PubMed İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/397
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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, MalikArticle Citation - WoS: 26Citation - Scopus: 33miRmoduleNet: Detecting miRNA-mRNA Regulatory Modules(Frontiers Media S.A., 2022-04-12) Yousef, Malik; Goy, Gokhan; Bakir-Gungor, BurcuIncreasing evidence that MicroRNAs (miRNAs) play a key role in carcinogenesis has revealed the need for elucidating the mechanisms of miRNA regulation and the roles of miRNAs in gene-regulatory networks. A better understanding of the interactions between miRNAs and their mRNA targets will provide a better understanding of the complex biological processes that occur during carcinogenesis. Increased efforts to reveal these interactions have led to the development of a variety of tools to detect and understand these interactions. We have recently described a machine learning approach miRcorrNet, based on grouping and scoring (ranking) groups of genes, where each group is associated with a miRNA and the group members are genes with expression patterns that are correlated with this specific miRNA. The miRcorrNet tool requires two types of -omics data, miRNA and mRNA expression profiles, as an input file. In this study we describe miRModuleNet, which groups mRNA (genes) that are correlated with each miRNA to form a star shape, which we identify as a miRNA-mRNA regulatory module. A scoring procedure is then applied to each module to further assess their contribution in terms of classification. An important output of miRModuleNet is that it provides a hierarchical list of significant miRNA-mRNA regulatory modules. miRModuleNet was further validated on external datasets for their disease associations, and functional enrichment analysis was also performed. The application of miRModuleNet aids the identification of functional relationships between significant biomarkers and reveals essential pathways involved in cancer pathogenesis.Article Citation - WoS: 20Citation - Scopus: 24miRdisNET: Discovering MicroRNA Biomarkers That Are Associated With Diseases Utilizing Biological Knowledge-Based Machine Learning(Frontiers Media S.A., 2023-01-12) Jabeer, Amhar; Temiz, Mustafa; Bakir-Gungor, Burcu; Yousef, MalikDuring recent years, biological experiments and increasing evidence have shown that MicroRNAs play an important role in the diagnosis and treatment of human complex diseases. Therefore, to diagnose and treat human complex diseases, it is necessary to reveal the associations between a specific disease and related miRNAs. Although current computational models based on machine learning attempt to determine miRNA-disease associations, the accuracy of these models need to be improved, and candidate miRNA-disease relations need to be evaluated from a biological perspective. In this paper, we propose a computational model named miRdisNET to predict potential miRNA-disease associations. Specifically, miRdisNET requires two types of data, i.e., miRNA expression profiles and known disease-miRNA associations as input files. First, we generate subsets of specific diseases by applying the grouping component. These subsets contain miRNA expressions with class labels associated with each specific disease. Then, we assign an importance score to each group by using a machine learning method for classification. Finally, we apply a modeling component and obtain outputs. One of the most important outputs of miRdisNET is the performance of miRNA-disease prediction. Compared with the existing methods, miRdisNET obtained the highest AUC value of .9998. Another output of miRdisNET is a list of significant miRNAs for disease under study. The miRNAs identified by miRdisNET are validated via referring to the gold-standard databases which hold information on experimentally verified MicroRNA-disease associations. miRdisNET has been developed to predict candidate miRNAs for new diseases, where miRNA-disease relation is not yet known. In addition, miRdisNET presents candidate disease-disease associations based on shared miRNA knowledge. The miRdisNET tool and other supplementary files are publicly available at: .Article Citation - WoS: 10Citation - Scopus: 15Textnettopics Pro, a Topic Model-Based Text Classification for Short Text by Integration of Semantic and Document-Topic Distribution Information(Frontiers Media S.A., 2023-10-05) Voskergian, Daniel; Bakir-Gungor, Burcu; Yousef, MalikWith the exponential growth in the daily publication of scientific articles, automatic classification and categorization can assist in assigning articles to a predefined category. Article titles are concise descriptions of the articles' content with valuable information that can be useful in document classification and categorization. However, shortness, data