Gorkem Durak

Dr. Gorkem Durak

orcid

Research Focus & Metrics

Academic Career Length

5Years (2022-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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8 November 2024 in Medical Image Analysis
Verified
Journal Article
Open access
ZZZheyuan Zhang
Zheyuan Zhang
EKElif Keles
Elif Keles
Gorkem DurakGorkem Durak
Gorkem Durak
YTYavuz Taktak
Yavuz Taktak
OSOnkar Susladkar
Onkar Susladkar
UBUlas Bagci
Ulas Bagci
Automated volumetric segmentation of the pancreas on cross-sectional imaging is needed for diagnosis and follow-up of pancreatic diseases. While CT-based pancreatic segmentation is more established, MRI-based segmentation methods are understudied, largely due to a lack of publicly available datasets, benchmarking research efforts, and domain-specific deep learning methods. In this retrospective study, we collected a large dataset (767 scans from 499 participants) of T1-weighted (T1 W) and T2-weighted (T2 W) abdominal MRI series from five centers between March 2004 and November 2022. We also collected CT scans of 1,350 patients from publicly available sources for benchmarking purposes. We introduced a new pancreas segmentation method, called PanSegNet, combining the strengths of nnUNet and a Transformer network with a new linear attention module enabling volumetric computation. We tested PanSegNet's accuracy in cross-modality (a total of 2,117 scans) and cross-center settings with Dice and Hausdorff distance (HD95) evaluation metrics. We used Cohen's kappa statistics for intra and inter-rater agreement evaluation and paired t-tests for volume and Dice comparisons, respectively. For segmentation accuracy, we achieved Dice coefficients of 88.3% (±7.2%, at case level) with CT, 85.0% (±7.9%) with T1 W MRI, and 86.3% (±6.4%) with T2 W MRI. There was a high correlation for pancreas volume prediction with R2 of 0.91, 0.84, and 0.85 for CT, T1 W, and T2 W, respectively. We found moderate inter-observer (0.624 and 0.638 for T1 W and T2 W MRI, respectively) and high intra-observer agreement scores. All MRI data is made available at https://osf.io/kysnj/. Our source code is available at https://github.com/NUBagciLab/PaNSegNet.

17 December 2024 in IEEE Transactions on Medical Imaging
Verified
Journal Article
Closed access
ZZZheyuan Zhang
Zheyuan Zhang
LYLanhong Yao
Lanhong Yao
BWBin Wang
Bin Wang
Debesh JhaDebesh Jha
Debesh Jha
Gorkem DurakGorkem Durak
Gorkem Durak
UBUlas Bagci
Ulas Bagci
Large-scale, big-variant, high-quality data are crucial for developing robust and successful deep-learning models for medical applications since they potentially enable better generalization performance and avoid overfitting. However, the scarcity of high-quality labeled data always presents significant challenges. This paper proposes a novel approach to address this challenge by developing controllable diffusion models for medical image synthesis, called DiffBoost. We leverage recent diffusion probabilistic models to generate realistic and diverse synthetic medical image data that preserve the essential characteristics of the original medical images by incorporating edge information of objects to guide the synthesis process. In our approach, we ensure that the synthesized samples adhere to medically relevant constraints and preserve the underlying structure of imaging data. Due to the random sampling process by the diffusion model, we can generate an arbitrary number of synthetic images with diverse appearances. To validate the effectiveness of our proposed method, we conduct an extensive set of medical image segmentation experiments on multiple datasets, including Ultrasound breast (+13.87%), CT spleen (+0.38%), and MRI prostate (+7.78%), achieving significant improvements over the baseline segmentation methods. The promising results demonstrate the effectiveness of our DiffBoost for medical image segmentation tasks and show the feasibility of introducing a first-ever text-guided diffusion model for general medical image segmentation tasks. With carefully designed ablation experiments, we investigate the influence of various data augmentations, hyper-parameter settings, patch size for generating random merging mask settings, and combined influence with different network architectures. Source code with checkpoints are available at https:// github.com/NUBagciLab/DiffBoost.

13 February 2025 in Bioengineering
Verified
Journal Article
Open access
PDF file
Debesh JhaDebesh Jha
Debesh Jha
Gorkem DurakGorkem Durak
Gorkem Durak
VSVanshali Sharma
Vanshali Sharma
EKElif Keles
Elif Keles
VÇVedat Çiçek
Vedat Çiçek
UBUlas Bagci
Ulas Bagci
Artificial Intelligence (AI) is reshaping healthcare through advancements in clinical decision support and diagnostic capabilities. While human expertise remains foundational to medical practice, AI-powered tools are increasingly matching or exceeding specialist-level performance across multiple domains, paving the way for a new era of democratized healthcare access. These systems promise to reduce disparities in care delivery across demographic, racial, and socioeconomic boundaries by providing high-quality diagnostic support at scale. As a result, advanced healthcare services can be affordable to all populations, irrespective of demographics, race, or socioeconomic background. The democratization of such AI tools can reduce the cost of care, optimize resource allocation, and improve the quality of care. In contrast to humans, AI can potentially uncover complex relationships in the data from a large set of inputs and generate new evidence-based knowledge in medicine. However, integrating AI into healthcare raises several ethical and philosophical concerns, such as bias, transparency, autonomy, responsibility, and accountability. In this study, we examine recent advances in AI-enabled medical image analysis, current regulatory frameworks, and emerging best practices for clinical integration. We analyze both technical and ethical challenges inherent in deploying AI systems across healthcare institutions, with particular attention to data privacy, algorithmic fairness, and system transparency. Furthermore, we propose practical solutions to address key challenges, including data scarcity, racial bias in training datasets, limited model interpretability, and systematic algorithmic biases. Finally, we outline a conceptual algorithm for responsible AI implementations and identify promising future research and development directions.

