arXiv subjects

İlkay Öksüz

Publications and source records attributed to İlkay Öksüz.

8 recordsLinked to original sources

arXiv2026

Sharpening the Ensemble: An SSIM-Aligned Residual Refiner for Brain-MRI Inpainting Post-Processing

Brain-MRI inpainting replaces a masked region of a scan with synthesized, anatomically plausible healthy tissue, so that analysis tools built for healthy brains can be applied to images they would otherwise reject. On the BraTS local-synthesis benchmark, which ranks submissions on the structural similarity index (SSIM), the peak signal-to-noise ratio, and the mean squared error (MSE) jointly, the strongest recent models are accurate, but several report blurry synthesized regions and attribute this to the mean-seeking behavior of the $\ell_1$ and MSE terms in their training losses. We address this in post-processing, forming a deep ensemble of the two co-first-place 2025 models and training a lightweight residual refiner on the ensemble's own outputs under an $\ell_1$ loss augmented with a structural-similarity term whose weight $\lambda$ we vary. At a moderate $\lambda$ the refiner improves SSIM over the ensemble, from $0.8767$ to $0.8780$ on a held-out reproduction of the official scorer and from $0.8555$ to $0.8572$ on the official validation leaderboard, with essentially no change in MSE. The gain is small but consistent, improving $62.6\%$ of the held-out cases with a signed-rank $p=2.2\times10^{-7}$, whereas over-weighting the structural term reverses it. Two ablations bound the effect. Adding any third model to the two-model ensemble degrades it, and classical unsharp masking fails to improve SSIM at any strength (best $0.8765$ against $0.8767$), so the gain reflects learned rather than indiscriminate sharpening. The result is a cheap, reproducible post-processing stage that improves an already strong ensemble without any large-scale retraining.

cs.CV↗

arXiv2026

VEELA: A Clinically-Constrained Benchmark for Liver Vessel Segmentation in Computed Tomography Angiography

Accurate segmentation of hepatic and portal vessels in contrast-enhanced computed tomography angiography (CTA) remains challenging due to complex vascular topology, peripheral visibility limitations, and acquisition-induced ambiguities. While existing public datasets offer valuable benchmarks, few include clinically realistic annotation constraints. We introduce VEELA (Vessel Extraction and Extrication for Liver Analysis), a rigorously curated liver vessel dataset derived from 40 CTA scans inherited from the CHAOS grand-challenge cohort. All vessels were manually delineated slice-by-slice under multi-expert consensus, using a strict visibility-driven annotation policy and avoiding anatomically inferred interpolation. This design explicitly captures anatomical variability and imaging-related uncertainty. As a continuation of the CHAOS challenge, VEELA enables reproducible cross-benchmark evaluation while extending the scope to fine-grained hepatic and portal vessel segmentation. We further establish a standardized benchmarking framework and analyze complementary evaluation metrics, including topology-aware (clDice), overlap-based (IoU), boundary-sensitive (NSD), and geometry-aware (area, length) measures. Our results demonstrate that different metrics capture distinct aspects of vascular integrity, underscoring the necessity of multi-perspective evaluation for clinically meaningful vessel segmentation. VEELA is publicly released to facilitate reproducible research and support the development of robust vascular segmentation methods. Researchers can access the evaluation metrics, dataset, and submission platform at https://www.synapse.org/Synapse:syn65471967.

cs.CV↗

arXiv2025

Beyond Pixels: Medical Image Quality Assessment with Implicit Neural Representations

Artifacts pose a significant challenge in medical imaging, impacting diagnostic accuracy and downstream analysis. While image-based approaches for detecting artifacts can be effective, they often rely on preprocessing methods that can lead to information loss and high-memory-demand medical images, thereby limiting the scalability of classification models. In this work, we propose the use of implicit neural representations (INRs) for image quality assessment. INRs provide a compact and continuous representation of medical images, naturally handling variations in resolution and image size while reducing memory overhead. We develop deep weight space networks, graph neural networks, and relational attention transformers that operate on INRs to achieve image quality assessment. Our method is evaluated on the ACDC dataset with synthetically generated artifact patterns, demonstrating its effectiveness in assessing image quality while achieving similar performance with fewer parameters.

eess.IV↗

arXiv2025

Pic2Diagnosis: A Method for Diagnosis of Cardiovascular Diseases from the Printed ECG Pictures

The electrocardiogram (ECG) is a vital tool for diagnosing heart diseases. However, many disease patterns are derived from outdated datasets and traditional stepwise algorithms with limited accuracy. This study presents a method for direct cardiovascular disease (CVD) diagnosis from ECG images, eliminating the need for digitization. The proposed approach utilizes a two-step curriculum learning framework, beginning with the pre-training of a classification model on segmentation masks, followed by fine-tuning on grayscale, inverted ECG images. Robustness is further enhanced through an ensemble of three models with averaged outputs, achieving an AUC of 0.9534 and an F1 score of 0.7801 on the BHF ECG Challenge dataset, outperforming individual models. By effectively handling real-world artifacts and simplifying the diagnostic process, this method offers a reliable solution for automated CVD diagnosis, particularly in resource-limited settings where printed or scanned ECG images are commonly used. Such an automated procedure enables rapid and accurate diagnosis, which is critical for timely intervention in CVD cases that often demand urgent care.

cs.CV↗

arXiv2025

Extreme Cardiac MRI Analysis under Respiratory Motion: Results of the CMRxMotion Challenge

