Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
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Article Citation - Scopus: 34Machine Learning Methods for Microrna Gene Prediction(Humana Press Inc., 2014) Saçar,M.D.; Allmer,J.MicroRNAs (miRNAs) are single-stranded, small, noncoding RNAs of about 22 nucleotides in length, which control gene expression at the posttranscriptional level through translational inhibition, degradation, adenylation, or destabilization of their target mRNAs. Although hundreds of miRNAs have been identified in various species, many more may still remain unknown. Therefore, discovery of new miRNA genes is an important step for understanding miRNA-mediated posttranscriptional regulation mechanisms. It seems that biological approaches to identify miRNA genes might be limited in their ability to detect rare miRNAs and are further limited to the tissues examined and the developmental stage of the organism under examination. These limitations have led to the development of sophisticated computational approaches attempting to identify possible miRNAs in silico. In this chapter, we discuss computational problems in miRNA prediction studies and review some of the many machine learning methods that have been tried to address the issues. © Springer Science+Business Media New York 2014.Review Citation - WoS: 103Citation - Scopus: 136Digital Twin of Electric Vehicle Battery Systems: Comprehensive Review of the Use Cases, Requirements, and Platforms(Elsevier, 2023) Naseri, Farshid; Gil, S.; Barbu, C.; Jensen, A. C.; Larsen, P. G.; Gomes, Claudio; Çetkin, Erdal; Yarımca, GülşahTransportation electrification has been fueled by recent advancements in the technology and manufacturing of battery systems, but the industry yet is facing serious challenges that could be addressed using cutting-edge digital technologies. One such novel technology is based on the digital twining of battery systems. Digital twins (DTs) of batteries utilize advanced multi-layer models, artificial intelligence, advanced sensing units, Internet-of-Things technologies, and cloud computing techniques to provide a virtual live representation of the real battery system (the physical twin) to improve the performance, safety, and cost-effectiveness. Furthermore, they orchestrate the operation of the entire battery value chain offering great advantages, such as improving the economy of manufacturing, re-purposing, and recycling processes. In this context, various studies have been carried out discussing the DT applications and use cases from cloud-enabled battery management systems to the digitalization of battery testing. This work provides a comprehensive review of different possible use cases, key enabling technologies, and requirements for battery DTs. The review inclusively discusses the use cases, development/integration platforms, as well as hardware and software requirements for implementation of the battery DTs, including electrical topics related to the modeling and algorithmic approaches, software architec-tures, and digital platforms for DT development and integration. The existing challenges are identified and circumstances that will create enough value to justify these challenges, such as the added costs, are discussed.Article Citation - WoS: 52Citation - Scopus: 60Applied Machine Learning for Prediction of Waste Plastic Pyrolysis Towards Valuable Fuel and Chemicals Production(Elsevier, 2023) Cheng, Yi; Yang, Yang; Coward, Brad; Wang, Jiawei; Yıldız, Güray; Ekici, Ecrin; Yıldız, GürayPyrolysis is a suitable conversion technology to address the severe ecological and environmental hurdles caused by waste plastics' ineffective pre- and/or post-user management and massive landfilling. By using machine learning (ML) algorithms, the present study developed models for predicting the products of continuous and non-catalytically processes for the pyrolysis of waste plastics. Along with different input datasets, four algorithms, including decision tree (DT), artificial neuron network (ANN), support vector machine (SVM), and Gaussian process (GP), were compared to select input variables for the most accurate models. Among these algorithms, the DT model exhibited generalisable and satisfactory accuracy (R2 > 0.99) with training data. The dataset with the elemental composition of waste plastics achieved better accuracy than that with the plastic-type for predicting liquid yields. These observations allow the predictions by the data from ultimate analysis when inaccessible to the plastic-type data in unknown plastic wastes. Besides, the combination of ultimate analysis input and the DT model also achieved excellent accuracy in liquid and gas composition predictions. © 2023 The AuthorsArticle Citation - WoS: 27Citation - Scopus: 34Multi-Zone Optimisation of High-Rise Buildings Using Artificial Intelligence for Sustainable Metropolises. Part 2: Optimisation Problems, Algorithms, Results, and Method Validation(Pergamon-Elsevier Science LTD, 2021) Ekici, Berk; Kazanasmaz, Zehra Tuğçe; Turrin, Michela; Taşgetiren, M. Fatih; Sarıyıldız, I. SevilHigh-rise building optimisation is becoming increasingly relevant owing to global population growth and urbanisation trends. Previous studies have demonstrated the potential of high-rise optimisation but have been focused on the use of the parameters of single floors for the entire design; thus, the differences related to the impact of the dense surroundings are not taken into consideration. Part 1 of this study presents a multi-zone optimisation (MUZO) methodology and surrogate models (SMs), which provide a swift and accurate prediction for the entire building design; hence, the SMs can be used for optimisation processes. Owing to the high number of parameters involved in the design process, the optimisation task remains challenging. This paper presents how MUZO can cope with an enormous number of parameters to optimise the entire design of high-rise buildings using three algorithms with an adaptive penalty function. Two design scenarios are considered for