Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
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Conference Object Citation - WoS: 16Citation - Scopus: 20Machine Learning Analysis of Inflammatory Bowel Disease-Associated Metagenomics Dataset(Institute of Electrical and Electronics Engineers Inc., 2018-09) Hacilar, Hilal; Nalbantoĝlu, Özkan Ufuk; Bakir-Güngör, BurcuThere is an ongoing interplay between humans and our microbial communities. The microorganisms living in our gut produce energy from our food, strengthen our immune system, break down foreign products, and release metabolites and hormones, which are significant for regulating our physiology. The shifts away from this 'healthy' gut microbiome is considered to be associated with many diseases. Inflammatory bowel diseases (IBD) including Crohn's disease and ulcerative colitis, are gut related disorders affecting the intestinal tract. Although some metagenomics studies are conducted on IBD recently, our current understanding of the precise relationships between the human gut microbiome and IBD remains limited. In this regard, the use of state-of-the art machine learning approaches became popular to address a variety of questions like early diagnosis of certain diseases using human microbiota. In this study, we investigate which subset of gut microbiota are mostly associated with IBD and if disease-associated biomarkers can be detected via applying state-of-the art machine learning algorithms and proper feature selection methods. © 2019 Elsevier B.V., All rights reserved.Conference Object Citation - WoS: 22Citation - Scopus: 52Evaluation of Classification Algorithms, Linear Discriminant Analysis and a New Hybrid Feature Selection Methodology for the Diagnosis of Coronary Artery Disease(Institute of Electrical and Electronics Engineers Inc., 2018-12) Kolukisa, Burak; Hacilar, Hilal; Göy, Gökhan; Kus, Mustafa; Bakir-Güngör, Burcu; Aral, Atilla; Güngör, Vehbi ÇağrıAccording to the World Health Organization (WHO), 31% of the world's total deaths in 2016 (17.9 million) was due to cardiovascular diseases (CVD). With the development of information technologies, it has become possible to predict whether people have heart diseases or not by checking certain physical and biochemical values at a lower cost. In this study, we have evalated a set of different classification algorithms, linear discriminant analysis and proposed a new hybrid feature selection methodology for the diagnosis of coronary heart diseases (CHD). Throughout this research effort, using three publicly available Heart Disease diagnosis datasets (UCI Machine Learning Repository), we have conducted comparative performance evaluations in terms of accuracy, sensitivity, specificity, F-measure, AUC and running time. © 2023 Elsevier B.V., All rights reserved.Article Citation - Scopus: 5CSA-DE-LR Enhancing Cardiovascular Disease Diagnosis With a Novel Hybrid Machine Learning Approach(PeerJ Inc., 2024-07-18) Dedeturk, Beyhan Adanur; Dedeturk, Bilge Kagan; Bakir-Güngör, BurcuCardiovascular diseases (CVD) are a leading cause of mortality globally, necessitating the development of efficient diagnostic tools. Machine learning (ML) and metaheuristic algorithms have become prevalent in addressing these challenges, providing promising solutions in medical diagnostics. However, traditional ML approaches often need to be improved in feature selection and optimization, leading to suboptimal performance in complex diagnostic tasks. To overcome these limitations, this study introduces a new hybrid method called CSA-DE-LR, which combines the clonal selection algorithm (CSA) and differential evolution (DE) with logistic regression. This integration is designed to optimize logistic regression weights efficiently for the accurate classification of CVD. The methodology employs three optimization strategies based on the F1 score, the Matthews correlation coefficient (MCC), and the mean absolute error (MAE). Extensive evaluations on benchmark datasets, namely Cleveland and Statlog, reveal that CSA-DELR outperforms state-of-the-art ML methods. In addition, generalization is evaluated using the Breast Cancer Wisconsin Original (WBCO) and Breast Cancer Wisconsin Diagnostic (WBCD) datasets. Significantly, the proposed model demonstrates superior efficacy compared to previous research studies in this domain. This study’s findings highlight the potential of hybrid machine learning approaches for improving diagnostic accuracy, offering a significant advancement in the fields of medical data analysis and CVD diagnosis. © 2024 Elsevier B.V., All rights reserved.Conference Object Protein-Protein Etkilesim Ağlarinda Aktif Alt Ağ Arama Yöntemlerinin Performans Degerlendirmeleri(Institute of Electrical and Electronics Engineers Inc., 2019-09) Güner, Pinar; Bakir-Güngör, BurcuProtein-protein interaction networks are mathematical representations of the physical contacts between proteins in the cell. A group of interconnected proteins in a protein-protein interaction network that contains most of the disease associated proteins and some interacting other proteins is called an active subnetwork. Active subnetwork search is important to understand mechanisms underlying diseases. Active subnetworks are used to discover disease related regulatory pathways, functional modules and to classify diseases. In the literature there are many methods to search for active subnetworks. The purpose of this study is to compare the performance of different subnetwork identification methods. By using the Rheumatoid Arthritis dataset, the performances of greedy approach, genetic algorithm, simulated annealing algorithm, prize collecting steiner forest and game theory based subnetwork search methods are compared. © 2020 Elsevier B.V., All rights reserved.Conference Object Image-Processing Based Signal Readout Method For MRD Biochip(Institute of Electrical and Electronics Engineers Inc., 2019-04) Uslu, Fatma; İçöz, Kutay; Taşdemir, KasímThe response of the cancer patients to chemotherapy treatment varies from person to person. For some patients cancer cells are resistant to treatment and these cells can relapse again which is known as minimal residual disease. A microfluidic-based biochip capable of monitoring minimal residual disease is under development by our research group. The role of the biochip