Displaying similar documents to “A sparse dynamic programming algorithm for alignment with non-overlapping inversions”

A new practical linear space algorithm for the longest common subsequence problem

Heiko Goeman, Michael Clausen (2002)

Kybernetika

Similarity:

This paper deals with a new practical method for solving the longest common subsequence (LCS) problem. Given two strings of lengths m and n , n ≥ m , on an alphabet of size s , we first present an algorithm which determines the length p of an LCS in O ( n s + min { m p , p ( n - p ) } ) time and O ( n s ) space. This result has been achieved before [ric94,ric95], but our algorithm is significantly faster than previous methods. We also provide a second algorithm which generates an LCS in O ( n s + min { m p , m log m + p ( n - p ) } ) time while preserving the linear space bound,...

Tuning the Zhu-Takaoka string matching algorithm and experimental results

Thomas Berry, Somasundaram Ravindran (2002)

Kybernetika

Similarity:

In this paper we present experimental results for string matching algorithms which have a competitive theoretical worst case run time complexity. Of these algorithms a few are already famous for their speed in practice, such as the Boyer–Moore and its derivatives. We chose to evaluate the algorithms by counting the number of comparisons made and by timing how long they took to complete a given search. Using the experimental results we were able to introduce a new string matching algorithm...

Reservation table scheduling: branch-and-bound based optimization . integer linear programming techniques

Hadda Cherroun, Alain Darte, Paul Feautrier (2007)

RAIRO - Operations Research

Similarity:

The recourse to operation research solutions has strongly increased the performances of scheduling task in the High-Level Synthesis (called hardware compilation). Scheduling a whole program is not possible as too many constraints and objectives interact. We decompose high-level scheduling in three steps. Step 1: Coarse-grain scheduling tries to exploit parallelism and locality of the whole program (in particular in loops, possibly imperfectly nested) with a rough view of the target...

An improved ant algorithm for Multi-mode Resource Constrained Project Scheduling Problem

Peng Wuliang, Huang Min, Hao Yongping (2014)

RAIRO - Operations Research - Recherche Opérationnelle

Similarity:

Many real-world scheduling problems can be modeled as Multi-mode Resource Constrained Project Scheduling Problems (MRCPSP). However, the MRCPSP is a strong NP-hard problem and very difficult to be solved. The purpose of this research is to investigate a more efficient alternative based on ant algorithm to solve MRCPSP. To enhance the generality along with efficiency of the algorithm, the rule pool is designed to manage numerous priority rules for MRCPSP. Each ant is provided with an...

Genetic and Tabu search algorithms for peptide assembly problem

Jacek Błażewicz, Marcin Borowski, Piotr Formanowicz, Tomasz Głowacki (2010)

RAIRO - Operations Research

Similarity:

Determining amino acid sequences of protein molecules is one of the most important issues in molecular biology. These sequences determine protein structure and functionality. Unfortunately, direct biochemical methods for reading amino acid sequences can be used for reading short sequences only. This is the reason, which makes peptide assembly algorithms an important complement of these methods. In this paper, a genetic algorithm solving the problem of short amino acid sequence assembly...