Contaminant oligonucleotide sequences such as primers and adapters can occur in both ends of high-throughput sequencing (HTS) reads. ALIENTRIMMER was developed in order to detect and remove such contaminants. Based on...
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Contaminant oligonucleotide sequences such as primers and adapters can occur in both ends of high-throughput sequencing (HTS) reads. ALIENTRIMMER was developed in order to detect and remove such contaminants. Based on the decomposition of specified alien nucleotide sequences into k-mers, ALIENTRIMMER is able to determine whether such alien k-mers are occurring in one or in both read ends by using a simple polynomial algorithm. Therefore, ALIENTRIMMER can process typical HTS single- or paired-end files with millions of reads in several minutes with very low computer resources. Based on the analysis of both simulated and real-case Illumina(R), 454(TM) and Ion Torrent(TM) read data, we show that ALIENTRIMMER performs with excellent accuracy and speed in comparison with other trimming tools. The program is freely available at ftp://***/pub/gensoft/projects/AlienTrimmer/. (C) 2013 Elsevier Inc. All rights reserved.
This paper extends the classical dynamic lot sizing model to the case with carbon emission and multi-mode production. Production activities generate emission and an emission cap is given for each period. The manufactu...
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ISBN:
(纸本)9781467352000;9781467351980
This paper extends the classical dynamic lot sizing model to the case with carbon emission and multi-mode production. Production activities generate emission and an emission cap is given for each period. The manufacturer is equipped with more than one mode for production. If a mode is less costly for producing one unit of product, it however yields more emission. As a consequence, the maximum production quantity in each period depends on the production mode selected and the emission cap. The model proposed in this paper represents applications in which the production is emission-dependent and constrained by the government-imposed emission regulation. Furthermore, with multi-mode production and emission regulation, emission abatement may be prompted through technological innovation and optimization of production planning. Compared with classical production planning problems, the problem considered here is challenging due to the emission constraint (therefore cumulative production capacity) and the multiple production modes (therefore multiple setup cost structures). In this paper, we present a general property of optimal solutions. Then, we consider a special but practical case involving two production modes. The practicalness stems from the fact that few manufacturers are equipped with more than two technologies, because of the heavy investment required for a new technology. We first prove some properties of optimal solutions. As a consequence, we can focus on solutions with these properties. This enables us to develop a polynomial dynamic programming algorithm to solve the model into optimality.
A word w is a fixed point of a nontrivial morphism h if w = h(w) and h is not the identity on the alphabet of w. The paper presents the first polynomial algorithm deciding whether a given finite word is such a fixed p...
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A word w is a fixed point of a nontrivial morphism h if w = h(w) and h is not the identity on the alphabet of w. The paper presents the first polynomial algorithm deciding whether a given finite word is such a fixed point. The algorithm also constructs the corresponding morphism, which has the smallest possible number of non-erased letters. (C) 2009 Elsevier B.V. All rights reserved.
Attention has been paid mostly to the new deterministic algorithm for primality testing AKS recently. However, probabilistic algorithms remain an efficient tool for primality testing. Our thesis focuses mostly on two ...
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Attention has been paid mostly to the new deterministic algorithm for primality testing AKS recently. However, probabilistic algorithms remain an efficient tool for primality testing. Our thesis focuses mostly on two most well-known probabilistic algorithms for primality testing. It describes the main idea and gives proofs of correctness of Solovay-Strassen and Rabin-Miller algorithms. Apart from that, it also tries to look at the subject of probabilistic algorithms from a wider perspective. It presents a definition of a probabilistic algorithm and various complexity classes that correspond to Monte Carlo or Las Vegas algorithms. Besides pure mathematical theory, we mention also some philosophical aspects that need to be considered when we decide to use the probabilistic method. Powered by TCPDF (***)
Let G = (V, E) be an undirected graph in which every vertex v. V is assigned a nonnegative integer w(v). A w- packing is a collection P of cycles (repetition allowed) in G such that every v. V is contained at most w(v...
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Let G = (V, E) be an undirected graph in which every vertex v. V is assigned a nonnegative integer w(v). A w- packing is a collection P of cycles (repetition allowed) in G such that every v. V is contained at most w(v) times by the members of P. Let < w > = 2|V | + Sigma(v is an element of V)[log(w(v)+ 1)] denote the binary encoding length (input size) of the vector (w(v): v is an element of V)(T). We present an efficient algorithm which finds in O(|V|(8) < w >(2) + |V|(14)) time a w- packing of maximum cardinality in G provided packing and covering cycles inGsatisfy the Z(+)-max-flow min-cut property.
The basic scheduling problem we are dealing with in this paper is the following one. A set of jobs has to be scheduled on a set of parallel uniform machines. Each machine can handle at most one job at a time. Each job...
