325 results on '"Kaya, Kamer"'
Search Results
152. Extracting Maximal Exact Matches on GPU
- Author
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Abu-Doleh, Anas, primary, Kaya, Kamer, additional, Abouelhoda, Mohamed, additional, and Catalyurek, Umit V., additional
- Published
- 2014
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153. MICA.
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Hatem, Ayat, Kaya, Kamer, Parvin, Jeffrey, Huang, Kun, and Çatalyürek, Ümit V.
- Published
- 2015
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154. Hypergraph Sparsification and Its Application to Partitioning
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Deveci, Mehmet, primary, Kaya, Kamer, additional, and Catalyurek, Umit V., additional
- Published
- 2013
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- View/download PDF
155. A Push-Relabel-Based Maximum Cardinality Bipartite Matching Algorithm on GPUs
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Deveci, Mehmet, primary, Kaya, Kamer, additional, Ucar, Bora, additional, and Catalyurek, Umit V., additional
- Published
- 2013
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- View/download PDF
156. Incremental algorithms for closeness centrality
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Sariyuce, Ahmet Erdem, primary, Kaya, Kamer, additional, Saule, Erik, additional, and Catalyurek, Umit V., additional
- Published
- 2013
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- View/download PDF
157. PRASE
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Hatem, Ayat, primary, Kaya, Kamer, additional, and Çatalyürek, Ümit V., additional
- Published
- 2013
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- View/download PDF
158. Masher
- Author
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Abu-Doleh, Anas, primary, Saule, Erik, additional, Kaya, Kamer, additional, and Çatalyürek, Ümit V., additional
- Published
- 2013
- Full Text
- View/download PDF
159. STREAMER: A distributed framework for incremental closeness centrality computation
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Sariyuce, Ahmet Erdem, primary, Saule, Erik, additional, Kaya, Kamer, additional, and Catalyurek, Umit V., additional
- Published
- 2013
- Full Text
- View/download PDF
160. Towards a personalized, scalable, and exploratory academic recommendation service
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Küçüktunç, Onur, primary, Saule, Erik, additional, Kaya, Kamer, additional, and Çatalyürek, Ümit V., additional
- Published
- 2013
- Full Text
- View/download PDF
161. TheAdvisor
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Küçüktunç, Onur, primary, Saule, Erik, additional, Kaya, Kamer, additional, and Çatalyürek, Ümit V., additional
- Published
- 2013
- Full Text
- View/download PDF
162. Diversified recommendation on graphs
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Küçüktunç, Onur, primary, Saule, Erik, additional, Kaya, Kamer, additional, and Çatalyürek, Ümit V., additional
- Published
- 2013
- Full Text
- View/download PDF
163. Shattering and Compressing Networks for Betweenness Centrality
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Sariyüce, Ahmet Erdem, primary, Saule, Erik, additional, Kaya, Kamer, additional, and Çatalyürek, Ümit V., additional
- Published
- 2013
- Full Text
- View/download PDF
164. Betweenness centrality on GPUs and heterogeneous architectures
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Sariyüce, Ahmet Erdem, primary, Kaya, Kamer, additional, Saule, Erik, additional, and Çatalyürek, Ümit V., additional
- Published
- 2013
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- View/download PDF
165. Constructing Elimination Trees for Sparse Unsymmetric Matrices
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Kaya, Kamer, primary and Uçar, Bora, additional
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- 2013
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- View/download PDF
166. UMPa: A multi-objective, multi-level partitioner for communication minimization
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Çatalyürek, Ümit, primary, Deveci, Mehmet, additional, Kaya, Kamer, additional, and Uçar, Bora, additional
- Published
- 2013
- Full Text
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167. A partitioning-based divisive clustering technique for maximizing the modularity
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Çatalyürek, Ümit, primary, Kaya, Kamer, additional, Langguth, Johannes, additional, and Uçar, Bora, additional
- Published
- 2013
- Full Text
- View/download PDF
168. Microarray vs. RNA-Seq
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Hatem, Ayat, primary, Kaya, Kamer, additional, and Çatalyürek, Ümit V., additional
- Published
- 2012
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169. On Shared-Memory Parallelization of a Sparse Matrix Scaling Algorithm
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Catalyurek, Umit V., primary, Kaya, Kamer, additional, and Ucar, Bora, additional
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- 2012
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170. Multithreaded Clustering for Multi-level Hypergraph Partitioning
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Catalyurek, Umit V., primary, Deveci, Mehmet, additional, Kaya, Kamer, additional, and Ucar, Bora, additional
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- 2012
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171. Design, implementation, and analysis of maximum transversal algorithms
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Duff, Iain S., primary, Kaya, Kamer, additional, and Uçcar, Bora, additional
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- 2011
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172. Integrated data placement and task assignment for scientific workflows in clouds
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Çatalyürek, Ümit V., primary, Kaya, Kamer, additional, and Uçar, Bora, additional
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- 2011
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173. EXACT ALGORITHMS FOR A TASK ASSIGNMENT PROBLEM
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KAYA, KAMER, primary and UÇAR, BORA, additional
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- 2009
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174. Generalized ID-based blind signatures from bilinear pairings
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Kalkan, Said, primary, Kaya, Kamer, additional, and Selcuk, Ali Aydin, additional
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- 2008
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175. Generalized ID-based ElGamal signatures
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Kalkan, Said, primary, Kaya, Kamer, additional, and Selcuk, Ali Aydin, additional
- Published
- 2007
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176. Diversifying Citation Recommendations.
- Author
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Küçüktunç, Onur, Saule, Erik, Kaya, Kamer, and Çatalyürek, Ümit V.
