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.
16182314
Improved Fixed-Parameter Algorithms for Two Feedback Set Problems
Settling a ten years open question, we show that the NP-complete Feedback Vertex Set problem is deterministically solvable in O(ck · m) time, where m denotes the number of graph edges, k denotes the size of the feedback vertex set searched for, and c is a constant. As a second result, we present a fixed-parameter algorithm for the NP-complete Edge Bipartization problem with runtime O(2k · m2).
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.
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.)


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.
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.
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.
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.
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.