75279
Error Compensation in Leaf Power Problems
AbstractThe k-Leaf Power recognition problem is a particular case of graph
 power problems: For a given graph it asks whether there exists an
 unrooted tree—the k-leaf root—with leaves one-to-one labeled by
 the graph vertices and where the leaves have distance at most k iff their corresponding vertices in the graph are connected by an
 edge. Here we study "error correction" versions of k-Leaf
 Power recognition—that is, adding or deleting at most l
 edges to generate a graph that has a k-leaf root. We provide
 several NP-completeness results in this context, and we show that
 the NP-complete Closest 3-Leaf Power problem (the error
 correction version of 3-Leaf Power) is fixed-parameter
 tractable with respect to the number of edge modifications or vertex
 deletions in the given graph. Thus, we provide the seemingly first
 nontrivial positive algorithmic results in the field of error
 compensation for leaf power problems with k > 2. To this end, as a
 result of independent interest, we develop a forbidden subgraph
 characterization of graphs with 3-leaf roots.
9767043
The Computational Complexity of Avoiding Forbidden Submatrices by Row Deletions
We initiate a systematic study of the ROW DELETION(B) problem on matrices: Given an input matrix A and a fixed "forbidden submatrix" B, the task is to remove a minimum number of rows from A such that no row or column permutation of B occurs as a submatrix in the resulting matrix. An application of this problem can be found, for instance, in the construction of perfect phylogenies. Establishing a strong connection to variants of the NP-complete HITTING SET problem, we describe and analyze structural properties of B that make ROW DELETION(B)NP-complete. On the positive side, the close relation with HITTING SET problems yields constant-factor polynomial-time approximation algorithms and fixed-parameter tractability results.
1715544
Pattern matching for arc-annotated sequences
We study pattern matching for arc-annotated sequences. An O(nm) time algorithm is given for the problem to determine whether a length m sequence with nested arc annotation is an arc-preserving subsequence (aps) of a length n sequence with nested arc annotation, called APS(NESTED,NESTED). Arc-annotated sequences and, in particular, those with nested arc annotation are motivated by applications in RNA structure comparison. Our algorithm generalizes results for ordered tree inclusion problems and it is useful for recent fixed-parameter algorithms for LAPCS(NESTED,NESTED), which is the problem of computing a longest arc-preserving common subsequence of two sequences with nested arc annotations. In particular, the presented dynamic programming methodology implies a quadratic-time algorithm for an open problem posed by Vialette.
6610579
Exact algorithms and applications for Tree-like Weighted Set Cover
We introduce an NP-complete special case of the Weighted Set Cover problem and show its fixed-parameter tractability with respect to the maximum subset size, a parameter that appears to be small in relevant applications. More precisely, in this practically relevant variant we require that the given collection C of subsets of a base set S should be ''tree-like''. That is, the subsets in C can be organized in a tree T such that every subset one-to-one corresponds to a tree node and, for each element s of S, the nodes corresponding to the subsets containing s induce a subtree of T. This is equivalent to the problem of finding a minimum edge cover in an edge-weighted acyclic hypergraph. Our main result is an algorithm running in O(3^[email protected]?mn) time where k denotes the maximum subset size, n:=|S|, and m:=|C|. The algorithm also implies a fixed-parameter tractability result for the NP-complete Multicut in Trees problem, complementing previous approximation results. Our results find applications in computational biology in phylogenomics and for saving memory in tree decomposition based graph algorithms.
919046
Fixed-Parameter Tractability Results for Feedback Set Problems in Tournaments
Complementing recent progress on classical complexity and polynomial-time approximability of feedback set problems in (bipartite) tournaments, we extend and partially improve fixed-parameter tractability results for these problems. We show that Feedback Vertex Set in tournaments is amenable to the novel iterative compression technique. Moreover, we provide data reductions and problem kernels for Feedback Vertex Set and Feedback Arc Set in tournaments, and a depth-bounded search tree for Feedback Arc Set in bipartite tournaments based on a new forbidden subgraph characterization.
