Mert Karabacak

Dr. Mert Karabacak

orcid

Research Focus & Metrics

Academic Career Length

9Years (2018-Present)

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

Representative Publications

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6 June 2023 in JMIR Medical Education
Verified
Journal Article
Open access
MKMert Karabacak
Mert Karabacak
BOBurak Berksu Ozkara
Burak Berksu Ozkara
KMKonstantinos Margetis
Konstantinos Margetis
MWMax Wintermark
Max Wintermark
SBSotirios Bisdas
Sotirios Bisdas
Artificial intelligence (AI) and generative language models (GLMs) present significant opportunities for enhancing medical education, including the provision of realistic simulations, digital patients, personalized feedback, evaluation methods, and the elimination of language barriers. These advanced technologies can facilitate immersive learning environments and enhance medical students' educational outcomes. However, ensuring content quality, addressing biases, and managing ethical and legal concerns present obstacles. To mitigate these challenges, it is necessary to evaluate the accuracy and relevance of AI-generated content, address potential biases, and develop guidelines and policies governing the use of AI-generated content in medical education. Collaboration among educators, researchers, and practitioners is essential for developing best practices, guidelines, and transparent AI models that encourage the ethical and responsible use of GLMs and AI in medical education. By sharing information about the data used for training, obstacles encountered, and evaluation methods, developers can increase their credibility and trustworthiness within the medical community. In order to realize the full potential of AI and GLMs in medical education while mitigating potential risks and obstacles, ongoing research and interdisciplinary collaboration are necessary. By collaborating, medical professionals can ensure that these technologies are effectively and responsibly integrated, contributing to enhanced learning experiences and patient care.

4 January 2023 in Cancers
Verified
Journal Article
Open access
PDF file
BOBurak Berksu Ozkara
Burak Berksu Ozkara
MCMelissa M. Chen
Melissa M. Chen
CFChristian Federau
Christian Federau
MKMert Karabacak
Mert Karabacak
TBTina Marie Briere
Tina Marie Briere
MWMax Wintermark
Max Wintermark
Since manual detection of brain metastases (BMs) is time consuming, studies have been conducted to automate this process using deep learning. The purpose of this study was to conduct a systematic review and meta-analysis of the performance of deep learning models that use magnetic resonance imaging (MRI) to detect BMs in cancer patients. A systematic search of MEDLINE, EMBASE, and Web of Science was conducted until 30 September 2022. Inclusion criteria were: patients with BMs; deep learning using MRI images was applied to detect the BMs; sufficient data were present in terms of detective performance; original research articles. Exclusion criteria were: reviews, letters, guidelines, editorials, or errata; case reports or series with less than 20 patients; studies with overlapping cohorts; insufficient data in terms of detective performance; machine learning was used to detect BMs; articles not written in English. Quality Assessment of Diagnostic Accuracy Studies-2 and Checklist for Artificial Intelligence in Medical Imaging was used to assess the quality. Finally, 24 eligible studies were identified for the quantitative analysis. The pooled proportion of patient-wise and lesion-wise detectability was 89%. Articles should adhere to the checklists more strictly. Deep learning algorithms effectively detect BMs. Pooled analysis of false positive rates could not be estimated due to reporting differences.


28 January 2023 in Cancers
Verified
Journal Article
Open access
PDF file
MKMert Karabacak
Mert Karabacak
KMKonstantinos Margetis
Konstantinos Margetis
Background: Preoperative prediction of short-term postoperative outcomes in spinal tumor patients can lead to more precise patient care plans that reduce the likelihood of negative outcomes. With this study, we aimed to develop machine learning algorithms for predicting short-term postoperative outcomes and implement these models in an open-source web application. Methods: Patients who underwent surgical resection of spinal tumors were identified using the American College of Surgeons, National Surgical Quality Improvement Program. Three outcomes were predicted: prolonged length of stay (LOS), nonhome discharges, and major complications. Four machine learning algorithms were developed and integrated into an open access web application to predict these outcomes. Results: A total of 3073 patients that underwent spinal tumor resection were included in the analysis. The most accurately predicted outcomes in terms of the area under the receiver operating characteristic curve (AUROC) was the prolonged LOS with a mean AUROC of 0.745 The most accurately predicting algorithm in terms of AUROC was random forest, with a mean AUROC of 0.743. An open access web application was developed for getting predictions for individual patients based on their characteristics and this web application can be accessed here: huggingface.co/spaces/MSHS-Neurosurgery-Research/NSQIP-ST. Conclusion: Machine learning approaches carry significant potential for the purpose of predicting postoperative outcomes following spinal tumor resections. Development of predictive models as clinically useful decision-making tools may considerably enhance risk assessment and prognosis as the amount of data in spinal tumor surgery continues to rise.

