Cemil Colak

Prof. Dr. Cemil Colak

Biostatisticas and Medical Informatics, Inonu University, Malatya, Turkey (Türkiye)
orcid

Research Focus & Metrics

Academic Career Length

20Years (2007-Present)

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

Representative Publications

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31 January 2023 in Computers in Biology and Medicine
Verified
Journal Article
Closed access
Fatma Hilal YaginFatma Hilal Yagin
Fatma Hilal Yagin
IÇipek balıkçı çiçek
ipek balıkçı çiçek
Abedalrhman AlkhateebAbedalrhman Alkhateeb
Abedalrhman Alkhateeb
BYBurak Yagin
Burak Yagin
Cemil ColakCemil Colak
Cemil Colak
Sami AkbulutSami Akbulut
Sami Akbulut

1 January 2020 in Brazilian Oral Research
Verified
Journal Article
Open access
GDGülsüm Duruk
Gülsüm Duruk
ZGZekiye Şeyma Gümüşboğa
Zekiye Şeyma Gümüşboğa
Cemil ColakCemil Colak
Cemil Colak
Currently, the whole world is under the threat of the COVID-19 pandemic, and dentists are at high risk. The aim of this study was to investigate what kind of precautions Turkish dentists take in dental clinics during the COVID-19 pandemic. The study population consisted of dentists in Turkey. An online questionnaire (23 questions–57 items) was sent to a sample of Turkish dentists from March 16 to March 20, 2020. The questionnaire comprised a series of questions about dentists’ demographic characteristics, their concerns, and the measures taken in dental clinics against COVID-19. This study included a total of 1,958 Turkish dentists. A total of 1,274 (65.1%) were general dentists, and 684 (34.9%) were specialists. Five hundred twenty-two (26.7%) dentists attended an informational meeting on COVID-19. Of these dentists, 69.8% were aware of COVID-19 according to their self-assessed knowledge scores. More than 90% of the dentists were concerned about themselves and their families. Only 12% of the dentists wore an N95 mask. Although Turkish dentists took some precautionary measures, they did not take enough precautions to protect themselves, the dental staff, and other patients from COVID-19. As the number of COVID-19 cases increased, the measures taken slightly increased in dental clinics as well. Dentists are strongly recommended to take maximum precautions in the clinical setting. The guidelines about the COVID-19 pandemic should be sent to all dentists by the regional and national dental associations.

26 October 2023 in Diagnostics
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Journal Article
Open access
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BYBurak Yagin
Burak Yagin
Fatma Hilal YaginFatma Hilal Yagin
Fatma Hilal Yagin
Cemil ColakCemil Colak
Cemil Colak
FİFeyza İnceoğlu
Feyza İnceoğlu
Seifedine KadrySeifedine Kadry
Seifedine Kadry
JKJungeun Kim
Jungeun Kim
Aim: Method: This research presents a model combining machine learning (ML) techniques and eXplainable artificial intelligence (XAI) to predict breast cancer (BC) metastasis and reveal important genomic biomarkers in metastasis patients. Method: A total of 98 primary BC samples was analyzed, comprising 34 samples from patients who developed distant metastases within a 5-year follow-up period and 44 samples from patients who remained disease-free for at least 5 years after diagnosis. Genomic data were then subjected to biostatistical analysis, followed by the application of the elastic net feature selection method. This technique identified a restricted number of genomic biomarkers associated with BC metastasis. A light gradient boosting machine (LightGBM), categorical boosting (CatBoost), Extreme Gradient Boosting (XGBoost), Gradient Boosting Trees (GBT), and Ada boosting (AdaBoost) algorithms were utilized for prediction. To assess the models’ predictive abilities, the accuracy, F1 score, precision, recall, area under the ROC curve (AUC), and Brier score were calculated as performance evaluation metrics. To promote interpretability and overcome the “black box” problem of ML models, a SHapley Additive exPlanations (SHAP) method was employed. Results: The LightGBM model outperformed other models, yielding remarkable accuracy of 96% and an AUC of 99.3%. In addition to biostatistical evaluation, in XAI-based SHAP results, increased expression levels of TSPYL5, ATP5E, CA9, NUP210, SLC37A1, ARIH1, PSMD7, UBQLN1, PRAME, and UBE2T (p ≤ 0.05) were found to be associated with an increased incidence of BC metastasis. Finally, decreased levels of expression of CACTIN, TGFB3, SCUBE2, ARL4D, OR1F1, ALDH4A1, PHF1, and CROCC (p ≤ 0.05) genes were also determined to increase the risk of metastasis in BC. Conclusion: The findings of this study may prevent disease progression and metastases and potentially improve clinical outcomes by recommending customized treatment approaches for BC patients.