6020472
Compression-based fixed-parameter algorithms for feedback vertex set and edge bipartization
We show that the NP-complete Feedback Vertex Set problem, which asks for the smallest set of vertices to remove from a graph to destroy all cycles, is deterministically solvable in O(c^[email protected]?m) time. Here, m denotes the number of graph edges, k denotes the size of the feedback vertex set searched for, and c is a constant. We extend this to an algorithm enumerating all solutions in O(d^[email protected]?m) time for a (larger) constant d. As a further result, we present a fixed-parameter algorithm with runtime O(2^[email protected]?m^2) for the NP-complete Edge Bipartization problem, which asks for at most k edges to remove from a graph to make it bipartite.
6234679
A Model-based Approach to Hair Region Segmentation
Hair regions represent an important external feature in many tasks involving the processing of human faces. Currently, the task of locating the hair region in a facial image requires manual intervention. In this paper we examine the different aspects of the hair region segmentation problem and develop an automatic system for such a problem. The system incorporates the human knowledge on where the hair is usually located in a facial image. Segmentation is performed via the classification of image pixels and is based on both textural and geometrical features. Experiments have shown that the segmentation results are generally satisfactory and are at least comparable to the performance of manual extraction.
13379605
Protein Fold Recognition Through Application of Residual Dipolar Coupling Data
Residual dipolar coupling (RDC) represents one of the most exciting emerging NMR techniques for studying protein structures. However, solving a protein structure using RDC data alone is a highly challenging problem as it often requires that the starting structure model be close to the actual structure of a protein, for the structure calculation procedure to be effective. We report in this paper a computer program, RDC-PROSPECT, for identification of a structural homolog or analog of a target protein in PDB, which best matches the 15N-1H RDC data of the protein recorded in a single ordering medium. The identified structural homolog/analog can then be used as a starting model for RDC-based structure calculation. Since RDC-PROSPECT uses only RDC data and predicted secondary structure information, its performance is virtually independent of sequence similarity between a target protein and its structural homolog/analog, making it applicable to protein targets out of the scope of current protein threading techniques. We have tested RDC-PROSPECT on all 15N-1H RDC data (representing 33 proteins) available in the BMRB database and the literature. The program correctly identified the structural folds for approximately 80% of the target proteins, significantly better than previously reported results, and achieved an average alignment accuracy of 97.9% residues within 4-residue shift. Through a careful algorithmic design, RDC-PROSPECT is at least one order of magnitude faster than previously reported algorithms for principal alignment frame search, making our algorithm fast enough for large-scale applications.
5572698
Concept exchange: constructing interoperable electronic product catalogues in an emergent environment
Research in interoperability of electronic product catalogues has primarily focused on resolving semantic conflicts arisen from the heterogeneously designed electronic product catalogues. We argue that while existing integration strategies providing static connections between various heterogeneous catalogues over mediating ontologies, ontologies themselves exhibit heterogeneity and lack of evolvability. What's more, reclassifying terms to link public ontologies is very difficult to avoid inaccuracy problem that is critical to electronic commerce. This paper highlights the problems of flexibility, exactness and evolvability that have received little attention in the literature and provides an overview of the concept exchange approach to interoperability. It illustrates why this is able to better solve the identified problems, presents the different features compared with other approaches and suggests how the concept exchange framework is working.
43856313
The waiting time distribution for a TDMA model with a finite buffer
Detailed analytic formulas for the density and probability distribution of the waiting time in a TDMA model with a finite buffer is obtained. On successive intervals of length equal to the duration of a slot, the density is expressed as (infinite) linear combinations of beta densities with positive coefficients. A recursive scheme, obtained by a matrix-analytic derivation, allows for the highly efficient computations of the coefficient sequences.
6950256
Context representation, transformation and comparison for ad hoc product data exchange
Product data exchange is the precondition of business interoperation between Web-based firms. However, millions of small and medium sized enterprises (SMEs) encode their Web product data in ad hoc formats for electronic product catalogues. This prevents product data exchange between business partners for business interoperation. To solve this problem, this paper has proposed a novel concept-centric catalogue engineering approach for representing, transforming and comparing semantic contexts in ad hoc product data exchange. In this approach, concepts and contexts of product data are specified along data exchange chain and are mapped onto several novel XML product map (XPM) documents by utilizing XML hierarchical structure and its syntax. The designed XPM has overcome the semantic limitations of XML markup and has achieved the semantic interoperation for ad hoc product data exchange.