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Publication Metadata only 3D shape correspondence by isometry-driven greedy optimization(IEEE Computer Soc, 2010) N/A; Department of Computer Engineering; Sahillioğlu, Yusuf; Yemez, Yücel; PhD Student; Faculty Member; Department of Computer Engineering; Graduate School of Sciences and Engineering; College of Engineering; 215195; 107907We present an automatic method that establishes 3D correspondence between isometric shapes. Our goal is to find an optimal correspondence between two given (nearly) isometric shapes, that minimizes the amount of deviation from isometry. We cast the problem as a complete surface correspondence problem. Our method first divides the given shapes to be matched into surface patches of equal area and then seeks for a mapping between the patch centers which we refer to as base vertices. Hence the correspondence is established in a fast and robust manner at a relatively coarse level as imposed by the patch radius. We optimize the isometry cost in two steps. in the first step, the base vertices are transformed into spectral domain based on geodesic affinity, where the isometry errors are minimized in polynomial time by complete bipartite graph matching. the resulting correspondence serves as a good initialization for the second step of optimization in which we explicitly minimize the isometry cost via an iterative greedy algorithm in the original 3D Euclidean space. We demonstrate the performance of our method on various isometric (or nearly isometric) pairs of shapes for some of which the ground-truth correspondence is available.Publication Metadata only Boxlib with tiling: an adaptive mesh refinement software framework(Siam Publications, 2016) Zhang, Weiqun; Almgren, Ann; Day, Marcus; Tan Nguyen; Shalf, John; Department of Computer Engineering; Erten, Didem Unat; Faculty Member; Department of Computer Engineering; College of Engineering; 219274In this paper we introduce a block-structured adaptive mesh refinement software framework that incorporates tiling, a well-known loop transformation. Because the multiscale, multiphysics codes built in BoxLib are designed to solve complex systems at high resolution, performance on current and next generation architectures is essential. With the expectation of many more cores per node on next generation architectures, the ability to effectively utilize threads within a node is essential, and the current model for parallelization will not be sufficient. We describe a new version of BoxLib in which the tiling constructs are embedded so that BoxLib-based applications can easily realize expected performance gains without extra effort on the part of the application developer. We also discuss a path forward to enable future versions of BoxLib to take advantage of NUMA-aware optimizations using the TiDA portable library.Publication Metadata only Context-sensitive mental model aggregation in a second-order adaptive network model for organisational learning(Springer International Publishing AG, 2022) Treur, Jan; Department of Computer Engineering; Canbaloğlu, Gülay; Undergraduate Student; Department of Computer Engineering; College of Engineering; N/AOrganisational learning processes often exploit developed individual mental models in order to obtain shared mental models for the organisation by some form of unification or aggregation. The focus in this paper is on this aggregation process, which may depend on a number of contextual factors. It is shown how a second-order adaptive network model for organisation learning can be used to model this process of aggregation of individual mental models in a context-dependent manner.Publication Metadata only Data decomposition for parallel K-means clustering(Springer-Verlag Berlin, 2004) Department of Computer Engineering; Gürsoy, Attila; Faculty Member; Department of Computer Engineering; College of Engineering; 8745Developing fast algorithms for clustering has been an important area of research in data mining and other fields. K-means is one of the widely used clustering algorithms. In this work, we have developed and evaluated parallelization of k-means method for low-dimensional data on message passing computers. Three different data decomposition schemes and their impact on the pruning of distance calculations in tree-based k-means algorithm have been studied. Random pattern decomposition has good load balancing but fails to prune distance calculations effectively. Compact spatial decomposition of patterns based on space filling curves outperforms random pattern decomposition even though it has load imbalance problem. In both cases, parallel tree-based k-means clustering runs significantly faster than the traditional parallel k-means.Publication Open Access HMI-PRED 2.0: a biologist-oriented web application for prediction of host-microbe protein-protein interaction by interface mimicry(Oxford University Press (OUP), 2022) Lim, H., Tsai, C.J.; Nussinov, R.; Department of Computer Engineering; Department of Chemical and Biological Engineering; Keskin, Özlem; Gürsoy, Attila; Faculty Member; Department of Computer Engineering; Department of Chemical and Biological Engineering; College of Engineering; 26605; 8745HMI-PRED 2.0 is a publicly available web service for the prediction of host-microbe protein-protein interaction by interface mimicry that is intended to be used without extensive computational experience. A microbial protein structure is screened against a database covering the entire available structural space of complexes of known human proteins.Publication Metadata only Network traffic properties of bimodal multicast protocol(TÜBİTAK, 2003) N/A; Department of Computer Engineering; Department of Mathematics; Özkasap, Öznur; Çağlar, Mine; Faculty Member; Faculty Member; Department of Computer Engineering; Department of Mathematics; College of Engineering; College of Sciences; 113507; 105131The popularity of large-scale distributed applications, such as videoconferencing, multimedia dissemination, electronic stock exchange and distributed cooperative work, has grown with the availability of high-speed networks and the expansion of the Internet. The key property of this type of applications is the need to distribute data among multiple participants together with an application-specific quality of service needs. This fact makes scalable multicast protocols an essential underlying communication structure. Although there exist several studies investigating the traffic characteristics of unicast communication, multicast traffic has not been examined extensively in previous studies. It is well known that the aggregate traffic properties of self-similarity and long-range dependence are ubiquitous in wide area networks and lead to adverse consequences in network performance. In this study, we analyze traffic characteristics of a novel scalable, reliable multicast protocol, Bimodal Multicast (Pbcast). In particular, our simulation studies demonstrate that epidemic approach of Bimodal Multicast generates short-range dependent traffic with low overhead traffic and transport delays. We elaborate on the protocol mechanisms as an underlying factor in our empirical results.Publication Metadata only Visualization literacy at elementary school(Assoc Computing Machinery, 2017) Alper, Başak; Riche, Nathalie Henry; Chevalier, Fanny; Boy, Jeremy; Department of Computer Engineering; Sezgin, Tevfik Metin; Faculty Member; Department of Computer Engineering; College of Engineering; 18632This work advances our understanding of children's visualization literacy, and aims to improve it with a novel approach for teaching visualization at elementary schools. We first contribute an analysis of data graphics and activities employed in grade K to 4 educational materials, and the results of a survey conducted with 16 elementary school teachers. We find that visualization education could benefit from integrating pedagogical strategies for teaching abstract concepts with established interactive visualization techniques. Building on these insights, we develop and study design principles for novel interactive teaching material aimed at increasing children's visualization literacy. We specifically contribute Cest la Vis, an online platform for teachers and students to respectively teach and learn about pictographs and bar charts, and report on our initial observations of its use in grades K and 2.