Next Issue
Previous Issue

Table of Contents

Algorithms, Volume 6, Issue 3 (September 2013), Pages 383-590

  • Issues are regarded as officially published after their release is announced to the table of contents alert mailing list.
  • You may sign up for e-mail alerts to receive table of contents of newly released issues.
  • PDF is the official format for papers published in both, html and pdf forms. To view the papers in pdf format, click on the "PDF Full-text" link, and use the free Adobe Readerexternal link to open them.
View options order results:
result details:
Displaying articles 1-14
Export citation of selected articles as:

Editorial

Jump to: Research, Review

Open AccessEditorial Special Issue on Graph Algorithms
Algorithms 2013, 6(3), 457-458; doi:10.3390/a6030457
Received: 9 August 2013 / Revised: 9 August 2013 / Accepted: 9 August 2013 / Published: 12 August 2013
PDF Full-text (38 KB) | HTML Full-text | XML Full-text
Abstract This special issue of Algorithms is devoted to the design and analysis of algorithms for solving combinatorial problems of a theoretical or practical nature involving graphs, with a focus on computational complexity. Full article
(This article belongs to the Special Issue Graph Algorithms)

Research

Jump to: Editorial, Review

Open AccessArticle Maximum Locally Stable Matchings
Algorithms 2013, 6(3), 383-395; doi:10.3390/a6030383
Received: 4 January 2013 / Revised: 2 June 2013 / Accepted: 4 June 2013 / Published: 24 June 2013
Cited by 2 | PDF Full-text (187 KB) | HTML Full-text | XML Full-text
Abstract
Motivated by the observation that most companies are more likely to consider job applicants referred by their employees than those who applied on their own, Arcaute and Vassilvitskii modeled a job market that integrates social networks into stable matchings in an interesting way.
[...] Read more.
Motivated by the observation that most companies are more likely to consider job applicants referred by their employees than those who applied on their own, Arcaute and Vassilvitskii modeled a job market that integrates social networks into stable matchings in an interesting way. We call their model HR+SN because an instance of their model is an ordered pair (I, G) where I is a typical instance of the Hospital/Residents problem (HR) and G is a graph that describes the social network (SN) of the residents in I. A matching p, of hospitals and residents has a local blocking pair (h, r) if (h, r) is a blocking pair of ii, and there is a resident r' such that r' is simultaneously an employee of h in the matching and a neighbor of r in G. Such a pair is likely to compromise the matching because the participants have access to each other through r': r can give her resume to r' who can then forward it to h. A locally stable matching is a matching with no local blocking pairs. The cardinality of the locally stable matchings of I can vary. This paper presents a variety of results on computing a locally stable matching with maximum cardinality. Full article
(This article belongs to the Special Issue Special Issue on Matching under Preferences)
Open AccessArticle New Heuristics for Rooted Triplet Consistency
Algorithms 2013, 6(3), 396-406; doi:10.3390/a6030396
Received: 14 April 2013 / Revised: 26 June 2013 / Accepted: 26 June 2013 / Published: 11 July 2013
Cited by 2 | PDF Full-text (222 KB)
Abstract
Rooted triplets are becoming one of the most important types of input for reconstructing rooted phylogenies. A rooted triplet is a phylogenetic tree on three leaves and shows the evolutionary relationship of the corresponding three species. In this paper, we investigate the problem
[...] Read more.
Rooted triplets are becoming one of the most important types of input for reconstructing rooted phylogenies. A rooted triplet is a phylogenetic tree on three leaves and shows the evolutionary relationship of the corresponding three species. In this paper, we investigate the problem of inferring the maximum consensus evolutionary tree from a set of rooted triplets. This problem is known to be APX-hard. We present two new heuristic algorithms. For a given set of m triplets on n species, the FastTree algorithm runs in O(m + α(n)n2) time, where α(n) is the functional inverse of Ackermann’s function. This is faster than any other previously known algorithms, although the outcome is less satisfactory. The Best Pair Merge with Total Reconstruction (BPMTR) algorithm runs in O(mn3) time and, on average, performs better than any other previously known algorithms for this problem. Full article
(This article belongs to the Special Issue Graph Algorithms)
Open AccessArticle Noise Reduction for Nonlinear Nonstationary Time Series Data using Averaging Intrinsic Mode Function
Algorithms 2013, 6(3), 407-429; doi:10.3390/a6030407
Received: 28 May 2013 / Revised: 13 June 2013 / Accepted: 4 July 2013 / Published: 19 July 2013
Cited by 3 | PDF Full-text (1140 KB) | HTML Full-text | XML Full-text
Abstract
