional Generative Adversarial Networks, but ignore the impact of adversarial loss on the quality of virtual staining. Furthermore, overlooking the issues of model evaluation, they claim improved performance based on metrics such as SSIM and PSNR, which are not sufficiently robust to evaluate the quality of virtually stained images. In this paper, we developed CSSP2P GAN, which we demonstrate to achieve heightened pathological fidelity through a blind pathological expert evaluation. Furthermore, while iteratively developing our model, we study the impact of the adversarial loss and demonstrate its crucial role in the quality of virtually stained images. Finally, while comparing our model with reference works in the field, we underscore the limitations of the currently used evaluation metrics and demonstrate the superior performance of CSSP2P GAN. △ Less

Submitted 24 November, 2025; originally announced November 2025.

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

Authors: Natalia Glazman, Jyoti Mangal, Pedro Borges, Sebastien Ourselin, M. Jorge Cardoso

Abstract: 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 independ… ▽ More 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. △ Less

Submitted 6 November, 2025; originally announced November 2025.

Comments: Accepted to the NeurIPS 2025 Workshop on CauScien: Uncovering Causality in Science

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

Authors: Mehmet Yigit Avci, Pedro Borges, Virginia Fernandez, Paul Wright, Mehmet Yigitsoy, Sebastien Ourselin, Jorge Cardoso

Abstract: 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… ▽ More 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. △ Less

Submitted 1 November, 2025; originally announced November 2025.

A methodology for clinically driven interactive segmentation evaluation

Authors: Parhom Esmaeili, Virginia Fernandez, Pedro Borges, Eli Gibson, Sebastien Ourselin, M. Jorge Cardoso

Abstract: 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… ▽ More 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. △ Less

Submitted 10 October, 2025; originally announced October 2025.

Comments: 10 pages, Medical Image Computing and Computed Assisted Intervention 2025

Controllable Surface Diffusion Generative Model for Neurodevelopmental Trajectories

Authors: Zhenshan Xie, Levente Baljer, M. Jorge Cardoso, Emma Robinson

Abstract: Preterm birth disrupts the typical trajectory of cortical neurodevelopment, increasing the risk of cognitive and behavioral difficulties. However, outcomes vary widely, posing a significant challenge for early prediction. To address this, individualized simulation offers a promising solution by modeling subject-specific neurodevelopmental trajectories, enabling the identification of subtle deviati… ▽ More Preterm birth disrupts the typical trajectory of cortical neurodevelopment, increasing the risk of cognitive and behavioral difficulties. However, outcomes vary widely, posing a significant challenge for early prediction. To address this, individualized simulation offers a promising solution by modeling subject-specific neurodevelopmental trajectories, enabling the identification of subtle deviations from normative patterns that might act as biomarkers of risk. While generative models have shown potential for simulating neurodevelopment, prior approaches often struggle to preserve subject-specific cortical folding patterns or to reproduce region-specific morphological variations. In this paper, we present a novel graph-diffusion network that supports controllable simulation of cortical maturation. Using cortical surface data from the developing Human Connectome Project (dHCP), we demonstrate that the model maintains subject-specific cortical morphology while modeling cortical maturation sufficiently well to fool an independently trained age regression network, achieving a prediction accuracy of $0.85 \pm 0.62$. △ Less

Submitted 18 September, 2025; v1 submitted 21 July, 2025; originally announced August 2025.

Disentanglement and Assessment of Shortcuts in Ophthalmological Retinal Imaging Exams

Authors: Leonor Fernandes, Tiago Gonçalves, João Matos, Luis Filipe Nakayama, Jaime S. Cardoso

Abstract: Diabetic retinopathy (DR) is a leading cause of vision loss in working-age adults. While screening reduces the risk of blindness, traditional imaging is often costly and inaccessible. Artificial intelligence (AI) algorithms present a scalable diagnostic solution, but concerns regarding fairness and generalization persist. This work evaluates the fairness and performance of image-trained models in… ▽ More Diabetic retinopathy (DR) is a leading cause of vision loss in working-age adults. While screening reduces the risk of blindness, traditional imaging is often costly and inaccessible. Artificial intelligence (AI) algorithms present a scalable diagnostic solution, but concerns regarding fairness and generalization persist. This work evaluates the fairness and performance of image-trained models in DR prediction, as well as the impact of disentanglement as a bias mitigation technique, using the diverse mBRSET fundus dataset. Three models, ConvNeXt V2, DINOv2, and Swin V2, were trained on macula images to predict DR and sensitive attributes (SAs) (e.g., age and gender/sex). Fairness was assessed between subgroups of SAs, and disentanglement was applied to reduce bias. All models achieved high DR prediction performance in diagnosing (up to 94% AUROC) and could reasonably predict age and gender/sex (91% and 77% AUROC, respectively). Fairness assessment suggests disparities, such as a 10% AUROC gap between age groups in DINOv2. Disentangling SAs from DR prediction had varying results, depending on the model selected. Disentanglement improved DINOv2 performance (2% AUROC gain), but led to performance drops in ConvNeXt V2 and Swin V2 (7% and 3%, respectively). These findings highlight the complexity of disentangling fine-grained features in fundus imaging and emphasize the importance of fairness in medical imaging AI to ensure equitable and reliable healthcare solutions. △ Less

Submitted 13 July, 2025; originally announced July 2025.

Comments: 10 pages. Under review

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

Authors: Mehmet Yigit Avci, Pedro Borges, Paul Wright, Mehmet Yigitsoy, Sebastien Ourselin, Jorge Cardoso

Abstract: 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 onl… ▽ More 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. △ Less

Submitted 1 August, 2025; v1 submitted 23 June, 2025; originally announced July 2025.

GANs vs. Diffusion Models for virtual staining with the HER2match dataset

Authors: Pascal Klöckner, José Teixeira, Diana Montezuma, Jaime S. Cardoso, Hugo M. Horlings, Sara P. Oliveira

Abstract: Virtual staining is a promising technique that uses deep generative models to recreate histological stains, providing a faster and more cost-effective alternative to traditional tissue chemical staining. Specifically for H&E-HER2 staining transfer, despite a rising trend in publications, the lack of sufficient public datasets has hindered progress in the topic. Additionally, it is currently unclea… ▽ More Virtual staining is a promising technique that uses deep generative models to recreate histological stains, providing a faster and more cost-effective alternative to traditional tissue chemical staining. Specifically for H&E-HER2 staining transfer, despite a rising trend in publications, the lack of sufficient public datasets has hindered progress in the topic. Additionally, it is currently unclear which model frameworks perform best for this particular task. In this paper, we introduce the HER2match dataset, the first publicly available dataset with the same breast cancer tissue sections stained with both H&E and HER2. Furthermore, we compare the performance of several Generative Adversarial Networks (GANs) and Diffusion Models (DMs), and implement a novel Brownian Bridge Diffusion Model for H&E-HER2 translation. Our findings indicate that, overall, GANs perform better than DMs, with only the BBDM achieving comparable results. Furthermore, we emphasize the importance of data alignment, as all models trained on HER2match produced vastly improved visuals compared to the widely used consecutive-slide BCI dataset. This research provides a new high-quality dataset ([available upon publication acceptance]), improving both model training and evaluation. In addition, our comparison of frameworks offers valuable guidance for researchers working on the topic. △ Less

Submitted 23 June, 2025; originally announced June 2025.