1 May 2015 in Computer Methods and Programs in Biomedicine
Verified
Journal Article
Closed access
Cemil ColakCemil Colak
Cemil Colak
EKEsra Karaman
Esra Karaman
MTM. Gokhan Turtay
M. Gokhan Turtay

19 March 2023 in Diagnostics
Verified
Journal Article
Open access
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Sami AkbulutSami Akbulut
Sami Akbulut
Fatma Hilal YaginFatma Hilal Yagin
Fatma Hilal Yagin
IÇipek balıkçı çiçek
ipek balıkçı çiçek
CKCemalettin Koc
Cemalettin Koc
Cemil ColakCemil Colak
Cemil Colak
SYSezai Yilmaz
Sezai Yilmaz
Background: The primary aim of this study was to create a machine learning (ML) model that can predict perforated and nonperforated acute appendicitis (AAp) with high accuracy and to demonstrate the clinical interpretability of the model with explainable artificial intelligence (XAI). Method: A total of 1797 patients who underwent appendectomy with a preliminary diagnosis of AAp between May 2009 and March 2022 were included in the study. Considering the histopathological examination, the patients were divided into two groups as AAp (n = 1465) and non-AAp (NA; n = 332); the non-AAp group is also referred to as negative appendectomy. Subsequently, patients confirmed to have AAp were divided into two subgroups: nonperforated (n = 1161) and perforated AAp (n = 304). The missing values in the data set were assigned using the Random Forest method. The Boruta variable selection method was used to identify the most important variables associated with AAp and perforated AAp. The class imbalance problem in the data set was resolved by the SMOTE method. The CatBoost model was used to classify AAp and non-AAp patients and perforated and nonperforated AAp patients. The performance of the model in the holdout test set was evaluated with accuracy, F1- score, sensitivity, specificity, and area under the receiver operator curve (AUC). The SHAP method, which is one of the XAI methods, was used to interpret the model results. Results: The CatBoost model could distinguish AAp patients from non-AAp individuals with an accuracy of 88.2% (85.6–90.8%), while distinguishing perforated AAp patients from nonperforated AAp individuals with an accuracy of 92% (89.6–94.5%). According to the results of the SHAP method applied to the CatBoost model, it was observed that high total bilirubin, WBC, Netrophil, WLR, NLR, CRP, and WNR values, and low PNR, PDW, and MCV values increased the prediction of AAp biochemically. On the other hand, high CRP, Age, Total Bilirubin, PLT, RDW, WBC, MCV, WLR, NLR, and Neutrophil values, and low Lymphocyte, PDW, MPV, and PNR values were observed to increase the prediction of perforated AAp. Conclusion: For the first time in the literature, a new approach combining ML and XAI methods was tried to predict AAp and perforated AAp, and both clinical conditions were predicted with high accuracy. This new approach proved successful in showing how well which demographic and biochemical parameters could explain the current clinical situation in predicting AAp and perforated AAp.

14 September 2023 in Diagnostics
Verified
Journal Article
Open access
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HBHarika Gozde Gozukara Bag
Harika Gozde Gozukara Bag
Fatma Hilal YaginFatma Hilal Yagin
Fatma Hilal Yagin
YGYasin Görmez
Yasin Görmez
PABLO PRIETO GONZALEZPABLO PRIETO GONZALEZ
PABLO PRIETO GONZALEZ
Cemil ColakCemil Colak
Cemil Colak
Luca Paolo ArdigòLuca Paolo Ardigò
Luca Paolo Ardigò
Obesity is the excessive accumulation of adipose tissue in the body that leads to health risks. The study aimed to classify obesity levels using a tree-based machine-learning approach considering physical activity and nutritional habits. Methods: The current study employed an observational design, collecting data from a public dataset via a web-based survey to assess eating habits and physical activity levels. The data included gender, age, height, weight, family history of being overweight, dietary patterns, physical activity frequency, and more. Data preprocessing involved addressing class imbalance using Synthetic Minority Over-sampling TEchnique-Nominal Continuous (SMOTE-NC) and feature selection using Recursive Feature Elimination (RFE). Three classification algorithms (logistic regression (LR), random forest (RF), and Extreme Gradient Boosting (XGBoost)) were used for obesity level prediction, and Bayesian optimization was employed for hyperparameter tuning. The performance of different models was evaluated using metrics such as accuracy, recall, precision, F1-score, area under the curve (AUC), and precision–recall curve. The LR model showed the best performance across most metrics, followed by RF and XGBoost. Feature selection improved the performance of LR and RF models, while XGBoost’s performance was mixed. The study contributes to the understanding of obesity classification using machine-learning techniques based on physical activity and nutritional habits. The LR model demonstrated the most robust performance, and feature selection was shown to enhance model efficiency. The findings underscore the importance of considering both physical activity and nutritional habits in addressing the obesity epidemic.