Elif Keles

Dr. Elif Keles

orcid

Research Focus & Metrics

Academic Career Length

21Years (2006-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.

27 November 2023 in npj Digital Medicine
Verified
Journal Article
Open access
PDF file
EKElif Keles
Elif Keles
UBUlas Bagci
Ulas Bagci
Machine learning and deep learning are two subsets of artificial intelligence that involve teaching computers to learn and make decisions from any sort of data. Most recent developments in artificial intelligence are coming from deep learning, which has proven revolutionary in almost all fields, from computer vision to health sciences. The effects of deep learning in medicine have changed the conventional ways of clinical application significantly. Although some sub-fields of medicine, such as pediatrics, have been relatively slow in receiving the critical benefits of deep learning, related research in pediatrics has started to accumulate to a significant level, too. Hence, in this paper, we review recently developed machine learning and deep learning-based solutions for neonatology applications. We systematically evaluate the roles of both classical machine learning and deep learning in neonatology applications, define the methodologies, including algorithmic developments, and describe the remaining challenges in the assessment of neonatal diseases by using PRISMA 2020 guidelines. To date, the primary areas of focus in neonatology regarding AI applications have included survival analysis, neuroimaging, analysis of vital parameters and biosignals, and retinopathy of prematurity diagnosis. We have categorically summarized 106 research articles from 1996 to 2022 and discussed their pros and cons, respectively. In this systematic review, we aimed to further enhance the comprehensiveness of the study. We also discuss possible directions for new AI models and the future of neonatology with the rising power of AI, suggesting roadmaps for the integration of AI into neonatal intensive care units.

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.

7 July 2022 in Neonatology
Verified
Journal Article
Open access
PDF file
EKElif Keles
Elif Keles
PWPia Wintermark
Pia Wintermark
FGFloris Groenendaal
Floris Groenendaal
NBNoor Borloo
Noor Borloo
ASAnne Smits
Anne Smits
Karel AllegaertKarel Allegaert
Karel Allegaert
Introduction: There is large variability in kidney function and injury in neonates with neonatal encephalopathy (NE) treated with therapeutic hypothermia (TH). Acute kidney injury (AKI) definitions that apply categorical approaches may lose valuable information about kidney function in individual patients. Centile serum creatinine (SCr) over postnatal age (PNA) may provide more valuable information in TH neonates. Methods: Data from seven TH neonates and one non-TH-treated, non-NE control cohorts were pooled in a retrospective study. SCr centiles over PNA, and AKI incidence (definition: SCr ↑≥0.3 mg/dL within 48 h, or ↑ ≥1.5 fold vs. the lowest prior SCr within 7 days) and mortality were calculated. Repeated measurement linear models were applied to SCr trends, modeling SCr on PNA, birth weight or gestational age (GA), using heterogeneous autoregressive residual covariance structure and maximum likelihood methods. Findings were compared to patterns in the control cohort. Results: Among 1,136 TH neonates, representing 4,724 SCr observations, SCr (10th–25th–50th–75th–90th–95th) PNA centiles (day 1–10) were generated. In TH neonates, the AKI incidence was 132/1,136 (11.6%), mortality 193/1,136 (17%). AKI neonates had a higher mortality (37.2–14.3%, p < 0.001). Median SCr patterns over PNA were significantly higher in nonsurvivors (p < 0.01) or AKI neonates (p < 0.001). In TH-treated neonates, PNA and GA or birth weight explained SCr variability. Patterns over PNA were significantly higher in TH neonates to controls (801 neonates, 2,779 SCr). Conclusions: SCr patterns in TH-treated NE neonates are specific. Knowing PNA-related patterns enable clinicians to better assess kidney function and tailor pharmacotherapy, fluids, or kidney supportive therapies.

1 January 2022 in TURKISH JOURNAL OF MEDICAL SCIENCES
Verified
Journal Article
Open access
PDF file
EKElif Keles
Elif Keles
HKHasan Huseyin Kazan
Hasan Huseyin Kazan
LALati̇fE Arzu Aral
Lati̇fE Arzu Aral
HBHayrunnisa Bolay
Hayrunnisa Bolay
Neonatal brain injury is a significant reason of neurodevelopmental abnormalities and long-term neurological impairments. Hypoxic-ischemic encephalopathy and preterm brain injury, including intraventricular hemorrhage are the most common grounds of brain injury for full-term and preterm neonates. The prevalence of hypoxic ischemic encephalopathy varies globally, ranging from 1 to 3.5/1000 live births in high-resource countries and 26/1000 in low-resource countries. Preterm birth's global incidence is 15 million, a significant reason for infant mortality and morbidity, permanent neurologic problems, and the associated social and economic burden. The widespread neurodevelopmental effects of neonatal brain injury could have an unfavorable impact on a variety of aspects of cognitive, linguistic, behavioral, sensory, and motor functions. Brain injury occurs via various mechanisms, including energy deprivation, excitatory amino acids, mitochondrial dysfunction, reactive oxygen species, and inflammation giving rise to different forms of cell death. The contribution of microglial activity in neonatal brain injury has widely been underlined by focusing on cell death mechanisms since the neuronal death pathways during their development are distinct from those in the adult brain. Iron accumulation and lipid peroxidation cause a relatively novel type of regulated cell death called ferroptosis. Neonates generally have biochemical iron inequalities, and their antioxidant potential is highly restricted, implying that ferroptosis may be significant in pathologic conditions. Moreover, inhaled nitric oxide therapy in infants may lead to microglial inflammation via ferroptosis and neuronal injury in the developing brain. This review article aims to summarize the studies that investigated the association between neonatal brain injury and iron metabolism, with a particular emphasis on the microglial activity and its application to the inhibition of neonatal brain injury.