Balancing Beyond Discrete Categories: Continuous Demographic Labels for Fair Face Recognition

Authors: Pedro C. Neto, Naser Damer, Jaime S. Cardoso, Ana F. Sequeira

Abstract: Bias has been a constant in face recognition models. Over the years, researchers have looked at it from both the model and the data point of view. However, their approach to mitigation of data bias was limited and lacked insight on the real nature of the problem. Here, in this document, we propose to revise our use of ethnicity labels as a continuous variable instead of a discrete value per identi… ▽ More Bias has been a constant in face recognition models. Over the years, researchers have looked at it from both the model and the data point of view. However, their approach to mitigation of data bias was limited and lacked insight on the real nature of the problem. Here, in this document, we propose to revise our use of ethnicity labels as a continuous variable instead of a discrete value per identity. We validate our formulation both experimentally and theoretically, showcasing that not all identities from one ethnicity contribute equally to the balance of the dataset; thus, having the same number of identities per ethnicity does not represent a balanced dataset. We further show that models trained on datasets balanced in the continuous space consistently outperform models trained on data balanced in the discrete space. We trained more than 65 different models, and created more than 20 subsets of the original datasets. △ Less

Submitted 6 June, 2025; v1 submitted 2 June, 2025; originally announced June 2025.

Comments: Under review

MAIS: Memory-Attention for Interactive Segmentation

Authors: Mauricio Orbes-Arteaga, Oeslle Lucena, Sabastien Ourselin, M. Jorge Cardoso

Abstract: Interactive medical segmentation reduces annotation effort by refining predictions through user feedback. Vision Transformer (ViT)-based models, such as the Segment Anything Model (SAM), achieve state-of-the-art performance using user clicks and prior masks as prompts. However, existing methods treat interactions as independent events, leading to redundant corrections and limited refinement gains.… ▽ More Interactive medical segmentation reduces annotation effort by refining predictions through user feedback. Vision Transformer (ViT)-based models, such as the Segment Anything Model (SAM), achieve state-of-the-art performance using user clicks and prior masks as prompts. However, existing methods treat interactions as independent events, leading to redundant corrections and limited refinement gains. We address this by introducing MAIS, a Memory-Attention mechanism for Interactive Segmentation that stores past user inputs and segmentation states, enabling temporal context integration. Our approach enhances ViT-based segmentation across diverse imaging modalities, achieving more efficient and accurate refinements. △ Less

Submitted 12 May, 2025; originally announced May 2025.

False Promises in Medical Imaging AI? Assessing Validity of Outperformance Claims

Authors: Evangelia Christodoulou, Annika Reinke, Pascaline Andrè, Patrick Godau, Piotr Kalinowski, Rola Houhou, Selen Erkan, Carole H. Sudre, Ninon Burgos, Sofiène Boutaj, Sophie Loizillon, Maëlys Solal, Veronika Cheplygina, Charles Heitz, Michal Kozubek, Michela Antonelli, Nicola Rieke, Antoine Gilson, Leon D. Mayer, Minu D. Tizabi, M. Jorge Cardoso, Amber Simpson, Annette Kopp-Schneider, Gaël Varoquaux, Olivier Colliot , et al. (1 additional authors not shown)

Abstract: Performance comparisons are fundamental in medical imaging Artificial Intelligence (AI) research, often driving claims of superiority based on relative improvements in common performance metrics. However, such claims frequently rely solely on empirical mean performance. In this paper, we investigate whether newly proposed methods genuinely outperform the state of the art by analyzing a representat… ▽ More Performance comparisons are fundamental in medical imaging Artificial Intelligence (AI) research, often driving claims of superiority based on relative improvements in common performance metrics. However, such claims frequently rely solely on empirical mean performance. In this paper, we investigate whether newly proposed methods genuinely outperform the state of the art by analyzing a representative cohort of medical imaging papers. We quantify the probability of false claims based on a Bayesian approach that leverages reported results alongside empirically estimated model congruence to estimate whether the relative ranking of methods is likely to have occurred by chance. According to our results, the majority (>80%) of papers claims outperformance when introducing a new method. Our analysis further revealed a high probability (>5%) of false outperformance claims in 86% of classification papers and 53% of segmentation papers. These findings highlight a critical flaw in current benchmarking practices: claims of outperformance in medical imaging AI are frequently unsubstantiated, posing a risk of misdirecting future research efforts. △ Less

Submitted 6 August, 2025; v1 submitted 7 May, 2025; originally announced May 2025.

CountPath: Automating Fragment Counting in Digital Pathology

Authors: Ana Beatriz Vieira, Maria Valente, Diana Montezuma, Tomé Albuquerque, Liliana Ribeiro, Domingos Oliveira, João Monteiro, Sofia Gonçalves, Isabel M. Pinto, Jaime S. Cardoso, Arlindo L. Oliveira

Abstract: Quality control of medical images is a critical component of digital pathology, ensuring that diagnostic images meet required standards. A pre-analytical task within this process is the verification of the number of specimen fragments, a process that ensures that the number of fragments on a slide matches the number documented in the macroscopic report. This step is important to ensure that the sl… ▽ More Quality control of medical images is a critical component of digital pathology, ensuring that diagnostic images meet required standards. A pre-analytical task within this process is the verification of the number of specimen fragments, a process that ensures that the number of fragments on a slide matches the number documented in the macroscopic report. This step is important to ensure that the slides contain the appropriate diagnostic material from the grossing process, thereby guaranteeing the accuracy of subsequent microscopic examination and diagnosis. Traditionally, this assessment is performed manually, requiring significant time and effort while being subject to significant variability due to its subjective nature. To address these challenges, this study explores an automated approach to fragment counting using the YOLOv9 and Vision Transformer models. Our results demonstrate that the automated system achieves a level of performance comparable to expert assessments, offering a reliable and efficient alternative to manual counting. Additionally, we present findings on interobserver variability, showing that the automated approach achieves an accuracy of 86%, which falls within the range of variation observed among experts (82-88%), further supporting its potential for integration into routine pathology workflows. △ Less

Submitted 13 March, 2025; originally announced March 2025.

