Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
Browse
5 results
Search Results
Article Topological Feature Generation for Link Prediction in Biological Networks(PeerJ Inc, 2023-05-09) Temiz, Mustafa; Bakir-Gungor, Burcu; Sahan, Pinar Guner; Coskun, Mustafa; Güner Şahan, PınarGraph or network embedding is a powerful method for extracting missing or potential information from interactions between nodes in biological networks. Graph embedding methods learn representations of nodes and interactions in a graph with low-dimensional vectors, which facilitates research to predict potential interactions in networks. However, most graph embedding methods suffer from high computational costs in the form of high computational complexity of the embedding methods and learning times of the classifier, as well as the high dimensionality of complex biological networks. To address these challenges, in this study, we use the Chopper algorithm as an alternative approach to graph embedding, which accelerates the iterative processes and thus reduces the running time of the iterative algorithms for three different (nervous system, blood, heart) undirected protein-protein interaction (PPI) networks. Due to the high dimensionality of the matrix obtained after the embedding process, the data are transformed into a smaller representation by applying feature regularization techniques. We evaluated the performance of the proposed method by comparing it with state-of-the-art methods. Extensive experiments demonstrate that the proposed approach reduces the learning time of the classifier and performs better in link prediction. We have also shown that the proposed embedding method is faster than state-of-the-art methods on three different PPI datasets.Article Citation - WoS: 3Citation - Scopus: 5Intrinsic Graph Topological Correlation for Graph Convolutional Network Propagation(Elsevier, 2023-01) Coskun, MustafaRecently, Graph Convolutional Networks (GCNs) and their variants become popular to learn graph-related tasks. These tasks include link prediction, node classification, and node embedding, among many others. In the node classification problem, the input is a graph with some labeled nodes and the features associated with these nodes and the objective is to predict the unlabeled nodes. While the GCNs have been successfully applied to this problem, some caveats that are inherited from classical deep learning remain unsolved. One such inherited caveat is that, during classification, GCNs only consider the nodes that are a few neighbors away from the labeled nodes. However, considering only a few steps away nodes could not effectively exploit the underlying graph topological information. To remedy this problem, the state-of-the-art methods leverage the network diffusion approaches, such as personalized PageRank and its variants, to fully account for the graph topology. However, these approaches overlook the fact that the network diffusion methods favour high degree nodes in the graph, resulting in the propagation of the labels to the unlabeled,hub nodes. In order to overcome bias, in this paper, we propose to utilize a dimensionality reduction technique, which is conjugate with personalized PageRank. Testing on four real-world networks that are commonly used in benchmarking GCNs' performance for the node classification task, we systematically evaluate the performance of the proposed methodology and show that our approach outperforms existing methods for wide ranges of parameter values. Since our method requires only a few training epochs, it releases the heavy training burden of GCNs. The source code of the proposed method is freely available at https://github.com/mustafaCoskunAgu/ScNP/blob/master/TRJMain.m.Article Citation - WoS: 1Citation - Scopus: 1Intelligent Traffic Light Systems Using Edge Flow Predictions(Elsevier, 2024-01) Thahir, Adam Rizvi; Coskun, Mustafa; Kilic, Sultan Kubra; Gungor, Vehbi CagriIn this paper, we propose a novel graph-based semi-supervised learning approach for traffic light management in multiple intersections. Specifically, the basic premise behind our paper is that if we know some of the occupied roads and predict which roads will be congested, we can dynamically change traffic lights at the intersections that are connected to the roads anticipated to be congested. Comparative performance evaluations show that the proposed approach can produce comparable average vehicle waiting time and reduce the training/learning time of learning adequate traffic light configurations for all intersections within a few seconds, while a deep learning-based approach can be trained in a few days for learning similar light configurations.Article Citation - WoS: 4Citation - Scopus: 6Fast Computation of Katz Index for Efficient Processing of Link Prediction Queries(Springer, 2021-04-16) Coskun, Mustafa; Baggag, Abdelkader; Koyuturk, MehmetNetwork proximity computations are among the most common operations in various data mining applications, including link prediction and collaborative filtering. A common measure of network proximity is Katz index, which has been shown to be among the best-performing path-based link prediction algorithms. With the emergence of very large network databases, such proximity computations become an important part of query processing in these databases. Consequently, significant effort has been devoted to developing algorithms for efficient computation of Katz index between a given pair of nodes or between a query node and every other node in the network. Here, we present LRC-Katz, an algorithm based on indexing and low rank correction to accelerate Katz index based network proximity queries. Using a variety of very large real-world networks, we show that LRC-Katzoutperforms the fastest existing method, Conjugate Gradient, for a wide range of parameter values. Taking advantage of the acceleration in the computation of Katz index, we propose a new link prediction algorithm that exploits locality of networks that are encountered in practical applications. Our experiments show that the resulting link prediction algorithm drastically outperforms state-of-the-art link prediction methods based on the vanilla and truncated Katz.Article Citation - WoS: 3Citation - Scopus: 3Consensus Embedding for Multiple Networks: Computation and Applications(Cambridge Univ Press, 2022-05-30) Li, Mengzhen; Coskun, Mustafa; Koyuturk, MehmetMachine learning applications on large-scale network-structured data commonly encode network information in the form of node embeddings. Network embedding algorithms map the nodes into a low-dimensional space such that the nodes that are "similar" with respect to network topology are also close to each other in the embedding space. Real-world networks often have multiple versions or can be "multiplex" with multiple types of edges with different semantics. For such networks, computation of Consensus Embeddings based on the node embeddings of individual versions can be useful for various reasons, including privacy, efficiency, and effectiveness of analyses. Here, we systematically investigate the performance of three dimensionality reduction methods in computing consensus embeddings on networks with multiple versions: singular value decomposition, variational auto-encoders, and canonical correlation analysis (CCA). Our results show that (i) CCA outperforms other dimensionality reduction methods in computing concensus embeddings, (ii) in the context of link prediction, consensus embeddings can be used to make predictions with accuracy close to that provided by embeddings of integrated networks, and (iii) consensus embeddings can be used to improve the efficiency of combinatorial link prediction queries on multiple networks by multiple orders of magnitude.