- Subjects
RECOMMENDER systems ,COMPUTER science ,CITATION analysis ,ALGORITHMS ,ONLINE bibliographic searching ,WEB services - Abstract
Literature search is one of the most important steps of academic research. With more than 100,000 papers published each year just in computer science, performing a complete literature search becomes a Herculean task. Some of the existing approaches and tools for literature search cannot compete with the characteristics of today’s literature, and they suffer from ambiguity and homonymy. Techniques based on citation information are more robust to the mentioned issues. Thus, we recently built a Web service called the advisor, which provides personalized recommendations to researchers based on their papers of interest. Since most recommendation methods may return redundant results, diversifying the results of the search process is necessary to increase the amount of information that one can reach via an automated search. This article targets the problem of result diversification in citation-based bibliographic search, assuming that the citation graph itself is the only information available and no categories or intents are known. The contribution of this work is threefold. We survey various random walk--based diversification methods and enhance them with the direction awareness property to allow users to reach either old, foundational (possibly well-cited and well-known) research papers or recent (most likely less-known) ones. Next, we propose a set of novel algorithms based on vertex selection and query refinement. A set of experiments with various evaluation criteria shows that the proposed γ-RLM algorithm performs better than the existing approaches and is suitable for real-time bibliographic search in practice. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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177. Towards a personalized, scalable, and exploratory academic recommendation service.
- Author
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Küçüktunç, Onur, Saule, Erik, Kaya, Kamer, and Çatalyürek, Ümit V.
- Published
- 2013
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178. Fast Recommendation on Bibliographic Networks.
- Author
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Kucuktunc, Onur, Kaya, Kamer, Saule, Erik, and Catalyurek, Umit V.
- Abstract
Graphs and matrices are widely used in algorithms for social network analyses. Since the number of interactions is much less than the possible number of interactions, the graphs and matrices used in the analyses are usually sparse. In this paper, we propose an efficient implementation of a sparse-matrix computation which arises in our publicly available citation recommendation service called the advisor. The recommendation algorithm uses a sparse matrix generated from the citation graph. We observed that the nonzero pattern of this matrix is highly irregular and the computation suffers from high number of cache misses. We propose techniques for storing the matrix in memory efficiently and reducing the number of cache misses. Experimental results show that our techniques are highly efficient on reducing the query processing time which is highly crucial for a web service. [ABSTRACT FROM PUBLISHER]
- Published
- 2012
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179. Practical Threshold Signatures with Linear Secret Sharing Schemes.
- Author
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Bozkurt, İlker Nadi, Kaya, Kamer, and Selçuk, Ali Aydın
- Abstract
Function sharing deals with the problem of distribution of the computation of a function (such as decryption or signature) among several parties. The necessary values for the computation are distributed to the participating parties using a secret sharing scheme (SSS). Several function sharing schemes have been proposed in the literature, with most of them using Shamir secret sharing as the underlying SSS. In this paper, we investigate how threshold cryptography can be conducted with any linear secret sharing scheme and present a function sharing scheme for the RSA cryptosystem. The challenge is that constructing the secret in a linear SSS requires the solution of a linear system, which normally involves computing inverses, while computing an inverse modulo ᵠ(N) cannot be tolerated in a threshold RSA system in any way. The threshold RSA scheme we propose is a generalization of Shoup΄s Shamir-based scheme. It is similarly robust and provably secure under the static adversary model. At the end of the paper, we show how this scheme can be extended to other public key cryptosystems and give an example on the Paillier cryptosystem. [ABSTRACT FROM AUTHOR]
- Published
- 2009
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180. Adapting Iterative-Improvement Heuristics for Scheduling File-Sharing Tasks on Heterogeneous Platforms.
- Author
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Kaya, Kamer, Uçar, Bora, and Aykanat, Cevdet
- Abstract
We consider the problem of scheduling an application on a computing system consisting of heterogeneous processors and one or more file repositories. The application consists of a large number of file-sharing, otherwise independent tasks. The files initially reside on the repositories. The interconnection network is heterogeneous. We focus on two disjoint problem cases. In the first case, there is only one file repository which is called as the master processor. In the second case, there are two or more repositories, each holding a distinct set of files. The problem is to assign the tasks to the processors, to schedule the file transfers from the repositories, and to order the executions of tasks on each processor in such a way that the turnaround time is minimized. This chapter surveys several solution techniques; but the stress is on our two recent works [22,23]. At the first glance, iterative-improvement-based heuristics do not seem to be suitable for the aforementioned scheduling problems. This is because their immediate application suggests iteratively improving a complete schedule, and hence building and exploring a complex neighborhood around the current schedule. Such complex neighborhood structures usually render the heuristics time-consuming and make them stuck to a part of the search space. However, in both of the our recent works, we show that these issues can be solved by using a three-phase approach: initial task assignment, refinement, and execution ordering. The main thrust of these two works is that iterative-improve-based heuristics can efficiently deliver effective solutions, implying that iterative-improve-based heuristics can provide highly competitive solutions to the similar scheduling problems. [ABSTRACT FROM AUTHOR]
- Published
- 2008
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181. A Verifiable Secret Sharing Scheme Based on the Chinese Remainder Theorem.
- Author
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Kaya, Kamer and Selçuk, Ali Aydın
- Abstract
In this paper, we investigate how to achieve verifiable secret sharing (VSS) schemes by using the Chinese Remainder Theorem (CRT). We first show that two schemes proposed earlier are not secure by an attack where the dealer is able to distribute inconsistent shares to the users. Then we propose a new VSS scheme based on the CRT and prove its security. Using the proposed VSS scheme, we develop a joint random secret sharing (JRSS) protocol, which, to the best of our knowledge, is the first JRSS protocol based on the CRT. [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
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182. Robust Threshold Schemes Based on the Chinese Remainder Theorem.
