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Algorithms, Volume 7, Issue 1 (March 2014), Pages 1-187

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Editorial

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Open AccessEditorial Acknowledgement to Reviewers of Algorithms in 2013
Algorithms 2014, 7(1), 60-61; doi:10.3390/a7010060
Received: 25 February 2014 / Accepted: 25 February 2014 / Published: 25 February 2014
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Abstract The editors of Algorithms would like to express their sincere gratitude to the following reviewers for assessing manuscripts in 2013. [...] Full article
Open AccessEditorial Editorial: Special Issue on Algorithms for Sequence Analysis and Storage
Algorithms 2014, 7(1), 186-187; doi:10.3390/a7010186
Received: 14 March 2014 / Revised: 19 March 2014 / Accepted: 19 March 2014 / Published: 25 March 2014
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Abstract This special issue of Algorithms is dedicated to approaches to biological sequence analysis that have algorithmic novelty and potential for fundamental impact in methods used for genome research. Full article
(This article belongs to the Special Issue Algorithms for Sequence Analysis and Storage)

Research

Jump to: Editorial

Open AccessArticle On Stable Matchings and Flows
Algorithms 2014, 7(1), 1-14; doi:10.3390/a7010001
Received: 1 August 2013 / Revised: 9 January 2014 / Accepted: 10 January 2014 / Published: 22 January 2014
Cited by 2 | PDF Full-text (231 KB) | HTML Full-text | XML Full-text
Abstract
We describe a flow model related to ordinary network flows the same way as stable matchings are related to maximum matchings in bipartite graphs. We prove that there always exists a stable flow and generalize the lattice structure of stable marriages to [...] Read more.
We describe a flow model related to ordinary network flows the same way as stable matchings are related to maximum matchings in bipartite graphs. We prove that there always exists a stable flow and generalize the lattice structure of stable marriages to stable flows. Our main tool is a straightforward reduction of the stable flow problem to stable allocations. For the sake of completeness, we prove the results we need on stable allocations as an application of Tarski’s fixed point theorem. Full article
(This article belongs to the Special Issue Special Issue on Matching under Preferences)
Open AccessArticle Bio-Inspired Meta-Heuristics for Emergency Transportation Problems
Algorithms 2014, 7(1), 15-31; doi:10.3390/a7010015
Received: 4 December 2013 / Revised: 28 January 2014 / Accepted: 30 January 2014 / Published: 11 February 2014
Cited by 8 | PDF Full-text (251 KB) | HTML Full-text | XML Full-text
Abstract
Emergency transportation plays a vital role in the success of disaster rescue and relief operations, but its planning and scheduling often involve complex objectives and search spaces. In this paper, we conduct a survey of recent advances in bio-inspired meta-heuristics, including genetic [...] Read more.
Emergency transportation plays a vital role in the success of disaster rescue and relief operations, but its planning and scheduling often involve complex objectives and search spaces. In this paper, we conduct a survey of recent advances in bio-inspired meta-heuristics, including genetic algorithms (GA), particle swarm optimization (PSO), ant colony optimization (ACO), etc., for solving emergency transportation problems. We then propose a new hybrid biogeography-based optimization (BBO) algorithm, which outperforms some state-of-the-art heuristics on a typical transportation planning problem. Full article
Open AccessArticle Choice Function-Based Two-Sided Markets: Stability, Lattice Property, Path Independence and Algorithms
Algorithms 2014, 7(1), 32-59; doi:10.3390/a7010032
Received: 23 June 2013 / Revised: 29 December 2013 / Accepted: 18 January 2014 / Published: 14 February 2014
Cited by 2 | PDF Full-text (312 KB) | HTML Full-text | XML Full-text
Abstract
We build an abstract model, closely related to the stable marriage problem and motivated by Hungarian college admissions. We study different stability notions and show that an extension of the lattice property of stable marriages holds in these more general settings, even [...] Read more.
We build an abstract model, closely related to the stable marriage problem and motivated by Hungarian college admissions. We study different stability notions and show that an extension of the lattice property of stable marriages holds in these more general settings, even if the choice function on one side is not path independent. We lean on Tarski’s fixed point theorem and the substitutability property of choice functions. The main virtue of the work is that it exhibits practical, interesting examples, where non-path independent choice functions play a role, and proves various stability-related results. Full article
(This article belongs to the Special Issue Special Issue on Matching under Preferences)
Open AccessArticle Modeling Dynamic Programming Problems over Sequences and Trees with Inverse Coupled Rewrite Systems
Algorithms 2014, 7(1), 62-144; doi:10.3390/a7010062