sparseness, limited word occurrences, and the inadequate contextual information of scientific document titles hinder the direct application of conventional text mining and machine learning algorithms on these short texts, making their classification a challenging task. This study firstly explores the performance of our earlier study, TextNetTopics on the short text. Secondly, here we propose an advanced version called TextNetTopics Pro, which is a novel short-text classification framework that utilizes a promising combination of lexical features organized in topics of words and topic distribution extracted by a topic model to alleviate the data-sparseness problem when classifying short texts. We evaluate our proposed approach using nine state-of-the-art short-text topic models on two publicly available datasets of scientific article titles as short-text documents. The first dataset is related to the Biomedical field, and the other one is related to Computer Science publications. Additionally, we comparatively evaluate the predictive performance of the models generated with and without using the abstracts. Finally, we demonstrate the robustness and effectiveness of the proposed approach in handling the imbalanced data, particularly in the classification of Drug-Induced Liver Injury articles as part of the CAMDA challenge. Taking advantage of the semantic information detected by topic models proved to be a reliable way to improve the overall performance of ML classifiers.Article Citation - WoS: 28Citation - Scopus: 31Proteomic and Biological Analysis of the Effects of Metformin Senomorphics on the Mesenchymal Stromal Cells(Frontiers Media S.A., 2021-10-05) Acar, Mustafa Burak; Ayaz-Guner, Serife; Gunaydin, Zeynep; Karakukcu, Musa; Peluso, Gianfranco; Di Bernardo, Giovanni; Galderisi, UmbertoSenotherapeutics are new drugs that can modulate senescence phenomena within tissues and reduce the onset of age-related pathologies. Senotherapeutics are divided into senolytics and senomorphics. The senolytics selectively kill senescent cells, while the senomorphics delay or block the onset of senescence. Metformin has been used to treat diabetes for several decades. Recently, it has been proposed that metformin may have anti-aging properties as it prevents DNA damage and inflammation. We evaluated the senomorphic effect of 6 weeks of therapeutic metformin treatment on the biology of human adipose mesenchymal stromal cells (MSCs). The study was combined with a proteome analysis of changes occurring in MSCs' intracellular and secretome protein composition in order to identify molecular pathways associated with the observed biological phenomena. The metformin reduced the replicative senescence and cell death phenomena associated with prolonged in vitro cultivation. The continuous metformin supplementation delayed and/or reduced the impairment of MSC functions as evidenced by the presence of three specific pathways in metformin-treated samples: 1) the alpha-adrenergic signaling, which contributes to regulation of MSCs physiological secretory activity, 2) the signaling pathway associated with MSCs detoxification activity, and 3) the aspartate degradation pathway for optimal energy production. The senomorphic function of metformin seemed related to its reactive oxygen species (ROS) scavenging activity. In metformin-treated samples, the CEBPA, TP53 and USF1 transcription factors appeared to be involved in the regulation of several factors (SOD1, SOD2, CAT, GLRX, GSTP1) blocking ROS.Article Citation - WoS: 16Citation - Scopus: 20Invention of 3Mint for Feature Grouping and Scoring in Multi-Omics(Frontiers Media S.A., 2023-03-15) Yazici, Miray Unlu; Marron, J. S.; Bakir-Gungor, Burcu; Zou, Fei; Yousef, Malik; Unlu Yazici, MirayAdvanced genomic and molecular profiling technologies accelerated the enlightenment of the regulatory mechanisms behind cancer development and progression, and the targeted therapies in patients. Along this line, intense studies with immense amounts of biological information have boosted the discovery of molecular biomarkers. Cancer is one of the leading causes of death around the world in recent years. Elucidation of genomic and epigenetic factors in Breast Cancer (BRCA) can provide a roadmap to uncover the disease mechanisms. Accordingly, unraveling the possible systematic connections between-omics data types and their contribution to BRCA tumor progression is crucial. In this study, we have developed a novel machine learning (ML) based integrative approach for multi-omics data analysis. This integrative approach combines information from gene expression (mRNA), MicroRNA (miRNA) and methylation data. Due to the complexity of cancer, this integrated data is expected to improve the prediction, diagnosis and treatment of disease through patterns only available from the 