<?xml version="1.0" encoding="utf-8" standalone="yes"?><rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom"><channel><title>Computational Neuroradiology |</title><link>https://albarqouni.github.io/areas/computational-neuroradiology/</link><atom:link href="https://albarqouni.github.io/areas/computational-neuroradiology/index.xml" rel="self" type="application/rss+xml"/><description>Computational Neuroradiology</description><generator>HugoBlox Kit (https://hugoblox.com)</generator><language>en-us</language><image><url>https://albarqouni.github.io/media/logo_hu_43a0798e7da4e673.png</url><title>Computational Neuroradiology</title><link>https://albarqouni.github.io/areas/computational-neuroradiology/</link></image><item><title>Eyelid Tumor Triage using Uncertainty-Aware and Explainable Artificial Intelligence</title><link>https://albarqouni.github.io/publications/shakarami-2026-eyelid/</link><pubDate>Fri, 25 Sep 2026 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/shakarami-2026-eyelid/</guid><description/></item><item><title>MRIQT – KI-gestützte Verbesserung der Bildqualität in der neonatalen Ultra-Niedrigfeld-MRT</title><link>https://albarqouni.github.io/publications/demir-2026-mriqt/</link><pubDate>Mon, 01 Jun 2026 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/demir-2026-mriqt/</guid><description/></item><item><title>MRIQT: Physics-Aware Diffusion Model for Image Quality Transfer in Neonatal Ultra-Low-Field MRI</title><link>https://albarqouni.github.io/publications/al-2026-mriqt/</link><pubDate>Mon, 17 Nov 2025 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/al-2026-mriqt/</guid><description/></item><item><title>Application of AI and Advanced MRI for a Better Prediction of Disease Progression in Neurological Disorders</title><link>https://albarqouni.github.io/projects/bonn-fellowship/</link><pubDate>Wed, 01 Jan 2025 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/projects/bonn-fellowship/</guid><description>&lt;p&gt;TBA&lt;/p&gt;</description></item><item><title>Leveraging Collective Intelligence for Inclusive Global Healthcare</title><link>https://albarqouni.github.io/publications/albarqouni-2025-leveraging/</link><pubDate>Wed, 01 Jan 2025 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/albarqouni-2025-leveraging/</guid><description/></item><item><title>Neonatal Ultra-Low-Field / High-Field MRI Dataset</title><link>https://albarqouni.github.io/datasets/neonatal-ulf-mri/</link><pubDate>Wed, 01 Jan 2025 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/datasets/neonatal-ulf-mri/</guid><description>&lt;p&gt;Curated with the Department of Experimental Neonatology, University Hospital Bonn. Basis of MRIQT, a physics-aware 3D diffusion model for image-quality transfer; expert clinicians rated 85% of generated images as diagnostically useful.&lt;/p&gt;</description></item><item><title>MRIQT: Image-quality transfer from ultra-low-field to high-field neonatal MRI</title><link>https://albarqouni.github.io/projects/mriqt/</link><pubDate>Mon, 01 Jan 2024 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/projects/mriqt/</guid><description>&lt;p&gt;This project addresses the limited diagnostic usability of portable ultra-low-field MRI (0.064 T) in neonatal neuroimaging, where reduced signal-to-noise ratio constrains clinical interpretation despite bedside accessibility.
Together with the clinical partners, we curated a unique in-house cohort comprising 50 paired ultra-low-field and high-field 3D neonatal brain MRI scans, complemented by 230 additional unpaired scans across nine pathologies.
