Browsing by Subject "Data structures"

Now showing 1 - 20 of 30

Open Access
Adaptive decomposition and remapping algorithms for object-space-parallel direct volume rendering of unstructured grids
(Academic Press, 2007-01) Aykanat, Cevdet; Cambazoglu, B. B.; Findik, F.; Kurc, T.
Object space (OS) parallelization of an efficient direct volume rendering algorithm for unstructured grids on distributed-memory architectures is investigated. The adaptive OS decomposition problem is modeled as a graph partitioning (GP) problem using an efficient and highly accurate estimation scheme for view-dependent node and edge weighting. In the proposed model, minimizing the cutsize corresponds to minimizing the parallelization overhead due to the data communication and redundant computation/storage while maintaining the GP balance constraint corresponds to maintaining the computational load balance in parallel rendering. A GP-based, view-independent cell clustering scheme is introduced to induce more tractable view-dependent computational graphs for successive visualizations. As another contribution, a graph-theoretical remapping model is proposed as a solution to the general remapping problem and is used in minimization of the cell-data migration overhead. The remapping tool RM-MeTiS is developed by modifying the GP tool MeTiS and is used in partitioning the remapping graphs. Experiments are conducted using benchmark datasets on a 28-node PC cluster to evaluate the performance of the proposed models. © 2006 Elsevier Inc. All rights reserved.
Open Access
Binary morphological subband decomposition for image coding
(IEEE, 1996) Gürcan, Metin Nafi; Gerek, Ömer Nezih; Çetin, A. Enis
In this paper a binary waveform coding method based on morphological subband decomposition coupled with embedded zero-tree and entropy coding is described. This method can be utilized in text compression or bit-plane coding of images. Binary morphological subband decomposition operations are carried out in the Gallois Field, resulting in a computationally efficient structure. Simulation studies are presented.
Open Access
CAPSULE: Language and system support for efficient state sharing in distributed stream processing systems
(ACM, 2012) Losa, G.; Kumar, V.; Andrade, H.; Gedik, Buğra; Hirzel, M.; Soulé, R.; Wu, K. -L.
Data stream processing applications are often expressed as data flow graphs, composed of operators connected via streams. This structured representation provides a simple yet powerful paradigm for building large-scale, distributed, high-performance applications. However, there are many tasks that require sharing data across operators, and across operators and the runtime using a less structured mechanism than point-to-point data flows. Examples include updating control variables, sending notifications, collecting metrics, building collective models, etc. In this paper we describe CAPSULE, which fills this gap. CAPSULE is a code generation and runtime framework that offers an easy to use and highly flexible framework for developers to realize shared variables (CAPSULE term for shared state) by specifying a data structure (at the programming-language level), and a few associated configuration parameters that qualify the expected usage scenario. Besides the easy of use and flexibility, CAPSULE offers the following important benefits: (1) Custom Code Generation - CAPSULE makes use of user-specified configuration parameters and information from the runtime to generate shared variable servers that are tailored for the specific usage scenario, (2) Composability - CAPSULE supports deployment time composition of the shared variable servers to achieve desired levels of scalability, performance and fault-tolerance, and (3) Extensibility - CAPSULE provides simple interfaces for extending the CAPSULE framework with more protocols, transports, caching mechanisms, etc. We describe the motivation for CAPSULE and its design, report on its implementation status, and then present experimental results. Copyright © 2012 ACM.
Open Access
A comparison of historical relational query languages
(ASME, 1994-07) Tansel, Abdullah Uz; Tin, E.
We introduce a historical relational data model in which N1NF relations are used and 1-level of nesting is allowed. Attributes can either be atomic or temporal atom. An atomic attribute represents a time invariant attribute. A temporal atom consists of two components, a value and a temporal set, which is a set of times denoting the validity period of the value. We define a relational tuple calculus for this model. We follow a comparative approach towards completeness of historical query languages.
Open Access
Computational pan-genomics: status, promises and challenges
(Oxford University Press, 2018-01-01) The Computational Pan-Genomics Consortium; Alkan, Can
Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic data sets. Instead, novel, qualitatively different computational methods and paradigms are needed.We will witness the rapid extension of computational pan-genomics, a new sub-area of research in computational biology. In this article, we generalize existing definitions and understand a pangenome as any collection of genomic sequences to be analyzed jointly or to be used as a reference. We examine already available approaches to construct and use pan-genomes, discuss the potential benefits of future technologies and methodologies and review open challenges from the vantage point of the above-mentioned biological disciplines. As a prominent example for a computational paradigm shift, we particularly highlight the transition from the representation of reference genomes as strings to representations as graphs. We outline how this and other challenges from different application domains translate into common computational problems, point out relevant bioinformatics techniques and identify open problems in computer science. With this review, we aim to increase awareness that a joint approach to computational pangenomics can help address many of the problems currently faced in various domains.