is to capture the target cells, which were separated by immunomagnetic beads on micro square tiles. Then biochips are imaged using a bright field optical microscope and it is planned to perform image-processing methods to detect the target cells, immunomagnetic beads and micro tiles. In this work the current progress of image processing methods for differentiating the immunomagnetic beads and micro tiles is presented. © 2020 Elsevier B.V., All rights reserved.Conference Object Papiller Tiroid Karsinom Oluşumunda Etkili Moleküler Mekanizmaların İn Siliko Yöntemlerle Tespit Edilmesi(Institute of Electrical and Electronics Engineers Inc., 2019-04) Ersöz, Nur Sebnem; Guzel, Yasin; Bakir-Güngör, BurcuRepresenting approximately 70% to 80% of thyroid cancers, papillary thyroid cancer (PTC) is the most common type of thyroid cancers. PTC is seen in all age groups, but it is seen more frequently in women than in men. Detection of biomarker proteins of papillary thyroid cancinoma plays an important role in the diagnosis of the disease. In this study, we aim to find target genes and pathways that are associated with papillar thyroid carcinoma, by integrating different bioinformatics methods. For this purpose, usingin-silico methodologies, candidate genes and pathways that could explain disease development mechanisms are identified. Throughout this study, firstly we identified differentially expressed genes as the amount of their protein product differ between patient and healthy groups. Secondly, by using active subnetworks search algorithms, topologic analyses and functional enrichment tests, candidate proteins,which could be thought as PTC biomarkers, and affected pathways are identified. © 2020 Elsevier B.V., All rights reserved.Conference Object Kolonoskopi Görüntülerinden Otomatik Ülseratif Kolit Teşhisi(Institute of Electrical and Electronics Engineers Inc., 2018-11) Kacmaz, Rukiye Nur; Yilmaz, BulentUlcerative colitis (UC) is a disease in which inner surface of colon is inflamed. Ulcers and open scars on the colon are observed. The complaint in the flare period is the frequent bloody diarrhea. Complaints of people with UC increase and decrease periodically. Colonoscopy is the most preferred approach for the visualization of the gastrointestinal tract for the diagnosis and follow-up of related diseases, and UC in particular. The lack of experience of the colonoscopist, complicated locality of the lesion, and the rush in the colonoscopy suite to complete the procedure as soon as possible may cause mistakes in visual analysis. In this study, 200 colonoscopy images (100 normal, 100 UC) were used. The statistical features such as gray level variance, gray level local variance, normalized variance, histogram range, and entropy were extracted from the images, and a normalized 200x5 feature matrix was formed. The normal images and images with UC were discriminated using support vector machines and k-nearest neighbors. It should be noted that the extraction of only 5 features from the colonoscopy images resulted in 95% accuracy. This study demonstrated the feasibility of the development of software tools for aiding the physicians in the diagnosis of colon diseases. © 2019 Elsevier B.V., All rights reserved.Conference Object Citation - WoS: 8Citation - Scopus: 9Meme Kanseri Histopatolojik Görüntülerinin Bilgisayar Destekli Sınıflandırılması(Institute of Electrical and Electronics Engineers Inc., 2017-10) Aksebzeci, Bekir Hakan; Kayaaltı, ÖmerNowadays, one of the most common types of cancer is breast cancer. The early and accurate diagnosis of breast cancer has great importance in the treatment of the disease. In the diagnosis of breast cancer, histopathological analysis of cell and tissue specimens taken by biopsy is considered as the gold standard. Histopathological analysis is a tedious process that is highly dependent on the knowledge and experience of the pathologists. In this study; it is aimed to develop a computer-Aided system that can reduce the workload of pathologists and help them in their diagnosis. An image set containing benign and malignant tumor images of breast cancer has been studied. To perform texture analysis on tumor images; first order statistics, Gabor and gray-level co-occurrence matrix (GLCM) feature extraction methods have been applied. Then, various classifiers were applied to the obtained feature matrices and their performances were compared. The highest classification accuracy was achieved 82.06% by Random Forests classifier with feature combination of Gabor and GLCM methods. The results presented here show that computer-Assisted diagnosis of breast cancer is a promising field. © 2018 Elsevier B.V., All rights reserved.Conference Object Citation - WoS: 1Citation - Scopus: 1Kolon Kanserinde Etkilenen Yolak Alt Ağlarini Ve Kümelenmelerini Belirlemek için Yeni Bir Yöntem(Institute of Electrical and Electronics Engineers Inc., 2019-09) Göy, Gökhan; Ünlü Yazici, Miray; Bakir-Güngör, BurcuNowadays new technological developments that play an important role in the production of big data have brought about the interpretation, sharing and storage of data related to complex diseases. Combining multi-omic data in different molecular levels is potentially important for understanding the biological origin of complex diseases. One of these complex diseases is cancer of different types, which has one of the highest causes of death worldwide. The integration of multiple omic data in the framework of a comprehensive analysis and identification of relevant pathways contribute to the development of therapeutic approaches related to disease. In this study, RNA and methylation data (genes and p values) of colon adenocarcinoma were obtained from TCGA data portal and combined with Fisher's method. While protein subnetworks affected by the disease were identified by using subnetwork algorithm, pathways related to the disease and genes associated with these pathways were determined by functional enrichment analysis. Using gene-pathway relationship matrix, kappa scores of pathways were determined by similarity calculation. In this way, the pathways were clustered according to the hierarchically optimal number, as a result, the most important pathway clusters and related genes that are effective in disease formation identified. © 2020 Elsevier B.V., All rights reserved.