arXiv subjects

Shadi Albarqouni

Publications and source records attributed to Shadi Albarqouni.

At least 19 recordsLinked to original sources

arXiv2026

SegSTRONG-C: Segmenting Surgical Tools Robustly On Non-adversarial Generated Corruptions -- An EndoVis'24 Challenge

Surgical data science has seen rapid advancement with the excellent performance of end-to-end deep neural networks (DNNs). Despite their successes, DNNs have been proven susceptible to minor "corruptions," introducing a major concern for the translation of cutting-edge technology, especially in high-stakes scenarios. We introduce the SegSTRONG-C challenge dedicated to better understanding model deterioration under unforeseen but plausible non-adversarial "corruption" and the capabilities of contemporary methods that seek to improve it. Built on a dataset generated through counterfactual robotic replay, SegSTRONG-C provides paired clean and "corrupted" samples, enabling reproducible evaluation of model robustness. Participants are challenged to train tool segmentation algorithms on "uncorrupted" data and evaluate them on "corrupted" test domains for the binary robot tool segmentation task. Through comprehensive baseline experiments and participating submissions from widespread community engagement, SegSTRONG-C reveals key themes for model failure and identifies promising directions for improving robustness. The performance of challenge winners, achieving an average 0.9394 DSC and 0.9301 NSD across the unreleased test sets with "corruption" types: bleeding, smoke, and low brightness. This highlights how prior knowledge, customized training strategies, and architectural choice can be leveraged to improve robustness. In conclusion, the SegSTRONG-C challenge has identified practical approaches for enhancing model robustness. However, most approaches rely on conventional techniques that have known limitations. Looking ahead, we advocate for expanding intellectual diversity and creativity in non-adversarial robustness beyond data augmentation, calling for new paradigms that enhance universal robustness to unforeseen "corruptions" to facilitate richer applications in surgical data science.

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arXiv2026

PromptGate Client Adaptive Vision Language Gating for Open Set Federated Active Learning

Deploying medical AI across resource-constrained institutions demands data-efficient learning pipelines that respect patient privacy. Federated Learning (FL) enables collaborative medical AI without centralising data, yet real-world clinical pools are inherently open-set, containing out-of-distribution (OOD) noise such as imaging artifacts and wrong modalities. Standard Active Learning (AL) query strategies mistake this noise for informative samples, wasting scarce annotation budgets. We propose PromptGate, a dynamic VLM-gated framework for Open-Set Federated AL that purifies unlabeled pools before querying. PromptGate introduces a federated Class-Specific Context Optimization: lightweight, learnable prompt vectors that adapt a frozen BiomedCLIP backbone to local clinical domains and aggregate globally via FedAvg -- without sharing patient data. As new annotations arrive, prompts progressively sharpen the ID/OOD boundary, turning the VLM into a dynamic gatekeeper that is strategy-agnostic: a plug-and-play pre-selection module enhancing any downstream AL strategy. Experiments on distributed dermatology and breast imaging benchmarks show that while static VLM prompting degrades to 50% ID purity, PromptGate maintains $>$95% purity with 98% OOD recall.

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arXiv2026

MRIQT: Physics-Aware Diffusion Model for Image Quality Transfer in Neonatal Ultra-Low-Field MRI

Portable ultra-low-field MRI (uLF-MRI, 0.064 T) offers accessible neuroimaging for neonatal care but suffers from low signal-to-noise ratio and poor diagnostic quality compared to high-field (HF) MRI. We propose MRIQT, a 3D conditional diffusion framework for image quality transfer (IQT) from uLF to HF MRI. MRIQT combines realistic K-space degradation for physics-consistent uLF simulation, v-prediction with classifier-free guidance for stable image-to-image generation, and an SNR-weighted 3D perceptual loss for anatomical fidelity. The model denoises from a noised uLF input conditioned on the same scan, leveraging volumetric attention-UNet architecture for structure-preserving translation. Trained on a neonatal cohort with diverse pathologies, MRIQT surpasses recent GAN and CNN baselines in PSNR 15.3% with 1.78% over the state of the art, while physicians rated 85% of its outputs as good quality with clear pathology present. MRIQT enables high-fidelity, diffusion-based enhancement of portable ultra-low-field (uLF) MRI for deliable neonatal brain assessment.