- Author
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Kaya, Kamer and Selçuk, Ali Aydın
- Abstract
Recently, Chinese Remainder Theorem (CRT) based function sharing schemes are proposed in the literature. In this paper, we investigate how a CRT-based threshold scheme can be enhanced with the robustness property. To the best of our knowledge, these are the first robust threshold cryptosystems based on a CRT-based secret sharing. [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
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183. Threshold Cryptography Based on Asmuth-Bloom Secret Sharing.
- Author
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Levi, Albert, Savaş, Erkay, Yenigün, Hüsnü, Balcısoy, Selim, Saygın, Yücel, Kaya, Kamer, Selçuk, Ali Aydın, and Tezcan, Zahir
- Abstract
In this paper, we investigate how threshold cryptography can be conducted with the Asmuth-Bloom secret sharing scheme and present two novel function sharing schemes, one for the RSA signature and the other for the ElGamal decryption functions, based on the Asmuth-Bloom scheme. To the best of our knowledge, these are the first threshold cryptosystems realized using the Asmuth-Bloom secret sharing. The proposed schemes compare favorably to the earlier function sharing schemes in performance as well as in certain theoretical aspects. [ABSTRACT FROM AUTHOR]
- Published
- 2006
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184. Capture Resilient ElGamal Signature Protocols.
- Author
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Levi, Albert, Savaş, Erkay, Yenigün, Hüsnü, Balcısoy, Selim, Saygın, Yücel, Acan, Hüseyin, Kaya, Kamer, and Selçuk, Ali Aydın
- Abstract
One of the fundamental problems of public key cryptography is protecting the private key. Private keys are too long to be remembered by the user, and storing them in the device which performs the private key operation is insecure as long as the device is subject to capture. In this paper, we propose server-assisted protocols for the ElGamal signature scheme which make the system capture resilient in the sense that the security of the system is not compromised even if the signature device is captured. The protocols also have a key disabling feature which allows a user to disable the device's private key in case both the device and the password of the user are compromised simultaneously. [ABSTRACT FROM AUTHOR]
- Published
- 2006
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185. Fast recommendation on bibliographic networks with sparse-matrix ordering and partitioning.
- Author
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Küçüktunç, Onur, Kaya, Kamer, Saule, Erik, and Çatalyürek, Ümit V.
- Abstract
Graphs and matrices are widely used in algorithms for social network analyses. Since the number of interactions is much less than the possible number of interactions, the graphs and matrices used in the analyses are usually sparse. In this paper, we propose an efficient implementation of a sparse-matrix computation which arises in our publicly available citation recommendation service the advisor as well as in many other recommendation systems. The recommendation algorithm uses a sparse matrix generated from the citation graph. We observed that the nonzero pattern of this matrix is highly irregular and the computation suffers from high number of cache misses. We propose techniques for storing the matrix in memory efficiently and we reduced the number of cache misses with ordering and partitioning. Experimental results show that our techniques are highly efficient in reducing the query processing time which is highly crucial for a web service. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
186. Boosting Graph Embedding on a Single GPU.
- Author
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Aljundi, Amro Alabsi, Akyildiz, Taha Atahan, and Kaya, Kamer
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GRAPH algorithms , *MACHINE learning , *GRAPHICS processing units , *CLASSIFICATION algorithms , *CHARTS, diagrams, etc. - Abstract
Graphs are ubiquitous, and they can model unique characteristics and complex relations of real-life systems. Although using machine learning (ML) on graphs is promising, their raw representation is not suitable for ML algorithms. Graph embedding represents each node of a graph as a $d$ d -dimensional vector which is more suitable for ML tasks. However, the embedding process is expensive, and CPU-based tools do not scale to real-world graphs. In this work, we present GOSH, a GPU-based tool for embedding large-scale graphs with minimum hardware constraints. GOSH employs a novel graph coarsening algorithm to enhance the impact of updates and minimize the work for embedding. It also incorporates a decomposition schema that enables any arbitrarily large graph to be embedded with a single GPU. As a result, GOSH sets a new state-of-the-art in link prediction both in accuracy and speed, and delivers high-quality embeddings for node classification at a fraction of the time compared to the state-of-the-art. For instance, it can embed a graph with over 65 million vertices and 1.8 billion edges in less than 30 minutes on a single GPU. [ABSTRACT FROM AUTHOR]
- Published
- 2022
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187. Efficient broadcast encryption with user profiles
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Ak, Murat, Kaya, Kamer, Onarlıoğlu, Kaan, and Selçuk, Ali Aydın
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DATA encryption , *COMPUTER users , *BROADCASTING industry , *TREE graphs , *DATA transmission systems , *MATHEMATICAL optimization , *ALGORITHMS , *DATA security - Abstract
Abstract: Broadcast encryption (BE) deals with secure transmission of a message to a group of users such that only an authorized subset of users can decrypt the message. Some of the most effective BE schemes in the literature are the tree-based schemes of complete subtree (CS) and subset difference (SD). The key distribution trees in these schemes are traditionally constructed without considering user preferences. In fact these schemes can be made significantly more efficient when user profiles are taken into account. In this paper, we consider this problem and study how to construct the CS and SD trees more efficiently according to user profiles. We first analyze the relationship between the transmission cost and the user profile distribution and prove a number of key results in this aspect. Then we propose several optimization algorithms which can reduce the bandwidth requirement of the CS and SD schemes significantly. This reduction becomes even more significant when a number of free riders can be allowed in the system. [Copyright &y& Elsevier]
- Published
- 2010
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188. Multilevel Threshold Secret Sharing based on the Chinese Remainder Theorem
- Author
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ERSOY, Oguzhan, KAYA, Kamer, and KASKALOGLU, Kerem
- Subjects
—Secret sharing,multilevel cryptography,Chinese Remainder Theorem - Abstract
In multilevel secret sharing, a secret is shared among a set of hierarchically organized participants in a way that the members of the superior compartments are more powerful and can replace the participants of an inferior one to form an authorized coalition during secret reconstruction. In this work, we first show that the only existing multilevel threshold secret sharing scheme based on the Chinese Remainder Theorem CRT is not secure and fails to work with certain natural threshold settings on compartments. As the main contribution, we propose a secure CRTbased scheme that works for all threshold settings. In the proposed scheme, we employ a refined version of Asmuth-Bloom secret sharing with a special and generic Asmuth-Bloom sequence called the anchor sequence. Based on this novel idea, we also propose the first multilevel conjunctive threshold secret sharing scheme based on the Chinese Remainder Theorem.