Comments: 10 pages, 3 figures

ACM Class: I.2; I.4

Resolution Invariant Autoencoder

Authors: Ashay Patel, Michela Antonelli, Sebastien Ourselin, M. Jorge Cardoso

Abstract: 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 r… ▽ More 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. △ Less

Submitted 12 March, 2025; originally announced March 2025.

Comments: 6 pages, 3 figures, preprint of paper submitted to MICCAI conference

Generalizable automated ischaemic stroke lesion segmentation with vision transformers

Authors: Chris Foulon, Robert Gray, James K. Ruffle, Jonathan Best, Tianbo Xu, Henry Watkins, Jane Rondina, Guilherme Pombo, Dominic Giles, Paul Wright, Marcela Ovando-Tellez, H. Rolf Jäger, Jorge Cardoso, Sebastien Ourselin, Geraint Rees, Parashkev Nachev

Abstract: 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 sig… ▽ More 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. △ Less

Submitted 10 February, 2025; originally announced February 2025.

Comments: 29 pages, 7 figures, 2 tables, 1 supplementary table, 2 supplementary figures

An inpainting approach to manipulate asymmetry in pre-operative breast images

Authors: Helena Montenegro, Maria J. Cardoso, Jaime S. Cardoso

Abstract: One of the most frequent modalities of breast cancer treatment is surgery. Breast surgery can cause visual alterations to the breasts, due to scars and asymmetries. To enable an informed choice of treatment, the patient must be adequately informed of the aesthetic outcomes of each treatment plan. In this work, we propose an inpainting approach to manipulate breast shape and nipple position in brea… ▽ More One of the most frequent modalities of breast cancer treatment is surgery. Breast surgery can cause visual alterations to the breasts, due to scars and asymmetries. To enable an informed choice of treatment, the patient must be adequately informed of the aesthetic outcomes of each treatment plan. In this work, we propose an inpainting approach to manipulate breast shape and nipple position in breast images, for the purpose of predicting the aesthetic outcomes of breast cancer treatment. We perform experiments with various model architectures for the inpainting task, including invertible networks capable of manipulating breasts in the absence of ground-truth breast contour and nipple annotations. Experiments on two breast datasets show the proposed models' ability to realistically alter a patient's breasts, enabling a faithful reproduction of breast asymmetries of post-operative patients in pre-operative images. △ Less

Submitted 8 February, 2025; originally announced February 2025.

Comments: Preprint

MSC Class: 68T45

Deep generative computed perfusion-deficit mapping of ischaemic stroke

Authors: Chayanin Tangwiriyasakul, Pedro Borges, Guilherme Pombo, Stefano Moriconi, Michael S. Elmalem, Paul Wright, Yee-Haur Mah, Jane Rondina, Sebastien Ourselin, Parashkev Nachev, M. Jorge Cardoso

Abstract: Focal deficits in ischaemic stroke result from impaired perfusion downstream of a critical vascular occlusion. While parenchymal lesions are traditionally used to predict clinical deficits, the underlying pattern of disrupted perfusion provides information upstream of the lesion, potentially yielding earlier predictive and localizing signals. Such perfusion maps can be derived from routine CT angi… ▽ More Focal deficits in ischaemic stroke result from impaired perfusion downstream of a critical vascular occlusion. While parenchymal lesions are traditionally used to predict clinical deficits, the underlying pattern of disrupted perfusion provides information upstream of the lesion, potentially yielding earlier predictive and localizing signals. Such perfusion maps can be derived from routine CT angiography (CTA) widely deployed in clinical practice. Analysing computed perfusion maps from 1,393 CTA-imaged-patients with acute ischaemic stroke, we use deep generative inference to localise neural substrates of NIHSS sub-scores. We show that our approach replicates known lesion-deficit relations without knowledge of the lesion itself and reveals novel neural dependents. The high achieved anatomical fidelity suggests acute CTA-derived computed perfusion maps may be of substantial clinical-and-scientific value in rich phenotyping of acute stroke. Using only hyperacute imaging, deep generative inference could power highly expressive models of functional anatomical relations in ischaemic stroke within the pre-interventional window. △ Less

Submitted 1 March, 2026; v1 submitted 3 February, 2025; originally announced February 2025.

CBVLM: Training-free Explainable Concept-based Large Vision Language Models for Medical Image Classification

Authors: Cristiano Patrício, Isabel Rio-Torto, Jaime S. Cardoso, Luís F. Teixeira, João C. Neves

Abstract: The main challenges limiting the adoption of deep learning-based solutions in medical workflows are the availability of annotated data and the lack of interpretability of such systems. Concept Bottleneck Models (CBMs) tackle the latter by constraining the model output on a set of predefined and human-interpretable concepts. However, the increased interpretability achieved through these concept-bas… ▽ More The main challenges limiting the adoption of deep learning-based solutions in medical workflows are the availability of annotated data and the lack of interpretability of such systems. Concept Bottleneck Models (CBMs) tackle the latter by constraining the model output on a set of predefined and human-interpretable concepts. However, the increased interpretability achieved through these concept-based explanations implies a higher annotation burden. Moreover, if a new concept needs to be added, the whole system needs to be retrained. Inspired by the remarkable performance shown by Large Vision-Language Models (LVLMs) in few-shot settings, we propose a simple, yet effective, methodology, CBVLM, which tackles both of the aforementioned challenges. First, for each concept, we prompt the LVLM to answer if the concept is present in the input image. Then, we ask the LVLM to classify the image based on the previous concept predictions. Moreover, in both stages, we incorporate a retrieval module responsible for selecting the best examples for in-context learning. By grounding the final diagnosis on the predicted concepts, we ensure explainability, and by leveraging the few-shot capabilities of LVLMs, we drastically lower the annotation cost. We validate our approach with extensive experiments across four medical datasets and twelve LVLMs (both generic and medical) and show that CBVLM consistently outperforms CBMs and task-specific supervised methods without requiring any training and using just a few annotated examples. More information on our project page: https://cristianopatricio.github.io/CBVLM/. △ Less

Submitted 6 October, 2025; v1 submitted 21 January, 2025; originally announced January 2025.

Comments: Accepted for publication in Computers in Biology and Medicine

Improving Sickle Cell Disease Classification: A Fusion of Conventional Classifiers, Segmented Images, and Convolutional Neural Networks

Authors: Victor Júnio Alcântara Cardoso, Rodrigo Moreira, João Fernando Mari, Larissa Ferreira Rodrigues Moreira

Abstract: Sickle cell anemia, which is characterized by abnormal erythrocyte morphology, can be detected using microscopic images. Computational techniques in medicine enhance the diagnosis and treatment efficiency. However, many computational techniques, particularly those based on Convolutional Neural Networks (CNNs), require high resources and time for training, highlighting the research opportunities in… ▽ More Sickle cell anemia, which is characterized by abnormal erythrocyte morphology, can be detected using microscopic images. Computational techniques in medicine enhance the diagnosis and treatment efficiency. However, many computational techniques, particularly those based on Convolutional Neural Networks (CNNs), require high resources and time for training, highlighting the research opportunities in methods with low computational overhead. In this paper, we propose a novel approach combining conventional classifiers, segmented images, and CNNs for the automated classification of sickle cell disease. We evaluated the impact of segmented images on classification, providing insight into deep learning integration. Our results demonstrate that using segmented images and CNN features with an SVM achieves an accuracy of 96.80%. This finding is relevant for computationally efficient scenarios, paving the way for future research and advancements in medical-image analysis. △ Less

Submitted 23 December, 2024; originally announced December 2024.

