Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
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Conference Object Citation - Scopus: 2miRcorrNetPro: Unraveling Algorithmic Insights Through Cross-Validation in Multi-Omics Integration for Comprehensive Data Analysis(Institute of Electrical and Electronics Engineers Inc., 2023-12-05) Ünlü Yazici, Miray; Yousef, Malik; Marron, J. S.; Bakir-Güngör, Burcu; Yazici, Miray UnluHigh throughput -omics technologies facilitate the investigation of regulatory mechanisms of complex diseases. Along this line, scientists develop promising tools and methods to extend our understanding at the molecular and functional levels. To this end, miRcorrNet tool performs integrative analysis of MicroRNA (miRNA) and gene expression profiles via machine learning (ML) approach to identify significant miRNA groups and their associated target genes. In this study, we propose miRcorrNetPro tool, which extends miRcorrNet by tracking group scoring, ranking and other information through the cross-validation iterations. Heatmap visualizations enable deep novel insights into the collective behavior of clusters of groups in cellular signaling and hence facilitate detection of potential biomarkers for the disease under investigation. Although miRcorrNetPro is designed as a generic tool, here we present our findings and potential miRNA biomarkers for Breast Cancer (BRCA). The miRcorrNetPro tool and all other supplementary files are available at https://github.com/Miray-Unlu/miRcorrNetPro. © 2024 Elsevier B.V., All rights reserved.Article Citation - Scopus: 1eTNT: Enhanced Textnettopics With Filtered LDA Topics and Sequential Forward / Backward Topic Scoring Approaches(Science and Information Organization, 2024) Voskergian, Daniel; Jayousi, Rashid; Bakir-Güngör, BurcuTextNetTopics is a novel text classification-based topic modelling approach that focuses on topic selection rather than individual word selection to train a machine learning algorithm. However, one key limitation of TextNetTopics is its scoring component, which evaluates each topic in isolation and ranks them accordingly, ignoring the potential relationships between topics. In addition, the chosen topics may contain redundant or irrelevant features, potentially increasing the feature set size and introducing noise that can degrade the overall model performance. To address these limitations and improve the classification performance, this study introduces an enhancement to TextNetTopics. eTNT integrates two novel scoring approaches: Sequential Forward Topic Scoring (SFTS) and Sequential Backward Topic Scoring (SBTS), which consider topic interactions by assessing sets of topics simultaneously. Moreover, it incorporates a filtering component that aims to enhance topics' quality and discriminative power by removing non-informative features from each topic using Random Forest feature importance values. These integrations aim to streamline the topic selection process and enhance classifier efficiency for text classification. The results obtained from the WOS-5736, LitCovid, and MultiLabel datasets provide valuable insights into the superior effectiveness of eTNT compared to its counterpart, TextNetTopics. © 2024 Elsevier B.V., All rights reserved.Conference Object Machine Learning Based Beamwidth Adaptation for mmWave Vehicular Communications(Institute of Electrical and Electronics Engineers Inc., 2023-12-10) Manic, Setinder; Heng Foh, Chuan; Köse, Abdulkadir; Lee, Haeyoung; Leow, Chee Yen; Chatzimisios, Periklis; Suthaputchakun, Chakkaphong; Foh, Chuan HengThe incorporation of mmWave technology in vehicular networks has unlocked a realm of possibilities, propelling the advancement of autonomous vehicles, enhancing interconnectedness, and facilitating communication for intelligent transportation systems (ITS). Despite these strides in connectivity, challenges such as high path-loss have arisen, impacting existing beam management procedures. This work aims to address this issue by improving beam management techniques, specifically focusing on enhancing the service time between vehicles and base stations through adaptive mmWave beamwidth adjustments, accomplished using a Contextual Multi-Armed Bandit Algorithm. By leveraging various conditions to train the ML agent of the Contextual Multi-Armed Bandit Algorithm, it seeks to learn about vehicle mobility profiles and optimize the usage of different antenna beamwidth settings to maximize seamless connection time. The extensive simulation results showcase the effectiveness of an adaptive beamwidth for mobility profiles, extending the connection time a vehicle experiences with a base station when compared to the existing strategies. © 2024 Elsevier B.V., All rights reserved.Conference Object Linear Vs. Non-Linear Embedding Methods in Recommendation Systems(Institute of Electrical and Electronics Engineers Inc., 2022-09-07) Gurler, Kerem; Cos¸kun, Mustafa; Karagenc, Safak; Orun, Gokhan; Kuleli Pak, Burcu Kuleli; Güngör, Vehbi Çağrı; Coskun, Mustafa; Pak, Burcu KuleliPredicting customer interest in items is very crucial in direct marketing as it can potentially boost sales. Data mining techniques are developed to predict which items a