189. TheAdvisor.
- Author
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Küçüktunç, Onur, Saule, Erik, Kaya, Kamer, and Çatalyürek, Ümit V.
- Published
- 2013
- Full Text
- View/download PDF
190. Multicore and manycore parallelization of cheap synchronizing sequence heuristics.
- Author
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Karahoda, Sertaç, Erenay, Osman Tufan, Kaya, Kamer, Türker, Uraz Cengiz, and Yenigün, Hüsnü
- Subjects
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MULTICORE processors , *GRAPHICS processing units , *FINITE state machines , *HEURISTIC , *PARALLEL processing , *MACHINE theory - Abstract
An important concept in finite state machine based testing is synchronization which is used to initialize an implementation to a particular state. Usually, synchronizing sequences are used for this purpose and the length of the sequence used is important since it determines the cost of the initialization process. Unfortunately, the shortest synchronization sequence problem is NP-Hard. Instead, heuristics are used to generate short sequences. However, the cubic complexity of even the fastest heuristic algorithms can be a problem in practice. In order to scale the performance of the heuristics for generating short synchronizing sequences, we propose algorithmic improvements together with a parallel implementation of the cheapest heuristics existing in the literature. To identify the bottlenecks of these heuristics, we experimented on random and slowly synchronizing automata. The identified bottlenecks in the algorithms are improved by using algorithmic modifications. We also implement the techniques on multicore CPUs and Graphics Processing Units (GPUs) to take benefit of the modern parallel computation architectures. The sequential implementation of the heuristic algorithms are compared to our parallel implementations by using a test suite consisting of 1200 automata. The speedup values obtained depend on the size and the nature of the automaton. In our experiments, we observe speedup values as high as 340x by using a 16-core CPU parallelization, and 496x by using a GPU. Furthermore, the proposed methods scale well and the speedup values increase as the size of the automata increases. • We propose algorithmic improvements together with an efficient parallelization approach for synchronizing sequence heuristics. • We experimented on random and slowly synchronizing automata. • We implement the proposed techniques on multicore CPUs and Graphics Processing Units (GPUs) to take benefit of the modern parallel architectures. • With the proposed techniques, we observe speedup values as high as 340x by using a 16-core CPU parallelization, and 496x by using a GPU. • The proposed methods scale well and the speedup values increase as the size of the automata increases. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
191. Second and fourth (2D:4D) digit ratio in heroin and cannabis addicted patients.
- Author
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Gurok, Mehmet Gurkan, Yıldız, Sevler, Bakış Aksoy, Dilek, Kılıçaslan, Aslı Kazğan, Tabara, Muhammed Fatih, Yılmaz, Tuba, Kaya, Kamer, Danacı Keleş, Denizhan, Karakaş, Şahin, Şimşek, Düzgün, and Atmaca, Murad
- Abstract
Abstract The etiology of addiction has not yet been fully elucidated. The ratio between the length of the second and fourth fingers (2D:4D ratio) has been linked with prenatal androgen concentrations, but also with addictive behvaiors. Aim: The present study aimed to evaluate the differences of 2D:4D ratio of individuals with cannabis and heroin addiction by examining them together with the control group. A total of sixty two male patients (33 opiate use disorder and 29 cannabis use disorder) with substance use disorder and the twenty-nine healthy controls were included in the present investigation. We obtained the lengths of 2D and 4D of the subjects by using sensitive calipers and calculated the 2D:4D. Heroin-addicted patients had lower 2D:4D ratio in in the right hand (significant difference between control group) (
p < 0.001), there was no significant difference found between heroin-cannabis (p = 0.242) and control-cannabis 2D:4D ratios (p < 0.06). In the left hand, it was significant between the heroin-control groups (p < 0.037) and the cannabis-control groups (p < 0.023), while it was not significant between the heroin-cannabis groups (p = 1). In conclusion, we suggest that heroin-and cannabis addicted patients seem to have a lower ratio of 2D:4D compared to healthy control subjects. Our findings can be considered promising as to whether prenatal hormonal factors are important in the etiopathogenesis of addiction. [ABSTRACT FROM AUTHOR]- Published
- 2023
- Full Text
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192. A hybrid CPU–GPU solver based on three-dimensional spectral Chebyshev technique for determining the dynamic behavior of thick sandwich panels.
