Güngör, Burcu
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Bakir Gungor, Burcu
Bakir-Gungor, Burcu
Bakir-Güngör, Burcu
Bakir-gungor, Burcu
Burcu Güngör
Gungor, Burcu Bakir
Bakir-Güngör, B.
Bakir-Gungor, Burcu
Bakir-Güngör, Burcu
Bakir-gungor, Burcu
Burcu Güngör
Gungor, Burcu Bakir
Bakir-Güngör, B.
Job Title
Doç. Dr.
Email Address
burcu.gungor@agu.edu.tr
Main Affiliation
02. 04. Bilgisayar Mühendisliği
02. Mühendislik Fakültesi
01. Abdullah Gül University
02. Mühendislik Fakültesi
01. Abdullah Gül University
Status
Current Staff
Website
ORCID ID
Scopus Author ID
Turkish CoHE Profile ID
Google Scholar ID
WoS Researcher ID
Sustainable Development Goals
1NO POVERTY
0
Research Products
2ZERO HUNGER
1
Research Products
3GOOD HEALTH AND WELL-BEING
51
Research Products
4QUALITY EDUCATION
0
Research Products
5GENDER EQUALITY
0
Research Products
6CLEAN WATER AND SANITATION
0
Research Products
7AFFORDABLE AND CLEAN ENERGY
1
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8DECENT WORK AND ECONOMIC GROWTH
0
Research Products
9INDUSTRY, INNOVATION AND INFRASTRUCTURE
1
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10REDUCED INEQUALITIES
0
Research Products
11SUSTAINABLE CITIES AND COMMUNITIES
0
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12RESPONSIBLE CONSUMPTION AND PRODUCTION
0
Research Products
13CLIMATE ACTION
0
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14LIFE BELOW WATER
2
Research Products
15LIFE ON LAND
2
Research Products
16PEACE, JUSTICE AND STRONG INSTITUTIONS
0
Research Products
17PARTNERSHIPS FOR THE GOALS
0
Research Products
Documents
101
Citations
1091
h-index
20
Documents
146
Citations
8923
Scholarly Output
128
Articles
58
Views / Downloads
2657/1872
Supervised MSc Theses
10
Supervised PhD Theses
7
WoS Citation Count
628
Scopus Citation Count
858
Patents
0
Projects
2
WoS Citations per Publication
4.91
Scopus Citations per Publication
6.70
Open Access Source
59
Supervised Theses
17
| Journal | Count |
|---|---|
| PeerJ Computer Science | 8 |
| Frontiers in Genetics | 7 |
| Applied Sciences-Basel | 5 |
| -- 3rd International Conference on Computer Science and Engineering, UBMK 2018 -- Sarajevo -- 143560 | 5 |
| PeerJ | 5 |
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128 results
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Now showing 1 - 10 of 128
Conference Object Citation - Scopus: 1TextNetTopics_TIS: Enhancing Textnettopics With Random Forest-Based Topic Importance Scoring(Institute of Electrical and Electronics Engineers Inc., 2024) Voskergian, Daniel; Bakir-Güngör, Burcu; Yousef, MalikTextNetTopics is an innovative Latent Dirichlet Allocation-based topic selection method for training text classification models. One main limitation is its computationally intensive scoring mechanism, especially when applied to many topics. This scoring mechanism involves training a machine learning model (i.e., Random Forest) on each topic using the Monte-Carlo Cross-Validation approach and assigning a score value based on a specific performance metric (e.g., accuracy or F1-score). Moreover, the measured score does not account for the interactions between all features residing in all topics. This paper presents a new topic-scoring mechanism called Topic Importance Scoring. This computationally efficient approach trains a Random Forest model on all topics simultaneously and leverages the extracted feature importance values to give each topic a score reflecting its classification potential. The experiments on three diverse datasets confirm that the proposed method's performance is superior to the Topic Performance Scoring, which was used in the original TextNetTopics method. © 2024 Elsevier B.V., All rights reserved.Article Cilt Kanseri Görüntü Sınıflandırması için Görüntü Ön İşlemenin Evrişimsel Sinir Ağları Performansı Üzerindeki Etkileri(2022) Dedeturk, Beyhan Adanur; Bakir-gungor, Burcu; Tasdemir, KasimCilt kanseri, dünya çapında yaygın olarak karşılaşılan kanser türleri arasındadır. Günümüzde pek çok kanser vakasının yanlış ya da geç teşhisi sonucunda, hasta ölümleri de dahil olmak üzere ciddi problemler yaşanmaktadır. Bu çalışmada, evrişimli sinir ağlarını kullanarak cilt kanseri sınıflandırması problemini ele almaktayız. Çalışmadaki temel amacımız farklı öğrenme mimarilerini karşılaştırmak yerine, görüntüleri farklı ön işlemlere tabi tutup, bu işlemin kullanılan mimari performansına etkisini incelemektir. Bu amaç doğrultusunda, ISIC 2018 