22 December 2024 in Cancers
Verified
Journal Article
Open access
PDF file
DSDeniz Seyithanoglu
Deniz Seyithanoglu
Gorkem DurakGorkem Durak
Gorkem Durak
EKElif Keles
Elif Keles
AMAlpay Medetalibeyoglu
Alpay Medetalibeyoglu
ZHZiliang Hong
Ziliang Hong
UBUlas Bagci
Ulas Bagci
Pancreatic cystic lesions (PCLs) represent a spectrum of non-neoplasms and neoplasms with varying malignant potential, posing significant challenges in diagnosis and management. While some PCLs are precursors to pancreatic cancer, others remain benign, necessitating accurate differentiation for optimal patient care. Conventional approaches to PCL management rely heavily on radiographic imaging, and endoscopic ultrasound (EUS) guided fine-needle aspiration (FNA), coupled with clinical and biochemical data. However, the observer-dependent nature of image interpretation and the complex morphology of PCLs can lead to diagnostic uncertainty and variability in patient management strategies. This review critically evaluates current PCL diagnosis and surveillance practices, showing features of the different lesions and highlighting the potential limitations of conventional methods. We then explore the potential of artificial intelligence (AI) to transform PCL management. AI-driven strategies, including deep learning algorithms for automated pancreas and lesion segmentation, and radiomics for analyzing heterogeneity, can improve diagnostic accuracy and risk stratification. These advanced techniques can provide more objective and reproducible assessments, aiding clinicians in decision-making regarding follow-up intervals and surgical interventions. Early results suggest that AI-driven methods can significantly improve patient outcomes by enabling earlier detection of high-risk lesions and reducing unnecessary procedures for benign cysts. Finally, this review emphasizes that AI-driven approaches could potentially reshape the landscape of PCL management, ultimately leading to improved pancreatic cancer prevention.

1 May 2023 in Diagnostic and Interventional Radiology
Verified
Journal Article
Open access
OIOkan İnCe
Okan İnCe
EUEmre Uysal
Emre Uysal
Gorkem DurakGorkem Durak
Gorkem Durak
SÖSuzan Önol
Suzan Önol
BYBinnur Dönmez Yılmaz
Binnur Dönmez Yılmaz
HÖHakan Önder
Hakan Önder
This study aimed to evaluate the potential of machine learning-based models for predicting carcinogenic human papillomavirus (HPV) oncogene types using radiomics features from magnetic resonance imaging (MRI). Pre-treatment MRI images of patients with cervical cancer were collected retrospectively. An HPV DNA oncogene analysis was performed based on cervical biopsy specimens. Radiomics features were extracted from contrast-enhanced T1-weighted images (CE-T1) and T2-weighted images (T2WI). A third feature subset was created as a combined group by concatenating the CE-T1 and T2WI subsets. Feature selection was performed using Pearson's correlation coefficient and wrapper- based sequential-feature selection. Two models were built with each feature subset, using support vector machine (SVM) and logistic regression (LR) classifiers. The models were validated using a five-fold cross-validation technique and compared using Wilcoxon's signed rank and Friedman's tests. Forty-one patients were enrolled in the study (26 were positive for carcinogenic HPV oncogenes, and 15 were negative). A total of 851 features were extracted from each imaging sequence. After feature selection, 5, 17, and 20 features remained in the CE-T1, T2WI, and combined groups, respectively. The SVM models showed 83%, 95%, and 95% accuracy scores, and the LR models revealed 83%, 81%, and 92.5% accuracy scores in the CE-T1, T2WI, and combined groups, respectively. The SVM algorithm performed better than the LR algorithm in the T2WI feature subset (P = 0.005), and the feature sets in the T2WI and the combined group performed better than CE-T1 in the SVM model (P = 0.033 and 0.006, respectively). The combined group feature subset performed better than T2WI in the LR model (P = 0.023). Machine learning-based radiomics models based on pre-treatment MRI can detect carcinogenic HPV status with discriminative accuracy.

16 June 2025 in Pancreatology
Verified
Journal Article
Closed access
EKElif Keles
Elif Keles
MYMerve Yazol
Merve Yazol
Gorkem DurakGorkem Durak
Gorkem Durak
ZHZiliang Hong
Ziliang Hong
HAHalil Ertugrul Aktas
Halil Ertugrul Aktas
UBUlas Bagci
Ulas Bagci