- Author
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Rafiei Anamagh, Mirmeysam, Gokalp, Kaya, Akyıldız, Taha Atahan, Alan, Salih, Kaya, Kamer, and Bediz, Bekir
- Subjects
- *
SANDWICH construction (Materials) , *HAMILTON'S equations , *HAMILTON'S principle function , *FINITE element method , *CHEBYSHEV polynomials , *GRAPHICS processing units - Abstract
In this study, static and vibration behavior of a curved thick sandwich-structured composite composed of a honeycomb core layer and two face-sheets reinforced with carbon nanotubes is investigated. The governing equations are derived using three-dimensional elasticity equations and Hamilton's principle. The problem domain is discretized following Gauss–Lobatto sampling approach. To numerically solve the governing equations, a spectral method based on Chebyshev polynomials is used and a CPU–GPU based hybrid solver is developed. The presented approach is validated by comparing the predicted natural frequencies and deformation of the structure to those obtained from finite element analysis. The results show that in-house CPU–GPU based spectral solution approach decreases the computational duration remarkably and predicts the dynamic and static behavior of the system accurately. Since composite materials offer great flexibility in tailoring the dynamic behavior of the structure, an optimization study is also performed to benefit from the developed computationally efficient solver. In this study, the CNT orientations are selected as design variables to maximize the fundamental frequency of the structure. Based on the analyzed cases for different thickness ratios, curvature amounts, volume content, and distributions of CNTs, it is shown that the vibration behavior of the structure can be significantly tailored. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
193. Incremental closeness centrality in distributed memory.
- Author
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Sarıyüce, Ahmet Erdem, Saule, Erik, Kaya, Kamer, and Çatalyürek, Ümit V.
- Subjects
- *
DISTRIBUTED computing , *COMPUTER networks , *WEBSITES , *ONLINE social networks , *SOCIAL interaction - Abstract
Networks are commonly used to model traffic patterns, social interactions, or web pages. The vertices in a network do not possess the same characteristics: some vertices are naturally more connected and some vertices can be more important. Closeness centrality (CC) is a global metric that quantifies how important is a given vertex in the network. When the network is dynamic and keeps changing, the relative importance of the vertices also changes. The best known algorithm to compute the CC scores makes it impractical to recompute them from scratch after each modification. In this paper, we propose S treamer , a distributed memory framework for incrementally maintaining the closeness centrality scores of a network upon changes. It leverages pipelined, replicated parallelism, and SpMM-based BFSs, and it takes NUMA effects into account. It makes maintaining the closeness centrality values of real-life networks with millions of interactions significantly faster and obtains almost linear speedups on a 64 nodes 8 threads/node cluster. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
194. Regularizing graph centrality computations.
- Author
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Sarıyüce, Ahmet Erdem, Saule, Erik, Kaya, Kamer, and Çatalyürek, Ümit V.
- Subjects
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GRAPH theory , *MATHEMATICAL regularization , *GRAPHICS processing units , *BETWEENNESS relations (Mathematics) , *ELECTRONIC data processing - Abstract
Centrality metrics such as betweenness and closeness have been used to identify important nodes in a network. However, it takes days to months on a high-end workstation to compute the centrality of today’s networks. The main reasons are the size and the irregular structure of these networks. While today’s computing units excel at processing dense and regular data, their performance is questionable when the data is sparse. In this work, we show how centrality computations can be regularized to reach higher performance. For betweenness centrality, we deviate from the traditional fine-grain approach by allowing a GPU to execute multiple BFSs at the same time. Furthermore, we exploit hardware and software vectorization to compute closeness centrality values on CPUs, GPUs and Intel Xeon Phi. Experiments show that only by reengineering the algorithms and without using additional hardware, the proposed techniques can speed up the centrality computations significantly: an improvement of a factor 5.9 on CPU architectures, 70.4 on GPU architectures and 21.0 on Intel Xeon Phi. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
195. İki mesafeli çizge boyama ve iki parçalı çizge boyama için açgözlü algoritmalar
- Author
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Taş, Mustafa Kemal, Kaya, Kamer, and Bilgisayar Mühendisliği Anabilim Dalı
- Subjects
Computer Engineering and Computer Science and Control ,Bilgisayar Mühendisliği Bilimleri-Bilgisayar ve Kontrol ,TK Electrical engineering. Electronics Nuclear engineering - Abstract
