31,353 research outputs found
Improved Approximate String Matching and Regular Expression Matching on Ziv-Lempel Compressed Texts
We study the approximate string matching and regular expression matching
problem for the case when the text to be searched is compressed with the
Ziv-Lempel adaptive dictionary compression schemes. We present a time-space
trade-off that leads to algorithms improving the previously known complexities
for both problems. In particular, we significantly improve the space bounds,
which in practical applications are likely to be a bottleneck
Path, theme and narrative in open plan exhibition settings
Three arguments are made based on the analysis of science exhibitions. First,sufficiently refined techniques of spatial analysis allow us to model the impact oflayout upon visitors' paths, even in moderately sized open plans which allow almostrandom patterns of movement and relatively unobstructed visibility. Second, newlydeveloped or adapted techniques of analysis allow us to make a transition frommodeling the mechanics of spatial movement (the way in which movement is affectedby the distribution of obstacles and boundaries), to modeling the manner in whichmovement might register additional aspects of visual information. Third, theadvantages of such purely spatial modes of analysis extend into providing us with asharper understanding of some of the pragmatic constrains within which exhibitioncontent is conceived and designed
Knowledge-based machine vision systems for space station automation
Computer vision techniques which have the potential for use on the space station and related applications are assessed. A knowledge-based vision system (expert vision system) and the development of a demonstration system for it are described. This system implements some of the capabilities that would be necessary in a machine vision system for the robot arm of the laboratory module in the space station. A Perceptics 9200e image processor, on a host VAXstation, was used to develop the demonstration system. In order to use realistic test images, photographs of actual space shuttle simulator panels were used. The system's capabilities of scene identification and scene matching are discussed
Path, theme and narrative in open plan exhibition settings
Three arguments are made based on the analysis of science exhibitions. First,sufficiently refined techniques of spatial analysis allow us to model the impact oflayout upon visitors' paths, even in moderately sized open plans which allow almostrandom patterns of movement and relatively unobstructed visibility. Second, newlydeveloped or adapted techniques of analysis allow us to make a transition frommodeling the mechanics of spatial movement (the way in which movement is affectedby the distribution of obstacles and boundaries), to modeling the manner in whichmovement might register additional aspects of visual information. Third, theadvantages of such purely spatial modes of analysis extend into providing us with asharper understanding of some of the pragmatic constrains within which exhibitioncontent is conceived and designed
Pattern Matching and Discourse Processing in Information Extraction from Japanese Text
Information extraction is the task of automatically picking up information of
interest from an unconstrained text. Information of interest is usually
extracted in two steps. First, sentence level processing locates relevant
pieces of information scattered throughout the text; second, discourse
processing merges coreferential information to generate the output. In the
first step, pieces of information are locally identified without recognizing
any relationships among them. A key word search or simple pattern search can
achieve this purpose. The second step requires deeper knowledge in order to
understand relationships among separately identified pieces of information.
Previous information extraction systems focused on the first step, partly
because they were not required to link up each piece of information with other
pieces. To link the extracted pieces of information and map them onto a
structured output format, complex discourse processing is essential. This paper
reports on a Japanese information extraction system that merges information
using a pattern matcher and discourse processor. Evaluation results show a high
level of system performance which approaches human performance.Comment: See http://www.jair.org/ for any accompanying file
Suffix Tree of Alignment: An Efficient Index for Similar Data
We consider an index data structure for similar strings. The generalized
suffix tree can be a solution for this. The generalized suffix tree of two
strings and is a compacted trie representing all suffixes in and
. It has leaves and can be constructed in time.
However, if the two strings are similar, the generalized suffix tree is not
efficient because it does not exploit the similarity which is usually
represented as an alignment of and .
In this paper we propose a space/time-efficient suffix tree of alignment
which wisely exploits the similarity in an alignment. Our suffix tree for an
alignment of and has leaves where is the sum of
the lengths of all parts of different from and is the sum of the
lengths of some common parts of and . We did not compromise the pattern
search to reduce the space. Our suffix tree can be searched for a pattern
in time where is the number of occurrences of in and
. We also present an efficient algorithm to construct the suffix tree of
alignment. When the suffix tree is constructed from scratch, the algorithm
requires time where is the sum of the lengths
of other common substrings of and . When the suffix tree of is
already given, it requires time.Comment: 12 page
An optimized TOPS+ comparison method for enhanced TOPS models
This article has been made available through the Brunel Open Access Publishing Fund.Background
Although methods based on highly abstract descriptions of protein structures, such as VAST and TOPS, can perform very fast protein structure comparison, the results can lack a high degree of biological significance. Previously we have discussed the basic mechanisms of our novel method for structure comparison based on our TOPS+ model (Topological descriptions of Protein Structures Enhanced with Ligand Information). In this paper we show how these results can be significantly improved using parameter optimization, and we call the resulting optimised TOPS+ method as advanced TOPS+ comparison method i.e. advTOPS+.
Results
We have developed a TOPS+ string model as an improvement to the TOPS [1-3] graph model by considering loops as secondary structure elements (SSEs) in addition to helices and strands, representing ligands as first class objects, and describing interactions between SSEs, and SSEs and ligands, by incoming and outgoing arcs, annotating SSEs with the interaction direction and type. Benchmarking results of an all-against-all pairwise comparison using a large dataset of 2,620 non-redundant structures from the PDB40 dataset [4] demonstrate the biological significance, in terms of SCOP classification at the superfamily level, of our TOPS+ comparison method.
Conclusions
Our advanced TOPS+ comparison shows better performance on the PDB40 dataset [4] compared to our basic TOPS+ method, giving 90 percent accuracy for SCOP alpha+beta; a 6 percent increase in accuracy compared to the TOPS and basic TOPS+ methods. It also outperforms the TOPS, basic TOPS+ and SSAP comparison methods on the Chew-Kedem dataset [5], achieving 98 percent accuracy. Software Availability: The TOPS+ comparison server is available at http://balabio.dcs.gla.ac.uk/mallika/WebTOPS/.This article is available through the Brunel Open Access Publishing Fun
FlashProfile: A Framework for Synthesizing Data Profiles
We address the problem of learning a syntactic profile for a collection of
strings, i.e. a set of regex-like patterns that succinctly describe the
syntactic variations in the strings. Real-world datasets, typically curated
from multiple sources, often contain data in various syntactic formats. Thus,
any data processing task is preceded by the critical step of data format
identification. However, manual inspection of data to identify the different
formats is infeasible in standard big-data scenarios.
Prior techniques are restricted to a small set of pre-defined patterns (e.g.
digits, letters, words, etc.), and provide no control over granularity of
profiles. We define syntactic profiling as a problem of clustering strings
based on syntactic similarity, followed by identifying patterns that succinctly
describe each cluster. We present a technique for synthesizing such profiles
over a given language of patterns, that also allows for interactive refinement
by requesting a desired number of clusters.
Using a state-of-the-art inductive synthesis framework, PROSE, we have
implemented our technique as FlashProfile. Across tasks over large
real datasets, we observe a median profiling time of only s.
Furthermore, we show that access to syntactic profiles may allow for more
accurate synthesis of programs, i.e. using fewer examples, in
programming-by-example (PBE) workflows such as FlashFill.Comment: 28 pages, SPLASH (OOPSLA) 201
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