Open Access
Distance-based classification methods
(Taylor & Francis, 1999) Ekin, O.; Hammer, P. L.; Kogan, A.; Winter, P.
Given a set of points in a Euclidean space, and a partitioning of this 'training set' into two or more subsets ('classes'), we consider the problem of identifying a 'reasonable' assignment of another point in the Euclidean space ('query point') to one of these classes. The various classifications proposed in this paper are determined by the distances between the query point and the points in the training set. We report results of extensive computational experiments comparing the new methods with two well-known distance-based classification methods (k-nearest neighbors and Parzen windows) on data sets commonly used in the literature. The results show that the performance of both new and old distance-based methods is on par with and often better than that of the other best classification methods known. Moreover, the new classification procedures proposed in this paper are: (i) easy to implement, (ii) extremely fast, and (iii) very robust (i.e. their performance is insignificantly affected by the choice of parameter values).
Open Access
Editing heightfield using history management and 3D widgets
(IEEE, 2009-09) Yalçın, M. Aydın; Çapin, Tolga K.
In virtual environments, terrain is generally modeled by heightfield, a 2D structure. To be able to create desired terrain geometry, software editors for this specific task have been developed. The graphics hardware, data structures and rendering techniques are developing fast to open up new possibilities to the user and terrain editor functionalities are following such improvements (such as real-time lighting updates during editing operations and multi-texture blending). Yet, current terrain editors mostly fail to give the user feedback about their actions and also fail to help the users understand and undo the editing operations on the terrain. The aim of this study is to investigate the 3d-widget based visualization of possible editing (sculpturing) actions on terrain and to help user undo previous operations. © 2009 IEEE.
Open Access
Effective use of space for pivot-based metric indexing structures
(IEEE, 2008-04) Çelik, Cengiz
Among the metric space indexing methods, AESA is known to produce the lowest query costs in terms of the number of distance computations. However, its quadratic construction cost and space consumption makes it infeasiblefor large dataseis. There have been some work on reducing the space requirements of AESA. Instead of keeping all the distances between objects, LAESA appoints a subset of the database as pivots, keeping only the distances between objects and pivots. Kvp uses the idea of prioritizing the pivots based on their distances to objects, only keeping pivot distances that it evaluates as promising. FQA discretizes the distances using a fixed amount of bits per distance instead of using system's floating point types. Varying the number of bits to produce a performance-space trade-off was also studied in Kvp. Recently, BAESA has been proposed based on the same idea, but using different distance ranges for each pivot. The t-spanner based indexing structure compacts the distance matrix by introducing an approximation factor that makes the pivots less effective. In this work, we show that the Kvp prioritization is oriented toward symmetric distance distributions. We offer a new method that evaluates the effectiveness of pivots in a better fashion by making use of the overall distance distribution. We also simulate the performance of our method combined with distance discretization. Our results show that our approach is able to offer very good space-performance trade-offs compared to AESA and tree-based methods. © 2008 IEEE.
Open Access
Efficiency and effectiveness of query processing in cluster-based retrieval
(Elsevier, 2004) Can, F.; Altingövde I.S.; Demir, E.
Our research shows that for large databases, without considerable additional storage overhead, cluster-based retrieval (CBR) can compete with the time efficiency and effectiveness of the inverted index-based full search (FS). The proposed CBR method employs a storage structure that blends the cluster membership information into the inverted file posting lists. This approach significantly reduces the cost of similarity calculations for document ranking during query processing and improves efficiency. For example, in terms of in-memory computations, our new approach can reduce query processing time to 39% of FS. The experiments confirm that the approach is scalable and system performance improves with increasing database size. In the experiments, we use the cover coefficient-based clustering methodology (C3M), and the Financial Times database of TREC containing 210158 documents of size 564 MB defined by 229748 terms with total of 29545234 inverted index elements. This study provides CBR efficiency and effectiveness experiments using the largest corpus in an environment that employs no user interaction or user behavior assumption for clustering. © 2003 Elsevier Ltd. All rights reserved.