Building on this paired–unpaired data structure, we developed &lt;em&gt;MRIQT&lt;/em&gt;, a 3D conditional diffusion framework for structure-preserving image quality transfer from ultra-low-field to high-field MRI. The method integrates physics-consistent k-space degradation, classifier-free guided diffusion, and an SNR-weighted volumetric perceptual loss.&lt;/p&gt;
&lt;p&gt;MRIQT outperformed CNN- and GAN-based baselines, achieving up to 15.3% improvement in PSNR, while expert clinicians rated 85% of generated images as diagnostically useful with preserved pathology.&lt;/p&gt;
&lt;h3 id="perspective"&gt;Perspective&lt;/h3&gt;
&lt;p&gt;The project provides a methodological foundation for automated MRI quality enhancement and modality-agnostic quality control. Building on the current results, the work is prepared for translational follow-up and prospective validation, with a planned submission to the &lt;em&gt;Go-Bio Initial&lt;/em&gt; funding program.&lt;/p&gt;</description></item><item><title>Joint self-supervised image-volume representation learning with intra-inter contrastive clustering</title><link>https://albarqouni.github.io/publications/nguyen-2023-joint/</link><pubDate>Sun, 01 Jan 2023 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/nguyen-2023-joint/</guid><description/></item><item><title>Lvm-med: Learning large-scale self-supervised vision models for medical imaging via second-order graph matching</title><link>https://albarqouni.github.io/publications/mh-2023-lvm/</link><pubDate>Sun, 01 Jan 2023 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/mh-2023-lvm/</guid><description/></item><item><title>Transformer based models for unsupervised anomaly segmentation in brain MR images</title><link>https://albarqouni.github.io/publications/ghorbel-2022-transformer/</link><pubDate>Sun, 01 Jan 2023 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/ghorbel-2022-transformer/</guid><description/></item><item><title>Federated disentangled representation learning for unsupervised brain anomaly detection</title><link>https://albarqouni.github.io/publications/bercea-2022-federated/</link><pubDate>Sat, 01 Oct 2022 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/bercea-2022-federated/</guid><description/></item><item><title>CTFSH: Full Head CT Anomaly Detection with Unsupervised Learning</title><link>https://albarqouni.github.io/publications/guerractfsh/</link><pubDate>Sat, 01 Jan 2022 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/guerractfsh/</guid><description/></item><item><title>ROAM: Random layer mixup for semi-supervised learning in medical images</title><link>https://albarqouni.github.io/publications/bdair-2022-roam/</link><pubDate>Sat, 01 Jan 2022 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/bdair-2022-roam/</guid><description/></item><item><title>SPA: Shape-Prior Variational Autoencoders for Unsupervised Brain Pathology Segmentation</title><link>https://albarqouni.github.io/publications/bercea-2022-spa/</link><pubDate>Sat, 01 Jan 2022 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/bercea-2022-spa/</guid><description/></item><item><title>Autoencoders for Unsupervised Anomaly Segmentation in Brain MR Images: A Comparative Study</title><link>https://albarqouni.github.io/publications/baur-2021-autoencoders/</link><pubDate>Fri, 01 Jan 2021 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/baur-2021-autoencoders/</guid><description/></item><item><title>FedDis: Disentangled Federated Learning for Unsupervised Brain Pathology Segmentation</title><link>https://albarqouni.github.io/publications/bercea-2021-feddis/</link><pubDate>Fri, 01 Jan 2021 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/bercea-2021-feddis/</guid><description/></item><item><title>Modeling Healthy Anatomy with Artificial Intelligence for Unsupervised Anomaly Detection in Brain MRI</title><link>https://albarqouni.github.io/publications/baur-2021-modeling/</link><pubDate>Fri, 01 Jan 2021 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/baur-2021-modeling/</guid><description/></item><item><title>The Federated Tumor Segmentation (FeTS) Challenge</title><link>https://albarqouni.github.io/publications/pati-2021-federated/</link><pubDate>Fri, 01 Jan 2021 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/pati-2021-federated/</guid><description/></item><item><title>The OOD Blind Spot of Unsupervised Anomaly Detection</title><link>https://albarqouni.github.io/publications/heer-2021-ood/</link><pubDate>Fri, 01 Jan 2021 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/heer-2021-ood/</guid><description/></item><item><title>Unsupervised anomaly detection in full-head CT for emergency triage</title><link>https://albarqouni.github.io/projects/deepc-ct-anomaly/</link><pubDate>Fri, 01 Jan 2021 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/projects/deepc-ct-anomaly/</guid><description>&lt;p&gt;In the emergency room, head CT scans must be read and prioritised quickly — and the findings range from bleeds to fractures. Supervised detectors need labelled examples of every pathology; unsupervised anomaly detection (UAD) instead learns what normal anatomy looks like and flags everything else, an inexpensive way to bring triage to the clinical workflow. Most UAD work, however, addressed 2D slices of brain MRI rather than volumetric CT.&lt;/p&gt;
