WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7150
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Article Citation - WoS: 2Citation - Scopus: 1A Novel Framework for Droplet/Particle Size Distribution in Suspension Polymerization Using Physics-Informed Neural Network (PINN)(Elsevier Science Sa, 2025) Turan, Meltem; Dutta, AbhishekA Machine Learning (ML) based neural network can capture the complex evolution of polymer chain distributions, accounting for factors such as initiation, propagation, and termination steps in a suspension polymerization process, by integrating stagewise molar balance model (MBM) and population balance model (PBM) with Physics-Informed Neural Network (PINN). The integrated PINN framework is proposed to efficiently solve these equations, incorporating known physical laws as constraints and minimizing errors in both the distribution and dynamics of the polymer chains. By optimizing the neural network parameters such as weight matrices and bias vector, the model reproduces the moments of the polymer molecular weight distribution in close alignment with numerical solutions, and it generates population balance solutions that exhibit excellent agreement with their analytical counterparts. Sensitivity analyses for the depth of the neural network architecture to quantify how structural choices affect model fidelity has been performed. The resulting MBM-PINN and PBM-PINN integrated framework demonstrates robustness and versatility in accurately capturing (96-97%) droplet/particle dynamics. The proposed methodology has the capability to provide a powerful tool for faster and scalable simulations of polymerization reactions, enabling better prediction of product properties which could be used for optimizing reaction conditions in industrial applications.Article Citation - WoS: 3Citation - Scopus: 3Data Driven Modeling and Design of Cellulose Acetate-Polysulfone Blend Ultrafiltration Membranes Based on Artificial Neural Networks(Elsevier Ltd, 2025) Gungormus, E.This study aimed to develop and validate an Artificial Neural Networks (ANNs) model for the design and optimization of cellulose acetate-polysulfone blend ultrafiltration membranes, produced via the Non-Solvent Induced Phase Separation method. After some data science applications on a comprehensive dataset obtained from literature studies, the ultimate ANNs model exhibited superior predictive capabilities and effectively captured complex nonlinear relationships in the data. The optimum model configuration with a single hidden layer containing six neurons provided reliable predictions by avoiding overfitting and underfitting risks and significantly reducing error metrics. The model analyzed the effects of input variables on outputs, revealing that different stages of the membrane preparation process had varying impacts on performance metrics. This finding emphasized the importance of systematically optimizing the preparation process to enhance overall membrane performance. The model's predictions showed strong agreement with experimental data, further validating its accuracy. The optimum production conditions identified by the model offered significant improvements in membrane performance. Moreover, the model accelerated the membrane development process by reducing the required number of experimental trials and promoting efficient resource utilization. This approach contributed to both economic and environmental sustainability by reducing production costs and energy consumption. This study highlighted the significant potential of machine learning techniques for future innovations and advancements in this field by enabling precise, efficient, and sustainable membrane design and synthesis. © 2025 Elsevier Ltd.Article Citation - WoS: 1Tcgex: a Powerful Visual Interface for Exploring and Analyzing Cancer Gene Expression Data(Springernature, 2025) Kus, M. Emre; Sahin, Cagatay; Kilic, Emre; Askin, Arda; Ozgur, M. Mert; Karahanogullari, Gokhan; Ekiz, H. AtakanAnalyzing gene expression data from the Cancer Genome Atlas (TCGA) and similar repositories often requires advanced coding skills, creating a barrier for many researchers. To address this challenge, we developed The Cancer Genome Explorer (TCGEx), a user-friendly, web-based platform for conducting sophisticated analyses such as survival modeling, gene set enrichment analysis, unsupervised clustering, and linear regression-based machine learning. TCGEx provides access to preprocessed TCGA data and immune checkpoint inhibition studies while allowing integration of user-uploaded data sets. Using TCGEx, we explore molecular subsets of human melanoma and identify microRNAs associated with intratumoral immunity. These findings are validated with independent clinical trial data on immune checkpoint inhibitors for melanoma and other cancers. In addition, we identify cytokine genes that can be used to predict treatment responses to various immune checkpoint inhibitors prior to treatment. Built on the R/Shiny framework, TCGEx offers customizable features to adapt analyses for diverse research contexts and generate