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arXiv2026

K-MaT: Knowledge-Anchored Manifold Transport for Cross-Modal Prompt Learning in Medical Imaging

Large-scale biomedical vision-language models (VLMs) adapted on high-end imaging (e.g., CT) often fail to transfer to frontline low-end modalities (e.g., radiography), collapsing into modality-specific shortcuts. We propose K-MaT (Knowledge-Anchored Manifold Transport), a prompt-learning framework that transfers decision structures to low-end modalities without requiring low-end training images. K-MaT factorizes prompts, anchors them to clinical text descriptions, and aligns the low-end prompt manifold to the visually-grounded high-end space using Fused Gromov-Wasserstein optimal transport. We evaluate K-MaT on four cross-modal benchmarks, including dermoscopy, mammography to ultrasound, and CT to chest X-ray. K-MaT achieves state-of-the-art results, improving the average harmonic mean of accuracy to 44.1% (from BiomedCoOp's 42.0%) and macro-F1 to 36.2%. Notably, on the challenging breast imaging task, it mitigates the catastrophic forgetting seen in standard methods like CoOp (which drops to 27.0% accuracy on the low-end), preserving robust performance across modalities. Aligning prompt manifolds via optimal transport provides a highly effective route for the zero-shot cross-modal deployment of medical VLMs.

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arXiv2025

INTERACT-CMIL: Multi-Task Shared Learning and Inter-Task Consistency for Conjunctival Melanocytic Intraepithelial Lesion Grading

Accurate grading of Conjunctival Melanocytic Intraepithelial Lesions (CMIL) is essential for treatment and melanoma prediction but remains difficult due to subtle morphological cues and interrelated diagnostic criteria. We introduce INTERACT-CMIL, a multi-head deep learning framework that jointly predicts five histopathological axes; WHO4, WHO5, horizontal spread, vertical spread, and cytologic atypia, through Shared Feature Learning with Combinatorial Partial Supervision and an Inter-Dependence Loss enforcing cross-task consistency. Trained and evaluated on a newly curated, multi-center dataset of 486 expert-annotated conjunctival biopsy patches from three university hospitals, INTERACT-CMIL achieves consistent improvements over CNN and foundation-model (FM) baselines, with relative macro F1 gains up to 55.1% (WHO4) and 25.0% (vertical spread). The framework provides coherent, interpretable multi-criteria predictions aligned with expert grading, offering a reproducible computational benchmark for CMIL diagnosis and a step toward standardized digital ocular pathology.

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arXiv2025

ProSona: Prompt-Guided Personalization for Multi-Expert Medical Image Segmentation

Automated medical image segmentation suffers from high inter-observer variability, particularly in tasks such as lung nodule delineation, where experts often disagree. Existing approaches either collapse this variability into a consensus mask or rely on separate model branches for each annotator. We introduce ProSona, a two-stage framework that learns a continuous latent space of annotation styles, enabling controllable personalization via natural language prompts. A probabilistic U-Net backbone captures diverse expert hypotheses, while a prompt-guided projection mechanism navigates this latent space to generate personalized segmentations. A multi-level contrastive objective aligns textual and visual representations, promoting disentangled and interpretable expert styles. Across the LIDC-IDRI lung nodule and multi-institutional prostate MRI datasets, ProSona reduces the Generalized Energy Distance by 17% and improves mean Dice by more than one point compared with DPersona. These results demonstrate that natural-language prompts can provide flexible, accurate, and interpretable control over personalized medical image segmentation. Our implementation is available online 1 .

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arXiv2025

Bias and Generalizability of Foundation Models across Datasets in Breast Mammography

Over the past decades, computer-aided diagnosis tools for breast cancer have been developed to enhance screening procedures, yet their clinical adoption remains challenged by data variability and inherent biases. Although foundation models (FMs) have recently demonstrated impressive generalizability and transfer learning capabilities by leveraging vast and diverse datasets, their performance can be undermined by spurious correlations that arise from variations in image quality, labeling uncertainty, and sensitive patient attributes. In this work, we explore the fairness and bias of FMs for breast mammography classification by leveraging a large pool of datasets from diverse sources-including data from underrepresented regions and an in-house dataset. Our extensive experiments show that while modality-specific pre-training of FMs enhances performance, classifiers trained on features from individual datasets fail to generalize across domains. Aggregating datasets improves overall performance, yet does not fully mitigate biases, leading to significant disparities across under-represented subgroups such as extreme breast densities and age groups. Furthermore, while domain-adaptation strategies can reduce these disparities, they often incur a performance trade-off. In contrast, fairness-aware techniques yield more stable and equitable performance across subgroups. These findings underscore the necessity of incorporating rigorous fairness evaluations and mitigation strategies into FM-based models to foster inclusive and generalizable AI.

