8805498
Bounded Degree Closest k-Tree Power Is NP-Complete
An undirected graph G=V,E is the k-power of an undirected tree T=V,E' if u,v∈ E iff u andi¾?v are connected by a path of length at mosti¾?k ini¾?T. The treei¾?T is called the tree root ofi¾?G. Tree powers can be recognized in polynomial time. The thus naturally arising question is whether a graphi¾?G can be modified by adding or deleting a specified number of edges such thati¾?G becomes a tree power. This problem becomes NP-complete for ki¾? 2. Strengthening this result, we answer the main open question of Tsukiji and Chen [COCOON 2004] by showing that the problem remains NP-complete when additionally demanding that the tree roots must have bounded degree.
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.

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.
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.
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.
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
8023010
PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction
Knowledge of the detailed structure of a protein is crucial to our understanding of the biological functions of that protein. The gap between the number of solved protein structures and the number of protein sequences continues to widen rapidly in the post-genomics era due to long and expensive processes for solving structures experimentally. Computational prediction of structures from amino acid sequence has come to play a key role in narrowing the gap and has been successful in providing useful information for the biological research community. We have developed a prediction pipeline, PROSPECT-PSPP, an integration of multiple computational tools, for fully automated protein structure prediction. The pipeline consists of tools for (i) preprocessing of protein sequences, which includes signal peptide prediction, protein type prediction (membrane or soluble) and protein domain partition, (ii) secondary structure prediction, (iii) fold recognition and (iv) atomic structural model generation. The centerpiece of the pipeline is our threading-based program PROSPECT. The pipeline is implemented using SOAP (Simple Object Access Protocol), which makes it easier to share our tools and resources. The pipeline has an easy-to-use user interface and is implemented on a 64-node dual processor Linux cluster. It can be used for genome-scale protein structure prediction. The pipeline is accessible at http://csbl.bmb.uga.edu/protein_pipeline.
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.
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.