particular user might be interested in based on their purchase history or explicit feedback in form of ratings or comments. Recently, non-linear and linear methods have been developed for this purpose. In this study, we applied Neighborhood based Collaborative Filtering (CF), Matrix Factorization (MF), Singular Value Decomposition (SVD), Neural Graph CF (NGCF) and Light Graph Convolutional Network (LightGCN) on explicit user product rating data which is acquired from the online gaming and mobile entertainment platform called HADI. We compared the results of node embedding methods in terms of Precision@k, Recall@k and NDCG@k values. SVD and LightGCN showed the best test performance and SVD was significantly superior to LightGCN in terms of training speed. To further increase predictive performance of SVD, we have applied classification with Logistic Regression and Deep Random Forest on user and item embeddings created by the SVD. © 2022 Elsevier B.V., All rights reserved.Article Citation - Scopus: 49EdgeAISim: A Toolkit for Simulation and Modelling of AI Models in Edge Computing Environments(Elsevier Ltd, 2024-02) Nandhakumar, Aadharsh Roshan; Baranwal, Ayush; Choudhary, Priyanshukumar; Golec, Muhammed; Gill, Sukhpal SinghTo meet next-generation Internet of Things (IoT) application demands, edge computing moves processing power and storage closer to the network edge to minimize latency and bandwidth utilization. Edge computing is becoming increasingly popular as a result of these benefits, but it comes with challenges such as managing resources efficiently. Researchers are utilising Artificial Intelligence (AI) models to solve the challenge of resource management in edge computing systems. However, existing simulation tools are only concerned with typical resource management policies, not the adoption and implementation of AI models for resource management, especially. Consequently, researchers continue to face significant challenges, making it hard and time-consuming to use AI models when designing novel resource management policies for edge computing with existing simulation tools. To overcome these issues, we propose a lightweight Python-based toolkit called EdgeAISim for the simulation and modelling of AI models for designing resource management policies in edge computing environments. In EdgeAISim, we extended the basic components of the EdgeSimPy framework and developed new AI-based simulation models for task scheduling, energy management, service migration, network flow scheduling, and mobility support for edge computing environments. In EdgeAISim, we have utilized advanced AI models such as Multi-Armed Bandit with Upper Confidence Bound, Deep Q-Networks, Deep Q-Networks with Graphical Neural Network, and Actor-Critic Network to optimize power usage while efficiently managing task migration within the edge computing environment. The performance of these proposed models of EdgeAISim is compared with the baseline, which uses a worst-fit algorithm-based resource management policy in different settings. Experimental results indicate that EdgeAISim exhibits a substantial reduction in power consumption, highlighting the compelling success of power optimization strategies in EdgeAISim. The development of EdgeAISim represents a promising step towards sustainable edge computing, providing eco-friendly and energy-efficient solutions that facilitate efficient task management in edge environments for different large-scale scenarios. © 2023 Elsevier B.V., All rights reserved.Article Citation - Scopus: 14CoviDetector: A Transfer Learning-Based Semi Supervised Approach to Detect COVID-19 Using CXR Images(Elsevier B.V., 2023-06) Chowdhury, Deepraj; Das, Anik; Dey, Ajoy; Banerjee, Soham; Golec, Muhammed; Kollias, Dimitrios; Arya, Rajesh Chand; Uhlig, SteveCOVID-19 was one of the deadliest and most infectious illnesses of this century. Research has been done to decrease pandemic deaths and slow down its spread. COVID-19 detection investigations have utilised Chest X-ray (CXR) images with deep learning techniques with its sensitivity in identifying pneumonic alterations. However, CXR images are not publicly available due to users’ privacy concerns, resulting in a challenge to train a highly accurate deep learning model from scratch. Therefore, we proposed CoviDetector, a new semi-supervised approach based on transfer learning and clustering, which displays improved performance and requires less training data. CXR images are given as input to this model, and individuals are categorised into three classes: (1) COVID-19 positive; (2) Viral pneumonia; and (3) Normal. The performance of CoviDetector has been evaluated on four different datasets, achieving over 99% accuracy on them. Additionally, we generate heatmaps utilising Grad-CAM and overlay them on the CXR images to present the highlighted areas that were deciding factors in detecting COVID-19. Finally, we developed an Android app to offer a user-friendly interface. We release the code, datasets and results’ scripts of CoviDetector for reproducibility purposes; they are available at: https://github.com/dasanik2001/CoviDetector © 2024 Elsevier B.V., All rights reserved.Article Citation - Scopus: 4CCPred: Global and