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.
14425036
Parameterized Intractability of Distinguishing Substring Selection
Abstract
A central question in computational biology is the design of genetic
markers to distinguish between two given sets of (DNA) sequences. This question is formalized as 
the NP-complete Distinguishing Substring Selection problem (DSSS for short) which asks, given a set of "good" strings and a set of "bad" strings, for a solution string which is, with respect to the Hamming metric, "away" from the good strings and "close" to the bad strings. More precisely, given integers dg, db, and L, we ask for a length-L string s such that s has Hamming distance at least dg to every length-L substring of the good strings and such that every bad string has a length-L substring with Hamming distance at most db to s. Studying the parameterized complexity of DSSS, we show that, already for binary alphabet, DSSS is W[1]-hard with respect to its natural parameters. This, in particular, implies that a recently given polynomial-time approximation scheme (PTAS) by Deng et al. cannot be replaced by a so-called efficient polynomial-time approximation scheme (EPTAS) unless an unlikely collapse in parameterized complexity theory occurs. This is seemingly the first computational biology problem for which such a border between PTAS (which exists) and EPTAS (which is unlikely to exist) could be established. By way of contrast, for a special case of DSSS, we present an exact fixed-parameter algorithm solving the problem efficiently. In this way we also exhibit a sharp border between fixed-parameter tractability and intractability 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.
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.
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.
14944633
On Exact and Approximation Algorithms for Distinguishing Substring Selection
The NP-complete Distinguishing Substring Selection problem (DSSS for short) asks, given a set of “good” strings and a set of “bad” strings, for a solution string which is, with respect to Hamming metric, “away” from the good strings and “close” to the bad strings.
10065672
The waiting time distribution for a TDMA model with a finite buffer and state-dependent service
We obtain detailed analytic formulas for the density and probability distribution of the waiting time in a time-division multiple-access (TDMA) model with a finite buffer and state-dependent service. On successive intervals of length equal to the duration of a slot, the density is expressed as a linear combination 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. An expression for the mean waiting time is derived using the classical queueing formula L=/spl lambda/W. We also demonstrate that our methodology provides a concise treatment of various special cases that have been studied over the past half century.
17686470
Inter-enterprise business document exchange
Electronic business document interoperation is the cornerstone of business process integration. An essential issue for business document interoperation is to maintain semantic consistency of the exchanged business documents between any two autonomous business communities, where the document sender and receiver have no misunderstanding in using the exchanged documents. Existing approaches to resolving this issue either adopts document standards to map heterogeneous document elements or applies business ontologies to mediate inconsistent document elements. While these approaches are effective in certain degree, the issues of limited flexibility and evolvability in using standards and the lack of accuracy in using ontologies to mediate document elements must be explored and resolved. This paper proposes a Collaborative Document Exchange (CODEX) approach to resolving the issues. In this approach, structures and concepts of business document are separated and layered in CODEX framework. Structures provide the commonality of business documents through classified concept identifiers while concepts support particularity of business documents through collaboration.
41178770
On matching coefficients
Abstract Explicit formulae are derived for the first four coefficients of the matching polynomial of a graph in terms of properties of the graph. An explicit formula is also derived for the number of triangles in the complement of a graph in terms of the parameters of the graph. Also, some extremal properties of regular multipartite graphs are identified.
14231112
A Transparent Collaborative Integration Approach for Ad Hoc Product Data
Product data integration is an essential issue for many e-commerce interoperable business systems. Core to this issue is how to maintain semantic consistency between heterogeneous product data that are semantically different in structure, concept and context. To resolve the issue, this paper proposes a transparent collaborative integration approach, which is built on a layered framework of messaging, structure, concept and collaboration. The key to this framework is three collaboration engines, which resolves semantic consistency issues between millions of contextual vocabularies of SMEs
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.