Cilt Görüntü Analizi Yarışması’na ait veri seti kullanılarak, iki farklı görüntü ön işleme yöntem dizisi ResNet50 mimarisi için uygulanmıştır. Bunlardan birincisinde sırasıyla ikili ve otsu eşikleme, CLAHE dönüşümü uygulanırken, ikincisinde morfolojik filtreleme, renk normalizasyonu ve dolgu işlemleri uygulanmıştır. F1 Puanı başta olmak üzere farklı performans metrikleri baz alındığında, cilt kanseri görüntüleri üzerinde ikinci ön işleme yöntem dizisinin performans iyileştirmesi yapabildiği gösterilmiştir.Master Thesis İstatistiksel Ön Puanlama Bileşeni ile Gruplama Puanlama Modellemesi (GSM) Yaklaşımın Geliştirilmesi: Yüksek Boyutlu Transkriptomik Veri Analizi için Bir Vaka Çalışması(Abdullah Gül Üniversitesi / Sosyal Bilimler Enstitüsü, 2024) Khokhar, Maham; Güngör, BurcuRapid advancements in transcriptomic technologies have significantly increased the volume of data available for analysis, which presents challenges in terms of efficiency and computational demand. This thesis introduces a Pre-Scoring component to the Grouping-Scoring-Modeling (G-S-M) framework to address inefficiencies caused by the excessive number of gene groups generated by traditional GSM. By selectively prioritizing gene groups based on their statistical significance, this innovation aims to reduce the computational demands associated with scoring these groups using machine learning models, thereby streamlining the analysis process. Assessed across nine diverse Gene Expression datasets, the Pre-Scoring G-S-M framework not only maintained accuracy comparable to the traditional approach but did so with significantly fewer genes. This refinement conserves resources while maintaining the robustness and reliability of the data analysis, crucial for advancing research in personalized medicine and therapeutic strategies. The findings suggest that the modified G-S-M framework serves as a valuable tool in bioinformatics, offering a more efficient approach to handling large-scale genomic datasets. Future work will focus on adapting this enhanced framework to incorporate diverse types of omics knowledge, such as proteomics and metabolomics, further optimizing its performance to broaden its applicability in both clinical and research settingsMaster Thesis Enhancing Breast Cancer Detection With a Hybrid Machine Learning Approach(2024) Etcil, Mustafa; Güngör, Burcu; Güngör, V. CagriDünya Sağlık Örgütü (WHO) tarafından belirlendiği üzere, göğüs kanseri, son beş yılda 7.8 milyon yeni vakayla en yaygın kanser türlerinden biri olarak ön plana çıkmaktadır. Bu çarpıcı istatistik, gelişmiş tanı yöntemlerine olan acil ihtiyacı vurgulamaktadır. Bu bağlamda, mevcut çalışma, göğüs kanseri tespiti için lojistik regresyon modeli eğitim sürecini iyileştirmek amacıyla klonal seçim algoritması (CSA) ile parçacık sürü optimizasyonunu (PSO) yenilikçi bir şekilde birleştiren CSA-PSO-LR sınıflandırıcısını önermektedir. Bu araştırma, geniş çapta tanınan iki veri seti olan Wisconsin Diagnostik Göğüs Kanseri (WDBC) ve Wisconsin Göğüs Kanseri Veritabanı (WBCD) kullanılarak, performans değerlendirmesi için 10 kat çapraz doğrulama ve Bayes hiperparametre optimizasyonunu içeren katı bir değerlendirme protokolü uygulamaktadır. Ayrıca, çalışma, model eğitim süresini önemli ölçüde kısaltmayı amaçlayan CPU paralelleştirme stratejilerini tanıtmaktadır. Karar ağaçları, aşırı gradyan artırma, en yakın komşular, lojistik regresyon, rastgele ormanlar ve destek vektör makineleri gibi makine öğrenimi algoritmalarına karşı yapılan karşılaştırmalı analizler, CSA-PSO-LR sınıflandırıcısının tespit doğruluğu ve F1-ölçütü açısından üstün performans sergilediğini göstermektedir. Bu araştırma, göğüs kanserinin erken tespitine yönelik yenilikçi bir yaklaşım sunarak, daha etkili tedavi planlarının kolaylaştırılmasına ve hastaların hayatta kalma beklentilerinin artırılmasına katkıda bulunmaktadır.Conference Object Citation - Scopus: 1Integrative Analyses in Omics Data: Machine Learning Perspective(Deutsche Gesellschaft fur Medizinische Informatik, Biometrie und Epidemiologie e.V., 2023) Ünlü Yazici, Miray; Bakir-Güngör, Burcu; Yousef, Malik; Yazici, Miray UnluDevelopments in the high throughput technologies have enabled the production of an immense amount of knowledge at the multi-omics level. Considering complex diseases which are affected by multi-factors, single omics datasets might not be sufficient to unveil the molecular mechanisms of heterogeneous diseases. Providing