Scopus İndeksli Yayınlar Koleksiyonu

Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395

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Department: search.filters.department.Abdullah Gul UniversitySubject: search.filters.subject.Machine Learning

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  • Article
    Developing a Label Propagation Approach for Cancer Subtype Classification Problem
    (TUBITAK, 2021) Güner, P.; Bakir-Güngör, B.; Coşkun, M.; Şahan, Pınar Güner
    Cancer is a disease in which abnormal cells grow uncontrollably and invade other tissues. Several types of cancer have various subtypes with different clinical and biological implications. Based on these differences, treatment methods need to be customized. The identification of distinct cancer subtypes is an important problem in bioinformatics, since it can guide future precision medicine applications. In order to design targeted treatments, bioinformatics methods attempt to discover common molecular pathology of different cancer subtypes. Along this line, several computational methods have been proposed to discover cancer subtypes or to stratify cancer into informative subtypes. However, existing works do not consider the sparseness of data (genes having low degrees) and result in an ill-conditioned solution. To address this shortcoming, in this paper, we propose an alternative unsupervised method to stratify cancer patients into subtypes using applied numerical algebra techniques. More specifically, we applied a label propagation-based approach to stratify somatic mutation profiles of colon, head and neck, uterine, bladder, and breast tumors. We evaluated the performance of our method by comparing it to the baseline methods. Extensive experiments demonstrate that our approach highly renders tumor classification tasks by largely outperforming the state-of-the-art unsupervised and supervised approaches. © 2022 Elsevier B.V., All rights reserved.
  • Correction
    Correction: Engineering Novel Features for Diabetes Complication Prediction Using Synthetic Electronic Health Records
    (Frontiers Media S.A., 2025-08-29) Voskergian, Daniel; Bakir-Gungor, Burcu; Yousef, Malik
  • Article
    Citation - WoS: 26
    Citation - Scopus: 31
    miRcorrNet: Machine Learning-Based Integration of miRNA and mRNA Expression Profiles, Combined with Feature Grouping and Ranking
    (PeerJ Inc., 2021-05-19) Yousef, M.; Göy, G.; Mitra, R.; Eischen, C.M.; Jabeer, A.; Bakir-Güngör, B.
    A better understanding of disease development and progression mechanisms at the molecular level is critical both for the diagnosis of a disease and for the development of therapeutic approaches. The advancements in high throughput technologies allowed to generate mRNA and microRNA (miRNA) expression profiles; and the integrative analysis of these profiles allowed to uncover the functional effects of RNA expression in complex diseases, such as cancer. Several researches attempt to integrate miRNA and mRNA expression profiles using statistical methods such as Pearson correlation, and then combine it with enrichment analysis. In this study, we developed a novel tool called miRcorrNet, which performs machine learning-based integration to analyze miRNA and mRNA gene expression profiles. miRcorrNet groups mRNAs based on their correlation to miRNA expression levels and hence it generates groups of target genes associated with each miRNA. Then, these groups are subject to a rank function for classification. We have evaluated our tool using miRNA and mRNA expression profiling data downloaded from The Cancer Genome Atlas (TCGA), and performed comparative evaluation with existing tools. In our experiments we show that miRcorrNet performs as good as other tools in terms of accuracy (reaching more than 95% AUC value). Additionally, miRcorrNet includes ranking steps to separate two classes, namely case and control, which is not available in other tools. We have also evaluated the performance of miRcorrNet using a completely independent dataset. Moreover, we conducted a comprehensive literature search to explore the biological functions of the identified miRNAs. We have validated our significantly identified miRNA groups against known databases, which yielded about 90% accuracy. Our results suggest that miRcorrNet is able to accurately prioritize pan-cancer regulating high-confidence miRNAs. miRcorrNet tool and all other supplementary files are available at https://github.com/ malikyousef/miRcorrNet. © 2021 Elsevier B.V., All rights reserved.
  • Conference Object
    Citation - Scopus: 1
    NLP-Driven Fake News Detection: A Machine Learning Perspective
    (IEEE, 2025-05-23) Coban, Mert Korkut; Bakal, Gokhan
    The rapid spread of fake news poses a significant challenge, impacting public opinion, decision-making, and societal trust. This study explores the application of Natural Language Processing (NLP) and Machine Learning (ML) techniques for robust fake news detection. Using datasets such as ISOT Fake News, WELFake, and Football Fake News, the project employs advanced preprocessing methods and feature extraction techniques, including TF-IDF, Word2Vec, and GloVe. A comprehensive evaluation of machine learning models-Random Forest, Support Vector Machines (SVM), and Neural Networks-was conducted to identify the optimal configuration. Results demonstrate that Random Forest with TF-IDF excels in in-domain detection, achieving an F1-score of 99.70%, while Neural Networks paired with Word2Vec and GloVe embeddings outperform in cross-dataset scenarios. The study highlights the importance of dataset size, domain relevance, and feature representation in achieving high generalizability. These findings provide a scalable framework for combating misinformation on digital platforms.
  • Conference Object
    Citation - Scopus: 1
    A Comprehensive Investigation into Strip Steel Defect Detection Using Traditional Machine Learning and Deep Learning Models
    (IEEE, 2025-05-23) Erkantarci, Betul; Kurban, Rifat; Bakal, Mehmet Gokhan; Kose, Abdulkadir
    The steel manufacturing sector places great importance on guaranteeing the quality of strip steel products, which has led to a thorough investigation of defect detection approaches. This work conducts a comparative analysis of traditional machine learning and deep learning models to determine their efficacy in detecting defects in strip steel. Our analysis is based on a dataset that includes a variety of images of strip steel surfaces showing different types of defects. In this work, we adopt image preprocessing techniques to improve the quality of input images prior to the application of classification methods. We employ traditional ML algorithms including Support Vector Machine and Random Forest, and deep learning model AlexNet Convolutional Neural Networks for effective defect classification. Consequently, we present comparative evaluations that highlight the strengths and weaknesses of each approach, considering accuracy scores.