Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
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Conference Object Metabolomics Data Analysis to Discover Chronic Granulomatous Disease-Associated Biomarkers Utilizing G-S-M Machine Learning Model via Grouping Metabolites According to Ion Type(Institute of Electrical and Electronics Engineers Inc., 2024-10-16) Ersöz, Nur Sebnem; Bakir-Güngör, Burcu; Yousef, MalikChronic Granulomatous Disease (CGD) is a rare, inherited immunodeficiency disorder characterized by white blood cells unable to effectively kill certain bacteria and fungi. This defect results in the formation of clusters of immune cells called granulomas that form at sites of infection or inflammation. Therefore, identification of disease-related biomarkers is a critical step in advancing precision medicine and improving diagnostic accuracy. In this study, we applied a G-S-M machine learning approach to metabolomics data to uncover CGD-Associated biomarkers. We obtained a metabolomics dataset from Gene Expression Omnibus with GSE220260 accession number. Data includes 85 samples (16 healthy controls and 69 CGD samples) with comprehensive metabolic profiles obtained using liquid chromatography-mass spectrometry analysis. Dataset includes metabolite names with their ion type and formula. In order to identify CGD related metabolites and their ion types, G-S-M was used as a grouping function when performing machine learning oriented metabolomics data analysis. We have performed the G-S-M approach by grouping metabolites according to their ion type. In the training part of the G-S-M approach, metabolites annotated with selected ion types have been utilized to perform a two-class classification task which generates an important set of ion type output. We also compared the performance results of the G-S-M machine learning model with traditional feature selection methods; XGB, SKB, IG, FCBF, MRMR, CMIM with random forest classifier. 100 times Monte-Carlo Cross Validation was used in our experiments. It was observed that G-S-M, XGB, SKB and FCBF methods similarly provided the best performances. In this study, besides its performance, G-S-M method used groups based on ion types unlike TFS, and then identified relevant Chronic Granulomatous Disease-associated metabolites. © 2024 Elsevier B.V., All rights reserved.Conference Object Citation - WoS: 16Citation - Scopus: 20Machine Learning Analysis of Inflammatory Bowel Disease-Associated Metagenomics Dataset(Institute of Electrical and Electronics Engineers Inc., 2018-09) Hacilar, Hilal; Nalbantoĝlu, Özkan Ufuk; Bakir-Güngör, BurcuThere is an ongoing interplay between humans and our microbial communities. The microorganisms living in our gut produce energy from our food, strengthen our immune system, break down foreign products, and release metabolites and hormones, which are significant for regulating our physiology. The shifts away from this 'healthy' gut microbiome is considered to be associated with many diseases. Inflammatory bowel diseases (IBD) including Crohn's disease and ulcerative colitis, are gut related disorders affecting the intestinal tract. Although some metagenomics studies are conducted on IBD recently, our current understanding of the precise relationships between the human gut microbiome and IBD remains limited. In this regard, the use of state-of-the art machine learning approaches became popular to address a variety of questions like early diagnosis of certain diseases using human microbiota. In this study, we investigate which subset of gut microbiota are mostly associated with IBD and if disease-associated biomarkers can be detected via applying state-of-the art machine learning algorithms and proper feature selection methods. © 2019 Elsevier B.V., All rights reserved.Article Citation - Scopus: 100An Optimally Configured and Improved Deep Belief Network (OCI-DBN) Approach for Heart Disease Prediction Based on Ruzzo-Tompa and Stacked Genetic Algorithm(Institute of Electrical and Electronics Engineers Inc., 2020) Ali, Syed Arslan; Raza, Basit; Malik, Ahmad Kamran Kamran; Shahid, Ahmad Raza; Faheem, Muhammed Yasir; Alquhayz, Hani Ali; Kumar, Y. J.A rapid increase in heart disease has occurred in recent years, which might be the result of unhealthy food, mental stress, genetic issues, and a sedentary lifestyle. There are many advanced automated diagnosis systems for heart disease prediction proposed in recent studies, but most of them focus only on feature preprocessing, some focus on feature selection, and some only on improving the predictive accuracy. In this study, we focus on every aspect that may have an influence on the final performance of the system, i.e., to avoid overfitting and underfitting problems or to solve network configuration issues and optimization problems. We introduce an optimally configured and improved deep belief network named OCI-DBN to solve these problems and improve the performance of the system. We used the Ruzzo-Tompa approach to remove those features that are not contributing enough to improve system performance. To find an optimal network configuration, we proposed a stacked genetic algorithm that stacks two genetic algorithms to give an optimally configured DBN. An analysis of a RBM and DBN trained is performed to give an insight how the system works. Six metrics were used to evaluate the proposed method, including accuracy, sensitivity, specificity, precision, F1 score, and Matthew's correlation coefficient. The experimental results are compared with other state-of-the-art methods, and OCI-DBN shows a better performance. The validation results assure that the proposed method can provide reliable recommendations to heart disease patients by improving the accuracy of heart disease predictions by up to 94.61%. © 2020 Elsevier B.V., All rights reserved.