A novel noise filtering algorithm based on averaging Intrinsic Mode Function (aIMF), which is a derivation of Empirical Mode Decomposition (EMD), is proposed to remove white-Gaussian noise of foreign currency exchange rates that are nonlinear nonstationary times series signals. Noise patterns with different
[...] Read more.
A novel noise filtering algorithm based on averaging Intrinsic Mode Function (aIMF), which is a derivation of Empirical Mode Decomposition (EMD), is proposed to remove white-Gaussian noise of foreign currency exchange rates that are nonlinear nonstationary times series signals. Noise patterns with different amplitudes and frequencies were randomly mixed into the five exchange rates. A number of filters, namely; Extended Kalman Filter (EKF), Wavelet Transform (WT), Particle Filter (PF) and the averaging Intrinsic Mode Function (aIMF) algorithm were used to compare filtering and smoothing performance. The aIMF algorithm demonstrated high noise reduction among the performance of these filters. Full article
Open AccessArticle Efficient in silico Chromosomal Representation of Populations via Indexing Ancestral Genomes
Algorithms 2013, 6(3), 430-441; doi:10.3390/a6030430
Received: 18 March 2013 / Revised: 18 July 2013 / Accepted: 23 July 2013 / Published: 30 July 2013
Cited by 5 | PDF Full-text (165 KB) | HTML Full-text | XML Full-text
Abstract
One of the major challenges in handling realistic forward simulations for plant and animal breeding is the sheer number of markers. Due to advancing technologies, the requirement has quickly grown from hundreds of markers to millions. Most simulators are lagging behind in handling
[...] Read more.
One of the major challenges in handling realistic forward simulations for plant and animal breeding is the sheer number of markers. Due to advancing technologies, the requirement has quickly grown from hundreds of markers to millions. Most simulators are lagging behind in handling these sizes, since they do not scale well. We present a scheme for representing and manipulating such realistic size genomes, without any loss of information. Usually, the simulation is forward and over tens to hundreds of generations with hundreds of thousands of individuals at each generation. We demonstrate through simulations that our representation can be two orders of magnitude faster and handle at least two orders of magnitude more markers than existing software on realistic breeding scenarios. Full article
(This article belongs to the Special Issue Algorithms for Sequence Analysis and Storage)
Open AccessArticle Ubiquitous Integrity via Network Integration and Parallelism—Sustaining Pedestrian/Bike Urbanism
Algorithms 2013, 6(3), 459-470; doi:10.3390/a6030459
Received: 12 April 2013 / Revised: 12 July 2013 / Accepted: 5 August 2013 / Published: 12 August 2013
Cited by 2 | PDF Full-text (776 KB) | HTML Full-text | XML Full-text
Abstract
Nowadays, due to the concern regarding environmental issues, establishing pedestrian/bike friendly urbanism is widely encouraged. To promote safety-assured, mobile communication environments, efficient, reliable maintenance, and information integrity need to be designed, especially in highly possibly interfered places. For busy traffic areas, regular degree-3
[...] Read more.
Nowadays, due to the concern regarding environmental issues, establishing pedestrian/bike friendly urbanism is widely encouraged. To promote safety-assured, mobile communication environments, efficient, reliable maintenance, and information integrity need to be designed, especially in highly possibly interfered places. For busy traffic areas, regular degree-3 dedicated short range communication (DSRC) networks are safety and information featured with availability, reliability, and maintainability in paths of multi-lanes. For sparsely populated areas, probes of wireless sensors are rational, especially if sensor nodes can be organized to enhance security, reliability, and flexibility. Applying alternative network topologies, such as spider-webs, generalized honeycomb tori, and cube-connected cycles, for comparing and analyzing is proposed in DSRC and cellular communications to enhance integrity in communications. Full article
Open AccessArticle Linear Time Local Approximation Algorithm for Maximum Stable Marriage
Algorithms 2013, 6(3), 471-484; doi:10.3390/a6030471
Received: 1 August 2013 / Revised: 6 August 2013 / Accepted: 7 August 2013 / Published: 15 August 2013
Cited by 7 | PDF Full-text (103 KB) | HTML Full-text | XML Full-text
Abstract
We consider a two-sided market under incomplete preference lists with ties, where the goal is to find a maximum size stable matching. The problem is APX-hard, and a 3/2-approximation was given by McDermid [1]. This algorithm has a non-linear running time, and, more
[...] Read more.
We consider a two-sided market under incomplete preference lists with ties, where the goal is to find a maximum size stable matching. The problem is APX-hard, and a 3/2-approximation was given by McDermid [1]. This algorithm has a non-linear running time, and, more importantly needs global knowledge of all preference lists. We present a very natural, economically reasonable, local, linear time algorithm with the same ratio, using some ideas of Paluch [2]. In this algorithm every person make decisions using only their own list, and some information asked from members of these lists (as in the case of the famous algorithm of Gale and Shapley). Some consequences to the Hospitals/Residents problem are also discussed. Full article
