arXiv subjects

Ilkay Oksuz

Publications and source records attributed to Ilkay Oksuz.

At least 19 recordsLinked to original sources

arXiv2026

Frequency-Hierarchical Active k-Space Sampling for Diagnostic MRI

Active sampling for accelerated MRI must distribute a tight sampling budget across spatial frequencies that carry very different kinds of information. Low frequencies hold most of the anatomical context; high frequencies carry the fine details that drive pathology assessment. Existing active samplers either treat both regions identically or restrict the action space to entire Cartesian rows, which forces a poor compromise at high acceleration. We propose HieraSample, a task-driven framework built around this hierarchy. A cosine-annealed curriculum lowers the acceleration factor from 20x to 4x across 80 acquisition steps while keeping a fully-sampled low-frequency disk at every step; a Mamba-based policy then picks individual high-frequency coordinates from features extracted by dual disease and severity classifiers. The reward is the per-sample reduction in class-weighted cross-entropy after each action, so a positive reward corresponds directly to a more confident correct prediction. On the fastMRI+ knee benchmark, HieraSample matches the fully-sampled oracle on ACL diagnosis from 4x to 10x acceleration, and improves on a recent Cartesian baseline by as much as 20.4 AUC points on ACL severity.

cs.CV↗

arXiv2025

Towards Modality- and Sampling-Universal Learning Strategies for Accelerating Cardiovascular Imaging: Summary of the CMRxRecon2024 Challenge

Cardiovascular health is vital to human well-being, and cardiac magnetic resonance (CMR) imaging is considered the {clinical reference standard} for diagnosing cardiovascular disease. However, its adoption is hindered by long scan times, complex contrasts, and inconsistent quality. While deep learning methods perform well on specific CMR imaging {sequences}, they often fail to generalize across modalities and sampling schemes. The lack of benchmarks for high-quality, fast CMR image reconstruction further limits technology comparison and adoption. The CMRxRecon2024 challenge, attracting over 200 teams from 18 countries, addressed these issues with two tasks: generalization to unseen {modalities} and robustness to diverse undersampling patterns. We introduced the largest public multi-{modality} CMR raw dataset, an open benchmarking platform, and shared code. Analysis of the best-performing solutions revealed that prompt-based adaptation and enhanced physics-driven consistency enabled strong cross-scenario performance. These findings establish principles for generalizable reconstruction models and advance clinically translatable AI in cardiovascular imaging.

eess.IV↗

arXiv2025

HierAdaptMR: Cross-Center Cardiac MRI Reconstruction with Hierarchical Feature Adapters

Deep learning-based cardiac MRI reconstruction faces significant domain shift challenges when deployed across multiple clinical centers with heterogeneous scanner configurations and imaging protocols. We propose HierAdaptMR, a hierarchical feature adaptation framework that addresses multi-level domain variations through parameter-efficient adapters. Our method employs Protocol-Level Adapters for sequence-specific characteristics and Center-Level Adapters for scanner-dependent variations, built upon a variational unrolling backbone. A Universal Adapter enables generalization to entirely unseen centers through stochastic training that learns center-invariant adaptations. The framework utilizes multi-scale SSIM loss with frequency domain enhancement and contrast-adaptive weighting for robust optimization. Comprehensive evaluation on the CMRxRecon2025 dataset spanning 5+ centers, 10+ scanners, and 9 modalities demonstrates superior cross-center generalization while maintaining reconstruction quality. code: https://github.com/Ruru-Xu/HierAdaptMR

cs.CV↗

arXiv2025

Adaptive k-space Radial Sampling for Cardiac MRI with Reinforcement Learning

Accelerated Magnetic Resonance Imaging (MRI) requires careful optimization of k-space sampling patterns to balance acquisition speed and image quality. While recent advances in deep learning have shown promise in optimizing Cartesian sampling, the potential of reinforcement learning (RL) for non-Cartesian trajectory optimization remains largely unexplored. In this work, we present a novel RL framework for optimizing radial sampling trajectories in cardiac MRI. Our approach features a dual-branch architecture that jointly processes k-space and image-domain information, incorporating a cross-attention fusion mechanism to facilitate effective information exchange between domains. The framework employs an anatomically-aware reward design and a golden-ratio sampling strategy to ensure uniform k-space coverage while preserving cardiac structural details. Experimental results demonstrate that our method effectively learns optimal radial sampling strategies across multiple acceleration factors, achieving improved reconstruction quality compared to conventional approaches. Code available: https://github.com/Ruru-Xu/RL-kspace-Radial-Sampling

