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Yayın Çizge evrişim ağı kullanarak patojen-konak ağlarında protein etkileşim tahmini(IEEE, 2021-06-09) Koca, Mehmet Burak; Karadeniz, İlknur; Nourani, Esmaeil; Sevilgen, Fatih ErdoğanProteinler yaşamsal faaliyetlerin gerçekleşmesinde kritik rol oynayan biyolojik moleküllerdir. Konak canlı proteinleri ile patojen proteinleri arasındaki etkileşimler patojenkonak etkileşim (PHI) ağlarını oluşturmaktadır. Bu iki parçalı etkileşim ağları patojenin hangi yaşamsal faaliyetleri etkilediğini belirlemede ve dolayısıyla sebep olabileceği hastalıkların tespitinde büyük öneme sahiptir. Proteinler arası etkileşimlerin laboratuvar ortamında tespiti hem zaman alıcı hem de maliyetlidir. Deneysel olarak saptanabilen etkileşim sayısının kısıtlı olması ve bazı etkileşimlerin gözden kaçması hesaplamalı tahmin yöntemlerinin geliştirilmesine önayak olmaktadır. Bu çalışmada PHI ağlarında protein etkileşim tahmini yapmayı sağlayan çizge evrişim ağı (GCN) tabanlı bir yöntem sunulmaktadır. Gözetimsiz olarak eğitilen GCN modeli (GraphSAGE) topolojik bilginin yanı sıra temel öznitelik olarak amino asit dizilimlerini kullanmaktadır. Bu çalışma bildiğimiz kadarıyla PHI ağlarında GCN tabanlı etkileşim tahmini sağlayan ilk çalışmadır. Deneysel sonuçlar geliştirilen modelin kıyaslama için kullanılan PHI veri seti üzerinde yüksek performanslı algoritmalardan %10 daha iyi performans göstererek %96 oranında doğrulukla etkileşim tahmini yaptığını göstermektedir.Yayın Hotel sales forecasting with LSTM and N-BEATS(IEEE, 2023-09-15) Özçelik, Şuayb Talha; Tek, Faik Boray; Şekerci, ErdalTime series forecasting aims to model the change in data points over time. It is applicable in many areas, such as energy consumption, solid waste generation, economic indicators (inflation, currency), global warming (heat, water level), and hotel sales forecasting. This paper focuses on hotel sales forecasting with machine learning and deep learning solutions. A simple forecast solution is to repeat the last observation (Naive method) or the average of the past observations (Average method). More sophisticated solutions have been developed over the years, such as machine learning methods that have linear (Linear Regression, ARIMA) and nonlinear (Polynomial Regression and Support Vector Regression) methods. Different kinds of neural networks are developed and used in time series forecasting problems, and two of the successful ones are Recurrent Neural Networks and N-BEATS. This paper presents a forecasting analysis of hotel sales from Türkiye and Cyprus. We showed that N-BEATS is a solid choice against LSTM, especially in long sequences. Moreover, N-BEATS has slightly better inference time results in long sequences, but LSTM is faster in short sequences.Yayın Predictive vector quantization of 3-D polygonal mesh geometry by representation of vertices in local coordinate systems(IEEE, 2005) Bayazıt, Uluğ; Orcay, Özgür; Konur, Umut; Gürgen, Sadık FikretA large family of lossy 3-D mesh geometry compression schemes operate by predicting the position of each vertex from the coded neighboring vertices and encoding the prediction error vectors. In this work, we first employ entropy constrained extensions of the predictive vector quantization and asymptotically closed loop predictive vector quantization techniques that have been suggested in [3] for coding these prediction error vectors. Then we propose the representation of the prediction error vectors in a local coordinate system with an axis coinciding with the surface normal vector in order to cluster the prediction error vectors around a 2-D subspace. We adopt a least squares approach to estimate the surface normal vector from the non-coplanar, previously coded neighboring vertices. Our simulation results demonstrate that the prediction error vectors can be more efficiently vector quantized by representation in local coordinate systems than in global coordinate systems.Yayın A novel regression method for software defect prediction with kernel methods(2013) Okutan, Ahmet; Yıldız, Olcay TanerIn this paper, we propose a novel method based on SVM to predict the number of defects in the files or classes of a software system. To model the relationship between source code similarity and defectiveness, we use SVM with a precomputed kernel matrix. Each value in the kernel matrix shows how much similarity exists between the files or classes of the software system tested. The experiments on 10 Promise datasets indicate that SVM with a precomputed kernel performs as good as the SVM with the usual linear or RBF kernels in terms of the root mean square error (RMSE). The method proposed is also comparable with other regression methods like linear regression and IBK. The results of this study suggest that source code similarity is a good means of predicting the number of defects in software modules. Based on the results of our analysis, the developers can focus on more defective modules rather than on less or non defective ones during testing activities.Yayın Forecasting and analysis of energy consumption and waste generation in Antalya with SVR(IEEE, 2023-12-24) Özçelik, Şuayb Talha; Tek, Faik Boray; Şekerci, ErdalAntalya, a rapidly expanding coastal city in Türkiye, has experienced significant changes due to urbanization and increasing tourism activities. Comprehending tourism trends is crucial for the city's sustainable development and environmental management. Based on this perspective, this paper aims to present a comprehensive retrospective analysis of Antalya's energy consumption, domestic solid waste generation, wastewater generation, population growth, and tourist numbers over the years. Antalya faces significant challenges due to escalating trends in listed areas. Utilizing the Support Vector Regression, this study projects a need for an additional 1715 GWh of electricity production capacity, an expansion of wastewater capacity by 85639 thousand m3, and an increase in domestic solid waste disposal capacity by 597745 tons by 2028 to accommodate growing demands. We emphasize the importance of adopting effective policies and strategies to support energy efficiency, waste reduction, and wastewater management alongside sustainable urban planning and tourism management for Antalya's long-Term environmental sustainability and development. The findings presented in this study provide valuable insights for policymakers, urban planners, and stakeholders to make informed decisions, ensuring a balanced approach toward economic growth and environmental conservation.
