Browsing by Author "Inal, Yasin"

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    Multi-Method Text Summarization: Evaluating Extractive and BART-Based Approaches on CNN/Daily Mail
    (Institute of Electrical and Electronics Engineers Inc., 2025) Inal, Yasin; Bakal, Gokhan; Esit, Muhammed
    With the exponential growth of digital content, efficient text summarization has become increasingly crucial for managing information overload. This paper presents a comprehensive approach to text summarization using both extractive and abstractive methods, implemented on the CNN/Daily Mail dataset. We leverage pre-trained BART (Bidirectional and AutoRegressive Transformers) models and fine-tuning techniques to generate high-quality summaries. Our approach demonstrates significant improvements, with our best model trained on 287 k samples achieving ROUGE-1 F1 scores of 0.4174, ROUGE-2 F1 scores of 0.1932, and ROUGE-L F1 scores of 0.2910. We provide detailed comparisons between extractive methods and various BART model configurations, analyzing the impact of training dataset size and model architecture on summarization quality. Additionally, we share our implementation through an opensource NLP toolkit to facilitate further research and practical applications in the field. © 2025 Elsevier B.V., All rights reserved.
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    Citation - Scopus: 4
    CCPred: Global and Population-Specific Colorectal Cancer Prediction and Metagenomic Biomarker Identification at Different Molecular Levels Using Machine Learning Techniques
    (Elsevier Ltd, 2024) Bakir-Güngör, Burcu; Temiz, Mustafa; Inal, Yasin; Cicekyurt, Emre; Yousef, Malik
    Colorectal cancer (CRC) ranks as the third most common cancer globally and the second leading cause of cancer-related deaths. Recent research highlights the pivotal role of the gut microbiota in CRC development and progression. Understanding the complex interplay between disease development and metagenomic data is essential for CRC diagnosis and treatment. Current computational models employ machine learning to identify metagenomic biomarkers associated with CRC, yet there is a need to improve their accuracy through a holistic biological knowledge perspective. This study aims to evaluate CRC-associated metagenomic data at species, enzymes, and pathway levels via conducting global and population-specific analyses. These analyses utilize relative abundance values from human gut microbiome sequencing data and robust classification models are built for disease prediction and biomarker identification. For global CRC prediction and biomarker identification, the features that are identified by SelectKBest (SKB), Information Gain (IG), and Extreme Gradient Boosting (XGBoost) methods are combined. Population-based analysis includes within-population, leave-one-dataset-out (LODO) and cross-population approaches. Four classification algorithms are employed for CRC classification. Random Forest achieved an AUC of 0.83 for species data, 0.78 for enzyme data and 0.76 for pathway data globally. On the global scale, potential taxonomic biomarkers include ruthenibacterium lactatiformanas; enzyme biomarkers include RNA 2′ 3′ cyclic 3′ phosphodiesterase; and pathway biomarkers include pyruvate fermentation to acetone pathway. This study underscores the potential of machine learning models trained on metagenomic data for improved disease prediction and biomarker discovery. The proposed model and associated files are available at https://github.com/TemizMus/CCPRED. © 2024 Elsevier B.V., All rights reserved.