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In this paper, we study the Steiner tree problem with minimum number of Steiner points and bounded edge-length (STPMSPBEL), which asks for a tree interconnecting a given set of n terminal points and a minimum number of Steiner points such that the Euclidean length of each edge is no more than a given positive constant. This problem has applications in VLSI(More)
Arc-annotated sequences are useful in representing the structural information of RNA sequences. In general, RNA secondary and tertiary structures can be represented as a set of nested arcs and a set of crossing arcs, respectively. Since RNA functions are largely determined by molecular confirmation and therefore secondary and tertiary structures, the(More)
Given n terminals in the Euclidean plane and a positive constant, find a Steiner tree interconnecting all terminals with the minimum number of Steiner points such that the Euclidean length of each edge is no more than the given positive constant. This problem is NP-hard with applications in VLSI design, WDM optical networks and wireless communications. In(More)
Microarray data analysis is notorious for involving a huge number of genes compared to a relatively small number of samples. Gene selection is to detect the most significantly differentially expressed genes under different conditions, and it has been a central research focus. In general, a better gene selection method can improve the performance of(More)
We investigate a practical variant of the well-known graph Steiner tree problem. In this variant, every target vertex is required to be a leaf vertex in the solution Steiner tree. We present hardness results for this variant as well as a polynomial time approximation algorithm with performance ratio ρ + 2, where ρ is the best-known approximation ratio for(More)
Given a graph G = (V; E) and a positive integer k, the Phylogenetic k-Root Problem asks for a (unrooted) tree T without degree-2 nodes such that its leaves are labeled by V and (u; v) 2 E if and only if dT (u; v) k. If the vertices in V are also allowed to be internal nodes in T , then we have the Steiner k-Root Problem. Moreover, if a particular subset S(More)
MOTIVATION The availability of the whole genomic sequences of HIV-1 viruses provides an excellent resource for studying the HIV-1 phylogenies using all the genetic materials. However, such huge volumes of data create computational challenges in both memory consumption and CPU usage. RESULTS We propose the complete composition vector representation for an(More)
Given a set of species and their similarity data, an important problem in evolutionary biology is how to reconstruct a phylogeny (also called evolutionary tree) so that species are close in the phylogeny if and only if they have high similarity. Assume that the similarity data are represented as a graph G = (V,E) where each vertex represents a species and(More)