Open Access
An efficient algorithm for the single machine total tardiness problem
(Taylor & Francis, 2001) Tansel, B. Ç.; Kara, B. Y.; Sabuncuoğlu İ.
This paper presents an exact algorithm for the single machine total tardiness problem (1// L T;). We present a new synthesis of various results from the literature which leads to a compact and concise representation of job precedences, a simple optimality check, new decomposition theory, a new lower bound, and a check for presolved subproblems. These are integrated through the use of an equivalenceconcept that permits a continuous reformation of the data to permit early detection of optimality at the nodes of an enumeration tree. The overall effect is a significant reduction in the size of the search tree, CPU times, and storage requirements. The algorithm is capable of handling much larger problems (e.g., 500 jobs) than its predecessors in the literature (:s; 150). In addition, a simple modification of the algorithm gives a new heuristic which significantly outperforms the best known heuristics in the literature.
Open Access
Efficient parallel spatial subdivision algorithm for object-based parallel ray tracing
(Pergamon Press, 1994) Aykanat, Cevdet; İşler, V.; Özgüç, B.
Parallel ray tracing of complex scenes on multicomputers requires the distribution of both computation and scene data to the processors. This is carried out during preprocessing and usually consumes too much time and memory. The paper presents an efficient parallel subdivision algorithm that decomposes a given scene into rectangular regions adaptively and maps the resultant regions to the node processors of a multicomputer. The proposed algorithm uses efficient data structures to identify the splitting planes quickly. Furthermore the mapping of the regions and the objects to the node processors is performed while parallel spatial subdivision proceeds. The proposed algorithm is implemented on an Intel iPSC/2 hypercube multicomputer and promising results have been obtained. © 1994.
Open Access
Efficient vectorization of forward/backward substitutions in solving sparse linear equations
(IEEE, 1994) Aykanat, Cevdet; Özgü, Özlem; Güven, N.
Vector processors have promised an enormous increase in computing speed for computationally intensive and time-critical power system problems which require the repeated solution of sparse linear equations. Due to short vectors processed in these applications, standard sparsity-based algorithms need to be restructured for efficient vectorization. This paper presents a novel data storage scheme and an efficient vectorization algorithm that exploits the intrinsic architectural features of vector computers such as sectioning and chaining. As the benchmark, the solution phase of the Fast Decoupled Load Flow algorithm is used in simulations. The relative performances of the proposed and existing vectorization schemes are evaluated, both theoretically and experimentally, on IBM 3090/VF.
Open Access
Energy efficient architecture for graph analytics accelerators
(IEEE, 2016-06) Özdal, Muhammet Mustafa; Yeşil, Şerif; Kim, T.; Ayupov, A.; Greth, J.; Burns, S.; Öztürk, Özcan
Specialized hardware accelerators can significantly improve the performance and power efficiency of compute systems. In this paper, we focus on hardware accelerators for graph analytics applications and propose a configurable architecture template that is specifically optimized for iterative vertex-centric graph applications with irregular access patterns and asymmetric convergence. The proposed architecture addresses the limitations of the existing multi-core CPU and GPU architectures for these types of applications. The SystemC-based template we provide can be customized easily for different vertex-centric applications by inserting application-level data structures and functions. After that, a cycle-accurate simulator and RTL can be generated to model the target hardware accelerators. In our experiments, we study several graph-parallel applications, and show that the hardware accelerators generated by our template can outperform a 24 core high end server CPU system by up to 3x in terms of performance. We also estimate the area requirement and power consumption of these hardware accelerators through physical-aware logic synthesis, and show up to 65x better power consumption with significantly smaller area. © 2016 IEEE.
Open Access
FAME: Face association through model evolution
(IEEE, 2015-06) Gölge, Eren; Duygulu, Pınar
We attack the problem of building classifiers for public faces from web images collected through querying a name. The search results are very noisy even after face detection, with several irrelevant faces corresponding to other people. Moreover, the photographs are taken in the wild with large variety in poses and expressions. We propose a novel method, Face Association through Model Evolution (FAME), that is able to prune the data in an iterative way, for the models associated to a name to evolve. The idea is based on capturing discriminative and representative properties of each instance and eliminating the outliers. The final models are used to classify faces on novel datasets with different characteristics. On benchmark datasets, our results are comparable to or better than the state-of-the-art studies for the task of face identification. © 2015 IEEE.