Comments: 14 pages

Journal ref: Encontro Nacional de Inteligência Artificial e Computacional (ENIAC) 2023

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

Authors: Zi Yang, Haojin Yang, Soumajit Majumder, Jorge Cardoso, Guillermo Gallego

Abstract: 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.… ▽ More 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. △ Less

Submitted 13 December, 2024; originally announced December 2024.

Journal ref: Transactions on Machine Learning Research - 2024

Command-line Risk Classification using Transformer-based Neural Architectures

Authors: Paolo Notaro, Soroush Haeri, Jorge Cardoso, Michael Gerndt

Abstract: 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 dam… ▽ More 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. △ Less

Submitted 2 December, 2024; originally announced December 2024.

Second FRCSyn-onGoing: Winning Solutions and Post-Challenge Analysis to Improve Face Recognition with Synthetic Data

Authors: Ivan DeAndres-Tame, Ruben Tolosana, Pietro Melzi, Ruben Vera-Rodriguez, Minchul Kim, Christian Rathgeb, Xiaoming Liu, Luis F. Gomez, Aythami Morales, Julian Fierrez, Javier Ortega-Garcia, Zhizhou Zhong, Yuge Huang, Yuxi Mi, Shouhong Ding, Shuigeng Zhou, Shuai He, Lingzhi Fu, Heng Cong, Rongyu Zhang, Zhihong Xiao, Evgeny Smirnov, Anton Pimenov, Aleksei Grigorev, Denis Timoshenko , et al. (34 additional authors not shown)

Abstract: Synthetic data is gaining increasing popularity for face recognition technologies, mainly due to the privacy concerns and challenges associated with obtaining real data, including diverse scenarios, quality, and demographic groups, among others. It also offers some advantages over real data, such as the large amount of data that can be generated or the ability to customize it to adapt to specific… ▽ More Synthetic data is gaining increasing popularity for face recognition technologies, mainly due to the privacy concerns and challenges associated with obtaining real data, including diverse scenarios, quality, and demographic groups, among others. It also offers some advantages over real data, such as the large amount of data that can be generated or the ability to customize it to adapt to specific problem-solving needs. To effectively use such data, face recognition models should also be specifically designed to exploit synthetic data to its fullest potential. In order to promote the proposal of novel Generative AI methods and synthetic data, and investigate the application of synthetic data to better train face recognition systems, we introduce the 2nd FRCSyn-onGoing challenge, based on the 2nd Face Recognition Challenge in the Era of Synthetic Data (FRCSyn), originally launched at CVPR 2024. This is an ongoing challenge that provides researchers with an accessible platform to benchmark i) the proposal of novel Generative AI methods and synthetic data, and ii) novel face recognition systems that are specifically proposed to take advantage of synthetic data. We focus on exploring the use of synthetic data both individually and in combination with real data to solve current challenges in face recognition such as demographic bias, domain adaptation, and performance constraints in demanding situations, such as age disparities between training and testing, changes in the pose, or occlusions. Very interesting findings are obtained in this second edition, including a direct comparison with the first one, in which synthetic databases were restricted to DCFace and GANDiffFace. △ Less

Submitted 10 March, 2025; v1 submitted 2 December, 2024; originally announced December 2024.

Comments: Accepted in Information Fusion

Classification of Keratitis from Eye Corneal Photographs using Deep Learning

Authors: Maria Miguel Beirão, João Matos, Tiago Gonçalves, Camila Kase, Luis Filipe Nakayama, Denise de Freitas, Jaime S. Cardoso

Abstract: Keratitis is an inflammatory corneal condition responsible for 10% of visual impairment in low- and middle-income countries (LMICs), with bacteria, fungi, or amoeba as the most common infection etiologies. While an accurate and timely diagnosis is crucial for the selected treatment and the patients' sight outcomes, due to the high cost and limited availability of laboratory diagnostics in LMICs, d… ▽ More Keratitis is an inflammatory corneal condition responsible for 10% of visual impairment in low- and middle-income countries (LMICs), with bacteria, fungi, or amoeba as the most common infection etiologies. While an accurate and timely diagnosis is crucial for the selected treatment and the patients' sight outcomes, due to the high cost and limited availability of laboratory diagnostics in LMICs, diagnosis is often made by clinical observation alone, despite its lower accuracy. In this study, we investigate and compare different deep learning approaches to diagnose the source of infection: 1) three separate binary models for infection type predictions; 2) a multitask model with a shared backbone and three parallel classification layers (Multitask V1); and, 3) a multitask model with a shared backbone and a multi-head classification layer (Multitask V2). We used a private Brazilian cornea dataset to conduct the empirical evaluation. We achieved the best results with Multitask V2, with an area under the receiver operating characteristic curve (AUROC) confidence intervals of 0.7413-0.7740 (bacteria), 0.8395-0.8725 (fungi), and 0.9448-0.9616 (amoeba). A statistical analysis of the impact of patient features on models' performance revealed that sex significantly affects amoeba infection prediction, and age seems to affect fungi and bacteria predictions. △ Less

Submitted 13 November, 2024; originally announced November 2024.

Comments: 6 pages; Accepted at IEEE's International Conference on Bioinformatics and Biomedicine (2024)

Confidence intervals uncovered: Are we ready for real-world medical imaging AI?