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arXiv2023

LVM-Med: Learning Large-Scale Self-Supervised Vision Models for Medical Imaging via Second-order Graph Matching

Obtaining large pre-trained models that can be fine-tuned to new tasks with limited annotated samples has remained an open challenge for medical imaging data. While pre-trained deep networks on ImageNet and vision-language foundation models trained on web-scale data are prevailing approaches, their effectiveness on medical tasks is limited due to the significant domain shift between natural and medical images. To bridge this gap, we introduce LVM-Med, the first family of deep networks trained on large-scale medical datasets. We have collected approximately 1.3 million medical images from 55 publicly available datasets, covering a large number of organs and modalities such as CT, MRI, X-ray, and Ultrasound. We benchmark several state-of-the-art self-supervised algorithms on this dataset and propose a novel self-supervised contrastive learning algorithm using a graph-matching formulation. The proposed approach makes three contributions: (i) it integrates prior pair-wise image similarity metrics based on local and global information; (ii) it captures the structural constraints of feature embeddings through a loss function constructed via a combinatorial graph-matching objective; and (iii) it can be trained efficiently end-to-end using modern gradient-estimation techniques for black-box solvers. We thoroughly evaluate the proposed LVM-Med on 15 downstream medical tasks ranging from segmentation and classification to object detection, and both for the in and out-of-distribution settings. LVM-Med empirically outperforms a number of state-of-the-art supervised, self-supervised, and foundation models. For challenging tasks such as Brain Tumor Classification or Diabetic Retinopathy Grading, LVM-Med improves previous vision-language models trained on 1 billion masks by 6-7% while using only a ResNet-50.

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arXiv2023

FLamby: Datasets and Benchmarks for Cross-Silo Federated Learning in Realistic Healthcare Settings

Federated Learning (FL) is a novel approach enabling several clients holding sensitive data to collaboratively train machine learning models, without centralizing data. The cross-silo FL setting corresponds to the case of few ($2$--$50$) reliable clients, each holding medium to large datasets, and is typically found in applications such as healthcare, finance, or industry. While previous works have proposed representative datasets for cross-device FL, few realistic healthcare cross-silo FL datasets exist, thereby slowing algorithmic research in this critical application. In this work, we propose a novel cross-silo dataset suite focused on healthcare, FLamby (Federated Learning AMple Benchmark of Your cross-silo strategies), to bridge the gap between theory and practice of cross-silo FL. FLamby encompasses 7 healthcare datasets with natural splits, covering multiple tasks, modalities, and data volumes, each accompanied with baseline training code. As an illustration, we additionally benchmark standard FL algorithms on all datasets. Our flexible and modular suite allows researchers to easily download datasets, reproduce results and re-use the different components for their research. FLamby is available at~\url{www.github.com/owkin/flamby}.

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arXiv2023

LYSTO: The Lymphocyte Assessment Hackathon and Benchmark Dataset

We introduce LYSTO, the Lymphocyte Assessment Hackathon, which was held in conjunction with the MICCAI 2019 Conference in Shenzen (China). The competition required participants to automatically assess the number of lymphocytes, in particular T-cells, in histopathological images of colon, breast, and prostate cancer stained with CD3 and CD8 immunohistochemistry. Differently from other challenges setup in medical image analysis, LYSTO participants were solely given a few hours to address this problem. In this paper, we describe the goal and the multi-phase organization of the hackathon; we describe the proposed methods and the on-site results. Additionally, we present post-competition results where we show how the presented methods perform on an independent set of lung cancer slides, which was not part of the initial competition, as well as a comparison on lymphocyte assessment between presented methods and a panel of pathologists. We show that some of the participants were capable to achieve pathologist-level performance at lymphocyte assessment. After the hackathon, LYSTO was left as a lightweight plug-and-play benchmark dataset on grand-challenge website, together with an automatic evaluation platform. LYSTO has supported a number of research in lymphocyte assessment in oncology. LYSTO will be a long-lasting educational challenge for deep learning and digital pathology, it is available at https://lysto.grand-challenge.org/.