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The basic scheduling problem we are dealing with in this paper is the following one. A set of jobs has to be scheduled on a set of parallel uniform machines. Each machine can handle at most one job at a time. Each job becomes available for processing at its release date. All jobs have the same execution requirement and arbitrary due dates. Each machine has a known speed. The processing of any job may be interrupted arbitrarily often and resumed later on any machine. The goal is to find a schedule that minimizes the sum of tardiness, i.e., we consider problem Q vertical bar r(j), p(j) = p, pmtn vertical bar Sigma T-j whose complexity status was open. Recently, Tian et al. (J. Sched. 9: 343-364, 2006) proposed a polynomial algorithm for problem 1 vertical bar r(j), p(j) = p, pmtn vertical bar Sigma T-j. We show that both the problem P vertical bar pmtn vertical bar Sigma T-j of minimizing total tardiness on a set of parallel machines with allowed preemptions and the problem P vertical bar r(j), p(j) = p, pmtn vertical bar Sigma T-j of minimizing total tardiness on a set of parallel machines with release dates, equal processing times and allowed preemptions are NP-hard. Moreover, we give a polynomial algorithm for the case of uniform machines without release dates, i.e., for problem Q vertical bar pj = p, pmtn vertical bar Sigma T-j.
We consider the problem of preemptive scheduling n jobs on two uniform parallel machines. All jobs have equal processing requirements. For each job we are given its due date. The objective is to find a schedule minimi...
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We consider the problem of preemptive scheduling n jobs on two uniform parallel machines. All jobs have equal processing requirements. For each job we are given its due date. The objective is to find a schedule minimizing total tardiness Sigma T-i. We suggest an O(n log n) algorithm to solve this problem. (C) 2011 Elsevier B.V. All rights reserved.
We consider the problem of optimally scheduling the restoration of edges of a transportation network destroyed/damaged by a disaster. The restoration is performed by service units (servers) which have fixed restoratio...
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We consider the problem of optimally scheduling the restoration of edges of a transportation network destroyed/damaged by a disaster. The restoration is performed by service units (servers) which have fixed restoration speeds. If several servers work simultaneously at the same point of the network, their collective restoration speed is the sum of their individual restoration speeds. The servers are initially located at some nodes. Each server can travel within the already restored part of the network with infinite speed, that is, at any time can immediately relocate to another point of the same connected component of the already restored part of the network. It is required to minimize a scheduling objective that can be expressed as the maximum or the sum of nondecreasing functions of the recovery times of the nodes, where the recovery time of a node is the time when the node is reached for the first time by a server. We present polynomial-time algorithms on path networks for problems with fixed initial locations of the servers. For problems with flexible locations that should also be optimized, we present polynomial-time algorithms for the case of equal restoration speeds of the servers, and prove that the problems are strongly NP-hard if the restoration speeds of the servers can be different. (C) 2012 Elsevier B.V. All rights reserved.
In this paper, we analyze some single machine scheduling problems with the aging effect. We extend the sum-of-processing-time-based aging model such that the fatigue caused by each job to the machine is equal to a non...
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In this paper, we analyze some single machine scheduling problems with the aging effect. We extend the sum-of-processing-time-based aging model such that the fatigue caused by each job to the machine is equal to a non-increasing function dependent on the normal processing time of a job and the aging effect is job dependent. Although the proposed model is more general and describes more precisely the real-life settings, we show that the special cases of the maximum completion time and the maximum lateness minimization problems with this model are still polynomially solvable. However, we prove the maximum completion time minimization problem with the sum-of-processing-time-based aging model is strongly NP-hard if some jobs have deadlines and constant processing times. On this basis, we show that the maximum lateness minimization problem with this aging model is also strongly NP-hard.
The well-known spanning tree packing theorem of Nash-Williams and Tutte characterizes graphs with k edge-disjoint spanning trees. Edmonds generalizes this theorem to matroids with k disjoint bases. For any graph G tha...
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The well-known spanning tree packing theorem of Nash-Williams and Tutte characterizes graphs with k edge-disjoint spanning trees. Edmonds generalizes this theorem to matroids with k disjoint bases. For any graph G that may not have k-edge-disjoint spanning trees, the problem of determining what edges should be added to G so that the resulting graph has k edge-disjoint spanning trees has been studied by Haas (2002) [11] and Liu et al. (2009) [17], among others. This paper aims to determine, for a matroid M that has k disjoint bases, the set E-k(M) of elements in M such that for any e is an element of E-k(M), M-e also has k disjoint bases. Using the matroid strength defined by Catlin et al. (1992) [4], we present a characterization of E-k(M) in terms of the strength of M. Consequently, this yields a characterization of edge sets E-k(G) in a graph G with at least k edge-disjoint spanning trees such that for all e is an element of E-k(G), G-e also has k edge-disjoint spanning trees. polynomial algorithms are also discussed for identifying the set E-k(M) in a matroid M, or the edge subset E-k(G) for a connected graph G. (C) 2012 Published by Elsevier B.V.
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