(This article belongs to the Special Issue Special Issue on Matching under Preferences)
Open AccessArticle A Simple Algorithm for Solving for the Generalized Longest Common Subsequence (LCS) Problem with a Substring Exclusion Constraint
Algorithms 2013, 6(3), 485-493; doi:10.3390/a6030485
Received: 14 June 2013 / Revised: 15 July 2013 / Accepted: 24 July 2013 / Published: 15 August 2013
PDF Full-text (164 KB) | HTML Full-text | XML Full-text
Abstract
This paper studies the string-excluding (STR-EC)-constrained longest common subsequence (LCS) problem, a generalized LCS problem. For the two input sequences, X and Y , of lengths n andmand a constraint string, P, of length r, the goal is to find the longest common
[...] Read more.
This paper studies the string-excluding (STR-EC)-constrained longest common subsequence (LCS) problem, a generalized LCS problem. For the two input sequences, X and Y , of lengths n andmand a constraint string, P, of length r, the goal is to find the longest common subsequence, Z, of X and Y that excludes P as a substring. The problem and its solution were first proposed by Chen and Chao, but we found that their algorithm cannot solve the problem correctly. A new dynamic programming solution for the STR-EC-LCS problem is then presented in this paper, and the correctness of the new algorithm is proven. The time complexity of the new algorithm is O(nmr). Full article
Open AccessArticle An Algorithm for Managing Aircraft Movement on an Airport Surface
Algorithms 2013, 6(3), 494-511; doi:10.3390/a6030494
Received: 8 June 2013 / Revised: 9 August 2013 / Accepted: 12 August 2013 / Published: 16 August 2013
Cited by 2 | PDF Full-text (714 KB) | HTML Full-text | XML Full-text
Abstract
The present paper focuses on the development of an algorithm for safely and optimally managing the routing of aircraft on an airport surface in future airport operations. This tool is intended to support air traffic controllers’ decision-making in selecting the paths of all
[...] Read more.
The present paper focuses on the development of an algorithm for safely and optimally managing the routing of aircraft on an airport surface in future airport operations. This tool is intended to support air traffic controllers’ decision-making in selecting the paths of all aircraft and the engine startup approval time for departing ones. Optimal routes are sought for minimizing the time both arriving and departing aircraft spend on an airport surface with engines on, with benefits in terms of safety, efficiency and costs. The proposed algorithm first computes a standalone, shortest path solution from runway to apron or vice versa, depending on the aircraft being inbound or outbound, respectively. For taking into account the constraints due to other traffic on an airport surface, this solution is amended by a conflict detection and resolution task that attempts to reduce and possibly nullify the number of conflicts generated in the first phase. An example application on a simple Italian airport exemplifies how the algorithm can be applied to true-world applications. Emphasis is given on how to model an airport surface as a weighted and directed graph with non-negative weights, as required for the input to the algorithm. Full article
Open AccessArticle Extraction and Segmentation of Sputum Cells for Lung Cancer Early Diagnosis
Algorithms 2013, 6(3), 512-531; doi:10.3390/a6030512
Received: 12 November 2012 / Revised: 14 August 2013 / Accepted: 15 August 2013 / Published: 21 August 2013
Cited by 8 | PDF Full-text (725 KB) | HTML Full-text | XML Full-text
Abstract
Lung cancer has been the largest cause of cancer deaths worldwide with an overall 5-year survival rate of only 15%. Its symptoms can be found exclusively in advanced stages where the chances for patients to survive are very low, thus making the mortality
[...] Read more.
Lung cancer has been the largest cause of cancer deaths worldwide with an overall 5-year survival rate of only 15%. Its symptoms can be found exclusively in advanced stages where the chances for patients to survive are very low, thus making the mortality rate the highest among all other types of cancer. The present work deals with the attempt to design computer-aided detection or diagnosis (CAD) systems for early detection of lung cancer based on the analysis of sputum color images. The aim is to reduce the false negative rate and to increase the true positive rate as much as possible. The early detection of lung cancer from sputum images is a challenging problem, due to both the structure of the cancer cells and the stained method which are employed in the formulation of the sputum cells. We present here a framework for the extraction and segmentation of sputum cells in sputum images using, respectively, a threshold classifier, a Bayesian classification and mean shift segmentation. Our methods are validated and compared with other competitive techniques via a series of experimentation conducted with a data set of 100 images. The extraction and segmentation results will be used as a base for a CAD system for early detection of lung cancer which will improve the chances of survival for the patient. Full article