oşut bir uygulamanın görev etkileşim çizgesi komşu görevlerin farklı renklerle boyandığında birbirleri ile aynı renkteki görevler aynı anda pahalı bir senkronizasyon veri yapısı kullanılmadan aynı anda çalıştırılabilmektedir. Bu tür bir çalıştırmada bir renkteki görevler bitirilmeden, başka bir renkteki görev koşut halde şlenemeyeceğinden boyama esnasında kullanılan renk sayısı koşut uygulamanın çalıştırılması esnasında karşılaşılacak senkronizasyon adım sayısını belirtmektedir. Literatürde çizge boyama problemi ''bir çizgeyi mümkün olan en az sayıda renk kullanarak komşu noktalara farklı renkler vermek'' olarak tanımlanmıştır ve bir optimizasyon problemi olarakgörüldüğünde NP-Hard sınıfındadır. Çizge boyama probleminin farklı çeşitleri de paralel hesaplama, özellikle paralel bilimsel hesaplama alanında önemlidir. Problemin yukarıda bahsedilen basit halinde 1-uzaklık kullanılırken, k-uzaklık tanımı da özellikle k = 2 için pratikte kullanılmaktadır. Bu tezde de bu problem üzerine yoğunlaşılmıştır. Problemin genel hali ''bir çizgeyi mümkün olan en az sayıda renk kullanarak birbirinden k ve daha az uzaklıktaki nokta ikililerine farklı renkler vermek'' olarak tanımlanabilir. Literatürde bu problem için az renk kullanan buluşsal yöntemler önerilmiştir ve bu yöntemler k = 1 için oldukça hızlıdır. Fakat k = 2 için özellikle büyük çizgelerde bu buluşsalyöntemler dakikalar mertebesinde zaman alabilmektedirler. Çizge boyamanın bir uygulamanın çalışması için sadece bir ön işlem olduğu düşünüldüğünde bu işlemin getirdiği ekstra zamanın mümkün olduğu kadar az olması işlemin uygulanabilirliği için önemlidir. Bu tezde 2-uzaklık çizge boyama ve bu problemin farklı bir türü olan iki parçalı çizge boyama problemleri için iyimser ve açgözlü buluşsal yöntemler önerilmiştir. Bu yöntemler çok çekirdekli işlemcilerde ve Grafik İşleme Ünitelerinde koşut olarak gerçeklenmiş, ve ölçeklenebilirlikleri analiz edilmiştir. Yapılan deneylerde önerilen yöntemlerin ölçeklenebilir ve 16 çekirdek kullanıldığında literatürdeki yöntemlerden ortalama 25 kat hızlı oldukları görülmüş, özellikle sosyal ağ karakteri taşıyan çizgeler için büyük performansartışı sağladığı saptanmıştır. Yine bu tez çerçevesinde aynı renge sahip nokta kümelerinin eleman sayılarının birbirine yakın olması üzerine de çalışılmıştır. Bu tür dengeli dağılımlı bir boyama, uygulamanın çok çekirdekli işlemciler ve özellikle GİÜ'ler üzerinde çalışması esnasında her senkronizasyon adımında bütün çekirdekleri doyuracak kadar iş yükü olmasını sağlayacağından yüksek performans için önemli olabilmektedir. Bu tezde neredeyse hiç ekstra külfet getirmeden bunu sağlayabilecek iki yöntem önerilmiştir. Yapılan deneylerde bu yöntemlerin başarılı olduğu sonucuna varılmıştır. In parallel computing, a valid graph coloring yields a lock-free processing of the colored tasks, data points, etc., without expensive synchronization mechanisms. However, the coloring stage is not free and the overhead can be significant. In particular, for distance-2 graph coloring (D2GC) and bipartite graph partial coloring (BGPC) problems, which have various use-cases within the scientific computing and numerical optimization domains, the coloring overhead can be in the order of minutes with a single thread for many real-life graphs, having millions and billions of vertices and edges.In this thesis, we propose a novel greedy algorithm for the distance-2 graph coloring problem on shared-memory architectures. We then extend the algorithm to bipartite graph partial coloring problem, which is structurally very similar to D2GC. The proposed algorithms yield a better parallel coloring performance compared to the existing shared-memory parallel coloring algorithms, by employing greedier and more optimistic techniques. In particular, when compared to the state-of-the-art, the proposed algorithms obtain 25x speedup with 16 cores, without decreasing the coloring quality. Moreover, we extend the existing distance-2 graph coloring algorithm to manycore architectures. Due to architectural limitations, the multicore algorithm can not easily be extended to manycore. Thus several optimizations and modifications are proposed to overcome such obstacles. In addition to multi and manycore implementations, we also offer novel optimizations for both D2GC and BGPC on social network graphs. Exploiting the structural properties of social graphs, we propose faster heuristics to increase the performance without decreasing the coloring quality. Finally, we propose two costless balancing heuristics that can be applied to both BGPC and D2GC, which would yield a better color-based parallelization performance with a better load-balancing, especially on manycore architectures. 92
- Published
- 2019
196. Optimal Hiperçizge Parçalama
- Author
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Usta, Baran, Kaya, Kamer, and Bilgisayar Bilimleri ve Mühendisliği Anabilim Dalı
- Subjects
TK7885-7895 Computer engineering. Computer hardware ,Computer Engineering and Computer Science and Control ,Bilgisayar Mühendisliği Bilimleri-Bilgisayar ve Kontrol - Abstract
Hiperçizge parçalama literatürde oldukça popüler bir problemdir. Dağıtık algoritmalar ve VLSI devre tasarımı gibi uygulamaların performasi bu yöntemle büyük ölçüde arttırılabilir. Son 20 yılda, hiperçizgeyi hızlı bir şekilde parçalayabilen araçlar geliştirilmiştir. Ancak bu problem NP-Zor olduğu için, bu araçlar sezgisel yöntemlere dayanmaktadır. Bu yüzden genelde optimal olmayan sonuçları bulmaktadırlar. Optimal hiperçizge problemi üzerine sezgisel yöntemlere dayalı çalışmalara nazaran çok daha az sayıda araştırma bulunmaktadır. Bu tezde, literatürdeki bir çok metriğe göre optimal parçalamayi bulan, PHaraoh isimli koşut hiperçizge parçalama aracı sunulmaktadır. Optimal sonuçların bulunması sayesinde, böyle bir araç, daha önceden geliştirilen hiperçizge parçalama araçlarının gerçek performansını, olası en iyi sonuçile karşılaştırarak ölçmemizi sağlar. PHaraoh herhangi bir parçalama ile başlatılabilir ve bu sonucu sürekli olarak geliştirmeye çalışır. Bu sayede, istenen optimal hiperçizge parçalama islemini verilen sürede tamamlayamasa bile, baslangıçta verilen parçalamanın