q-bio.TO↗

arXiv2024

HyperCMR: Enhanced Multi-Contrast CMR Reconstruction with Eagle Loss

Accelerating image acquisition for cardiac magnetic resonance imaging (CMRI) is a critical task. CMRxRecon2024 challenge aims to set the state of the art for multi-contrast CMR reconstruction. This paper presents HyperCMR, a novel framework designed to accelerate the reconstruction of multi-contrast cardiac magnetic resonance (CMR) images. HyperCMR enhances the existing PromptMR model by incorporating advanced loss functions, notably the innovative Eagle Loss, which is specifically designed to recover missing high-frequency information in undersampled k-space. Extensive experiments conducted on the CMRxRecon2024 challenge dataset demonstrate that HyperCMR consistently outperforms the baseline across multiple evaluation metrics, achieving superior SSIM and PSNR scores.

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arXiv2024

Mammographic Breast Positioning Assessment via Deep Learning

Breast cancer remains a leading cause of cancer-related deaths among women worldwide, with mammography screening as the most effective method for the early detection. Ensuring proper positioning in mammography is critical, as poor positioning can lead to diagnostic errors, increased patient stress, and higher costs due to recalls. Despite advancements in deep learning (DL) for breast cancer diagnostics, limited focus has been given to evaluating mammography positioning. This paper introduces a novel DL methodology to quantitatively assess mammogram positioning quality, specifically in mediolateral oblique (MLO) views using attention and coordinate convolution modules. Our method identifies key anatomical landmarks, such as the nipple and pectoralis muscle, and automatically draws a posterior nipple line (PNL), offering robust and inherently explainable alternative to well-known classification and regression-based approaches. We compare the performance of proposed methodology with various regression and classification-based models. The CoordAtt UNet model achieved the highest accuracy of 88.63% $\pm$ 2.84 and specificity of 90.25% $\pm$ 4.04, along with a noteworthy sensitivity of 86.04% $\pm$ 3.41. In landmark detection, the same model also recorded the lowest mean errors in key anatomical points and the smallest angular error of 2.42 degrees. Our results indicate that models incorporating attention mechanisms and CoordConv module increase the accuracy in classifying breast positioning quality and detecting anatomical landmarks. Furthermore, we make the labels and source codes available to the community to initiate an open research area for mammography, accessible at https://github.com/tanyelai/deep-breast-positioning.

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arXiv2024

QUBIQ: Uncertainty Quantification for Biomedical Image Segmentation Challenge

Uncertainty in medical image segmentation tasks, especially inter-rater variability, arising from differences in interpretations and annotations by various experts, presents a significant challenge in achieving consistent and reliable image segmentation. This variability not only reflects the inherent complexity and subjective nature of medical image interpretation but also directly impacts the development and evaluation of automated segmentation algorithms. Accurately modeling and quantifying this variability is essential for enhancing the robustness and clinical applicability of these algorithms. We report the set-up and summarize the benchmark results of the Quantification of Uncertainties in Biomedical Image Quantification Challenge (QUBIQ), which was organized in conjunction with International Conferences on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2020 and 2021. The challenge focuses on the uncertainty quantification of medical image segmentation which considers the omnipresence of inter-rater variability in imaging datasets. The large collection of images with multi-rater annotations features various modalities such as MRI and CT; various organs such as the brain, prostate, kidney, and pancreas; and different image dimensions 2D-vs-3D. A total of 24 teams submitted different solutions to the problem, combining various baseline models, Bayesian neural networks, and ensemble model techniques. The obtained results indicate the importance of the ensemble models, as well as the need for further research to develop efficient 3D methods for uncertainty quantification methods in 3D segmentation tasks.