quad-grid and diagrid shading devices, glazing type, and building-shape parameters using the setup, and the SMs developed in part 1. The optimisation part of the MUZO methodology reported satisfactory results for spatial daylight autonomy and annual sunlight exposure by meeting the Leadership in Energy and Environmental Design standards in 19 of 20 optimisation problems. To validate the impact of the methodology, optimised designs were compared with 8748 and 5832 typical quad-grid and diagrid scenarios, respectively, using the same design parameters for all floor levels. The findings indicate that the MUZO methodology provides significant improvements in the optimisation of high-rise buildings in dense urban areas.Article Citation - WoS: 38Citation - Scopus: 50Multi-Zone Optimisation of High-Rise Buildings Using Artificial Intelligence for Sustainable Metropolises. Part 1: Background, Methodology, Setup, and Machine Learning Results(Elsevier Ltd., 2021) Ekici, Berk; Kazanasmaz, Zehra Tuğçe; Turrin, Michela; Taşgetiren, M. Fatih; Sarıyıldız, I. SevilDesigning high-rise buildings is one of the complex tasks of architecture because it involves interdisciplinary performance aspects in the conceptual phase. The necessity for sustainable high-rise buildings has increased owing to the demand for metropolises based on population growth and urbanisation trends. Although artificial intelligence (AI) techniques support swift decision-making when addressing multiple performance aspects related to sustainable buildings, previous studies only examined single floors because modelling and optimising the entire building requires extensive computational time. However, different floor levels require various design decisions because of the performance variances between the ground and sky levels of high-rises in dense urban districts. This paper presents a multi-zone optimisation (MUZO) methodology to support decision-making for an entire high-rise building considering multiple floor levels and performance aspects. The proposed methodology includes parametric modelling and simulations of high-rise buildings, as well as machine learning and optimisation as AI methods. The specific setup focuses on the quad-grid and diagrid shading devices using two daylight metrics of LEED: spatial daylight autonomy and annual sunlight exposure. The parametric model generated samples to develop surrogate models using an artificial neural network. The results of 40 surrogate models indicated that the machine learning part of the MUZO methodology can report very high prediction accuracies for 31 models and high accuracies for six quad-grid and three diagrid models. The findings indicate that the MUZO can be an important part of designing high-rises in metropolises while predicting multiple performance aspects related to sustainable buildings during the conceptual design phase. © 2021 The Author(s)Article Citation - WoS: 5Citation - Scopus: 7Fast Texture Classification of Denoised Sar Image Patches Using Glcm on Spark(Türkiye Klinikleri Journal of Medical Sciences, 2020) Özcan, Caner; Ersoy, Okan; Oğul, İskender ÜlgenClassification of a synthetic aperture radar (SAR) image is an essential process for SAR image analysis and interpretation. Recent advances in imaging technologies have allowed data sizes to grow, and a large number of applications in many areas have been generated. However, analysis of high-resolution SAR images, such as classification, is a time-consuming process and high-speed algorithms are needed. In this study, classification of high-speed denoised SAR image patches by using Apache Spark clustering framework is presented. Spark is preferred due to its powerful open-source cluster-computing framework with fast, easy-to-use, and in-memory analytics. Classification of SAR images is realized on patch level by using the supervised learning algorithms embedded in the Spark machine learning library. The feature vectors used as the classifier input are obtained using gray-level cooccurrence matrix which is chosen to quantitatively evaluate textural parameters and representations. SAR image patches used to construct the feature vectors are first applied to the noise reduction algorithm to obtain a more accurate classification accuracy. Experimental studies were carried out using naive Bayes, decision tree, and random forest algorithms to provide comparative results, and significant accuracies were achieved. The results were also compared with a state-of-the-art deep learning method. TerraSAR-X images of high-resolution real-world SAR images were used as data.Article Citation - WoS: 4Citation - Scopus: 4Improving the Quality of Positive Datasets for the Establishment of Machine Learning Models for Pre-Microrna Detection(Informationsmanagement in der Biotechnologie e.V. (IMBio e.V.), 2017) Saçar Demirci, Müşerref Duygu; Allmer, JensMicroRNAs (miRNAs) are involved in the post-transcriptional regulation of protein abundance and thus have a great impact on the resulting phenotype. It is, therefore, no wonder that they have been implicated in many diseases ranging from virus infections to cancer. This impact on the phenotype leads to a great interest in establishing the miRNAs of an organism. Experimental methods are complicated which led to the development of computational methods for pre-miRNA detection. Such methods generally employ machine learning to establish models for the discrimination between miRNAs and other sequences. Positive training data for model establishment, for the most part, stems from miRBase, the miRNA registry. The quality of the entries in miRBase has been questioned, though. This unknown quality led to the development of filtering strategies in attempts to produce high quality positive datasets which can lead to a scarcity of positive data. To analyze the quality of filtered data we developed a machine learning model and found it is well able to establish data quality based on intrinsic measures. Additionally, we analyzed which features describing pre-miRNAs could discriminate between low and