Authors: Evangelia Christodoulou, Annika Reinke, Rola Houhou, Piotr Kalinowski, Selen Erkan, Carole H. Sudre, Ninon Burgos, Sofiène Boutaj, Sophie Loizillon, Maëlys Solal, Nicola Rieke, Veronika Cheplygina, Michela Antonelli, Leon D. Mayer, Minu D. Tizabi, M. Jorge Cardoso, Amber Simpson, Paul F. Jäger, Annette Kopp-Schneider, Gaël Varoquaux, Olivier Colliot, Lena Maier-Hein

Abstract: Medical imaging is spearheading the AI transformation of healthcare. Performance reporting is key to determine which methods should be translated into clinical practice. Frequently, broad conclusions are simply derived from mean performance values. In this paper, we argue that this common practice is often a misleading simplification as it ignores performance variability. Our contribution is three… ▽ More Medical imaging is spearheading the AI transformation of healthcare. Performance reporting is key to determine which methods should be translated into clinical practice. Frequently, broad conclusions are simply derived from mean performance values. In this paper, we argue that this common practice is often a misleading simplification as it ignores performance variability. Our contribution is threefold. (1) Analyzing all MICCAI segmentation papers (n = 221) published in 2023, we first observe that more than 50% of papers do not assess performance variability at all. Moreover, only one (0.5%) paper reported confidence intervals (CIs) for model performance. (2) To address the reporting bottleneck, we show that the unreported standard deviation (SD) in segmentation papers can be approximated by a second-order polynomial function of the mean Dice similarity coefficient (DSC). Based on external validation data from 56 previous MICCAI challenges, we demonstrate that this approximation can accurately reconstruct the CI of a method using information provided in publications. (3) Finally, we reconstructed 95% CIs around the mean DSC of MICCAI 2023 segmentation papers. The median CI width was 0.03 which is three times larger than the median performance gap between the first and second ranked method. For more than 60% of papers, the mean performance of the second-ranked method was within the CI of the first-ranked method. We conclude that current publications typically do not provide sufficient evidence to support which models could potentially be translated into clinical practice. △ Less

Submitted 27 September, 2024; v1 submitted 26 September, 2024; originally announced September 2024.

Comments: Paper accepted at MICCAI 2024 conference

MST-KD: Multiple Specialized Teachers Knowledge Distillation for Fair Face Recognition

Authors: Eduarda Caldeira, Jaime S. Cardoso, Ana F. Sequeira, Pedro C. Neto

Abstract: As in school, one teacher to cover all subjects is insufficient to distill equally robust information to a student. Hence, each subject is taught by a highly specialised teacher. Following a similar philosophy, we propose a multiple specialized teacher framework to distill knowledge to a student network. In our approach, directed at face recognition use cases, we train four teachers on one specifi… ▽ More As in school, one teacher to cover all subjects is insufficient to distill equally robust information to a student. Hence, each subject is taught by a highly specialised teacher. Following a similar philosophy, we propose a multiple specialized teacher framework to distill knowledge to a student network. In our approach, directed at face recognition use cases, we train four teachers on one specific ethnicity, leading to four highly specialized and biased teachers. Our strategy learns a project of these four teachers into a common space and distill that information to a student network. Our results highlighted increased performance and reduced bias for all our experiments. In addition, we further show that having biased/specialized teachers is crucial by showing that our approach achieves better results than when knowledge is distilled from four teachers trained on balanced datasets. Our approach represents a step forward to the understanding of the importance of ethnicity-specific features. △ Less

Submitted 29 August, 2024; originally announced August 2024.

Comments: Accepted at ECCV 2024 ABAW

Evaluating the Impact of Pulse Oximetry Bias in Machine Learning under Counterfactual Thinking

Authors: Inês Martins, João Matos, Tiago Gonçalves, Leo A. Celi, A. Ian Wong, Jaime S. Cardoso

Abstract: Algorithmic bias in healthcare mirrors existing data biases. However, the factors driving unfairness are not always known. Medical devices capture significant amounts of data but are prone to errors; for instance, pulse oximeters overestimate the arterial oxygen saturation of darker-skinned individuals, leading to worse outcomes. The impact of this bias in machine learning (ML) models remains uncl… ▽ More Algorithmic bias in healthcare mirrors existing data biases. However, the factors driving unfairness are not always known. Medical devices capture significant amounts of data but are prone to errors; for instance, pulse oximeters overestimate the arterial oxygen saturation of darker-skinned individuals, leading to worse outcomes. The impact of this bias in machine learning (ML) models remains unclear. This study addresses the technical challenges of quantifying the impact of medical device bias in downstream ML. Our experiments compare a "perfect world", without pulse oximetry bias, using SaO2 (blood-gas), to the "actual world", with biased measurements, using SpO2 (pulse oximetry). Under this counterfactual design, two models are trained with identical data, features, and settings, except for the method of measuring oxygen saturation: models using SaO2 are a "control" and models using SpO2 a "treatment". The blood-gas oximetry linked dataset was a suitable test-bed, containing 163,396 nearly-simultaneous SpO2 - SaO2 paired measurements, aligned with a wide array of clinical features and outcomes. We studied three classification tasks: in-hospital mortality, respiratory SOFA score in the next 24 hours, and SOFA score increase by two points. Models using SaO2 instead of SpO2 generally showed better performance. Patients with overestimation of O2 by pulse oximetry of > 3% had significant decreases in mortality prediction recall, from 0.63 to 0.59, P < 0.001. This mirrors clinical processes where biased pulse oximetry readings provide clinicians with false reassurance of patients' oxygen levels. A similar degradation happened in ML models, with pulse oximetry biases leading to more false negatives in predicting adverse outcomes. △ Less

Submitted 8 August, 2024; originally announced August 2024.

Comments: 10 pages; accepted at MICCAI's Third Workshop on Applications of Medical AI (2024)

Learning Ordinality in Semantic Segmentation

Authors: Ricardo P. M. Cruz, Rafael Cristino, Jaime S. Cardoso

Abstract: Semantic segmentation consists of predicting a semantic label for each image pixel. While existing deep learning approaches achieve high accuracy, they often overlook the ordinal relationships between classes, which can provide critical domain knowledge (e.g., the pupil lies within the iris, and lane markings are part of the road). This paper introduces novel methods for spatial ordinal segmentati… ▽ More Semantic segmentation consists of predicting a semantic label for each image pixel. While existing deep learning approaches achieve high accuracy, they often overlook the ordinal relationships between classes, which can provide critical domain knowledge (e.g., the pupil lies within the iris, and lane markings are part of the road). This paper introduces novel methods for spatial ordinal segmentation that explicitly incorporate these inter-class dependencies. By treating each pixel as part of a structured image space rather than as an independent observation, we propose two regularization terms and a new metric to enforce ordinal consistency between neighboring pixels. Two loss regularization terms and one metric are proposed for structural ordinal segmentation, which penalizes predictions of non-ordinal adjacent classes. Five biomedical datasets and multiple configurations of autonomous driving datasets demonstrate the efficacy of the proposed methods. Our approach achieves improvements in ordinal metrics and enhances generalization, with up to a 15.7% relative increase in the Dice coefficient. Importantly, these benefits come without additional inference time costs. This work highlights the significance of spatial ordinal relationships in semantic segmentation and provides a foundation for further exploration in structured image representations. △ Less

Submitted 5 February, 2025; v1 submitted 30 July, 2024; originally announced July 2024.