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arXiv2023

Explainable Image Quality Assessment for Medical Imaging

Medical image quality assessment is an important aspect of image acquisition, as poor-quality images may lead to misdiagnosis. Manual labelling of image quality is a tedious task for population studies and can lead to misleading results. While much research has been done on automated analysis of image quality to address this issue, relatively little work has been done to explain the methodologies. In this work, we propose an explainable image quality assessment system and validate our idea on two different objectives which are foreign object detection on Chest X-Rays (Object-CXR) and Left Ventricular Outflow Tract (LVOT) detection on Cardiac Magnetic Resonance (CMR) volumes. We apply a variety of techniques to measure the faithfulness of the saliency detectors, and our explainable pipeline relies on NormGrad, an algorithm which can efficiently localise image quality issues with saliency maps of the classifier. We compare NormGrad with a range of saliency detection methods and illustrate its superior performance as a result of applying these methodologies for measuring the faithfulness of the saliency detectors. We see that NormGrad has significant gains over other saliency detectors by reaching a repeated Pointing Game score of 0.853 for Object-CXR and 0.611 for LVOT datasets.

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arXiv2023

Semi-Supervised Segmentation of Multi-vendor and Multi-center Cardiac MRI using Histogram Matching

Automatic segmentation of the heart cavity is an essential task for the diagnosis of cardiac diseases. In this paper, we propose a semi-supervised segmentation setup for leveraging unlabeled data to segment Left-ventricle, Right-ventricle, and Myocardium. We utilize an enhanced version of residual U-Net architecture on a large-scale cardiac MRI dataset. Handling the class imbalanced data issue using dice loss, the enhanced supervised model is able to achieve better dice scores in comparison with a vanilla U-Net model. We applied several augmentation techniques including histogram matching to increase the performance of our model in other domains. Also, we introduce a simple but efficient semi-supervised segmentation method to improve segmentation results without the need for large labeled data. Finally, we applied our method on two benchmark datasets, STACOM2018, and M\&Ms 2020 challenges, to show the potency of the proposed model. The effectiveness of our proposed model is demonstrated by the quantitative results. The model achieves average dice scores of 0.921, 0.926, and 0.891 for Left-ventricle, Right-ventricle, and Myocardium respectively.

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arXiv2023

Prostate Lesion Estimation using Prostate Masks from Biparametric MRI

Biparametric MRI has emerged as an alternative to multiparametric prostate MRI, which eliminates the need for the potential harms to the patient due to the contrast medium. One major issue with biparametric MRI is difficulty to detect clinically significant prostate cancer (csPCA). Deep learning algorithms have emerged as an alternative solution to detect csPCA in cohort studies. We present a workflow which predicts csPCA on biparametric prostate MRI PI-CAI 2022 Challenge with over 10,000 carefully-curated prostate MRI exams. We propose to to segment the prostate gland first to the central gland (transition + central zone) and the peripheral gland. Then we utilize these predcitions in combination with T2, ADC and DWI images to train an ensemble nnU-Net model. Finally, we utilize clinical indices PSA and ADC intensity distributions of lesion regions to reduce the false positives. Our method achieves top results on open-validation stage with a AUROC of 0.888 and AP of 0.732.

physics.med-ph↗

arXiv2022

Transfer Learning for Electricity Price Forecasting

Electricity price forecasting is an essential task in all the deregulated markets of the world. The accurate prediction of the day-ahead electricity prices is an active research field and available data from various markets can be used as an input for forecasting. A collection of models have been proposed for this task, but the fundamental question on how to use the available big data is often neglected. In this paper, we propose to use transfer learning as a tool for utilizing information from other electricity price markets for forecasting. We pre-train a neural network model on source markets and finally do a fine-tuning for the target market. Moreover, we test different ways to use the rich input data from various electricity price markets. Our experiments on four different day-ahead markets indicate that transfer learning improves the electricity price forecasting performance in a statistically significant manner. Furthermore, we compare our results with stateof-the-art methods in a rolling window scheme to demonstrate the performance of the transfer learning approach.

eess.SP↗

arXiv2022

Detecting respiratory motion artefacts for cardiovascular MRIs to ensure high-quality segmentation