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arXiv2022

Joint Self-Supervised Image-Volume Representation Learning with Intra-Inter Contrastive Clustering

Collecting large-scale medical datasets with fully annotated samples for training of deep networks is prohibitively expensive, especially for 3D volume data. Recent breakthroughs in self-supervised learning (SSL) offer the ability to overcome the lack of labeled training samples by learning feature representations from unlabeled data. However, most current SSL techniques in the medical field have been designed for either 2D images or 3D volumes. In practice, this restricts the capability to fully leverage unlabeled data from numerous sources, which may include both 2D and 3D data. Additionally, the use of these pre-trained networks is constrained to downstream tasks with compatible data dimensions. In this paper, we propose a novel framework for unsupervised joint learning on 2D and 3D data modalities. Given a set of 2D images or 2D slices extracted from 3D volumes, we construct an SSL task based on a 2D contrastive clustering problem for distinct classes. The 3D volumes are exploited by computing vectored embedding at each slice and then assembling a holistic feature through deformable self-attention mechanisms in Transformer, allowing incorporating long-range dependencies between slices inside 3D volumes. These holistic features are further utilized to define a novel 3D clustering agreement-based SSL task and masking embedding prediction inspired by pre-trained language models. Experiments on downstream tasks, such as 3D brain segmentation, lung nodule detection, 3D heart structures segmentation, and abnormal chest X-ray detection, demonstrate the effectiveness of our joint 2D and 3D SSL approach. We improve plain 2D Deep-ClusterV2 and SwAV by a significant margin and also surpass various modern 2D and 3D SSL approaches.

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arXiv2022

What can we learn about a generated image corrupting its latent representation?

Generative adversarial networks (GANs) offer an effective solution to the image-to-image translation problem, thereby allowing for new possibilities in medical imaging. They can translate images from one imaging modality to another at a low cost. For unpaired datasets, they rely mostly on cycle loss. Despite its effectiveness in learning the underlying data distribution, it can lead to a discrepancy between input and output data. The purpose of this work is to investigate the hypothesis that we can predict image quality based on its latent representation in the GANs bottleneck. We achieve this by corrupting the latent representation with noise and generating multiple outputs. The degree of differences between them is interpreted as the strength of the representation: the more robust the latent representation, the fewer changes in the output image the corruption causes. Our results demonstrate that our proposed method has the ability to i) predict uncertain parts of synthesized images, and ii) identify samples that may not be reliable for downstream tasks, e.g., liver segmentation task.

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arXiv2022

Transformer based Models for Unsupervised Anomaly Segmentation in Brain MR Images

The quality of patient care associated with diagnostic radiology is proportionate to a physician workload. Segmentation is a fundamental limiting precursor to both diagnostic and therapeutic procedures. Advances in machine learning (ML) aim to increase diagnostic efficiency by replacing a single application with generalized algorithms. The goal of unsupervised anomaly detection (UAD) is to identify potential anomalous regions unseen during training, where convolutional neural network (CNN) based autoencoders (AEs) and variational autoencoders (VAEs) are considered a de facto approach for reconstruction based-anomaly segmentation. The restricted receptive field in CNNs limits the CNN to model the global context. Hence, if the anomalous regions cover large parts of the image, the CNN-based AEs are not capable of bringing a semantic understanding of the image. Meanwhile, vision transformers (ViTs) have emerged as a competitive alternative to CNNs. It relies on the self-attention mechanism that can relate image patches to each other. We investigate in this paper Transformer capabilities in building AEs for the reconstruction-based UAD task to reconstruct a coherent and more realistic image. We focus on anomaly segmentation for brain magnetic resonance imaging (MRI) and present five Transformer-based models while enabling segmentation performance comparable to or superior to state-of-the-art (SOTA) models. The source code is made publicly available on GitHub: https://github.com/ahmedgh970/Transformers_Unsupervised_Anomaly_Segmentation.git.

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arXiv2022

Anomaly-aware multiple instance learning for rare anemia disorder classification

Deep learning-based classification of rare anemia disorders is challenged by the lack of training data and instance-level annotations. Multiple Instance Learning (MIL) has shown to be an effective solution, yet it suffers from low accuracy and limited explainability. Although the inclusion of attention mechanisms has addressed these issues, their effectiveness highly depends on the amount and diversity of cells in the training samples. Consequently, the poor machine learning performance on rare anemia disorder classification from blood samples remains unresolved. In this paper, we propose an interpretable pooling method for MIL to address these limitations. By benefiting from instance-level information of negative bags (i.e., homogeneous benign cells from healthy individuals), our approach increases the contribution of anomalous instances. We show that our strategy outperforms standard MIL classification algorithms and provides a meaningful explanation behind its decisions. Moreover, it can denote anomalous instances of rare blood diseases that are not seen during the training phase.

