Scopus İndeksli Yayınlar Koleksiyonu

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

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Publisher: search.filters.publisher.IEEESubject: search.filters.subject.Feature Selection

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  • Conference Object
    Enhancing Complex Disease Group Scoring with Mirgedinet: A Multi-Algorithm Machine Learning Framework Based on the GSM Approach
    (IEEE, 2025-06-25) Qumsiyeh, Emma; Bakir-Gungor, Burcu; Yousef, Malik
    Integrating biological prior knowledge for disease gene associations has shown significant promise in discovering new biomarkers with potential translational applications. This work investigates the application of a multi-algorithm machine learning framework based on the Grouping-Scoring-Modeling (G-S-M) approach for improving the prediction of complex diseases. The study identifies the primary gene and miRNA interactions in various complex diseases with the help of miRGediNET, which is a machine-learning based tool that integrates data from three biological databases. Traditional methods have only focused on independence between features; the G-S-M method focuses on aggregating genes based on biological interactions, pinpointing the scoring of gene groups for a disease, and modeling its predictive capability using advanced machine learning algorithms. In this research paper, seven algorithms, including Support Vector Machine, Decision Tree, and CatBoost, were applied to eight datasets extracted from the GEO database. This framework proved very robust in ranking gene clusters, thus predicting critical biomarkers while doing 100-fold randomized cross-validation within the evaluation. The results indicate this approach's high potential for refining disease and supporting research for choosing the best algorithm that can provide biological insights and computational advances.
  • Conference Object
    Citation - WoS: 2
    Citation - Scopus: 1
    Feature Selection for Protein Dihedral Angle Prediction
    (IEEE, 2017) Aydin, Zafer; Kaynar, Oguz; Gormez, Yasin
    Three-dimensional structure prediction has crucial importance for bioinformatics and theoretical chemistry. One of the main steps of three-dimensional structure prediction is dihedral (torsion) angle prediction. As new feature extraction methods are developed the dimension of the input space increases considerably yielding longer model training and less accurate models due to noisy or redundant features. In this study, feature selection is employed for dimensionality reduction on one of the established benchmarks of protein 1D structure prediction. Experimental results show that the feature selection improves the accuracy of protein dihedral angle class prediction by 2% and can eliminate up to %82 of the features when random forest classifier is used. Accurate prediction of dihedral angles will eventually contribute to protein structure prediction.
  • Conference Object
    Citation - WoS: 1
    Citation - Scopus: 1
    The Identification of Discriminative Single Nucleotide Polymorphism Sets for the Classification of Behcet's Disease
    (IEEE, 2018-09) Gormez, Yasin; Isik, Yunus Emre; Bakir-Gungor, Burcu
    Behcet's disease is a long-term multisystem inflammatory disorder, characterized by recurrent attacks affecting several organs. As the genotyping individuals get cheaper and easier following the developments in genomic technologies, genome-wide association studies (GWAS) emerged. By this means, via studying big-sized case-control groups for a specific disease, potential genetic variations, single nucleotide polymorphisms (SNPs) are identified. Although several genetic risk factors are identified for Behcet's disease with the help of these studies via scanning around a million of SNPs, these variations could only explain up to 200/u of the disease's genetic risk. In this study, for Behcet's disease classification, via comparing all the SNPs genotyped in GWAS, with the SNPs selected via using genetic knowledge, gain ratio and information gain; both reduction in the feature size and improvement in the classification accuracy is aimed. Also, using different classification algorithms such as random forest, k-nearest neighbour and logistic regression, their effects on the classification accuracy are investigated. Our results showed that compared to other feature selection methods, with at least 81% success rate, the selection of the SNPs using the genetic information (of their GWAS p-values, indicating the significance of the SNP against the disease) provides 15% to 42% improvement in all classification algorithms. This improvement is statistically sound. While gain ratio and information gain feature selection techniques yield similar classification accuracies, the models using all SNPs could not exceed 50% accuracies and results in the worst performance.
  • Conference Object
    Citation - WoS: 1
    Citation - Scopus: 5
    Credit Risk Analysis Based on Hybrid Classification: Case Studies on German and Turkish Credit Datasets
    (IEEE, 2018-05) Cetiner, Erkan; Kocak, Taskin; Gungor, V. Cagri
    In finance sector, credit risk analysis plays a major role in decision process. Banks and finance institutions gather large amounts of raw data from their customers. Data mining techniques can be employed to obtain useful information from this raw data. Several data mining techniques, such as support-vector machines (SVM), neural networks, naive-bayes, have already been used to classify customers. In this paper, we propose hybrid classification approaches, which try to combine several classifiers and ensemble learners to boost accuracy on classification results. Furthermore, we compare these approaches' performance with respect to their classification accuracy. We work with two diverse datasets; namely, German credit dataset and Turkish bank dataset. The goal of using such diverse dataset is to show generalization capabality of our approaches. Experimental results provide three important consequences. First, feature selection stage has a major role both on result accuracy and calculation complexity. Second, hybrid approaches have better generalability over single classifiers. Third, using SVM-Radial Basis Function (RBF) as the base classifier and a hybrid model member gives the best accuracy and type-1 accuracy results among others.