Algorithms

71 KiB

Open AccessEditorial

Editorial: Special Issue on Algorithms for Sequence Analysis and Storage

by Veli Mäkinen

Algorithms 2014, 7(1), 186-187; https://doi.org/10.3390/a7010186 - 25 Mar 2014

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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)

507 KiB

Open AccessArticle

Pareto Optimization or Cascaded Weighted Sum: A Comparison of Concepts

by Wilfried Jakob and Christian Blume

Algorithms 2014, 7(1), 166-185; https://doi.org/10.3390/a7010166 - 21 Mar 2014

Cited by 80 | Viewed by 10457 | 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 have [...] 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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708 KiB

Open AccessArticle

The Minimum Scheduling Time for Convergecast in Wireless Sensor Networks

by Changyong Jung, Suk Jin Lee and Vijay Bhuse

Algorithms 2014, 7(1), 145-165; https://doi.org/10.3390/a7010145 - 17 Mar 2014

Cited by 6 | Viewed by 5971

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, we [...] 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

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613 KiB

Open AccessArticle

Modeling Dynamic Programming Problems over Sequences and Trees with Inverse Coupled Rewrite Systems

by Robert Giegerich and H´el'ene Touzet

Algorithms 2014, 7(1), 62-144; https://doi.org/10.3390/a7010062 - 7 Mar 2014

Cited by 13 | Viewed by 10794

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 often [...] 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)

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80 KiB

Open AccessEditorial

Acknowledgement to Reviewers of Algorithms in 2013

by Algorithms Editorial Office

Algorithms 2014, 7(1), 60-61; https://doi.org/10.3390/a7010060 - 25 Feb 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

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Open AccessArticle

Choice Function-Based Two-Sided Markets: Stability, Lattice Property, Path Independence and Algorithms

by Tamàs Fleiner and Zsuzsanna Jankó

Algorithms 2014, 7(1), 32-59; https://doi.org/10.3390/a7010032 - 14 Feb 2014

Cited by 13 | Viewed by 6171

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 if [...] 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)

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251 KiB

Open AccessArticle

Bio-Inspired Meta-Heuristics for Emergency Transportation Problems

by Min-Xia Zhang, Bei Zhang and Yu-Jun Zheng

Algorithms 2014, 7(1), 15-31; https://doi.org/10.3390/a7010015 - 11 Feb 2014

Cited by 18 | Viewed by 7258

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 algorithms [...] 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

(This article belongs to the Special Issue Novel Meta-heuristic Approaches and Their Applications to Preemptive Operational Planning and Logistics in Disaster Management)

231 KiB

Open AccessArticle

On Stable Matchings and Flows

by Tamás Fleiner

Algorithms 2014, 7(1), 1-14; https://doi.org/10.3390/a7010001 - 22 Jan 2014

Cited by 10 | Viewed by 6459

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 stable [...] 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)

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Algorithms, Volume 7, Issue 1 (March 2014) – 8 articles , Pages 1-187

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