high quality data. Both models are applicable to data from miRBase and can be used for establishing high quality positive data. This will facilitate the development of better miRNA detection tools which will make the prediction of miRNAs in disease states more accurate. Finally, we applied both models to all miRBase data and provide the list of high quality hairpins.Article Citation - WoS: 11Citation - Scopus: 14Categorization of Species Based on Their Micrornas Employing Sequence Motifs, Information-Theoretic Sequence Feature Extraction, and K-Mers(Springer Verlag, 2017) Yousef, Malik; Nigatu, Dawit; Levy, Dalit; Allmer, Jens; Henkel, WernerBackground: Diseases like cancer can manifest themselves through changes in protein abundance, and microRNAs (miRNAs) play a key role in the modulation of protein quantity. MicroRNAs are used throughout all kingdoms and have been shown to be exploited by viruses to modulate their host environment. Since the experimental detection of miRNAs is difficult, computational methods have been developed. Many such tools employ machine learning for pre-miRNA detection, and many features for miRNA parameterization have been proposed. To train machine learning models, negative data is of importance yet hard to come by; therefore, we recently started to employ pre-miRNAs from one species as positive data versus another species’ pre-miRNAs as negative examples based on sequence motifs and k-mers. Here, we introduce the additional usage of information-theoretic (IT) features. Results: Pre-miRNAs from one species were used as positive and another species’ pre-miRNAs as negative training data for machine learning. The categorization capability of IT and k-mer features was investigated. Both feature sets and their combinations yielded a very high accuracy, which is as good as the previously suggested sequence motif and k-mer based method. However, for obtaining a high performance, a sufficiently large phylogenetic distance between the species and sufficiently high number of pre-miRNAs in the training set is required. To examine the contribution of the IT and k-mer features, an information gain-based feature ranking was performed. Although the top 3 are IT features, 80% of the top 100 features are k-mers. The comparison of all three individual approaches (motifs, IT, and k-mers) shows that the distinction of species based on their pre-miRNAs k-mers are sufficient. Conclusions: IT sequence feature extraction enables the distinction among species and is less computationally expensive than motif calculations. However, since IT features need larger amounts of data to have enough statistics for producing highly accurate results, future categorization into species can be effectively done using k-mers only. The biological reasoning for this is the existence of a codon bias between species which can, at least, be observed in exonic miRNAs. Future work in this direction will be the ab initio detection of pre-miRNA. In addition, prediction of pre-miRNA from RNA-seq can be done.Article Citation - WoS: 37Citation - Scopus: 45On the Performance of Pre-Microrna Detection Algorithms(Nature Publishing Group, 2017) Saçar Demirci, Müşerref Duygu; Baumbach, Jan; Allmer, JensMicroRNAs are crucial for post-transcriptional gene regulation, and their dysregulation has been associated with diseases like cancer and, therefore, their analysis has become popular. The experimental discovery of miRNAs is cumbersome and, thus, many computational tools have been proposed. Here we assess 13 ab initio pre-miRNA detection approaches using all relevant, published, and novel data sets while judging algorithm performance based on ten intrinsic performance measures. We present an extensible framework, izMiR, which allows for the unbiased comparison of existing algorithms, adding new ones, and combining multiple approaches into ensemble methods. In an exhaustive attempt, we condense the results of millions of computations and show that no method is clearly superior; however, we provide a guideline for biomedical researchers to select a tool. Finally, we demonstrate that combining all of the methods into one ensemble approach, for the first time, allows reliable purely computational pre-miRNA detection in large eukaryotic genomes.Article Citation - WoS: 20Citation - Scopus: 25Microrna Categorization Using Sequence Motifs and K-Mers(BioMed Central Ltd., 2017) Yousef, Malik; Khalifa, Waleed; Acar, İlhan Erkin; Allmer, JensBackground: Post-transcriptional gene dysregulation can be a hallmark of diseases like cancer and microRNAs (miRNAs) play a key role in the modulation of translation efficiency. Known pre-miRNAs are listed in miRBase, and they have been discovered in a variety of organisms ranging from viruses and microbes to eukaryotic organisms. The computational detection of pre-miRNAs is of great interest, and such approaches usually employ machine learning to discriminate between miRNAs and other sequences. Many features have been proposed describing pre-miRNAs, and we have previously introduced the use of sequence motifs and k-mers as useful ones. There have been reports of xeno-miRNAs detected via next generation sequencing. However, they may be contaminations and to aid that important decision-making process, we aimed to establish a means to differentiate pre-miRNAs from different species. Results: To achieve distinction into species, we used one species' pre-miRNAs as the positive and another species' pre-miRNAs as the negative training and test data for the establishment of machine learned models based on sequence motifs and k-mers as features. This approach resulted in higher accuracy values between distantly related species while species with closer relation produced lower accuracy values. Conclusions: We were able to differentiate among species with increasing success when the evolutionary distance increases. This conclusion is supported by previous reports of fast evolutionary changes in miRNAs since even in relatively closely related species a fairly good discrimination was possible.