kalitesini iyileştirebilir. Gerçek hayattaki uygulamalarda karşılaşılan hiperçizge modelleri üzerinde yaptığımız deneylere göre, PHaraoh pratikte en çok kullanılan araçların ürettiği parçalamaların kalitesini dal ve sınır arama yöntemini kullanarak büyük ölçüde iyileştirmektedir. Arama uzayında bulunan optimal parçalamanın bulunma süresini kısaltmak icin, `usta yamak` ve `iş çalma` yöntemlerine dayalı koşut algoritmalardan faydalandik. Daha önceki çalışmalarımızda ve bu tezde yaptığımız deneylere göre hiperçizge parçalama problemi icin dal ve sınır ağacındaki öğelerin sırası PHaraoh'ın performansını önemli oranda etkilemektedir. Bu tezde, değişik sıralama yöntemleri önerip, bunların PHaraoh'ın çalışma süresini nasıl değiştirdiğini ve bu değişikliğin nedenlerini hiperçizgelerin özelliklerine bağlayarak açıkladık. Hypergraph partitioning into K parts has many applications in practice such as distributed algorithms and very large scale integrated circuit (VLSI) design. There are various tools proposed in the literature which can partition a given hypergraph very fast. However, since the problem is NP-Hard and the traditional approaches heavily use heuristics, these tools do not provide an optimal partition. There is limited research on partitioning hypergraphs optimally. In this thesis, we proposePHaraoh, a parallel hypergraph partitioner that can provide optimal partitions for many metrics used in the literature. Such a partitioner is important in practice since it enables us to evaluate the true performance of the existing tools. Furthermore, PHaraoh can be started with an initial partition. Thanks to that, even an optimal solution is not found within the given time limit, PHaraoh improves the cost of the provided initial partition. Experimental results on hypergraphs obtained from real life matrices show that the quality of the partitions of existing tools can be improved significantly for most of the hypergraphs. In order to increase the speed up the search-space exploration, we experimented with both master-slave and work-stealing parallelization. It also has been shown that the runtime of the algorithm highly depends on the order of the items in the branch and bound tree. In this study, we propose different ordering strategies which can offer great speed ups depending on the characteristics of the hypergraph. 85
- Published
- 2018
197. Algorithmic optimization and parallelization of Eppstein's synchronizing heuristic
- Author
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Karahoda, Sertaç, Yenigün, Hüsnü, Kaya, Kamer, and Bilgisayar Bilimleri ve Mühendisliği Anabilim Dalı
- Subjects
TK7885-7895 Computer engineering. Computer hardware ,Computer Engineering and Computer Science and Control ,Bilgisayar Mühendisliği Bilimleri-Bilgisayar ve Kontrol - Abstract
Karmaşık sistemlerin geliştirilmesinde, test etme en pahalı ve en çok zaman alan evredir. Model tabanlı testler yüksek kaliteli deney kurgusunu otomatik üretmede kullanılan yaklaşımlardan birisidir. Deney kurgusunu otomatik üretme test etmenin en zorlu parçalarından biridir. Sonlu durum makineleri ya da özdevinimler gibi biçimsel modeller, otomatik deney grubunu üretmek için kullanılmaktadır. Sistem belirli bir duruma senkronize edildikten sonra testler uygulanır ve bu belirli duruma gelebilmek için sıfırlama kelimeleri kullanılmaktadır. Daha kısa deney süreleri için en kısa sıfırlama kelimesini hesaplamak önemlidir, ancak en kısa sıfırlama kelimesini hesaplamak NP–hard bir problemdir. Bu nedenle kısa sıfırlama kelimelerini hesaplamak için sezgisel yöntemler kullanılmaktadır. GREEDY algoritması bu alanda bilinen en hızlı sezgisel algoritmadır. Bu tezde, GREEDY algoritmasını hızlandıran yaklaşımlar sunulmaktadır. İlk olarak GREEDY algoritmasının paralelleştirilmesine odaklanılmaktadır. İkinci olarak ise tembel bir yaklaşım önererek sıfırlama kelimesinin üretilmesi için gerekli bilgilerin hazırlanma süreci ertelenmektedir. Aynı zamanda, GREEDY algoritması için benzer algoritmik iyileştirilmeler önerilmektedir. Deney sonuçlarımız özdevinim büyüklügüne bağlı olarak GREEDY algoritmasının 500 kat daha hızlı hale getirilebileceğini göstermektedir. Önerilen geliştirmeler özdevinim büyüklügü arttıkça daha etkili hale gelmektedir. Testing is the most expensive and time consuming phase in the development of complex systems. Model–based testing is an approach that can be used to automate the generation of high quality test suites, which is the most challenging part of testing. Formal models, such as finite state machines or automata, have been used as specifications from which the test suites can be automatically generated. The tests are applied after the system is synchronized to a particular state, which can be accomplished by using a synchronizing word. Computing a shortest synchronizing word is of interest for practical purposes, e.g. for a shorter testing time. However, computing a shortest synchronizing word is an NP–hard problem. Therefore, heuristics are used to compute short synchronizing words. GREEDY is one of the fastest synchronizing heuristics currently known. In this thesis, we present approaches to accelerate GREEDY algorithm. Firstly, we focus on parallelization of GREEDY. Second, we propose a lazy execution of the preprocessing phase of the algorithm, by postponing the preparation of the required information until it is to be used in the reset word generation phase. We suggest other algorithmic enhancements as well for the implementation of the heuristics. Our experimental results show that depending on the automata size, GREEDY can be made 500⇥ faster. The suggested improvements become more effective as the size of the automaton increases. 52