a comprehensive and systematic overview to explain disease hallmarks in significant depth is critical. Utilizing multi-omics datasets has led to the development of a variety of tools and platforms. Machine learning models are utilized in a wide variety of tools to tackle the complexity of disorders and to identify new biomolecular signatures and potential markers. Underlying aspects of these approaches are based on training the models for making predictions and classification of the given data. In this review, we describe current machine learning-based approaches and available implementations. Challenges in the enlightenment of disease mechanisms of onset and progression and future development of the field of medicine will be discussed. The prominence of biological interpretation of model output with corresponding biological knowledge will be also covered in this review. © 2023 Elsevier B.V., All rights reserved.Article Citation - WoS: 9Citation - Scopus: 12AMP-GSM: Prediction of Antimicrobial Peptides via a Grouping-Scoring Approach(MDPI, 2023) Soylemez, Ummu Gulsum; Yousef, Malik; Bakir-Gungor, BurcuDue to the increasing resistance of bacteria to antibiotics, scientists began seeking new solutions against this problem. One of the most promising solutions in this field are antimicrobial peptides (AMP). To identify antimicrobial peptides, and to aid the design and production of novel antimicrobial peptides, there is a growing interest in the development of computational prediction approaches, in parallel with the studies performing wet-lab experiments. The computational approaches aim to understand what controls antimicrobial activity from the perspective of machine learning, and to uncover the biological properties that define antimicrobial activity. Throughout this study, we aim to develop a novel prediction approach that can identify peptides with high antimicrobial activity against selected target bacteria. Along this line, we propose a novel method called AMP-GSM (antimicrobial peptide-grouping-scoring-modeling). AMP-GSM includes three main components: grouping, scoring, and modeling. The grouping component creates sub-datasets via placing the physicochemical, linguistic, sequence, and structure-based features into different groups. The scoring component gives a score for each group according to their ability to distinguish whether it is an antimicrobial peptide or not. As the final part of our method, the model built using the top-ranked groups is evaluated (modeling component). The method was tested for three AMP prediction datasets, and the prediction performance of AMP-GSM was comparatively evaluated with several feature selection methods and several classifiers. When we used 10 features (which are members of the physicochemical group), we obtained the highest area under curve (AUC) value for both the Gram-negative (99%) and Gram-positive (98%) datasets. AMP-GSM investigates the most significant feature groups that improve AMP prediction. A number of physico-chemical features from the AMP-GSM's final selection demonstrate how important these variables are in terms of defining peptide characteristics and how they should be taken into account when creating models to predict peptide activity.Article Enlightening the Molecular Mechanisms of Type 2 Diabetes With a Novel Pathway Clustering and Pathway Subnetwork Approach(Tubitak Scientific & Technological Research Council Turkey, 2022) Bakir-Gungor, Burcu; Yazici, Miray Unlu; Goy, Gokhan; Temiz, Mustafa; Ünlü Yazici, MirayType 2 diabetes mellitus (T2D) constitutes 90% of the diabetes cases, and it is a complex multifactorial disease. In the last decade, genome-wide association studies (GWASs) for T2D successfully pinpointed the genetic variants (typically single nucleotide polymorphisms, SNPs) that associate with disease risk. In order to diminish the burden of multiple testing in GWAS, researchers attempted to evaluate the collective effects of interesting variants. In this regard, pathway-based analyses of GWAS became popular to discover novel multigenic functional associations. Still, to reveal the unaccounted 85 to 90% of T2D variation, which lies hidden in GWAS datasets, new post-GWAS strategies need to be developed. In this respect, here we reanalyze three metaanalysis data of GWAS in T2D, using the methodology that we have developed to identify disease-associated pathways by combining nominally significant evidence of