Performance of SSE and AVX Instruction Sets

SSE (streaming SIMD extensions) and AVX (advanced vector extensions) are SIMD (single instruction multiple data streams) instruction sets supported by recent CPUs manufactured in Intel and AMD. This SIMD programming allows parallel processing by multiple cores in a single CPU. Basic arithmetic and data transfer operations such as sum, multiplication and square root can be processed simultaneously. Although popular compilers such as GNU compilers and Intel compilers provide automatic SIMD optimization options, one can obtain better performance by a manual SIMD programming with proper optimization: data packing, data reuse and asynchronous data transfer. In particular, linear algebraic operations of vectors and matrices can be easily optimized by the SIMD programming. Typical calculations in lattice gauge theory are composed of linear algebraic operations of gauge link matrices and fermion vectors, and so can adopt the manual SIMD programming to improve the performance.Comment: 7 pages, 5 figures, 4 tables, Contribution to proceedings of the 30th International Symposium on Lattice Field Theory (Lattice 2012), June 24-29, 201

Young Wall Realization of Crystal Bases for Classical Lie Algebras

In this paper, we give a new realization of crystal bases for finite dimensional irreducible modules over classical Lie algebras. The basis vectors are parameterized by certain Young walls lying between highest weight and lowest weight vectors.Comment: 27page

Construction of biorthogonal wavelet vectors

AbstractThe construction of all possible biorthogonal wavelet vectors corresponding to a given biorthogonal scaling vector may not be easy as that of biorthogonal uniwavelets. In this paper, we give some theorems about the construction of biorthogonal wavelet vectors, which is followed by simple computations for constructing all parametrized biorthogonal wavelet vectors supported in [-1,1]. This approach is also suitable for the case of compactly supported orthogonal uniwavelet. Moreover, we give examples parametrizing all biorthogonal wavelet vectors corresponding to well known biorthogonal scaling vectors

Progressive Processing of Continuous Range Queries in Hierarchical Wireless Sensor Networks

In this paper, we study the problem of processing continuous range queries in a hierarchical wireless sensor network. Contrasted with the traditional approach of building networks in a "flat" structure using sensor devices of the same capability, the hierarchical approach deploys devices of higher capability in a higher tier, i.e., a tier closer to the server. While query processing in flat sensor networks has been widely studied, the study on query processing in hierarchical sensor networks has been inadequate. In wireless sensor networks, the main costs that should be considered are the energy for sending data and the storage for storing queries. There is a trade-off between these two costs. Based on this, we first propose a progressive processing method that effectively processes a large number of continuous range queries in hierarchical sensor networks. The proposed method uses the query merging technique proposed by Xiang et al. as the basis and additionally considers the trade-off between the two costs. More specifically, it works toward reducing the storage cost at lower-tier nodes by merging more queries, and toward reducing the energy cost at higher-tier nodes by merging fewer queries (thereby reducing "false alarms"). We then present how to build a hierarchical sensor network that is optimal with respect to the weighted sum of the two costs. It allows for a cost-based systematic control of the trade-off based on the relative importance between the storage and energy in a given network environment and application. Experimental results show that the proposed method achieves a near-optimal control between the storage and energy and reduces the cost by 0.989~84.995 times compared with the cost achieved using the flat (i.e., non-hierarchical) setup as in the work by Xiang et al.Comment: 41 pages, 20 figure

Predicting and improving the protein sequence alignment quality by support vector regression

Abstract Background For successful protein structure prediction by comparative modeling, in addition to identifying a good template protein with known structure, obtaining an accurate sequence alignment between a query protein and a template protein is critical. It has been known that the alignment accuracy can vary significantly depending on our choice of various alignment parameters such as gap opening penalty and gap extension penalty. Because the accuracy of sequence alignment is typically measured by comparing it with its corresponding structure alignment, there is no good way of evaluating alignment accuracy without knowing the structure of a query protein, which is obviously not available at the time of structure prediction. Moreover, there is no universal alignment parameter option that would always yield the optimal alignment. Results In this work, we develop a method to predict the quality of the alignment between a query and a template. We train the support vector regression (SVR) models to predict the MaxSub scores as a measure of alignment quality. The alignment between a query protein and a template of length n is transformed into a (n + 1)-dimensional feature vector, then it is used as an input to predict the alignment quality by the trained SVR model. Performance of our work is evaluated by various measures including Pearson correlation coefficient between the observed and predicted MaxSub scores. Result shows high correlation coefficient of 0.945. For a pair of query and template, 48 alignments are generated by changing alignment options. Trained SVR models are then applied to predict the MaxSub scores of those and to select the best alignment option which is chosen specifically to the query-template pair. This adaptive selection procedure results in 7.4% improvement of MaxSub scores, compared to those when the single best parameter option is used for all query-template pairs. Conclusion The present work demonstrates that the alignment quality can be predicted with reasonable accuracy. Our method is useful not only for selecting the optimal alignment parameters for a chosen template based on predicted alignment quality, but also for filtering out problematic templates that are not suitable for structure prediction due to poor alignment accuracy. This is implemented as a part in FORECAST, the server for fold-recognition and is freely available on the web at http://pbil.kaist.ac.kr/forecast</p