(This article belongs to the Special Issue Machine Learning for Medical Imaging 2012)
Open AccessArticle Stable Flows over Time
Algorithms 2013, 6(3), 532-545; doi:10.3390/a6030532
Received: 31 December 2012 / Revised: 27 July 2013 / Accepted: 9 August 2013 / Published: 21 August 2013
Cited by 1 | PDF Full-text (223 KB) | HTML Full-text | XML Full-text
Abstract
In this paper, the notion of stability is extended to network flows over time. As a useful device in our proofs, we present an elegant preflow-push variant of the Gale-Shapley algorithm that operates directly on the given network and computes stable flows in
[...] Read more.
In this paper, the notion of stability is extended to network flows over time. As a useful device in our proofs, we present an elegant preflow-push variant of the Gale-Shapley algorithm that operates directly on the given network and computes stable flows in pseudo-polynomial time, both in the static flow and the flow over time case. We show periodical properties of stable flows over time on networks with an infinite time horizon. Finally, we discuss the influence of storage at vertices, with different results depending on the priority of the corresponding holdover edges. Full article
(This article belongs to the Special Issue Special Issue on Matching under Preferences)
Open AccessArticle Quantitative Trait Loci Mapping Problem: An Extinction-Based Multi-Objective Evolutionary Algorithm Approach
Algorithms 2013, 6(3), 546-564; doi:10.3390/a6030546
Received: 28 May 2013 / Revised: 9 August 2013 / Accepted: 26 August 2013 / Published: 2 September 2013
Cited by 7 | PDF Full-text (424 KB) | HTML Full-text | XML Full-text
Abstract
The Quantitative Trait Loci (QTL) mapping problem aims to identify regions in the genome that are linked to phenotypic features of the developed organism that vary in degree. It is a principle step in determining targets for further genetic analysis and is key
[...] Read more.
The Quantitative Trait Loci (QTL) mapping problem aims to identify regions in the genome that are linked to phenotypic features of the developed organism that vary in degree. It is a principle step in determining targets for further genetic analysis and is key in decoding the role of specific genes that control quantitative traits within species. Applications include identifying genetic causes of disease, optimization of cross-breeding for desired traits and understanding trait diversity in populations. In this paper a new multi-objective evolutionary algorithm (MOEA) method is introduced and is shown to increase the accuracy of QTL mapping identification for both independent and epistatic loci interactions. The MOEA method optimizes over the space of possible partial least squares (PLS) regression QTL models and considers the conflicting objectives of model simplicity versus model accuracy. By optimizing for minimal model complexity, MOEA has the advantage of solving the over-fitting problem of conventional PLS models. The effectiveness of the method is confirmed by comparing the new method with Bayesian Interval Mapping approaches over a series of test cases where the optimal solutions are known. This approach can be applied to many problems that arise in analysis of genomic data sets where the number of features far exceeds the number of observations and where features can be highly correlated. Full article
Open AccessArticle An Emergent Approach to Text Analysis Based on a Connectionist Model and the Web
Algorithms 2013, 6(3), 565-590; doi:10.3390/a6030565
Received: 5 August 2013 / Revised: 5 September 2013 / Accepted: 10 September 2013 / Published: 17 September 2013
PDF Full-text (899 KB) | HTML Full-text | XML Full-text
Abstract
In this paper, we present a method to provide proactive assistance in text checking, based on usage relationships between words structuralized on the Web. For a given sentence, the method builds a connectionist structure of relationships between word n-grams. Such structure is
[...] Read more.
In this paper, we present a method to provide proactive assistance in text checking, based on usage relationships between words structuralized on the Web. For a given sentence, the method builds a connectionist structure of relationships between word n-grams. Such structure is then parameterized by means of an unsupervised and language agnostic optimization process. Finally, the method provides a representation of the sentence that allows emerging the least prominent usage-based relational patterns, helping to easily find badly-written and unpopular text. The study includes the problem statement and its characterization in the literature, as well as the proposed solving approach and some experimental use. Full article