Population-Specific Colorectal Cancer Prediction and Metagenomic Biomarker Identification at Different Molecular Levels Using Machine Learning Techniques(Elsevier Ltd, 2024-11) Bakir-Güngör, Burcu; Temiz, Mustafa; Inal, Yasin; Cicekyurt, Emre; Yousef, MalikColorectal 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.Article Citation - Scopus: 8Building a Challenging Medical Dataset for Comparative Evaluation of Classifier Capabilities(Elsevier Ltd, 2024-08) Bozkurt, Berat; Coskun, Kerem; Bakal, GokhanSince the 2000s, digitalization has been a crucial transformation in our lives. Nevertheless, digitalization brings a bulk of unstructured textual data to be processed, including articles, clinical records, web pages, and shared social media posts. As a critical analysis, the classification task classifies the given textual entities into correct categories. Categorizing documents from different domains is straightforward since the instances are unlikely to contain similar contexts. However, document classification in a single domain is more complicated due to sharing the same context. Thus, we aim to classify medical articles about four common cancer types (Leukemia, Non-Hodgkin Lymphoma, Bladder Cancer, and Thyroid Cancer) by constructing machine learning and deep learning models. We used 383,914 medical articles about four common cancer types collected by the PubMed API. To build classification models, we split the dataset into 70% as training, 20% as testing, and 10% as validation. We built widely used machine-learning (Logistic Regression, XGBoost, CatBoost, and Random Forest Classifiers) and modern deep-learning (convolutional neural networks - CNN, long short-term memory - LSTM, and gated recurrent unit - GRU) models. We computed the average classification performances (precision, recall, F-score) to evaluate the models over ten distinct dataset splits. The best-performing deep learning model(s) yielded a superior F1 score of 98%. However, traditional machine learning models also achieved reasonably high F1 scores, 95% for the worst-performing case. Ultimately, we constructed multiple models to classify articles, which compose a hard-to-classify dataset in the medical domain. © 2024 Elsevier B.V., All rights reserved.Conference Object Citation - Scopus: 4A Transfer Learning Application on the Reliability of Psychological Drugs' Comments(Institute of Electrical and Electronics Engineers Inc., 2023-07-25) Sen, Tarik Uveys; Bakal, GokhanAs digitalization and the Internet stay emerging concepts by gaining popularity, the accuracy of personal reviews/opinions will be a critical issue. This circumstance also particularly applies to patients taking psychological drugs, where accurate information is crucial for other patients and medical professionals. In this study, we analyze drug reviews from drugs.com to determine the effectiveness of reviews for psychological drugs. Our dataset includes over 200,000 drug reviews, which we labeled as positive, negative, or neutral according to their rating scores. We apply machine learning (ML) models, including Logistic Regression, Recurrent Neural Network (RNN), and Long Short-Term Memory (LSTM) algorithms, to predict the sentiment class of each review. Our results demonstrate an F1-Weighted score of 85.3% for the LSTM model. However, by applying the transfer learning technique, we further improved the F1 score (nearly 3% increase) obtained by the LSTM model. Our findings proved that there is no contextual difference between the comments made by the patients suffering from psychological or other diseases. © 2023 Elsevier B.V., All rights reserved.Conference Object Citation - Scopus: 3A Computational Drug Repositioning Effort Using Patients' Reviews Dataset(Institute of Electrical and Electronics Engineers Inc., 2023-07-25) Akkaya, Ali; Bakal, GokhanThe drug discovery process is one of the core motivations in both medical and, specifically, pharmaceutical disciplines. Due to the nature of the process, it requires an excessive amount of time, clinical experiments, and budget to cover each discovery phase. In this sense, computational drug discovery efforts can shorten the discovery process by providing plausible candidates since many of the attempts fail for several reasons, such as a lack of participants, financial problems, or ineffective results. In this study, the goal is to identify plausible candidate drugs for diseases. To do that, we utilize a personal experience of drugs dataset generated by patients. Beyond the user-generated comments, the users also give a rate between 1 and 10. Since we want to ensure the dataset quality, we first performed sentiment analysis experiments to prove that the reviews/comments are consistent with the given rating score. Then, only the review pairs having an effectiveness rate of 6 or more are selected as pre-filtered drug-disease pairs. We also build a knowledge graph using treatment-related biomedical relations using predications from Semantic Medline Database to identify drug similarities utilizing the Simrank similarity algorithm. As a result, we reported a list of plausible drugs as repurposing/repositioning candidates for further experiments. © 2023 Elsevier B.V., All rights reserved.