26295637
A Linear-Time Algorithm for Computing Translocation Distance between Signed Genomes
The study of evolution based on rearrangements leads to a rearrangement distance problem, i.e., computing the minimum number of rearrangement events required to transform one geonome to another. In this paper we study the translocation distance problem, modeling the evolution of genomes by translocations. We present a linear-time algorithm for computing the translocation distance between signed genomes in this paper, improving a previous O(n 3) bound by Hannenhalli in 1996.
40174055
A PTAS for Distinguishing (Sub)string Selection
Consider two sets of strings, B (bad genes) and G (good genes), as well as two integers db and dg (db ? dg). A frequently occurring problem in computational biology (andother fields) is to finda (distinguishing) substring s of length L that distinguishes the bad strings from goodstrings, i.e., for each string si ? B there exists a length-L substring ti of si with d(s, ti) ? db (close to badstrings) andfor every substring ui of length L of every string gi ? G, d(s, ui) ? dg (far from goodstrings). We present a polynomial time approximation scheme to settle the problem, i.e., for any constant ? > 0, the algorithm finds a string s of length L such that for every si ? B, there is a length-L substring ti of si with d(ti, s) ? (1+?)db and for every substring ui of length L of every gi ? G, d(ui, s) ? (1 - ?)dg, if a solution to the original pair (db ? dg) exists.
37978882
Hamiltonian cycles in 3-connected Claw-free graphs
It is shown that every 3-connected claw-free graph having at most 6δ - 7 vertices is hamiltonian, where δ is the minimum degree.
7451094
Orthogonal (g, f)-factorizations in networks
Let G = (V,E) be a graph and let g and f be two integer-valued functions defined on V such that k ≤ g(x) ≤ f(x) for all x ∈ V . Let H1,H2, · · · ,Hk be subgraphs of G such that |E(Hi)| = m, 1 ≤ i ≤ k, and V (Hi) ∩ V (Hj) = ∅ when i 6= j. In this paper it is proved that every (mg + m − 1,mf −m + 1)-graph G has a (g, f)-factorization orthogonal to Hi for i = 1, 2, · · · , k and shown that there are polynomial-time algorithms to find the desired (g, f)-factorizations.
1876314
A 2-Approximation Algorithm for Path Coloring on Trees of Rings
A tree of rings is an undirected graph obtained from a tree by replacing each node of the tree with a cycle and then contracting the edges of the tree so that two cycles corresponding to the two end-nodes of any edge have precisely one node in common. Given a set of paths on a tree of rings, the routing problem is to color the paths with the smallest number of colors so that any two paths sharing an edge are assigned different colors. We present a 2-approximation algorithm in this paper.
9766004
A PTAS for Minimizing Total Completion Time of Bounded Batch Scheduling
We consider a batch processing system {pi : i = 1, 2,..., n} where pi is the processing time of job i, and up to B jobs can be processed together such that the handling time of a batch is the longest processing time among jobs in the batch. The number of job types m is not fixed and all the jobs are released at the same time. Jobs are executed nonpreemptively. Our objective is to assign jobs to batches and sequence the batches so as to minimize the total completion time. The best previously known result is a 2-approximation algorithm due to D. S. Hochbaum and D. Landy [6]. In this paper, we establish the first polynomial time approximation scheme (PTAS) for the problem.
33634319
A genetic algorithm for the multiple destination routing problems
The multiple destination routing (MDR) problem can be formulated as finding a minimal cost tree which contains designated source and multiple destination nodes so that certain constraints in a given communication network are satisfied. This is a typical NP-hard problem, and therefore only heuristic algorithms are of practical value. As a first step, a new genetic algorithm is developed to solve the MDR problems without constraints. It is based on the transformation of the underlying network of an MDR problem into its distance complete form, a natural chromosome representation of a minimal spanning tree (an individual), and a completely new computation of the fitness of individual. Compared with the known genetic algorithms and heuristic algorithms for the same problem, the proposed algorithm has several advantages. First, it guarantees convergence to an optimal solution with probability one. Second, not only are the resultant solutions all feasible, the solution quality is also much higher than that obtained by the other methods (indeed, in almost every case in our simulations, the algorithm can find the optimal solution of the problem). Third, the algorithm is of low computational complexity, and this can be decreased dramatically as the number of destination nodes in the problem increases. The simulation studies for the sparse and dense networks all demonstrate that the proposed algorithm is highly robust and very efficient in the sense of yielding high-quality solutions.
1032115
Incremental Mining of Frequent Query Patterns from XML Queries for Caching
Existing studies for mining frequent XML query patterns mainly introduce a straightforward candidate generate-and-test strategy and compute frequencies of candidate query patterns from scratch periodically by checking the entire transaction database, which consists of XML query patterns transformed from user queries. However, it is nontrivial to maintain such discovered frequent patterns in real XML databases because there may incur frequent updates that may not only invalidate some existing frequent query patterns but also generate some new frequent ones. Accordingly, existing proposals are inefficient for the evolution of the transaction database. To address these problems, this paper presents an efficient algorithm IPS-FXQPMiner for mining frequent XML query patterns without candidate maintenance and costly tree-containment checking. We transform XML queries into sequences through a one- to-one mapping and then mine the frequent sequences to generate frequent XML query patterns. More importantly, based on IPS-FXQPMiner, an efficient incremental algorithm, Incre-FXQPMiner is proposed to incrementally mine frequent XML query patterns, which can minimize the I/O and computation requirements for handling incremental updates. Our experimental study on various real-life datasets demonstrates the efficiency and scalability of our algorithms over previous known alternatives.
2186483
Improvements for the Symbolic Verification of Timed Automata
Based on the equivalence relation for location based reachability between continuous and integer semantics of closed timed automata, Beyer et al. have implemented the verifier Rabbit, with the uniform representation of reachable configurations. However, the growth of maximal constant of clock variables will decline the performance of Rabbit. The paper proposes an improved symbolic method, using binary decision diagrams (BDDs) to store the symbolic representation of discretized states, for the verification of timed systems. Compared with Rabbit, experiments demonstrate that besides the memory reduction, our implementation is also less sensitive to the size of clock domain.
16653782
Genetic Algorithm Based on Independent Component Analysis for Global Optimization
We design a new Genetic Algorithm based on Independent Component Analysis for unconstrained global optimization of continuous function. We use Independent Component Analysis to linearly transform the original dimensions of the problem into new components which are independent from each other with respect to the fitness. We project the population on the independent components and obtain corresponding sub-populations. We apply genetic operators on the sub-populations to generate new sub-populations, and combine them as a new population. In other words, we use Genetic Algorithm to find the optima on the independent components, and combine the optima as the global optimum for the problem. As we actually reduce the original high-dimensional problem into sub-problems of much fewer dimensions, the solution space decreases exponentially and thus the problem becomes easier for Genetic Algorithm to solve. The experiment results verified that our algorithm produced optimal or close-to-optimal solutions better than or comparable to those produced by some of other Genetic Algorithms and it required much less fitness evaluations of individuals.
2367308
ClaiMaker: Weaving a Semantic Web of Research Papers
The usability of research papers on the Web would be enhanced by a system that explicitly modelled the rhetorical relations between claims in related papers. We describe ClaiMaker, a system for modelling readers' interpretations of the core content of papers. ClaiMaker provides tools to build a Semantic Web representation of the claims in research papers using an ontology of relations. We demonstrate how the system can be used to make inter-document queries.