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arXiv2022

Unsupervised Cross-Domain Feature Extraction for Single Blood Cell Image Classification

Diagnosing hematological malignancies requires identification and classification of white blood cells in peripheral blood smears. Domain shifts caused by different lab procedures, staining, illumination, and microscope settings hamper the re-usability of recently developed machine learning methods on data collected from different sites. Here, we propose a cross-domain adapted autoencoder to extract features in an unsupervised manner on three different datasets of single white blood cells scanned from peripheral blood smears. The autoencoder is based on an R-CNN architecture allowing it to focus on the relevant white blood cell and eliminate artifacts in the image. To evaluate the quality of the extracted features we use a simple random forest to classify single cells. We show that thanks to the rich features extracted by the autoencoder trained on only one of the datasets, the random forest classifier performs satisfactorily on the unseen datasets, and outperforms published oracle networks in the cross-domain task. Our results suggest the possibility of employing this unsupervised approach in more complicated diagnosis and prognosis tasks without the need to add expensive expert labels to unseen data.

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arXiv2022

Virtual embeddings and self-consistency for self-supervised learning

Self-supervised Learning (SSL) has recently gained much attention due to the high cost and data limitation in the training of supervised learning models. The current paradigm in the SSL is to utilize data augmentation at the input space to create different views of the same images and train a model to maximize the representations between similar images and minimize them for different ones. While this approach achieves state-of-the-art (SOTA) results in various downstream tasks, it still lakes the opportunity to investigate the latent space augmentation. This paper proposes TriMix, a novel concept for SSL that generates virtual embeddings through linear interpolation of the data, thus providing the model with novel representations. Our strategy focuses on training the model to extract the original embeddings from virtual ones, hence, better representation learning. Additionally, we propose a self-consistency term that improves the consistency between the virtual and actual embeddings. We validate TriMix on eight benchmark datasets consisting of natural and medical images with an improvement of 2.71% and 0.41% better than the second-best models for both data types. Further, our approach outperformed the current methods in semi-supervised learning, particularly in low data regimes. Besides, our pre-trained models showed better transfer to other datasets.

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arXiv2022

FedNorm: Modality-Based Normalization in Federated Learning for Multi-Modal Liver Segmentation

Given the high incidence and effective treatment options for liver diseases, they are of great socioeconomic importance. One of the most common methods for analyzing CT and MRI images for diagnosis and follow-up treatment is liver segmentation. Recent advances in deep learning have demonstrated encouraging results for automatic liver segmentation. Despite this, their success depends primarily on the availability of an annotated database, which is often not available because of privacy concerns. Federated Learning has been recently proposed as a solution to alleviate these challenges by training a shared global model on distributed clients without access to their local databases. Nevertheless, Federated Learning does not perform well when it is trained on a high degree of heterogeneity of image data due to multi-modal imaging, such as CT and MRI, and multiple scanner types. To this end, we propose Fednorm and its extension \fednormp, two Federated Learning algorithms that use a modality-based normalization technique. Specifically, Fednorm normalizes the features on a client-level, while Fednorm+ employs the modality information of single slices in the feature normalization. Our methods were validated using 428 patients from six publicly available databases and compared to state-of-the-art Federated Learning algorithms and baseline models in heterogeneous settings (multi-institutional, multi-modal data). The experimental results demonstrate that our methods show an overall acceptable performance, achieve Dice per patient scores up to 0.961, consistently outperform locally trained models, and are on par or slightly better than centralized models.

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arXiv2022

Semi-Supervised Federated Peer Learning for Skin Lesion Classification

Globally, Skin carcinoma is among the most lethal diseases. Millions of people are diagnosed with this cancer every year. Sill, early detection can decrease the medication cost and mortality rate substantially. The recent improvement in automated cancer classification using deep learning methods has reached a human-level performance requiring a large amount of annotated data assembled in one location, yet, finding such conditions usually is not feasible. Recently, federated learning (FL) has been proposed to train decentralized models in a privacy-preserved fashion depending on labeled data at the client-side, which is usually not available and costly. To address this, we propose \verb!FedPerl!, a semi-supervised federated learning method. Our method is inspired by peer learning from educational psychology and ensemble averaging from committee machines. FedPerl builds communities based on clients' similarities. Then it encourages communities members to learn from each other to generate more accurate pseudo labels for the unlabeled data. We also proposed the peer anonymization (PA) technique to anonymize clients. As a core component of our method, PA is orthogonal to other methods without additional complexity and reduces the communication cost while enhancing performance. Finally, we propose a dynamic peer-learning policy that controls the learning stream to avoid any degradation in the performance, especially for individual clients. Our experimental setup consists of 71,000 skin lesion images collected from 5 publicly available datasets. We test our method in four different scenarios in SSFL. With few annotated data, FedPerl is on par with a state-of-the-art method in skin lesion classification in the standard setup while outperforming SSFLs and the baselines by 1.8% and 15.8%, respectively. Also, it generalizes better to unseen clients while being less sensitive to noisy ones.

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