14019711
Fixed-parameter tractability and data reduction for multicut in trees
We study an NP-complete (and MaxSNP-hard) communication problem on tree networks, the so-called Multicut in Trees: given an undirected tree and some pairs of nodes of the tree, find out whether there is a set of at most k tree edges whose removal separates all given pairs of nodes. Multicut has been intensively studied for trees as well as for general graphs mainly from the viewpoint of polynomialtime approximation algorithms. By way of contrast, we provide a simple fixed-parameter algorithm for Multicut in Trees showing ∗Supported by the Deutsche Forschungsgemeinschaft (DFG), Emmy Noether research group PIAF (fixed-parameter algorithms), NI 369/4. Parts of this work have been done while the authors were at the Universität Tübingen.
2256716
Minimum Membership Set Covering and the Consecutive Ones Property
The Minimum Membership Set Cover problem has recently been introduced and studied in the context of interference reduction in cellular networks. It has been proven to be notoriously hard in several aspects. Here, we investigate how natural generalizations and variations of this problem behave in terms of the consecutive ones property: While it is well-known that classical set covering problems become polynomial-time solvable when restricted to instances obeying the consecutive ones property, we experience a significantly more intricate complexity behavior in the case of Minimum Membership Set Cover. We provide polynomial-time solvability, NP-completeness, and approximability results for various cases here. In addition, a number of interesting challenges for future research is exhibited
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.
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.
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.
539228
Towards Optimally Solving the LONGEST COMMON SUBSEQUENCE Problem for Sequences with Nested Arc Annotations in Linear Time
We present exact algorithms for the NP-complete Longest Common Subsequence problem for sequences with nested arc annotations, a problem occurring in structure comparison of RNA. Given two sequences of length at most n and nested arc structure, our algorithm determines (if existent) in time O(3.31k1+k2?n) an arc-preserving subsequence of both sequences, which can be obtained by deleting (together with corresponding arcs) k1 letters from the first and k2 letters from the second sequence. Thus, the problem is fixed-parameter tractable when parameterized by the number of deletions. This complements known approximation results which give a quadratic time factor-2-approximation for the general and polynomial time approximation schemes for restricted versions of the problem. In addition, we obtain further fixed-parameter tractability results for these restricted versions.
9204785
Achieving Transparent Integration of Information, Documents and Processes
While progress is made in the individual integration of business information, documents and processes, the issue of how to vertically integrate these individually integrated results needs to be resolved. This paper proposes a novel TRANSCODE approach to the issue. The approach represents business information, business documents and business processes in three TRANSCODE structures, which are then implemented, conceptualized and reified in an integrated and flexible 3-layer TRANSCODE model
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.
30330476
Measurement Models for Survivability and Competitiveness of Very Large E-marketplace
E-Marketplace is a man-made profit center with emergent customer requirements. This emergence nature poses many difficulties for e-marketplace to satisfy its customers and thus affects its survivability and competitiveness. To challenge this issue, this paper has introduced a novel emergent emarketplace model, and analyzed and quantified the emergent properties of emarketplace from simple ESMs to very large complex electronic intermediary EIMs. The measurement models developed in this paper are very useful for producing dynamic interaction records appropriate for further simulation model of e-marketplaces.
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.
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.