Comments: 13 pages

Journal ref: IEEE Access (2025)

A Survey on Cell Nuclei Instance Segmentation and Classification: Leveraging Context and Attention

Authors: João D. Nunes, Diana Montezuma, Domingos Oliveira, Tania Pereira, Jaime S. Cardoso

Abstract: Manually annotating nuclei from the gigapixel Hematoxylin and Eosin (H&E)-stained Whole Slide Images (WSIs) is a laborious and costly task, meaning automated algorithms for cell nuclei instance segmentation and classification could alleviate the workload of pathologists and clinical researchers and at the same time facilitate the automatic extraction of clinically interpretable features. But due t… ▽ More Manually annotating nuclei from the gigapixel Hematoxylin and Eosin (H&E)-stained Whole Slide Images (WSIs) is a laborious and costly task, meaning automated algorithms for cell nuclei instance segmentation and classification could alleviate the workload of pathologists and clinical researchers and at the same time facilitate the automatic extraction of clinically interpretable features. But due to high intra- and inter-class variability of nuclei morphological and chromatic features, as well as H&E-stains susceptibility to artefacts, state-of-the-art algorithms cannot correctly detect and classify instances with the necessary performance. In this work, we hypothesise context and attention inductive biases in artificial neural networks (ANNs) could increase the generalization of algorithms for cell nuclei instance segmentation and classification. We conduct a thorough survey on context and attention methods for cell nuclei instance segmentation and classification from H&E-stained microscopy imaging, while providing a comprehensive discussion of the challenges being tackled with context and attention. Besides, we illustrate some limitations of current approaches and present ideas for future research. As a case study, we extend both a general instance segmentation and classification method (Mask-RCNN) and a tailored cell nuclei instance segmentation and classification model (HoVer-Net) with context- and attention-based mechanisms, and do a comparative analysis on a multi-centre colon nuclei identification and counting dataset. Although pathologists rely on context at multiple levels while paying attention to specific Regions of Interest (RoIs) when analysing and annotating WSIs, our findings suggest translating that domain knowledge into algorithm design is no trivial task, but to fully exploit these mechanisms, the scientific understanding of these methods should be addressed. △ Less

Submitted 26 July, 2024; originally announced July 2024.

Investigating Memory Failure Prediction Across CPU Architectures

Authors: Qiao Yu, Wengui Zhang, Min Zhou, Jialiang Yu, Zhenli Sheng, Jasmin Bogatinovski, Jorge Cardoso, Odej Kao

Abstract: 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… ▽ More 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. △ Less

Submitted 8 June, 2024; originally announced June 2024.

Comments: Accepted by 2024 54th Annual IEEE/IFIP International Conference on Dependable Systems and Networks (DSN), Industry Track

Journal ref: 2024 54th Annual IEEE/IFIP International Conference on Dependable Systems and Networks - Supplemental Volume (DSN-S)

AutoNet: Automatic Reachability Policy Management in Public Cloud Networks

Authors: German Sviridov, Zheng Tao Shen, Jorge Cardoso

Abstract: 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,… ▽ More 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. △ Less

Submitted 30 April, 2024; originally announced April 2024.

On Software Ageing Indicators in OpenStack

Authors: Yevhen Yazvinskyi, Jasmin Bogatinovski, Jorge Cardoso, Odej Kao

Abstract: 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 increas… ▽ More 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. △ Less

Submitted 25 April, 2024; originally announced April 2024.

Deep Learning-based Prediction of Breast Cancer Tumor and Immune Phenotypes from Histopathology

Authors: Tiago Gonçalves, Dagoberto Pulido-Arias, Julian Willett, Katharina V. Hoebel, Mason Cleveland, Syed Rakin Ahmed, Elizabeth Gerstner, Jayashree Kalpathy-Cramer, Jaime S. Cardoso, Christopher P. Bridge, Albert E. Kim

Abstract: The interactions between tumor cells and the tumor microenvironment (TME) dictate therapeutic efficacy of radiation and many systemic therapies in breast cancer. However, to date, there is not a widely available method to reproducibly measure tumor and immune phenotypes for each patient's tumor. Given this unmet clinical need, we applied multiple instance learning (MIL) algorithms to assess activi… ▽ More The interactions between tumor cells and the tumor microenvironment (TME) dictate therapeutic efficacy of radiation and many systemic therapies in breast cancer. However, to date, there is not a widely available method to reproducibly measure tumor and immune phenotypes for each patient's tumor. Given this unmet clinical need, we applied multiple instance learning (MIL) algorithms to assess activity of ten biologically relevant pathways from the hematoxylin and eosin (H&E) slide of primary breast tumors. We employed different feature extraction approaches and state-of-the-art model architectures. Using binary classification, our models attained area under the receiver operating characteristic (AUROC) scores above 0.70 for nearly all gene expression pathways and on some cases, exceeded 0.80. Attention maps suggest that our trained models recognize biologically relevant spatial patterns of cell sub-populations from H&E. These efforts represent a first step towards developing computational H&E biomarkers that reflect facets of the TME and hold promise for augmenting precision oncology. △ Less

Submitted 25 April, 2024; originally announced April 2024.

Comments: Paper accepted at the First Workshop on Imageomics (Imageomics-AAAI-24) - Discovering Biological Knowledge from Images using AI (https://sites.google.com/vt.edu/imageomics-aaai-24/home), held as part of the 38th Annual AAAI Conference on Artificial Intelligence (https://aaai.org/aaai-conference/)

MSC Class: 92C55 ACM Class: I.5.1; I.5.4; I.2.10; J.3

Second Edition FRCSyn Challenge at CVPR 2024: Face Recognition Challenge in the Era of Synthetic Data

Authors: Ivan DeAndres-Tame, Ruben Tolosana, Pietro Melzi, Ruben Vera-Rodriguez, Minchul Kim, Christian Rathgeb, Xiaoming Liu, Aythami Morales, Julian Fierrez, Javier Ortega-Garcia, Zhizhou Zhong, Yuge Huang, Yuxi Mi, Shouhong Ding, Shuigeng Zhou, Shuai He, Lingzhi Fu, Heng Cong, Rongyu Zhang, Zhihong Xiao, Evgeny Smirnov, Anton Pimenov, Aleksei Grigorev, Denis Timoshenko, Kaleb Mesfin Asfaw , et al. (33 additional authors not shown)

Abstract: Synthetic data is gaining increasing relevance for training machine learning models. This is mainly motivated due to several factors such as the lack of real data and intra-class variability, time and errors produced in manual labeling, and in some cases privacy concerns, among others. This paper presents an overview of the 2nd edition of the Face Recognition Challenge in the Era of Synthetic Data… ▽ More Synthetic data is gaining increasing relevance for training machine learning models. This is mainly motivated due to several factors such as the lack of real data and intra-class variability, time and errors produced in manual labeling, and in some cases privacy concerns, among others. This paper presents an overview of the 2nd edition of the Face Recognition Challenge in the Era of Synthetic Data (FRCSyn) organized at CVPR 2024. FRCSyn aims to investigate the use of synthetic data in face recognition to address current technological limitations, including data privacy concerns, demographic biases, generalization to novel scenarios, and performance constraints in challenging situations such as aging, pose variations, and occlusions. Unlike the 1st edition, in which synthetic data from DCFace and GANDiffFace methods was only allowed to train face recognition systems, in this 2nd edition we propose new sub-tasks that allow participants to explore novel face generative methods. The outcomes of the 2nd FRCSyn Challenge, along with the proposed experimental protocol and benchmarking contribute significantly to the application of synthetic data to face recognition. △ Less

Submitted 16 April, 2024; originally announced April 2024.