Deep learning models have achieved state-of-the-art performance in automated Cardiac Magnetic Resonance (CMR) analysis. However, the efficacy of these models is highly dependent on the availability of high-quality, artifact-free images. In clinical practice, CMR acquisitions are frequently degraded by respiratory motion, yet the robustness of deep learning models against such artifacts remains an underexplored problem. To promote research in this domain, we organized the MICCAI CMRxMotion challenge. We curated and publicly released a dataset of 320 CMR cine series from 40 healthy volunteers who performed specific breathing protocols to induce a controlled spectrum of motion artifacts. The challenge comprised two tasks: 1) automated image quality assessment to classify images based on motion severity, and 2) robust myocardial segmentation in the presence of motion artifacts. A total of 22 algorithms were submitted and evaluated on the two designated tasks. This paper presents a comprehensive overview of the challenge design and dataset, reports the evaluation results for the top-performing methods, and further investigates the impact of motion artifacts on five clinically relevant biomarkers. All resources and code are publicly available at: https://github.com/CMRxMotion

eess.IV↗

arXiv2024

GLIMS: Attention-Guided Lightweight Multi-Scale Hybrid Network for Volumetric Semantic Segmentation

Convolutional Neural Networks (CNNs) have become widely adopted for medical image segmentation tasks, demonstrating promising performance. However, the inherent inductive biases in convolutional architectures limit their ability to model long-range dependencies and spatial correlations. While recent transformer-based architectures address these limitations by leveraging self-attention mechanisms to encode long-range dependencies and learn expressive representations, they often struggle to extract low-level features and are highly dependent on data availability. This motivated us for the development of GLIMS, a data-efficient attention-guided hybrid volumetric segmentation network. GLIMS utilizes Dilated Feature Aggregator Convolutional Blocks (DACB) to capture local-global feature correlations efficiently. Furthermore, the incorporated Swin Transformer-based bottleneck bridges the local and global features to improve the robustness of the model. Additionally, GLIMS employs an attention-guided segmentation approach through Channel and Spatial-Wise Attention Blocks (CSAB) to localize expressive features for fine-grained border segmentation. Quantitative and qualitative results on glioblastoma and multi-organ CT segmentation tasks demonstrate GLIMS' effectiveness in terms of complexity and accuracy. GLIMS demonstrated outstanding performance on BraTS2021 and BTCV datasets, surpassing the performance of Swin UNETR. Notably, GLIMS achieved this high performance with a significantly reduced number of trainable parameters. Specifically, GLIMS has 47.16M trainable parameters and 72.30G FLOPs, while Swin UNETR has 61.98M trainable parameters and 394.84G FLOPs. The code is publicly available on https://github.com/yaziciz/GLIMS.

cs.CV↗

arXiv2024

Attention-Enhanced Hybrid Feature Aggregation Network for 3D Brain Tumor Segmentation

Glioblastoma is a highly aggressive and malignant brain tumor type that requires early diagnosis and prompt intervention. Due to its heterogeneity in appearance, developing automated detection approaches is challenging. To address this challenge, Artificial Intelligence (AI)-driven approaches in healthcare have generated interest in efficiently diagnosing and evaluating brain tumors. The Brain Tumor Segmentation Challenge (BraTS) is a platform for developing and assessing automated techniques for tumor analysis using high-quality, clinically acquired MRI data. In our approach, we utilized a multi-scale, attention-guided and hybrid U-Net-shaped model -- GLIMS -- to perform 3D brain tumor segmentation in three regions: Enhancing Tumor (ET), Tumor Core (TC), and Whole Tumor (WT). The multi-scale feature extraction provides better contextual feature aggregation in high resolutions and the Swin Transformer blocks improve the global feature extraction at deeper levels of the model. The segmentation mask generation in the decoder branch is guided by the attention-refined features gathered from the encoder branch to enhance the important attributes. Moreover, hierarchical supervision is used to train the model efficiently. Our model's performance on the validation set resulted in 92.19, 87.75, and 83.18 Dice Scores and 89.09, 84.67, and 82.15 Lesion-wise Dice Scores in WT, TC, and ET, respectively. The code is publicly available at https://github.com/yaziciz/GLIMS.

eess.IV↗

arXiv2023

Interpretable ECG Analysis for Myocardial Infarction Detection through Counterfactuals

In the evolving landscape of ECG signal analysis, the challenge of limited transparency in machine learning models remains a significant barrier to their effective integration into clinical practice. This study addresses this issue by investigating the use of counterfactual explanations to improve model interpretability for clinicians, particularly in differentiating healthy subjects from myocardial infarction patients. Utilizing the PTB-XL dataset, we developed a methodology for systematic feature extraction and refinement to prepare for counterfactual analysis. This led to the creation of the Visualizing Counterfactual Clues on Electrocardiograms (VCCE) method, designed to improve the practicality of counterfactual explanations in a clinical setting. The validity of our approach was assessed using custom metrics that reflect the diagnostic relevance of counterfactuals, evaluated with the help of two cardiologists. Our findings suggest that this approach could support future efforts in using ECGs to predict patient outcomes for cardiac conditions, achieving interpretation validity scores of 23.29 $\pm$ 1.04 and 20.28 $\pm$ 0.99 out of 25 for high and moderate-quality interpretations, respectively. Clinical alignment scores of 0.83 $\pm$ 0.12 for high-quality and 0.57 $\pm$ 0.10 for moderate-quality interpretations underscore the potential clinical applicability of our method. The methodology and findings of this study contribute to the ongoing discussion on enhancing the interpretability of machine learning models in cardiology, offering a concept that bridges the gap between advanced data analysis techniques and clinical decision-making. The source code for this study is available at https://github.com/tanyelai/vcce.

eess.SP↗