10069776
Automated Generation of Search Tree Algorithms for Hard Graph
Modification Problems
Abstract
We present a framework for an automated 
generation of exact search tree algorithms for NP-hard problems.
The purpose of our approach is twofold—rapid development and 
improved upper bounds. 
Many search tree algorithms for various problems
in the literature are based on complicated
case distinctions. Our approach may lead to a much 
simpler process of developing and analyzing these algorithms.
Moreover, using the sheer computing power of machines it may also 
lead to improved upper bounds on
search tree sizes (i.e., faster exact solving algorithms) in comparison
with previously developed “hand-made” search trees.
Among others, such an example is given with the NP-complete 
Cluster Editing problem (also known as Correlation
Clustering on complete unweighted graphs), which asks for the minimum
number of edge additions and deletions to create a graph which is a
disjoint union of cliques. The
hand-made search tree
for Cluster Editing
had worst-case size O(2.27k), which now is improved to 
O(1.92k) due to our new method.
(Herein, k denotes the number of edge modifications allowed.)


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.

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.
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.
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.
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.
15601163
High Efficiency Digital Halftoning with Two-Element Error Kernel
A high efficiency and good quality error-diffused halftoning is proposed in this paper. An objective halftone image quality evaluation method based on human visual system obtained by least-mean-square is also introduced. The error diffusion algorithm, first introduced by Floyd and Steinberg in 1975, is currently the most popular method of digital halftoning. However, some annoying shortcomings, such as patches of regular textures, worm effect, and computational complexity still need to be improved. Ostromoukhov proposed a three-element error diffusion solving the problems described above, and achieved excellent performance. In this paper, we further reduced the complexity with the proposed two-element error diffusion by cooperating with the proposed LMS-trained quality evaluation. As demonstrated in experiments, the proposed technique further reduced the complexity by 33% compared to Ostromoukhov's method, and it is still comparable in image quality.
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.
18367158
A distributed database server for continuous media
In our project, we are adopting a new approach for handling video data. We view the video as a well-defined data type with its own description, parameters and applicable methods. The system is based on PREDATOR, an open-source object-relational DBMS. PREDATOR uses Shore as the underlying storage manager. Supporting video operations (storing, searching-by-content and streaming) and new query types (query-by-example and multi-feature similarity searching) requires major changes in many of the traditional system components. More specifically, the storage and buffer manager has to deal with huge volumes of data with real-time constraints. Query processing has to consider the video methods and operators in generating, optimizing and executing the query plans.
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.
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