12 December 2022 in Acta Radiologica
Verified
Journal Article
Closed access
MKMert Karabacak
Mert Karabacak
BOBurak Berksu Ozkara
Burak Berksu Ozkara
AOAdmir Ozturk
Admir Ozturk
BKBusra Kaya
Busra Kaya
ZCZeynep Cirak
Zeynep Cirak
ZOZeynep Ozcan
Zeynep Ozcan
Background: Medulloblastomas are a major cause of cancer-related mortality in the pediatric population. Four molecular groups have been identified, and these molecular groups drive risk stratification, prognostic modeling, and the development of novel treatment modalities. It has been demonstrated that radiomics-based machine learning (ML) models are effective at predicting the diagnosis, molecular class, and grades of CNS tumors. Purpose: To assess radiomics-based ML models’ diagnostic performance in predicting medulloblastoma subgroups and the methodological quality of the studies. Material and Methods: A comprehensive literature search was performed on PubMed; the last search was conducted on 1 May 2022. Studies that predicted all four medulloblastoma subgroups in patients with histopathologically confirmed medulloblastoma and reporting area under the curve (AUC) values were included in the study. The quality assessments were conducted according to the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) and Checklist for Artificial Intelligence in Medical Imaging (CLAIM). A meta-analysis of radiomics-based ML studies’ diagnostic performance for the preoperative evaluation of medulloblastoma subgrouping was performed. Results: Five studies were included in this meta-analysis. Regarding patient selection, two studies indicated an unclear risk of bias according to the QUADAS-2. The five studies had an average CLAIM score and compliance score of 23.2 and 0.57, respectively. The meta-analysis showed pooled AUCs of 0.88, 0.82, 0.83, and 0.88 for WNT, SHH, group 3, and group 4 for classification, respectively. Conclusion: Radiomics-based ML studies have good classification performance in predicting medulloblastoma subgroups, with AUCs >0.80 in every subgroup. To be applied to clinical practice, they need methodological quality improvement and stability.

7 March 2022 in JMIR Medical Education
Verified
Journal Article
Open access
BOBurak Berksu Ozkara
Burak Berksu Ozkara
MKMert Karabacak
Mert Karabacak
DADuygu Demet Alpaydin
Duygu Demet Alpaydin
Background: Since the closure of university campuses due to COVID-19 in spring 2020 necessitated a quick transition to online courses, medical students were isolated from hospitals and universities, negatively impacting their education. During this time, medical students had no opportunity to participate in academic discussions and were also socially isolated. Furthermore, medical doctors and professors of medical schools were given additional responsibilities during the pandemic because they were the frontliners in the fight against COVID-19. As a result, they did not have enough time to contribute effectively to medical student education. Objective: This paper describes the establishment of the Cerrahpasa Neuroscience Society Journal Clubs, a group of entirely student-run online journal clubs at Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa. Methods: The website, mass emailing, and social media accounts were used to announce the online journal clubs. Only medical students were eligible to apply. Journal clubs included psychiatry, neuroradiology, neurosurgery, neurology, and neuroscience. Following the last journal club meeting, a questionnaire created by the society’s board was distributed to the participants. SPSS Statistics (version 26) was used for statistical analysis. Results: Since March 15, 2021, synchronous online journal club meetings have been held every 2 weeks on a weekday using Google Meet, Microsoft Teams, or Zoom. Meetings of each journal club lasted approximately 1 hour on average. Interstudent interaction across multiple institutions was achieved since a total of 45 students from 11 different universities attended the meetings on a regular basis. Students on the society’s board served as academic mentors for the clubs. The clubs received excellent feedback from participants, with an overall contentment score of 4.32 out of 5. Conclusions: By establishing these clubs, we have created a venue for academic discussions, which helps to reduce the negative impact of the pandemic on education. In addition, we believe it greatly aided students in staying in touch with their peers, thereby reducing the sense of isolation. We realize that traditional journal clubs are run by faculty; however, we believe that this experience demonstrated that medical students could run a journal club on their own since the feedback from participants was excellent. Additionally, as a medical student, being a journal club academic mentor is a challenging responsibility; however, having this responsibility significantly improved our academic mentors’ leadership abilities.