&lt;h3 id="what-we-did"&gt;What we did&lt;/h3&gt;
&lt;ul&gt;
&lt;li&gt;&lt;strong&gt;UAD for volumetric head CT.&lt;/strong&gt; We compared two widely used reconstruction-based baselines on full 3D head CT, and improved their reconstruction quality with two recent computer-vision contributions — raising anomaly-detection AUROC from 0.70 to 0.77 for one baseline.&lt;/li&gt;
&lt;li&gt;&lt;strong&gt;Keep the skull.&lt;/strong&gt; Testing on skull-stripped and unstripped volumes showed that leaving the skull in lets the model detect fractures too — to our knowledge the first comparison of this kind.&lt;/li&gt;
&lt;li&gt;&lt;strong&gt;Open labels and code.&lt;/strong&gt; Supplementary labels for the public CQ500 head-CT dataset and the
were released to support further research.&lt;/li&gt;
&lt;/ul&gt;
&lt;h3 id="our-role"&gt;Our role&lt;/h3&gt;
&lt;p&gt;Academic lead and supervision, together with Daniel Rueckert (TU Munich) and Mehmet Yigitsoy and Abhijeet Parida (deepc GmbH).&lt;/p&gt;</description></item><item><title>An Uncertainty-Driven GCN Refinement Strategy for Organ Segmentation</title><link>https://albarqouni.github.io/publications/soberanis-2020-uncertainty/</link><pubDate>Tue, 01 Dec 2020 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/soberanis-2020-uncertainty/</guid><description/></item><item><title>FedDis: Federated disentangled representation learning for brain anomaly detection</title><link>https://albarqouni.github.io/projects/feddis/</link><pubDate>Mon, 01 Jun 2020 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/projects/feddis/</guid><description>&lt;p&gt;This research line addressed one of the central methodological challenges in collaborative medical AI: how to learn clinically meaningful representations across institutions without sharing patient data and without relying on pixel-level pathology annotations. In the context of brain MRI, unsupervised anomaly detection is particularly attractive because lesion annotation is expensive, heterogeneous, and often unavailable, while privacy and governance constraints limit centralized multi-site learning.&lt;/p&gt;
&lt;p&gt;Together with the collaborators, we developed &lt;em&gt;FedDis&lt;/em&gt;, a federated disentangled representation-learning framework for unsupervised brain anomaly detection. The key methodological idea was to separate the representation space into &lt;em&gt;global shape&lt;/em&gt; components, learned collaboratively across institutions, and &lt;em&gt;local appearance&lt;/em&gt; components, trained locally to capture client-specific intensity and scanner characteristics. This disentanglement strategy was designed to address statistical heterogeneity across sites while preserving the privacy-preserving benefits of federated learning.&lt;/p&gt;
&lt;p&gt;The resulting system was trained collaboratively on &lt;strong&gt;1,532 healthy MRI scans from four institutions&lt;/strong&gt; and evaluated on &lt;strong&gt;538 pathological volumes from six institutions&lt;/strong&gt;, covering multiple sclerosis, vascular lesions, and brain tumors. Compared with locally trained unsupervised models, the approach achieved substantial improvements in anomaly segmentation performance, including marked gains for multiple sclerosis, vascular lesions, and tumors, while requiring neither pathology annotations nor raw data sharing. The work was published in &lt;em&gt;&lt;strong&gt;Nature Machine Intelligence&lt;/strong&gt;&lt;/em&gt; and became one of the most visible methodological outputs of my collaborative research in federated medical imaging.&lt;/p&gt;
&lt;h3 id="perspective"&gt;Perspective&lt;/h3&gt;
