31,709 research outputs found
Adder Based Residue to Binary Number Converters for (2n - 1; 2n; 2n + 1)
Copyright © 2002 IEEEBased on an algorithm derived from the new Chinese remainder theorem I, we present three new residue-to-binary converters for the residue number system (2n-1, 2n, 2n+1) designed using 2n-bit or n-bit adders with improvements on speed, area, or dynamic range compared with various previous converters. The 2n-bit adder based converter is faster and requires about half the hardware required by previous methods. For n-bit adder-based implementations, one new converter is twice as fast as the previous method using a similar amount of hardware, whereas another new converter achieves improvement in either speed, area, or dynamic range compared with previous convertersYuke Wang, Xiaoyu Song, Mostapha Aboulhamid and Hong She
SWAPHI: Smith-Waterman Protein Database Search on Xeon Phi Coprocessors
The maximal sensitivity of the Smith-Waterman (SW) algorithm has enabled its
wide use in biological sequence database search. Unfortunately, the high
sensitivity comes at the expense of quadratic time complexity, which makes the
algorithm computationally demanding for big databases. In this paper, we
present SWAPHI, the first parallelized algorithm employing Xeon Phi
coprocessors to accelerate SW protein database search. SWAPHI is designed based
on the scale-and-vectorize approach, i.e. it boosts alignment speed by
effectively utilizing both the coarse-grained parallelism from the many
co-processing cores (scale) and the fine-grained parallelism from the 512-bit
wide single instruction, multiple data (SIMD) vectors within each core
(vectorize). By searching against the large UniProtKB/TrEMBL protein database,
SWAPHI achieves a performance of up to 58.8 billion cell updates per second
(GCUPS) on one coprocessor and up to 228.4 GCUPS on four coprocessors.
Furthermore, it demonstrates good parallel scalability on varying number of
coprocessors, and is also superior to both SWIPE on 16 high-end CPU cores and
BLAST+ on 8 cores when using four coprocessors, with the maximum speedup of
1.52 and 1.86, respectively. SWAPHI is written in C++ language (with a set of
SIMD intrinsics), and is freely available at http://swaphi.sourceforge.net.Comment: A short version of this paper has been accepted by the IEEE ASAP 2014
conferenc
Fast matrix multiplication techniques based on the Adleman-Lipton model
On distributed memory electronic computers, the implementation and
association of fast parallel matrix multiplication algorithms has yielded
astounding results and insights. In this discourse, we use the tools of
molecular biology to demonstrate the theoretical encoding of Strassen's fast
matrix multiplication algorithm with DNA based on an -moduli set in the
residue number system, thereby demonstrating the viability of computational
mathematics with DNA. As a result, a general scalable implementation of this
model in the DNA computing paradigm is presented and can be generalized to the
application of \emph{all} fast matrix multiplication algorithms on a DNA
computer. We also discuss the practical capabilities and issues of this
scalable implementation. Fast methods of matrix computations with DNA are
important because they also allow for the efficient implementation of other
algorithms (i.e. inversion, computing determinants, and graph theory) with DNA.Comment: To appear in the International Journal of Computer Engineering
Research. Minor changes made to make the preprint as similar as possible to
the published versio
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