Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Citation - WoS: 1Citation - Scopus: 1Automating Software Size Measurement With Language Models: Insights From Industrial Case Studies(Elsevier Science Inc, 2026) Unlu, Huseyin; Tenekeci, Samet; Kennouche, Dhia Eddine; Demirors, OnurObjective software size measurement is critical for accurate effort estimation, yet many organizations avoid it due to high costs, required expertise, and time-consuming manual effort. This often leads to vague predictions, poor planning, and project overruns. To address this challenge, we investigate the use of pre-trained language models - BERT and SE-BERT - to automate size measurement based on textual requirements using COSMIC and MicroM methods. We constructed one heterogeneous dataset and two industrial datasets, each manually measured by experienced analysts. Models were evaluated in three settings: (i) generic model evaluation, where the models are trained and tested on heterogeneous data, (ii) internal evaluation, where the models are trained and tested on organization-specific data, and (iii) external evaluation, where generic models were tested on organization-specific data. Results show that organization-specific models significantly outperform generic models, indicating that aligning training data with the target organization's requirement style is critical for accuracy. SE-BERT, a domain-adapted variant of BERT, improves performance, particularly in low-resource settings. These findings highlight the practical potential of tailoring training data for broader adoption and cost-effective software size measurement in industrial contexts.Article Citation - WoS: 4Citation - Scopus: 4Integrative Biological Network Analysis To Identify Shared Genes in Metabolic Disorders(Institute of Electrical and Electronics Engineers, 2022) Tenekeci, Samet; Işık, ZerrinIdentification of common molecular mechanisms in interrelated diseases is essential for better prognoses and targeted therapies. However, complexity of metabolic pathways makes it difficult to discover common disease genes underlying metabolic disorders; and it requires more sophisticated bioinformatics models that combine different types of biological data and computational methods. Accordingly, we built an integrative network analysis model to identify shared disease genes in metabolic syndrome (MS), type 2 diabetes (T2D), and coronary artery disease (CAD). We constructed weighted gene co-expression networks by combining gene expression, protein-protein interaction, and gene ontology data from multiple sources. For 90 different configurations of disease networks, we detected the significant modules by using MCL, SPICi, and Linkcomm graph clustering algorithms. We also performed a comparative evaluation on disease modules to determine the best method providing the highest biological validity. By overlapping the disease modules, we identified 22 shared genes for MS-CAD and T2D-CAD. Moreover, 19 out of these genes were directly or indirectly associated with relevant diseases in the previous medical studies. This study does not only demonstrate the performance of different biological data sources and computational methods in disease-gene discovery, but also offers potential insights into common genetic mechanisms of the metabolic disorders.