Received: 19 March 2013 / Revised: 6 February 2014 / Accepted: 14 February 2014 / Published: 7 March 2014
Cited by 6 | PDF Full-text (613 KB)
Abstract
Dynamic programming is a classical algorithmic paradigm, which often allows the evaluation of a search space of exponential size in polynomial time. Recursive problem decomposition, tabulation of intermediate results for re-use, and Bellman’s Principle of Optimality are its well-understood ingredients. However, algorithms [...] Read more.
Dynamic programming is a classical algorithmic paradigm, which often allows the evaluation of a search space of exponential size in polynomial time. Recursive problem decomposition, tabulation of intermediate results for re-use, and Bellman’s Principle of Optimality are its well-understood ingredients. However, algorithms often lack abstraction and are difficult to implement, tedious to debug, and delicate to modify. The present article proposes a generic framework for specifying dynamic programming problems. This framework can handle all kinds of sequential inputs, as well as tree-structured data. Biosequence analysis, document processing, molecular structure analysis, comparison of objects assembled in a hierarchic fashion, and generally, all domains come under consideration where strings and ordered, rooted trees serve as natural data representations. The new approach introduces inverse coupled rewrite systems. They describe the solutions of combinatorial optimization problems as the inverse image of a term rewrite relation that reduces problem solutions to problem inputs. This specification leads to concise yet translucent specifications of dynamic programming algorithms. Their actual implementation may be challenging, but eventually, as we hope, it can be produced automatically. The present article demonstrates the scope of this new approach by describing a diverse set of dynamic programming problems which arise in the domain of computational biology, with examples in biosequence and molecular structure analysis. Full article
(This article belongs to the Special Issue Algorithms for Sequence Analysis and Storage)
Open AccessArticle The Minimum Scheduling Time for Convergecast in Wireless Sensor Networks
Algorithms 2014, 7(1), 145-165; doi:10.3390/a7010145
Received: 11 November 2013 / Revised: 25 February 2014 / Accepted: 25 February 2014 / Published: 17 March 2014
Cited by 3 | PDF Full-text (708 KB) | HTML Full-text | XML Full-text
Abstract
We study the scheduling problem for data collection from sensor nodes to the sink node in wireless sensor networks, also referred to as the convergecast problem. The convergecast problem in general network topology has been proven to be NP-hard. In this paper, [...] Read more.
We study the scheduling problem for data collection from sensor nodes to the sink node in wireless sensor networks, also referred to as the convergecast problem. The convergecast problem in general network topology has been proven to be NP-hard. In this paper, we propose our heuristic algorithm (finding the minimum scheduling time for convergecast (FMSTC)) for general network topology and evaluate the performance by simulation. The results of the simulation showed that the number of time slots to reach the sink node decreased with an increase in the power. We compared the performance of the proposed algorithm to the optimal time slots in a linear network topology. The proposed algorithm for convergecast in a general network topology has 2.27 times more time slots than that of a linear network topology. To the best of our knowledge, the proposed method is the first attempt to apply the optimal algorithm in a linear network topology to a general network topology. Full article
Open AccessArticle Pareto Optimization or Cascaded Weighted Sum: A Comparison of Concepts
Algorithms 2014, 7(1), 166-185; doi:10.3390/a7010166
Received: 22 January 2014 / Revised: 3 March 2014 / Accepted: 14 March 2014 / Published: 21 March 2014
Cited by 1 | PDF Full-text (507 KB) | HTML Full-text | XML Full-text | Correction
Abstract
Looking at articles or conference papers published since the turn of the century, Pareto optimization is the dominating assessment method for multi-objective nonlinear optimization problems. However, is it always the method of choice for real-world applications, where either more than four objectives [...] Read more.
Looking at articles or conference papers published since the turn of the century, Pareto optimization is the dominating assessment method for multi-objective nonlinear optimization problems. However, is it always the method of choice for real-world applications, where either more than four objectives have to be considered, or the same type of task is repeated again and again with only minor modifications, in an automated optimization or planning process? This paper presents a classification of application scenarios and compares the Pareto approach with an extended version of the weighted sum, called cascaded weighted sum, for the different scenarios. Its range of application within the field of multi-objective optimization is discussed as well as its strengths and weaknesses. Full article

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