genetic association with the known biochemical pathways, protein-protein interaction (PPI) networks, and the functional information of selected SNPs. In this research effort, to enlighten the molecular mechanisms underlying T2D development and progress, we integrated different in silico approaches that proceed in top-down manner and bottom-up manner, and presented a comprehensive analysis at protein subnetwork, pathway, and pathway subnetwork levels. Using the mutual information based on the shared genes, the identified protein subnetworks and the affected pathways of each dataset were compared. While most of the identified pathways recapitulate the pathophysiology of T2D, our results show that incorporating SNP functional properties, PPI networks into GWAS can dissect leading molecular pathways, and it could offer improvement over traditional enrichment strategies.Article Citation - WoS: 20Citation - Scopus: 24miRdisNET: Discovering MicroRNA Biomarkers That Are Associated With Diseases Utilizing Biological Knowledge-Based Machine Learning(Frontiers Media S.A., 2023) Jabeer, Amhar; Temiz, Mustafa; Bakir-Gungor, Burcu; Yousef, MalikDuring recent years, biological experiments and increasing evidence have shown that MicroRNAs play an important role in the diagnosis and treatment of human complex diseases. Therefore, to diagnose and treat human complex diseases, it is necessary to reveal the associations between a specific disease and related miRNAs. Although current computational models based on machine learning attempt to determine miRNA-disease associations, the accuracy of these models need to be improved, and candidate miRNA-disease relations need to be evaluated from a biological perspective. In this paper, we propose a computational model named miRdisNET to predict potential miRNA-disease associations. Specifically, miRdisNET requires two types of data, i.e., miRNA expression profiles and known disease-miRNA associations as input files. First, we generate subsets of specific diseases by applying the grouping component. These subsets contain miRNA expressions with class labels associated with each specific disease. Then, we assign an importance score to each group by using a machine learning method for classification. Finally, we apply a modeling component and obtain outputs. One of the most important outputs of miRdisNET is the performance of miRNA-disease prediction. Compared with the existing methods, miRdisNET obtained the highest AUC value of .9998. Another output of miRdisNET is a list of significant miRNAs for disease under study. The miRNAs identified by miRdisNET are validated via referring to the gold-standard databases which hold information on experimentally verified MicroRNA-disease associations. miRdisNET has been developed to predict candidate miRNAs for new diseases, where miRNA-disease relation is not yet known. In addition, miRdisNET presents candidate disease-disease associations based on shared miRNA knowledge. The miRdisNET tool and other supplementary files are publicly available at: .Conference Object Citation - Scopus: 10Sağlıkta Blokzincir Tabanlı Sistem Bilişimi Uygulamaları(Institute of Electrical and Electronics Engineers Inc., 2020) Dedeturk, Beyhan Adanur; Bakir-Güngör, Burcu; Soran, AhmetRecently, the use of blockchain technology in the field of healthcare has increased. Although blockchain technology brought several innovations to healthcare, still there are problems waiting to be resolved. In order to provide alternative solutions to these problems, the use of fog computing together with blockchain technology has been proposed. In this study, the applications of blockchain based fog computing technology in healthcare are investigated. The aim of this study is to provide the readers an idea about the interactive use of blockchain and fog computing in the field of healthcare. For this purpose, firstly, fog computing and blockchain technologies are introduced. Afterwards, the integration of these areas, the advantages and disadvantages of using these technologies in the field of healthcare is discussed and a new system architecture is proposed. © 2021 Elsevier B.V., All rights reserved.Conference Object Performance Evaluations of Active Subnetwork Search Methods in Protein-Protein Interaction Networks(IEEE, 2019) Gunter, Pinar; Bakir-Gungor, 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 arc 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.
