Siang Wun Song

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In this paper we present deterministic parallel algorithms for the coarse-grained multicomputer (CGM) and bulk synchronous parallel (BSP) models for solving the following well-known graph problems: (1) list ranking, (2) Euler tour construction in a tree, (3) computing the connected components and spanning forest, (4) lowest common ancestor preprocessing,(More)
In this paper we present a parallel wavefront algorithm for computing an alignment between two strings A and C, with |A| = m and |C| = n. On a distributed memory parallel computer of p processors each with O((m+ n)/p) memory, the proposed algorithm requires O(p) communication rounds and O(mn/p) local computing time. The novelty of this algorithm is based on(More)
Several loop transformations techniques have been designed to extract parallelism from nested loop structures. We rst review two important approaches, known as Generalized Cycle Shrinking presented by Shang, O'Keefe and Fortes and the Index Shift Method introduced by Liu, Ho and Sheu. The main result of the paper is a new methodology that permits to combine(More)
We present a CGM/BSP algorithm for computing an alignment (or string editing) between two strings A and C, with jAj = m and jCj = n. The algorithm requires O(p) communication rounds and O( p ) local computing time, on a distributed memory parallel computer of p processors each with O(nm=p) memory. We also present implementation results obtained on Beowulf(More)
Given two strings X and Y of lengths m and n, respectively, the all-substrings longest common subsequence (ALCS) problem obtains the lengths of the subsequences common to X and any substring of Y . The sequential algorithm takes O(mn) time and O(n) space. We present a parallel algorithm for ALCS on a coarse-grained multicomputer (BSP/CGM) model with p < p m(More)
Given two strings A and B of lengths na and nb, respectively, the All-substrings Longest Common Subsequence (ALCS) problem obtains, for any substring B ′ of B, the length of the longest string that is a subsequence of both A and B . The sequential algorithm takes O(nanb) time and O(nb) space. We present a parallel algorithm for the ALCS on the Coarse(More)
We present a randomized parallel list ranking algorithm for distributed memory multiprocessors, using a BSP type model. We first describe a simple version which requires, with high probability, log(3p)+log ln(n)=Õ(logp+log logn) communication rounds (h-relations withh=Õ(n/p)) andÕ(n/p)) local computation. We then outline an improved version that requires(More)
Large-scale simulations of parts of the brain using detailed neuronal models to improve our understanding of brain functions are becoming a reality with the usage of supercomputers and large clusters. However, the high acquisition and maintenance cost of these computers, including the physical space, air conditioning, and electrical power, limits the number(More)