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Cacheefficient Dynamic Programming Algorithms for Multicores
, 2008
"... We present cacheefficient chip multiprocessor (CMP) algorithms with good speedup for some widely used dynamic programming algorithms. We consider three types of caching systems for CMPs: DCMP with a private cache for each core, SCMP with a single cache shared by all cores, and Multicore, which h ..."
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Cited by 27 (4 self)
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We present cacheefficient chip multiprocessor (CMP) algorithms with good speedup for some widely used dynamic programming algorithms. We consider three types of caching systems for CMPs: DCMP with a private cache for each core, SCMP with a single cache shared by all cores, and Multicore, which
Efficient Dynamic Programming Algorithms for Ordering Expensive Joins and Selections
 In Proc. of EDBT
, 1998
"... 1 Introduction Traditional work on algebraic query optimization has mainly focused on the problem of ordering joins in a query. Restrictions like selections and projections are generally treated by "pushdown rules". According to these, selections and projections should be pushed d ..."
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Cited by 11 (3 self)
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1 Introduction Traditional work on algebraic query optimization has mainly focused on the problem of ordering joins in a query. Restrictions like selections and projections are generally treated by "pushdown rules". According to these, selections and projections should be pushed down the query plan as far as possible. These heuristic rules worked quite well for traditional relational database systems where the evaluation of selection predicates is of neglectable cost and every selection reduces the cost of subsequent joins. As pointed out by Hellerstein, Stonebraker [5], this is no longer true for modern database systems like objectoriented DBMSs? Research supported by the German Research Association (DFG) under contract
A MemoryEfficient Dynamic Programming Algorithm for Optimal Alignment of a Sequence to an RNA Secondary Structure
, 2002
"... Background: Covariance models (CMs) are probabilistic models of RNA secondary structure, analogous to profile hidden Markov models of linear sequence. The dynamic programming algorithm for aligning a CM to an RNA sequence of length N is O(N³) in memory. This is only practical for small RNAs ..."
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Cited by 104 (11 self)
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Background: Covariance models (CMs) are probabilistic models of RNA secondary structure, analogous to profile hidden Markov models of linear sequence. The dynamic programming algorithm for aligning a CM to an RNA sequence of length N is O(N³) in memory. This is only practical for small
An Efficient Dynamic Programming Algorithm for the Generalized LCS Problem with Multiple Substring Exclusion Constrains
, 2014
"... In this paper, we consider a generalized longest common subsequence problem with multiple substring exclusion constrains. For the two input sequences X and Y of lengths n and m, and a set of d constrains P = {P1, · · · , Pd} of total length r, the problem is to find a common subsequence Z of X an ..."
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and Y excluding each of constrain string in P as a substring and the length of Z is maximized. The problem was declared to be NPhard[1], but we finally found that this is not true. A new dynamic programming solution for this problem is presented in this paper. The correctness of the new algorithm
Dynamic programming algorithm optimization for spoken word recognition
 IEEE TRANSACTIONS ON ACOUSTICS, SPEECH, AND SIGNAL PROCESSING
, 1978
"... This paper reports on an optimum dynamic programming (DP) based timenormalization algorithm for spoken word recognition. First, a general principle of timenormalization is given using timewarping function. Then, two timenormalized distance definitions, ded symmetric and asymmetric forms, are der ..."
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Cited by 788 (3 self)
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This paper reports on an optimum dynamic programming (DP) based timenormalization algorithm for spoken word recognition. First, a general principle of timenormalization is given using timewarping function. Then, two timenormalized distance definitions, ded symmetric and asymmetric forms
An Efficient ContextFree Parsing Algorithm
, 1970
"... A parsing algorithm which seems to be the most efficient general contextfree algorithm known is described. It is similar to both Knuth's LR(k) algorithm and the familiar topdown algorithm. It has a time bound proportional to n 3 (where n is the length of the string being parsed) in general; i ..."
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Cited by 798 (0 self)
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A parsing algorithm which seems to be the most efficient general contextfree algorithm known is described. It is similar to both Knuth's LR(k) algorithm and the familiar topdown algorithm. It has a time bound proportional to n 3 (where n is the length of the string being parsed) in general
Fast Parallel Algorithms for ShortRange Molecular Dynamics
 JOURNAL OF COMPUTATIONAL PHYSICS
, 1995
"... Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of interatomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dyn ..."
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Cited by 653 (7 self)
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Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of interatomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular
Scalable molecular dynamics with NAMD.
 J Comput Chem
, 2005
"... Abstract: NAMD is a parallel molecular dynamics code designed for highperformance simulation of large biomolecular systems. NAMD scales to hundreds of processors on highend parallel platforms, as well as tens of processors on lowcost commodity clusters, and also runs on individual desktop and la ..."
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Cited by 849 (63 self)
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and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion
The algorithmic analysis of hybrid systems
 THEORETICAL COMPUTER SCIENCE
, 1995
"... We present a general framework for the formal specification and algorithmic analysis of hybrid systems. A hybrid system consists of a discrete program with an analog environment. We model hybrid systems as nite automata equipped with variables that evolve continuously with time according to dynamica ..."
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Cited by 778 (71 self)
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We present a general framework for the formal specification and algorithmic analysis of hybrid systems. A hybrid system consists of a discrete program with an analog environment. We model hybrid systems as nite automata equipped with variables that evolve continuously with time according
Pin: building customized program analysis tools with dynamic instrumentation
 IN PLDI ’05: PROCEEDINGS OF THE 2005 ACM SIGPLAN CONFERENCE ON PROGRAMMING LANGUAGE DESIGN AND IMPLEMENTATION
, 2005
"... Robust and powerful software instrumentation tools are essential for program analysis tasks such as profiling, performance evaluation, and bug detection. To meet this need, we have developed a new instrumentation system called Pin. Our goals are to provide easytouse, portable, transparent, and eff ..."
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Cited by 991 (35 self)
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original, uninstrumented behavior. Pin uses dynamic compilation to instrument executables while they are running. For efficiency, Pin uses several techniques, including inlining, register reallocation, liveness analysis, and instruction scheduling to optimize instrumentation. This fully automated approach
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