Comments: arXiv admin note: text overlap with arXiv:2311.10476

Journal ref: IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRw 2024)

Framework to generate perfusion map from CT and CTA images in patients with acute ischemic stroke: A longitudinal and cross-sectional study

Authors: Chayanin Tangwiriyasakul, Pedro Borges, Stefano Moriconi, Paul Wright, Yee-Haur Mah, James Teo, Parashkev Nachev, Sebastien Ourselin, M. Jorge Cardoso

Abstract: Stroke is a leading cause of disability and death. Effective treatment decisions require early and informative vascular imaging. 4D perfusion imaging is ideal but rarely available within the first hour after stroke, whereas plain CT and CTA usually are. Hence, we propose a framework to extract a predicted perfusion map (PPM) derived from CT and CTA images. In all eighteen patients, we found signif… ▽ More Stroke is a leading cause of disability and death. Effective treatment decisions require early and informative vascular imaging. 4D perfusion imaging is ideal but rarely available within the first hour after stroke, whereas plain CT and CTA usually are. Hence, we propose a framework to extract a predicted perfusion map (PPM) derived from CT and CTA images. In all eighteen patients, we found significantly high spatial similarity (with average Spearman's correlation = 0.7893) between our predicted perfusion map (PPM) and the T-max map derived from 4D-CTP. Voxelwise correlations between the PPM and National Institutes of Health Stroke Scale (NIHSS) subscores for L/R hand motor, gaze, and language on a large cohort of 2,110 subjects reliably mapped symptoms to expected infarct locations. Therefore our PPM could serve as an alternative for 4D perfusion imaging, if the latter is unavailable, to investigate blood perfusion in the first hours after hospital admission. △ Less

Submitted 5 April, 2024; originally announced April 2024.

Comments: Accepted and presented in SWITCH2023: Stroke Workshop on Imaging and Treatment CHallenges (MICCAI 2023, Vancouver Canada)

Impact of Employing Weather Forecast Data as Input to the Estimation of Evapotranspiration by Deep Neural Network Models

Authors: Pedro J. Vaz, Gabriela Schütz, Carlos Guerrero, Pedro J. S. Cardoso

Abstract: Reference Evapotranspiration (ET0) is a key parameter for designing smart irrigation scheduling, since it is related by a coefficient to the water needs of a crop. The United Nations Food and Agriculture Organization, proposed a standard method for ET0 computation (FAO56PM), based on the parameterization of the Penman-Monteith equation, that is widely adopted in the literature. To compute ET0 usin… ▽ More Reference Evapotranspiration (ET0) is a key parameter for designing smart irrigation scheduling, since it is related by a coefficient to the water needs of a crop. The United Nations Food and Agriculture Organization, proposed a standard method for ET0 computation (FAO56PM), based on the parameterization of the Penman-Monteith equation, that is widely adopted in the literature. To compute ET0 using the FAO56-PM method, four main weather parameters are needed: temperature, humidity, wind, and solar radiation (SR). One way to make daily ET0 estimations for future days is to use freely available weather forecast services (WFSs), where many meteorological parameters are estimated up to the next 15 days. A problem with this method is that currently, SR is not provided as a free forecast parameter on most of those online services or, normally, such forecasts present a financial cost penalty. For this reason, several ET0 estimation models using machine and deep learning were developed and presented in the literature, that use as input features a reduced set of carefully selected weather parameters, that are compatible with common freely available WFSs. However, most studies on this topic have only evaluated model performance using data from weather stations (WSs), without considering the effect of using weather forecast data. In this study, the performance of authors' previous models is evaluated when using weather forecast data from two online WFSs, in the following scenarios: (i) direct ET0 estimation by an ANN model, and (ii) estimate SR by ANN model, and then use that estimation for ET0 computation, using the FAO56-PM method. Employing data collected from two WFSs and a WS located in Vale do Lobo, Portugal, the latter approach achieved the best result, with a coefficient of determination (R2) ranging between 0.893 and 0.667, when considering forecasts up to 15 days. △ Less

Submitted 27 March, 2024; originally announced March 2024.

Comments: A partial version of the work submitted to ESRE/INTERNATIONAL CONFERENCE ON ENVIRONMENTAL SCIENCES AND RENEWABLE ENERGY

Cortical Surface Diffusion Generative Models

Authors: Zhenshan Xie, Simon Dahan, Logan Z. J. Williams, M. Jorge Cardoso, Emma C. Robinson

Abstract: Cortical surface analysis has gained increased prominence, given its potential implications for neurological and developmental disorders. Traditional vision diffusion models, while effective in generating natural images, present limitations in capturing intricate development patterns in neuroimaging due to limited datasets. This is particularly true for generating cortical surfaces where individua… ▽ More Cortical surface analysis has gained increased prominence, given its potential implications for neurological and developmental disorders. Traditional vision diffusion models, while effective in generating natural images, present limitations in capturing intricate development patterns in neuroimaging due to limited datasets. This is particularly true for generating cortical surfaces where individual variability in cortical morphology is high, leading to an urgent need for better methods to model brain development and diverse variability inherent across different individuals. In this work, we proposed a novel diffusion model for the generation of cortical surface metrics, using modified surface vision transformers as the principal architecture. We validate our method in the developing Human Connectome Project (dHCP), the results suggest our model demonstrates superior performance in capturing the intricate details of evolving cortical surfaces. Furthermore, our model can generate high-quality realistic samples of cortical surfaces conditioned on postmenstrual age(PMA) at scan. △ Less

Submitted 7 February, 2024; originally announced February 2024.