3-way interactions between these 3-omics datasets. In addition, the proposed method bridges the interpretation gap between the disease mechanisms that drive onset and progression. Our fundamental contribution is the 3 Multi-omics integrative tool (3Mint). This tool aims to perform grouping and scoring of groups using biological knowledge. Another major goal is improved gene selection via detection of novel groups of cross-omics biomarkers. Performance of 3Mint is assessed using different metrics. Our computational performance evaluations showed that the 3Mint classifies the BRCA molecular subtypes with lower number of genes when compared to the miRcorrNet tool which uses miRNA and mRNA gene expression profiles in terms of similar performance metrics (95% Accuracy). The incorporation of methylation data in 3Mint yields a much more focused analysis. The 3Mint tool and all other supplementary files are available at .Article Citation - WoS: 15Citation - Scopus: 18Histopathology Image Classification: Highlighting the Gap Between Manual Analysis and AI Automation(Frontiers Media S.A., 2024-01-17) Dogan, Refika Sultan; Yilmaz, BulentThe field of histopathological image analysis has evolved significantly with the advent of digital pathology, leading to the development of automated models capable of classifying tissues and structures within diverse pathological images. Artificial intelligence algorithms, such as convolutional neural networks, have shown remarkable capabilities in pathology image analysis tasks, including tumor identification, metastasis detection, and patient prognosis assessment. However, traditional manual analysis methods have generally shown low accuracy in diagnosing colorectal cancer using histopathological images. This study investigates the use of AI in image classification and image analytics using histopathological images using the histogram of oriented gradients method. The study develops an AI-based architecture for image classification using histopathological images, aiming to achieve high performance with less complexity through specific parameters and layers. In this study, we investigate the complicated state of histopathological image classification, explicitly focusing on categorizing nine distinct tissue types. Our research used open-source multi-centered image datasets that included records of 100.000 non-overlapping images from 86 patients for training and 7180 non-overlapping images from 50 patients for testing. The study compares two distinct approaches, training artificial intelligence-based algorithms and manual machine learning models, to automate tissue classification. This research comprises two primary classification tasks: binary classification, distinguishing between normal and tumor tissues, and multi-classification, encompassing nine tissue types, including adipose, background, debris, stroma, lymphocytes, mucus, smooth muscle, normal colon mucosa, and tumor. Our findings show that artificial intelligence-based systems can achieve 0.91 and 0.97 accuracy in binary and multi-class classifications. In comparison, the histogram of directed gradient features and the Random Forest classifier achieved accuracy rates of 0.75 and 0.44 in binary and multi-class classifications, respectively. Our artificial intelligence-based methods are generalizable, allowing them to be integrated into histopathology diagnostics procedures and improve diagnostic accuracy and efficiency. The CNN model outperforms existing machine learning techniques, demonstrating its potential to improve the precision and effectiveness of histopathology image analysis. This research emphasizes the importance of maintaining data consistency and applying normalization methods during the data preparation stage for analysis. It particularly highlights the potential of artificial intelligence to assess histopathological images.Article Citation - WoS: 16Citation - Scopus: 21GeNetOntology: Identifying Affected Gene Ontology Terms via Grouping, Scoring, and Modeling of Gene Expression Data Utilizing Biological Knowledge-Based Machine Learning(Frontiers Media S.A., 2023-08-21) Ersoz, Nur Sebnem; Bakir-Gungor, Burcu; Yousef, MalikIntroduction: Identifying significant sets of genes that are up/downregulated under specific conditions is vital to understand disease development mechanisms at the molecular level. Along this line, in order to analyze transcriptomic data, several computational feature selection (i.e., gene selection) methods have been proposed. On the other hand, uncovering the core functions of the selected genes provides a deep understanding of diseases. In order to address this problem, biological domain knowledge-based feature selection methods have been proposed. Unlike computational gene selection approaches, these domain knowledge-based methods take the