Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Citation - WoS: 40Citation - Scopus: 38Anisotropic and Outstanding Mechanical, Thermal Conduction, Optical, and Piezoelectric Responses in a Novel Semiconducting Bcn Monolayer Confirmed by First-Principles and Machine Learning(Elsevier, 2022) Mortazavi, Bohayra; Fazel Shojaei; Yağmurcukardeş, Mehmet; Alexander Shapeev; Xiaoying ZhuangGraphene-like nanomembranes made of the neighboring elements of boron, carbon and nitrogen elements, are well-known of showing outstanding physical properties. Herein, with the aid of density functional theory (DFT) calculations, various atomic configurations of the graphene-like BCN nanosheets are investigated. DFT results reveal that depending on the atomic arrangement, the BCN monolayers may display semimetallic Dirac cone or semiconducting electronic nature. BCN nanosheets are also found to exhibit high piezoelectricity and carrier mobilities with considerable in-plane anisotropy, depending on the atomic arrangement. For the predicted most stable BCN monolayer, thermal and mechanical properties are explored using machine learning interatomic potentials. The room temperature tensile strength and lattice thermal conductivity of the most stable BCN monolayer are estimated to be orientation-dependent and remarkably high, over 78 GPa and 290 W/m.K, respectively. In addition, the thermal expansion coefficient of the monolayer BCN at room temperature is estimated to be −3.2 × 10−6 K−1, which is close to that of the graphene. The piezoelectric response of the herein proposed BCN lattice is also predicted to be close to that of the h-BN monolayer. Presented results highlight outstanding physics of the BCN nanosheets.Conference Object Citation - Scopus: 13Feature Selection for Microrna Target Prediction Comparison of One-Class Feature Selection Methodologies(Hindawi Publishing Corporation, 2016) Yousef, Malik; Allmer, Jens; Khalifa, WaleedTraditionally, machine learning algorithms build classification models from positive and negative examples. Recently, one-class classification (OCC) receives increasing attention in machine learning for problems where the negative class cannot be defined unambiguously. This is specifically problematic in bioinformatics since for some important biological problems the target class (positive class) is easy to obtain while the negative one cannot be measured. Artificially generating the negative class data can be based on unreliable assumptions. Several studies have applied two-class machine learning to predict microRNAs (miRNAs) and their target. Different approaches for the generation of an artificial negative class have been applied, but may lead to a biased performance estimate. Feature selection has been well studied for the two-class classification problem, while fewer methods are available for feature selection in respect to OCC. In this study, we present a feature selection approach for applying one-class classification to the prediction of miRNA targets. A comparison between one-class and two-class approaches is presented to highlight that their performance are similar while one-class classification is not based on questionable artificial data for training and performance evaluation. We further show that the feature selection method we tried works to a degree, but needs improvement in the future. Perhaps it could be combined with other approaches.Article Citation - Scopus: 19Feature Selection Has a Large Impact on One-Class Classification Accuracy for Micrornas in Plants(Hindawi Publishing Corporation, 2016) Yousef, Malik; Demirci, Müşerref Duygu Saçar; Khalifa, Waleed; Allmer, JensMicroRNAs (miRNAs) are short RNA sequences involved in posttranscriptional gene regulation. Their experimental analysis is complicated and, therefore, needs to be supplemented with computational miRNA detection. Currently computational miRNA detection is mainly performed using machine learning and in particular two-class classification. For machine learning, the miRNAs need to be parametrized and more than 700 features have been described. Positive training examples for machine learning are readily available, but negative data is hard to come by. Therefore, it seems prerogative to use one-class classification instead of two-class classification. Previously, we were able to almost reach two-class classification accuracy using one-class classifiers. In this work, we employ feature selection procedures in conjunction with one-class classification and show that there is up to 36% difference in accuracy among these feature selection methods. The best feature set allowed the training of a one-class classifier which achieved an average accuracy of 95.6% thereby outperforming previous two-class-based plant miRNA detection approaches by about 0.5%. We believe that this can be improved upon in the future by rigorous filtering of the positive training examples and by improving current feature clustering algorithms to better target pre-miRNA feature selection.Conference Object Citation - Scopus: 19Data Mining for Microrna Gene Prediction: on the Impact of Class Imbalance and Feature Number for Microrna Gene Prediction(Institute of Electrical and Electronics Engineers Inc., 2013) Saçar, Müşerref Duygu; Allmer, JensMicroRNAs (miRNAs) are small, non-coding RNAs which are involved in the posttranscriptional modulation of gene expression. Their short (18-24) single stranded mature sequences are involved in targeting specific genes. It turns out that experimental methods are limited and that it is difficult, if not impossible, to establish all miRNAs and their targets experimentally. Therefore, many tools for the prediction of miRNA genes and miRNA targets have been proposed. Most of these tools are based on machine learning methods and within that area mostly two-class classification is employed. Unfortunately, truly negative data is impossible to attain and only approximations of negative data are currently available. Also, we recently showed that the available positive data is not flawless. Here we investigate the impact of class imbalance on the learner accuracy and find that there is a difference of up to 50% between the best and worst precision and recall values. In addition, we looked at increasing number of features and found a curve maximizing at 0.97 recall and 0.91 precision with quickly decaying performance after inclusion of more than 100 features. © 2013 IEEE.Conference Object Citation - WoS: 18Citation - Scopus: 25Adaptation and Use of Subjectivity Lexicons for Domain Dependent Sentiment Classification(Institute of Electrical and Electronics Engineers Inc., 2012) Dehkharghani, Rahim; Yanıkoğlu, Berrin; Tapucu, Dilek; Saygın, YücelSentiment analysis refers to the automatic extraction of sentiments from a natural language text. We study the effect of subjectivity-based features on sentiment classification on two lexicons and also propose new subjectivity-based features for sentiment classification. The subjectivity-based features we experiment with are based on the average word polarity and the new features that we propose are based on the occurrence of subjective words in review texts. Experimental results on hotel and movie reviews show an overall accuracy of about 84% and 71% in hotel and movie review domains respectively; improving the baseline using just the average word polarities by about 2% points. © 2012 IEEE.Conference Object Citation - WoS: 22Citation - Scopus: 29Learning Domain-Specific Polarity Lexicons(Institute of Electrical and Electronics Engineers Inc., 2012) Demiröz, Gülşen; Yanıkoğlu, Berrin; Tapucu, Dilek; Saygın, YücelSentiment analysis aims to automatically estimate the sentiment in a given text as positive or negative. Polarity lexicons, often used in sentiment analysis, indicate how positive or negative each term in the lexicon is. However, since creating domain-specific polarity lexicons is expensive and time-consuming, researchers often use a general purpose or domain-independent lexicon. In this work, we address the problem of adapting a general purpose polarity lexicon to a specific domain and propose a simple yet effective adaptation algorithm. We experimented with two sets of reviews from the hotel and movie domains and observed that while our adaptation techniques changed the polarity values for only a small set of words, the overall test accuracy increased significantly: 77% to 83% in the hotel dataset and 61% to 66% in the movie dataset. © 2012 IEEE.