Comments: 4 pages

Re:Draw -- Context Aware Translation as a Controllable Method for Artistic Production

Authors: Joao Liborio Cardoso, Francesco Banterle, Paolo Cignoni, Michael Wimmer

Abstract: We introduce context-aware translation, a novel method that combines the benefits of inpainting and image-to-image translation, respecting simultaneously the original input and contextual relevance -- where existing methods fall short. By doing so, our method opens new avenues for the controllable use of AI within artistic creation, from animation to digital art. As an use case, we apply our met… ▽ More We introduce context-aware translation, a novel method that combines the benefits of inpainting and image-to-image translation, respecting simultaneously the original input and contextual relevance -- where existing methods fall short. By doing so, our method opens new avenues for the controllable use of AI within artistic creation, from animation to digital art. As an use case, we apply our method to redraw any hand-drawn animated character eyes based on any design specifications - eyes serve as a focal point that captures viewer attention and conveys a range of emotions, however, the labor-intensive nature of traditional animation often leads to compromises in the complexity and consistency of eye design. Furthermore, we remove the need for production data for training and introduce a new character recognition method that surpasses existing work by not requiring fine-tuning to specific productions. This proposed use case could help maintain consistency throughout production and unlock bolder and more detailed design choices without the production cost drawbacks. A user study shows context-aware translation is preferred over existing work 95.16% of the time. △ Less

Submitted 7 January, 2024; originally announced January 2024.

ACM Class: I.2.6; I.2.1; J.5

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

Authors: Qiao Yu, Wengui Zhang, Jorge Cardoso, Odej Kao

Abstract: 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 occu… ▽ More 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%. △ Less

Submitted 18 December, 2023; v1 submitted 5 December, 2023; originally announced December 2023.

Comments: Published at ICCAD 2023

Journal ref: 2023 IEEE/ACM International Conference on Computer Aided Design (ICCAD), San Francisco, CA, USA, 2023, pp. 01-09

RAISE -- Radiology AI Safety, an End-to-end lifecycle approach

Authors: M. Jorge Cardoso, Julia Moosbauer, Tessa S. Cook, B. Selnur Erdal, Brad Genereaux, Vikash Gupta, Bennett A. Landman, Tiarna Lee, Parashkev Nachev, Elanchezhian Somasundaram, Ronald M. Summers, Khaled Younis, Sebastien Ourselin, Franz MJ Pfister

Abstract: The integration of AI into radiology introduces opportunities for improved clinical care provision and efficiency but it demands a meticulous approach to mitigate potential risks as with any other new technology. Beginning with rigorous pre-deployment evaluation and validation, the focus should be on ensuring models meet the highest standards of safety, effectiveness and efficacy for their intende… ▽ More The integration of AI into radiology introduces opportunities for improved clinical care provision and efficiency but it demands a meticulous approach to mitigate potential risks as with any other new technology. Beginning with rigorous pre-deployment evaluation and validation, the focus should be on ensuring models meet the highest standards of safety, effectiveness and efficacy for their intended applications. Input and output guardrails implemented during production usage act as an additional layer of protection, identifying and addressing individual failures as they occur. Continuous post-deployment monitoring allows for tracking population-level performance (data drift), fairness, and value delivery over time. Scheduling reviews of post-deployment model performance and educating radiologists about new algorithmic-driven findings is critical for AI to be effective in clinical practice. Recognizing that no single AI solution can provide absolute assurance even when limited to its intended use, the synergistic application of quality assurance at multiple levels - regulatory, clinical, technical, and ethical - is emphasized. Collaborative efforts between stakeholders spanning healthcare systems, industry, academia, and government are imperative to address the multifaceted challenges involved. Trust in AI is an earned privilege, contingent on a broad set of goals, among them transparently demonstrating that the AI adheres to the same rigorous safety, effectiveness and efficacy standards as other established medical technologies. By doing so, developers can instil confidence among providers and patients alike, enabling the responsible scaling of AI and the realization of its potential benefits. The roadmap presented herein aims to expedite the achievement of deployable, reliable, and safe AI in radiology. △ Less

Submitted 24 November, 2023; originally announced November 2023.

Comments: 14 pages, 3 figures

Anonymizing medical case-based explanations through disentanglement

Authors: Helena Montenegro, Jaime S. Cardoso

Abstract: Case-based explanations are an intuitive method to gain insight into the decision-making process of deep learning models in clinical contexts. However, medical images cannot be shared as explanations due to privacy concerns. To address this problem, we propose a novel method for disentangling identity and medical characteristics of images and apply it to anonymize medical images. The disentangleme… ▽ More Case-based explanations are an intuitive method to gain insight into the decision-making process of deep learning models in clinical contexts. However, medical images cannot be shared as explanations due to privacy concerns. To address this problem, we propose a novel method for disentangling identity and medical characteristics of images and apply it to anonymize medical images. The disentanglement mechanism replaces some feature vectors in an image while ensuring that the remaining features are preserved, obtaining independent feature vectors that encode the images' identity and medical characteristics. We also propose a model to manufacture synthetic privacy-preserving identities to replace the original image's identity and achieve anonymization. The models are applied to medical and biometric datasets, demonstrating their capacity to generate realistic-looking anonymized images that preserve their original medical content. Additionally, the experiments show the network's inherent capacity to generate counterfactual images through the replacement of medical features. △ Less

Submitted 8 November, 2023; originally announced November 2023.

MSC Class: 68T45

A 3D generative model of pathological multi-modal MR images and segmentations

Authors: Virginia Fernandez, Walter Hugo Lopez Pinaya, Pedro Borges, Mark S. Graham, Tom Vercauteren, M. Jorge Cardoso

Abstract: Generative modelling and synthetic data can be a surrogate for real medical imaging datasets, whose scarcity and difficulty to share can be a nuisance when delivering accurate deep learning models for healthcare applications. In recent years, there has been an increased interest in using these models for data augmentation and synthetic data sharing, using architectures such as generative adversari… ▽ More Generative modelling and synthetic data can be a surrogate for real medical imaging datasets, whose scarcity and difficulty to share can be a nuisance when delivering accurate deep learning models for healthcare applications. In recent years, there has been an increased interest in using these models for data augmentation and synthetic data sharing, using architectures such as generative adversarial networks (GANs) or diffusion models (DMs). Nonetheless, the application of synthetic data to tasks such as 3D magnetic resonance imaging (MRI) segmentation remains limited due to the lack of labels associated with the generated images. Moreover, many of the proposed generative MRI models lack the ability to generate arbitrary modalities due to the absence of explicit contrast conditioning. These limitations prevent the user from adjusting the contrast and content of the images and obtaining more generalisable data for training task-specific models. In this work, we propose brainSPADE3D, a 3D generative model for brain MRI and associated segmentations, where the user can condition on specific pathological phenotypes and contrasts. The proposed joint imaging-segmentation generative model is shown to generate high-fidelity synthetic images and associated segmentations, with the ability to combine pathologies. We demonstrate how the model can alleviate issues with segmentation model performance when unexpected pathologies are present in the data. △ Less

Submitted 8 November, 2023; originally announced November 2023.

Comments: Accepted for publication at the 2023 Deep Generative Models (DGM4MICCAI) MICCAI workshop (Vancouver, Canada)