underlying biology into account and integrate knowledge from external biological resources. Gene Ontology (GO) is one such biological resource that provides ontology terms for defining the molecular function, cellular component, and biological process of the gene product.Methods: In this study, we developed a tool named GeNetOntology which performs GO-based feature selection for gene expression data analysis. In the proposed approach, the process of Grouping, Scoring, and Modeling (G-S-M) is used to identify significant GO terms. GO information has been used as the grouping information, which has been embedded into a machine learning (ML) algorithm to select informative ontology terms. The genes annotated with the selected ontology terms have been used in the training part to carry out the classification task of the ML model. The output is an important set of ontologies for the two-class classification task applied to gene expression data for a given phenotype.Results: Our approach has been tested on 11 different gene expression datasets, and the results showed that GeNetOntology successfully identified important disease-related ontology terms to be used in the classification model.Discussion: GeNetOntology will assist geneticists and scientists to identify a range of disease-related genes and ontologies in transcriptomic data analysis, and it will also help doctors design diagnosis platforms and improve patient treatment plans.Article Citation - WoS: 1Citation - Scopus: 3Engineering Novel Features for Diabetes Complication Prediction Using Synthetic Electronic Health Records(Frontiers Media S.A., 2025-04-14) Voskergian, Daniel; Bakir-Gungor, Burcu; Yousef, MalikDiabetes significantly affects millions of people worldwide, leading to substantial morbidity, disability, and mortality rates. Predicting diabetes-related complications from health records is crucial for early prevention and for the development of effective treatment plans. In order to predict four different complications of diabetes mellitus, i.e., retinopathy, chronic kidney disease, ischemic heart disease, and amputations, this study introduces a novel feature engineering approach. While developing the classification models, we utilize XGBoost feature selection method and various supervised machine learning algorithms, including Random Forest, XGBoost, LogitBoost, AdaBoost, and Decision Tree. These models were trained on synthetic electronic health records (EHR) generated by dual-adversarial autoencoders. These EHRs represent nearly 1 million synthetic patients derived from an authentic cohort of 979,308 individuals with diabetes. The variables considered in the models were the age range accompanied by chronic diseases that occur during patient visits starting from the onset of diabetes. Throughout the experiments, XGBoost and Random Forest demonstrated the best overall prediction performance. The final models, which are tailored to each complication and trained using our feature engineering approach, achieved an accuracy between 69% and 77% and an AUC between 77% and 84% using cross-validation, while the partitioned validation approach yielded an accuracy between 59% and 78% and an AUC between 66% and 85%. These findings imply that the performance of our method surpass the performance of the traditional Bag-of-Features approach, highlighting the effectiveness of our approach in enhancing model accuracy and robustness.Article Citation - WoS: 102Citation - Scopus: 122A Human-Robot Interaction Perspective on Assistive and Rehabilitation Robotics(Frontiers Media S.A., 2017-05-23) Beckerle, Philipp; Salvietti, Gionata; Unal, Ramazan; Prattichizzo, Domenico; Rossi, Simone; Castellini, Claudio; Bianchi, MatteoAssistive and rehabilitation devices are a promising and challenging field of recent robotics research. Motivated by societal needs such as aging populations, such devices can support motor functionality and subject training. The design, control, sensing, and assessment of the devices become more sophisticated due to a human in the loop. This paper gives a human-robot interaction perspective on current issues and opportunities in the field. On the topic of control and machine learning, approaches that support but do not distract subjects are reviewed. Options to provide sensory user feedback that are currently missing from robotic devices are outlined. Parallels between device acceptance and affective computing are made. Furthermore, requirements for functional assessment protocols that relate to real-world tasks are discussed. In all topic areas, the design of human-oriented frameworks and methods is dominated by challenges related to the close interaction between the human and robotic device. This paper discusses the aforementioned aspects in order to open up new perspectives for future robotic solutions.