publication-ready visualizations. TCGEx is freely available at https://tcgex.iyte.edu.tr, providing an accessible tool to extract insights from cancer transcriptomics data.Article Citation - WoS: 3Citation - Scopus: 4Comparison of Conventional and Machine Learning Models for Kinetic Modelling of Biomethane Production From Pretreated Tomato Plant Residues(Elsevier, 2025) Fidan, Berrak; Bodur, Fatma-Gamze; Oztep, Gulsh; Gungoren-Madenoglu, Tuelay; Baba, Alper; Kabay, NalanTomato plant residues (Solanum lycopersicum L.) lack sustainable applications as abundant lignocellulosic biomass after harvest. These residues can be utilized as substrates in anaerobic digestion for biomethane production, generating energy and reducing waste. The purpose of this study was to investigate the sustainable utilization of tomato plant residues for biomethane production at varying conditions and to model biological kinetics. The study aimed to evaluate the effects of varying substrate/inoculum ratios, sulfuric acid pretreatment concentrations, and yeast (Saccharomyces cerevisiae) addition on biogas and biomethane yields under mesophilic conditions (37 degrees C). Maximum biogas and biomethane yields in the studied range were obtained when the substrate/inoculum ratio was 3 (g substrate/g inoculum), the sulfuric acid concentration used for residue pretreatment was 2 %v/v, and the substrate/yeast ratio was 10 (g substrate/g yeast). The yeast ratio of 10 increased the cumulative biogas and biomethane production by 96.5 and 128.9%, respectively. Conventional models (Modified Gompertz, Cone, First-order, Logistic) and Machine Learning models (Support Vector Machine and Neural Network) were compared for biological kinetics. Machine Learning models were also observed to give good fitting results similar to conventional models. Results suggest that Machine Learning models (RMSE: 2.5833-12.0500) are reliable methods like conventional kinetic models (RMSE: 2.1796-13.4880) for forecasting biomethane production in anaerobic digestion processes and Machine Learning models can be applied without needing prior understanding of biomethane production kinetics.Conference Object Citation - WoS: 1Konteyner Görüntülerini Kullanarak Hasar Tespiti ve Sınıflandırması(IEEE, 2020) Imamoglu, Zeynep Ekici; Tuglular, Tugkan; Bastanlar, YalinIn the logistics sector, digital transformation is of great importance in terms of competition. In the present case, container warehouse entry / exit operations are carried out manually by the logistics personnel including container damage detection. During container warehouse entry / exit process, the process of detecting damaged containers is carried out by the personnel and several minutes are required to upload to the IT system. The aim of our work is to automate the detection of damaged containers. This way, the mistakes made by the personnel will be eliminated and the process will be accelerated. In this work, we propose to use a convolutional neural network (CNN) that takes the container images and classify them as damaged or undamaged. We modeled the problem as a binary classification and employed different CNN models. The result we obtained shows that there is no single best method for the classification. It is shown how the dataset was created and how the parameters used in the layered structures affect the models employed in this study.Conference Object Citation - WoS: 3Citation - Scopus: 8Distinguishing Between Microrna Targets From Diverse Species Using Sequence Motifs and K-Mers(SCITEPRESS, 2017) Yousef, Malik; Khalifa, Waleed; Acar, İlhan Erkin; Allmer, JensA disease phenotype is often due to dysregulation of gene expression. Post-translational regulation of protein abundance by microRNAs (miRNAs) is, therefore, of high importance in, for example, cancer studies. MicroRNAs provide a complementary sequence to their target messenger RNA (mRNA) as part of a complex molecular machinery. Known miRNAs and targets are listed in miRTarBase for a variety of organisms. The experimental detection of such pairs is convoluted and, therefore, their computational detection is desired which is complicated by missing negative data. For machine learning, many features for parameterization of the miRNA targets are available and k-mers and sequence motifs have previously been used. Unrelated organisms like intracellular pathogens and their hosts may communicate via miRNAs and, therefore, we investigated whether miRNA targets from one species can be differentiated from miRNA targets of another. To achieve this end, we employed target information of one species as positive and the other as negative training and testing data. Models of species with higher evolutionary distance generally achieved better results of up to 97% average accuracy (mouse versus Caenorhabditis elegans) while more closely related species did not lead to successful models (human versus mouse; 60%). In the future, when more targeting data becomes available, models can be established which will be able to more precisely determine miRNA targets in hostpathogen systems using this approach.