We study a fast algorithm for on-line approximate string matching. It is based on a non-deterministic nite automaton, which is simulated using bit-parallelism. If the automaton does not t in a computer word, we partition the problem into subproblems. We show experimentally that this algorithm is the fastest for typical text search. We also show which algorithms are the best in other cases, and ...

Program understanding can be assisted by tools that match patterns in the program source. Lexical pattern matchers provide excellent performance and ease of use, but have a limited vocabulary. Syntactic matchers provide more precision, but may sacrifice performance, retargetability, ease of use, or generality. To achieve more of the benefits of both models, we extend the pattern syntax of AWK t...

We introduce several new families of string kernels designed in particular for use with support vector machines (SVMs) for classification of protein sequence data. These kernels – restricted gappy kernels, substitution kernels, and wildcard kernels – are based on feature spaces indexed by k-length subsequences from the string alphabet Σ (or the alphabet augmented by a wildcard character), and h...

Template matching is one of the most basic techniques in computer vision, where the algorithm should search for a template image T in an image to analyze I. This paper considers the rotation, scale, brightness and contrast invariant grayscale template matching problem. The proposed algorithm uses a sufficient condition for distinguishing between candidate matching positions and other positions ...

A string matching—andmore generally, sequence matching—algorithm is presented that has a linear worst-case computing time bound, a low worst-case bound on the number of comparisons (2n), and sublinear average-case behavior that is better than that of the fastest versions of the Boyer-Moore algorithm. The algorithm retains its efficiency advantages in a wide variety of sequence matching problems...

In this paper, we propose a fast algorithm for speeding up the process of template matching that uses M-estimators for dealing with outliers. We propose a particular image hierarchy called the p-pyramid that can be exploited to generate a list of ascending lower bounds of the minimal matching errors when a non-decreasing robust error measure is adopted. Then, the set of lower bounds can be used...

Searching for all occurrences of a pattern in a text is a fundamental problem in computer science with applications in many other fields, like natural language processing, information retrieval and computational biology. In the last two decades a general trend has appeared trying to exploit the power of the word RAM model to speed-up the performances of classical string matching algorithms. In ...

In this paper, we study the problem of computing the similarity of two protein structures by measuring their contact-map overlap. Contact-map overlap abstracts the problem of computing the similarity of two polygonal chains as a graph-theoretic problem. In R3, we present the first polynomial time algorithm with any guarantee on the approximation ratio for the 3-dimensional problem. More precise...

The problem of optimal approximation of members of a vector space by a linear combination of members of a large overcomplete library of vectors is of importance in many areas including image and video coding, image analysis, control theory, and statistics. Finding the optimal solution in the general case is mathematically intractable. Matching pursuit, and its orthogonal version, provide greedy...

We present an index that stores a text of length n such that given a pattern of length m, all the substrings of the text that are within Hamming distance (or edit distance) at most k from the pattern are reported in O(m+ log log n + #matches) time (for constant k). The space complexity of the index is O(n1+ǫ) for any constant ǫ > 0.