Review

Jump to: Editorial, Research

Open AccessReview A Review of Routing Protocols Based on Ant-Like Mobile Agents
Algorithms 2013, 6(3), 442-456; doi:10.3390/a6030442
Received: 17 June 2013 / Revised: 15 July 2013 / Accepted: 31 July 2013 / Published: 6 August 2013
Cited by 5 | PDF Full-text (239 KB) | HTML Full-text | XML Full-text
Abstract
A survey on the routing protocols based on ant-like mobile agents is given. These protocols are often employed in Mobile Ad Hoc Networks (MANET). Mobile Ad Hoc Networks are collections of wireless mobile nodes such as PDAs, laptop computers, and cellular phones having
[...] Read more.
A survey on the routing protocols based on ant-like mobile agents is given. These protocols are often employed in Mobile Ad Hoc Networks (MANET). Mobile Ad Hoc Networks are collections of wireless mobile nodes such as PDAs, laptop computers, and cellular phones having wireless communication capability that dynamically form a temporary network without using any existing network infrastructures such as wireless access points. The only infrastructure in MANET is the wireless communication interfaces on the devices. In such a circumstance, where some of the wireless devices are not within wireless range of each other, multi-hop routing is required to transmit messages to the destination. A node that wants to start communication with other nodes that are not within its one-hop wireless transmission range has to request intermediate nodes to forward their communication packets to the destination. In this paper, we survey a variety of proposed network protocols to accommodate this situation. We focus especially on biologically-inspired routing algorithms that are based on the ant colony optimization algorithm. Full article
(This article belongs to the Special Issue Bio-inspired Algorithms for Combinatorial Problems)

Journal Contact

MDPI AG
Algorithms Editorial Office
St. Alban-Anlage 66, 4052 Basel, Switzerland
algorithms@mdpi.com
Tel. +41 61 683 77 34
Fax: +41 61 302 89 18
Editorial Board
Contact Details Submit to Algorithms
Back to Top