&lt;p&gt;This project established an important methodological foundation for my later work on federated and collaborative learning, benchmark development, and multi-institutional validation in medical imaging. Conceptually, it shaped my subsequent research agenda by demonstrating that privacy-preserving learning across hospital networks must address not only optimization and communication constraints, but also representation-level heterogeneity across institutions. The insights from this project continue to inform my current and planned work on collaborative validation, foundation models under distribution shift, and trustworthy medical AI infrastructures such as OMI.&lt;/p&gt;</description></item><item><title>Uncertainty-based graph convolutional networks for organ segmentation refinement</title><link>https://albarqouni.github.io/publications/soberanis-2019-uncertainty/</link><pubDate>Wed, 01 Apr 2020 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/soberanis-2019-uncertainty/</guid><description/></item><item><title>Bayesian Skip-Autoencoders for Unsupervised Hyperintense Anomaly Detection in High Resolution Brain Mri</title><link>https://albarqouni.github.io/publications/baur-2020-bayesian/</link><pubDate>Wed, 01 Jan 2020 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/baur-2020-bayesian/</guid><description/></item><item><title>Modelling Uncertainty in Deep Learning for Medical Applications</title><link>https://albarqouni.github.io/projects/uncertainty/</link><pubDate>Wed, 01 Jan 2020 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/projects/uncertainty/</guid><description>&lt;p&gt;Deep Learning has emerged as a leading technology for accomplishing many challenging tasks showing outstanding performance in a broad range of applications in computer vision and medical applications. Despite its success and merit in recent state-of-the-art methods, DL tools still lack in robustness hindering its adoption in medical applications. Modeling uncertainty, through Bayesian Inference and Monte-Carlo dropout, has been successfully introduced to computer vision for better understanding the underlying deep learning models. In this proposal, we investigate modeling the uncertainty for medical applications given the well-known challenges in medical image analysis, namely severe class-imbalance, few amounts of labeled data, domain shift, and noisy annotations.&lt;/p&gt;</description></item><item><title>Scale-Space Autoencoders for Unsupervised Anomaly Segmentation in Brain MRI</title><link>https://albarqouni.github.io/publications/baur-2020-scale/</link><pubDate>Wed, 01 Jan 2020 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/baur-2020-scale/</guid><description/></item><item><title>SteGANomaly: Inhibiting CycleGAN Steganography for Unsupervised Anomaly Detection in Brain MRI</title><link>https://albarqouni.github.io/publications/baur-2020-steganomaly/</link><pubDate>Wed, 01 Jan 2020 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/baur-2020-steganomaly/</guid><description/></item><item><title>Deep autoencoding models for unsupervised anomaly segmentation in brain MR images</title><link>https://albarqouni.github.io/publications/baur-2018-deep/</link><pubDate>Tue, 01 Jan 2019 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/baur-2018-deep/</guid><description/></item><item><title>Graph Convolution Based Attention Model for Personalized Disease Prediction</title><link>https://albarqouni.github.io/publications/kazi-2019-graph/</link><pubDate>Tue, 01 Jan 2019 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/kazi-2019-graph/</guid><description/></item><item><title>Learn to estimate labels uncertainty for quality assurance</title><link>https://albarqouni.github.io/publications/tomczack-2019-learn/</link><pubDate>Tue, 01 Jan 2019 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/tomczack-2019-learn/</guid><description/></item><item><title>Preliminary results of DSA denoising based on a weighted low-rank approach using an advanced neurovascular replication system</title><link>https://albarqouni.github.io/publications/hariharan-2019-preliminary/</link><pubDate>Tue, 01 Jan 2019 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/hariharan-2019-preliminary/</guid><description/></item><item><title>Fusing unsupervised and supervised deep learning for white matter lesion segmentation</title><link>https://albarqouni.github.io/publications/baur-2019-fusing/</link><pubDate>Thu, 13 Dec 2018 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/baur-2019-fusing/</guid><description/></item><item><title>Deep learning with synthetic data for free water elimination in diffusion MRI</title><link>https://albarqouni.github.io/publications/molina-2018-deep/</link><pubDate>Mon, 01 Jan 2018 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/molina-2018-deep/</guid><description/></item><item><title>Fully Automated Multiple Sclerosis lesion detection on multi-channel subtraction images through an integrated Computer Vision-Machine Learning pipeline</title><link>https://albarqouni.github.io/publications/wiestler-2017-fully/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://albarqouni.github.io/publications/wiestler-2017-fully/</guid><description/></item></channel></rss>