- Published
- 2018
198. Boosting expensive synchronizing heuristics.
- Author
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Saraç, N. Ege, Altun, Ömer Faruk, Atam, Kamil Tolga, Karahoda, Sertaç, Kaya, Kamer, and Yenigün, Hüsnü
- Subjects
- *
GRAPHICS processing units , *HEURISTIC , *MACHINE theory , *PARALLEL algorithms , *ROBOTS - Abstract
For automata, synchronization, the problem of bringing an automaton to a particular state regardless of its initial state, is important. It has several applications in practice and is related to a fifty-year-old conjecture on the length of the shortest synchronizing word. Although using shorter words increases the effectiveness in practice, finding a shortest one (which is not necessarily unique) is NP-hard. For this reason, there exist various heuristics in the literature. However, high-quality heuristics such as SynchroP producing relatively shorter sequences are very expensive and can take hours when the automaton has tens of thousands of states. The SynchroP heuristic has been frequently used as a benchmark to evaluate the performance of the new heuristics. In this work, we first improve the runtime of SynchroP and its variants by using algorithmic techniques. We then focus on adapting SynchroP for many-core architectures, and overall, we obtain more than 1000 × speedup on GPUs compared to naive sequential implementation that has been frequently used as a benchmark to evaluate new heuristics in the literature. We also propose two SynchroP variants and evaluate their performance. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
199. Türkiye akademik eşyazarlık ağlarında tavsiye için bağlantı tahmin modelleri
- Author
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Aydin, Soner, Birbil, Şevket İlker, Kaya, Kamer, and Endüstri Mühendisliği Anabilim Dalı
- Subjects
Subgradient method ,Big data ,Sparse matrixes ,T055.4-60.8 Industrial engineering. Management engineering ,Endüstri ve Endüstri Mühendisliği ,Industrial and Industrial Engineering ,Logistic regression models - Abstract
Profesyonel ağlarda bireylerin birbirine tavsiye edilmesi bir bağlantı tahmini problemi olarak ele alınabilir. Bu amaç doğrultusunda öğrenme tabanlı yöntemler, hem tahmin hem de çıkarsama yapma hedefleri için uygundur. Bu yöntemlerin uygulanması kolaydır ve büyük ölçekli veri setleri için hesaplanabilirlik açısından da uygundurlar. Bu tezde, Türkiye'nin akademik işbirliği ağında, yazarların ve makalelerin önerilmesi için bağlantı tahmin modelleri araştırılmıştır. Modeller ve hipotezler için kavramsal bir arka plan oluşturmak amacıyla veri setini belirli görselleştirme araçları ve temel istatistikler kullanarak inceliyoruz. Bir yan ürün olarak, mevcut modellerin ve kullandıkları bilgi kaynaklarının olası eksikliklerini de vurguluyoruz. Kavramsal arka planı ve potansiyel dezavantajları hesaba katarak mevcut modelleri uyguluyor, karşılaştırıyor ve farklılıklarını ortaya koyuyor ve hipotezimizi test ediyoruz. Tüm bu modelleri eniyileme problemleri olarak ele alıyor ve birinci dereceden eniyileme yöntemlerini kullanarak çözüyoruz. Sonuçları, tahmin isabeti açısından değerlendiriyor ve anlamlarını da yorumluyoruz. Elde ettiğimiz sonuçlar, sahip olduğumuz veri seti için özel olsa da, kullandığımız teknikler diğer ağ veri setleri ile uygulanabilecek kadar geneldir. Recommendation of individuals in a professional network can be thought as a link prediction problem. For this purpose, learning based methods are suitable for both prediction and inference goals. These methods are also easy to implement and they are computationally tractable for large scale datasets. In this thesis, we investigate link prediction models for recommendation of authors and papers in academic collaboration network of Turkey. We examine the dataset with certain visualization tools and basic statistics, in order to form a conceptual background for our models and hypothesis. As a byproduct, we highlight potential drawbacks of existing models and the information resources they use. Taking the conceptual background and potential drawbacks into account, we implement, compare and contrast existing models, and test our hypothesis. We cast all of these models as optimization problems and solve them by using first order optimization methods. We evaluate their results in terms of prediction accuracy and provide interpretation about their meaning as well. While the results that we have obtained are special for the given dataset that we have, techniques that we have used are generic enough to be implemented with other graph datasets. 45
- Published
- 2017
200. Parallel implementations for solving matrix factorization problems with optimization
- Author
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Emami Gohari, Amir, Birbil, Şevket İlker, Kaya, Kamer, and Endüstri Mühendisliği Anabilim Dalı
- Subjects
T055.4-60.8 Industrial engineering. Management engineering ,Endüstri ve Endüstri Mühendisliği ,Industrial and Industrial Engineering - Abstract
Günümüzde, veri setlerinin boyutundaki artış ile tavsiye sistemleri gibi uygulamalardaki bu verilerle çalışmayı sağlayacak hızlı ve tutarlı araçların gereksinimi, en kısa sürede tüm kaynakları kullanarak istenen çalışmaları yapabilen yeni düzenlenmiş modeller üzerinde büyük bir ilgi oluşmasını sağladı.Bu çalışmada, paralelleşmiş büyük ölçekli matris faktorizasyon problemi için bir sistem oluşturduk.Bu tür problemleri çözmek için en çok kullanılan, en başarılı yöntemlerden biri optimizasyon teknikleridir. Optimizasyon yöntemleri, iterasyonları gerçekleştirmek için gradyan vektörlerine gerek duymaktadır. Bu tür problemlerin çözümünde zamanın çoğu gradyan ve fonksiyon değerlerinin hesaplanmasında harcanmaktadır. Bu çalışmada, matris faktorizasyonunda daha önce kullanılmayan, yeni bir yöntem uyguladık. Paralelizasyon için CPU ve GPU uygulamalarını gösterdik. Çalışmamızda da görüldüğü gibi, önerilen paralelizasyon oldukça iyi ölçeklenmektedir. MovieLens veri seti üzerindeki çalışmamızı raporladık. Sonuçlarımız gösteriyor ki iterasyon sayısını azaltmada önerdiğimiz yöntem oldukça başarılı. İstenilen RMSE değerleri ile birlikte umut vadeden ölçeklenir değerlere ulaştık. During recent years, the exponential increase in data sets' sizes and the need for fast and accurate tools which can operate on these huge data sets in applications such as recommendation systems has led to an ever growing attention towards devising novelmethods which can incorporate all the available resources to execute desired operations in the least possible time. In this work, we provide a framework for parallelized large-scale matrix factorization problems. One of the most successful and used methods to solve these problems is solving them via optimization techniques. Optimization methods require gradient vectors to update the iterates. The time spent to solve such a problem is mostly spent on calls to gradient and function value evaluations. In this work, we have used a recent method, which has not been used before for matrix factorization. When it comes to parallelization, we present both CPU and GPU implementations. As our experiments show, the proposed parallelization scales quite well. We report our results on Movie- Lens data set. Our results show that the new method is quite successful in reducing the number of iterations. We obtain very good RMSE values with significant promising scaling figures. 54
- Published
- 2016
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