While machine learning approaches perform well on their training domain, they generally tend to fail in a real-world application. In cardiovascular magnetic resonance imaging (CMR), respiratory motion represents a major challenge in terms of acquisition quality and therefore subsequent analysis and final diagnosis. We present a workflow which predicts a severity score for respiratory motion in CMR for the CMRxMotion challenge 2022. This is an important tool for technicians to immediately provide feedback on the CMR quality during acquisition, as poor-quality images can directly be re-acquired while the patient is still available in the vicinity. Thus, our method ensures that the acquired CMR holds up to a specific quality standard before it is used for further diagnosis. Therefore, it enables an efficient base for proper diagnosis without having time and cost-intensive re-acquisitions in cases of severe motion artefacts. Combined with our segmentation model, this can help cardiologists and technicians in their daily routine by providing a complete pipeline to guarantee proper quality assessment and genuine segmentations for cardiovascular scans. The code base is available at https://github.com/MECLabTUDA/QA_med_data/tree/dev_QA_CMRxMotion.

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arXiv2022

Shifted Windows Transformers for Medical Image Quality Assessment

To maintain a standard in a medical imaging study, images should have necessary image quality for potential diagnostic use. Although CNN-based approaches are used to assess the image quality, their performance can still be improved in terms of accuracy. In this work, we approach this problem by using Swin Transformer, which improves the poor-quality image classification performance that causes the degradation in medical image quality. We test our approach on Foreign Object Classification problem on Chest X-Rays (Object-CXR) and Left Ventricular Outflow Tract Classification problem on Cardiac MRI with a four-chamber view (LVOT). While we obtain a classification accuracy of 87.1% and 95.48% on the Object-CXR and LVOT datasets, our experimental results suggest that the use of Swin Transformer improves the Object-CXR classification performance while obtaining a comparable performance for the LVOT dataset. To the best of our knowledge, our study is the first vision transformer application for medical image quality assessment.

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arXiv2022

A Deep Learning-based Integrated Framework for Quality-aware Undersampled Cine Cardiac MRI Reconstruction and Analysis

Cine cardiac magnetic resonance (CMR) imaging is considered the gold standard for cardiac function evaluation. However, cine CMR acquisition is inherently slow and in recent decades considerable effort has been put into accelerating scan times without compromising image quality or the accuracy of derived results. In this paper, we present a fully-automated, quality-controlled integrated framework for reconstruction, segmentation and downstream analysis of undersampled cine CMR data. The framework enables active acquisition of radial k-space data, in which acquisition can be stopped as soon as acquired data are sufficient to produce high quality reconstructions and segmentations. This results in reduced scan times and automated analysis, enabling robust and accurate estimation of functional biomarkers. To demonstrate the feasibility of the proposed approach, we perform realistic simulations of radial k-space acquisitions on a dataset of subjects from the UK Biobank and present results on in-vivo cine CMR k-space data collected from healthy subjects. The results demonstrate that our method can produce quality-controlled images in a mean scan time reduced from 12 to 4 seconds per slice, and that image quality is sufficient to allow clinically relevant parameters to be automatically estimated to within 5% mean absolute difference.

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arXiv2022

MyoPS: A Benchmark of Myocardial Pathology Segmentation Combining Three-Sequence Cardiac Magnetic Resonance Images

Assessment of myocardial viability is essential in diagnosis and treatment management of patients suffering from myocardial infarction, and classification of pathology on myocardium is the key to this assessment. This work defines a new task of medical image analysis, i.e., to perform myocardial pathology segmentation (MyoPS) combining three-sequence cardiac magnetic resonance (CMR) images, which was first proposed in the MyoPS challenge, in conjunction with MICCAI 2020. The challenge provided 45 paired and pre-aligned CMR images, allowing algorithms to combine the complementary information from the three CMR sequences for pathology segmentation. In this article, we provide details of the challenge, survey the works from fifteen participants and interpret their methods according to five aspects, i.e., preprocessing, data augmentation, learning strategy, model architecture and post-processing. In addition, we analyze the results with respect to different factors, in order to examine the key obstacles and explore potential of solutions, as well as to provide a benchmark for future research. We conclude that while promising results have been reported, the research is still in the early stage, and more in-depth exploration is needed before a successful application to the clinics. Note that MyoPS data and evaluation tool continue to be publicly available upon registration via its homepage (www.sdspeople.fudan.edu.cn/zhuangxiahai/0/myops20/).

