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Yayın Graph convolutional network based virus-human protein-protein interaction prediction for novel viruses(Elsevier Ltd, 2022-08-13) Koca, Mehmet Burak; Nourani, Esmaeil; Abbasoğlu, Ferda; Karadeniz, İlknur; Sevilgen, Fatih ErdoğanComputational identification of human-virus protein-protein interactions (PHIs) is a worthwhile step towards understanding infection mechanisms. Analysis of the PHI networks is important for the determination of path-ogenic diseases. Prediction of these interactions is a popular problem since experimental detection of PHIs is both time-consuming and expensive. The available methods use biological features like amino acid sequences, molecular structure, or biological activities for prediction. Recent studies show that the topological properties of proteins in protein-protein interaction (PPI) networks increase the performance of the predictions. The basic network projections, random-walk-based models, or graph neural networks are used for generating topologically enriched (hybrid) protein embeddings. In this study, we propose a three-stage machine learning pipeline that generates and uses hybrid embeddings for PHI prediction. In the first stage, numerical features are extracted from the amino acid sequences using the Doc2Vec and Byte Pair Encoding method. The amino acid embeddings are used as node features while training a modified GraphSAGE model, which is an improved version of the graph convolutional network. Lastly, the hybrid protein embeddings are used for training a binary interaction classifier model that predicts whether there is an interaction between the given two proteins or not. The proposed method is evaluated with comprehensive experiments to test its functionality and compare it with the state-of-art methods. The experimental results on the benchmark dataset prove the efficiency of the proposed model by having a 3–23% better area under curve (AUC) score than its competitors.Yayın Mental disorder and suicidal ideation detection from social media using deep neural networks(Springer, 2024-12) Ezerceli, Özay; Dehkharghani, RahimDepression and suicidal ideation are global reasons for life-threatening injury and death. Mental disorders have increased especially among young people in recent years, and early detection of those cases can prevent suicide attempts. Social media platforms provide users with an anonymous space to interact with others, making them a secure environment to discuss their mental disorders. This paper proposes a solution to detect depression/suicidal ideation using natural language processing and deep learning techniques. We used Transformers and a unique model to train the proposed model and applied it to three diferent datasets: SuicideDetection, CEASEv2.0, and SWMH. The proposed model is evaluated using the accuracy, precision, recall, and ROC curve. The proposed model outperforms the state-of-theart in the SuicideDetection and CEASEv2.0 datasets, achieving F1 scores of 0.97 and 0.75, respectively. However, in the SWMH data set, the proposed model is 4% points behind the state-of-the-art precision providing the F1 score of 0.68. In the real world, this project could help psychologists in the early detection of depression and suicidal ideation for a more efcient treatment. The proposed model achieves state-of-the-art performance in two of the three datasets, so they could be used to develop a screening tool that could be used by mental health professionals or individuals to assess their own risk of suicide. This could lead to early intervention and treatment, which could save lives.Yayın Text-to-SQL: a methodical review of challenges and models(TÜBİTAK, 2024-05-20) Kanburoğlu, Ali Buğra; Tek, Faik BorayThis survey focuses on Text-to-SQL, automated translation of natural language queries into SQL queries. Initially, we describe the problem and its main challenges. Then, by following the PRISMA systematic review methodology, we survey the existing Text-to-SQL review papers in the literature. We apply the same method to extract proposed Text-to-SQL models and classify them with respect to used evaluation metrics and benchmarks. We highlight the accuracies achieved by various models on Text-to-SQL datasets and discuss execution-guided evaluation strategies. We present insights into model training times and implementations of different models. We also explore the availability of Text-to-SQL datasets in non-English languages. Additionally, we focus on large language model (LLM) based approaches for the Text-to-SQL task, where we examine LLM-based studies in the literature and subsequently evaluate the LLMs on the cross-domain Spider dataset. Finally, we conclude with a discussion of future directions for Text-to-SQL research, identifying potential areas of improvement and advancements in this field.Yayın Real-time 3D inspection of large civil structures using a stereoscopic camera system equipped UAV(International Society for Photogrammetry and Remote Sensing, 2024-12-13) Akça, Devrim; Torkut, Çağın; Kemper, Gerhard; Kunz, Noah; Caner, Doğa; Gruen, ArminREALTIME3D is an innovative Mixed-Reality (MR) photogrammetry system that integrates photogrammetry, UAV technology, and VR/AR solutions to enable real-time 3D infrastructure inspection. By combining these technologies, the system allows users to remotely access, visualize, and measure 3D stereoscopic models in real time. An operator on-site pilots a UAV equipped with the stereo cameras, while experts, utilizing VR headsets, can observe and analyze the object of interest from remote locations. This approach enhances cost efficiency and safety during inspections of large-scale, critical structures. The paper introduces the first prototype of the system, detailing its hardware and software components.