Open Access
Human action recognition using distribution of oriented rectangular patches
(Springer, 2007-10) İkizler, Nazlı; Duygulu, Pınar
We describe a "bag-of-rectangles" method for representing and recognizing human actions in videos. In this method, each human pose in an action sequence is represented by oriented rectangular patches extracted over the whole body. Then, spatial oriented histograms are formed to represent the distribution of these rectangular patches. In order to carry the information from the spatial domain described by the bag-of-rectangles descriptor to temporal domain for recognition of the actions, four different methods are proposed. These are namely, (i) frame by frame voting, which recognizes the actions by matching the descriptors of each frame, (ii) global histogramming, which extends the idea of Motion Energy Image proposed by Bobick and Davis by rectangular patches, (iii) a classifier based approach using SVMs, and (iv) adaptation of Dynamic Time Warping on the temporal representation of the descriptor. The detailed experiments are carried out on the action dataset of Blank et. al. High success rates (100%) prove that with a very simple and compact representation, we can achieve robust recognition of human actions, compared to complex representations. © Springer-Verlag Berlin Heidelberg 2007.
Open Access
Incremental materialization of object-oriented views
(Elsevier, 1999) Alhajj, R.; Elnagar, A.
We present an approach to handle incremental materialization of object-oriented views. Queries that define views are implemented as methods that are invoked to compute corresponding views. To avoid computation from scratch each time a view is accessed, we introduce some deferred update algorithms that reflect for a view only related modifications introduced into the database while that view was inactive. A view is updated by considering modifications performed within all classes along the inheritance and class-composition subhierarchies rooted at every class used in deriving that view. To each class, we add a modification list to keep one modification tuple per view dependent on that class. Such a tuple acts as a reference point that marks the start of the next update to the corresponding view. © 1999 Elsevier Science B.V. All rights reserved.
Open Access
Lossless image compression by LMS adaptive filter banks
(Elsevier, 2001) Öktem, R.; Çetin, A. Enis; Gerek, O. N.; Öktem, L.; Egiazarian, K.
A lossless image compression algorithm based on adaptive subband decomposition is proposed. The subband decomposition is achieved by a two-channel LMS adaptive filter bank. The resulting coefficients are lossy coded first, and then the residual error between the lossy and error-free coefficients is compressed. The locations and the magnitudes of the nonzero coefficients are encoded separately by an hierarchical enumerative coding method. The locations of the nonzero coefficients in children bands are predicted from those in the parent band. The proposed compression algorithm, on the average, provides higher compression ratios than the state-of-the-art methods.
Open Access
Mars: A tool-based modeling, animation, and parallel rendering system
(Springer, 1994) Aktıhanoğlu, M.; Özgüç, B.; Aykanat, Cevdet
This paper describes a system for modeling, animating, previewing and rendering articulated objects. The system has a modeler of objects that consists of joints and segments. The animator interactively positions the articulated object in its stick, control vertex, or rectangular prism representation and previews the motion in real time. Then the data representing the motion and the models is sent to a multicomputer [iPSC/2 Hypercube (Intel)]. The frames are rendered in parallel, exploiting the coherence between successive frames, thus cutting down the rendering time significantly. Our main aim is to make a detailed study on rendering of a sequence of 3D scenes. The results show that due to an inherent correlation between the 3D scenes, an efficient rendering can be achieved. © 1994 Springer-Verlag.
Open Access
MLFMA memory reduction techniques for solving large-scale problems
(IEEE, 2014) Hidayetoğlu, Mert; Gürel, Levent
We present two memory reduction methods for the parallel multilevel fast multipole algorithm. One of these methods uses data structures out of core, and the other parallelizes the data structures related to input geometry. With these methods, large-scale electromagnetic scattering problems can be solved on modest parallel computers. © 2014 IEEE.
Open Access
Morphological subband decomposition structure using GF(N) arithmetic
(IEEE, 1996-09) Gürcan, Metin Nafi; Çetin, A. Enis; Gerek, Ömer, N.
Linear filter banks with critical subsampling and perfect reconstruction (PR) property have received much interest and found numerous applications in signal and image processing. Recently, nonlinear filter bank structures with PR and critical subsampling have been proposed and used in image coding. In this paper, it is shown that PR nonlinear subband decomposition can be performed using the Gallois Field (GF) arithmetic. The result of the decomposition of an n-ary (e.g. 256-ary) input signal is still n-ary at different resolutions. This decomposition structure can be utilized for binary and 2k (k is an integer) level signal decompositions. Simulation studies are presented.