eess.IV↗

arXiv2021

A survey on shape-constraint deep learning for medical image segmentation

Since the advent of U-Net, fully convolutional deep neural networks and its many variants have completely changed the modern landscape of deep learning based medical image segmentation. However, the over dependence of these methods on pixel level classification and regression has been identified early on as a problem. Especially when trained on medical databases with sparse available annotation, these methods are prone to generate segmentation artifacts such as fragmented structures, topological inconsistencies and islands of pixel. These artefacts are especially problematic in medical imaging since segmentation is almost always a pre-processing step for some downstream evaluation. The range of possible downstream evaluations is rather big, for example surgical planning, visualization, shape analysis, prognosis, treatment planning etc. However, one common thread across all these downstream tasks is the demand of anatomical consistency. To ensure the segmentation result is anatomically consistent, approaches based on Markov/ Conditional Random Fields, Statistical Shape Models are becoming increasingly popular over the past 5 years. In this review paper, a broad overview of recent literature on bringing anatomical constraints for medical image segmentation is given, the shortcomings and opportunities of the proposed methods are thoroughly discussed and potential future work is elaborated. We review the most relevant papers published until the submission date. For quick access, important details such as the underlying method, datasets and performance are tabulated.

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arXiv2020

Channel Attention Networks for Robust MR Fingerprinting Matching

Magnetic Resonance Fingerprinting (MRF) enables simultaneous mapping of multiple tissue parameters such as T1 and T2 relaxation times. The working principle of MRF relies on varying acquisition parameters pseudo-randomly, so that each tissue generates its unique signal evolution during scanning. Even though MRF provides faster scanning, it has disadvantages such as erroneous and slow generation of the corresponding parametric maps, which needs to be improved. Moreover, there is a need for explainable architectures for understanding the guiding signals to generate accurate parametric maps. In this paper, we addressed both of these shortcomings by proposing a novel neural network architecture consisting of a channel-wise attention module and a fully convolutional network. The proposed approach, evaluated over 3 simulated MRF signals, reduces error in the reconstruction of tissue parameters by 8.88% for T1 and 75.44% for T2 with respect to state-of-the-art methods. Another contribution of this study is a new channel selection method: attention-based channel selection. Furthermore, the effect of patch size and temporal frames of MRF signal on channel reduction are analyzed by employing a channel-wise attention.

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arXiv2020

A Topological Loss Function for Deep-Learning based Image Segmentation using Persistent Homology

We introduce a method for training neural networks to perform image or volume segmentation in which prior knowledge about the topology of the segmented object can be explicitly provided and then incorporated into the training process. By using the differentiable properties of persistent homology, a concept used in topological data analysis, we can specify the desired topology of segmented objects in terms of their Betti numbers and then drive the proposed segmentations to contain the specified topological features. Importantly this process does not require any ground-truth labels, just prior knowledge of the topology of the structure being segmented. We demonstrate our approach in three experiments. Firstly we create a synthetic task in which handwritten MNIST digits are de-noised, and show that using this kind of topological prior knowledge in the training of the network significantly improves the quality of the de-noised digits. Secondly we perform an experiment in which the task is segmenting the myocardium of the left ventricle from cardiac magnetic resonance images. We show that the incorporation of the prior knowledge of the topology of this anatomy improves the resulting segmentations in terms of both the topological accuracy and the Dice coefficient. Thirdly, we extend the method to 3D volumes and demonstrate its performance on the task of segmenting the placenta from ultrasound data, again showing that incorporating topological priors improves performance on this challenging task. We find that embedding explicit prior knowledge in neural network segmentation tasks is most beneficial when the segmentation task is especially challenging and that it can be used in either a semi-supervised or post-processing context to extract a useful training gradient from images without pixelwise labels.

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