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Verifying Candidate Matches in Sparse and Wildcard Matching (Extended Abstract)
, 2002
"... This paper obtains the following results on pattern matching problems in which the text has length n and the pattern has length m. ..."
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Cited by 40 (3 self)
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This paper obtains the following results on pattern matching problems in which the text has length n and the pattern has length m.
Pattern Matching for Spatial Point Sets
 PROC. 39TH ANNU. IEEE SYMPOS. FOUND. COMPUT. SCI
, 1998
"... Two sets of points in ddimensional space are given: a data set D consisting of N points, and a pattern set or probe P consisting of k points. We address the problem of determining whether there is a transformation, among a specified group of transformations of the space, carrying P into or near (me ..."
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Cited by 36 (0 self)
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Two sets of points in ddimensional space are given: a data set D consisting of N points, and a pattern set or probe P consisting of k points. We address the problem of determining whether there is a transformation, among a specified group of transformations of the space, carrying P into or near (meaning at a small directed Hausdorff distance of) D. The groups we consider are translations and rigid motions. Runtimes of approximately O(n log n) and O(n d log n) respectively are obtained (letting n = maxfN; kg and omitting the effects of several secondary parameters). For translations, a runtime of approximately O(n(ak + 1) log² n) is obtained for the case that a constant fraction a ! 1 of the points of the probe is allowed to fail to match.
Geometric Pattern Matching: A Performance Study
, 1999
"... In this paper, we undertake a performance study of some recent algorithms for geometric pattern matching. These algorithms cover two general paradigms for pattern matching; alignment and combinatorial pattern matching. We present analytical and empirical evaluations of these schemes. Our results ind ..."
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Cited by 14 (1 self)
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In this paper, we undertake a performance study of some recent algorithms for geometric pattern matching. These algorithms cover two general paradigms for pattern matching; alignment and combinatorial pattern matching. We present analytical and empirical evaluations of these schemes. Our results indicate that a proper implementation of an alignmentbased method outperforms other (often asymptotically better) approaches.
Efficient patternmatching with don’t cares
 In Proceedings of the thirteenth annual ACMSIAM symposium on Discrete algorithms
, 2002
"... Abstract We present a randomized algorithm for the string matching with don't cares problem. Based on the simple fingerprint method of Karp and Rabin for ordinary string matching [4], our algorithm runs in time O(n log m) for a text of length n and a pattern of length m and is simpler and slightly f ..."
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Cited by 14 (0 self)
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Abstract We present a randomized algorithm for the string matching with don't cares problem. Based on the simple fingerprint method of Karp and Rabin for ordinary string matching [4], our algorithm runs in time O(n log m) for a text of length n and a pattern of length m and is simpler and slightly faster than the previous algorithms [3, 5, 1]. 1 Introduction. We extend the simple randomized fingerprinting algorithm of Karp and Rabin [4] to the problem of string matching with don't cares. Our algorithm uses a single, simple convolution. This is optimal in the sense that the string matching with don't cares problem is at least as hard as the boolean convolution problem [6]. Thus, to improve our run time of O(n log m) on text of length n and pattern of length m, one would have to improve on the Fast Fourier Transform.
kmismatch with don’t cares
 In ESA
, 2007
"... Abstract. We give the first nontrivial algorithms for the kmismatch pattern matching problem with don’t cares. Given a text t of length n and a pattern p of length m with don’t care symbols and a bound k,our algorithms find all the places that the pattern matches the text with at most k mismatches ..."
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Cited by 13 (6 self)
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Abstract. We give the first nontrivial algorithms for the kmismatch pattern matching problem with don’t cares. Given a text t of length n and a pattern p of length m with don’t care symbols and a bound k,our algorithms find all the places that the pattern matches the text with at most k mismatches.WefirstgiveanO(n(k +lognlog log n)logm)time randomised solution which finds the correct answer with high probability. We then present a new deterministic O(nk 2 log 3 m) time solution that uses tools developed for group testing and finally an approach based on kselectors that runs in O(nk polylog m) time but requires O(poly m) time preprocessing. In each case, the location of the mismatches at each alignment is also given at no extra cost. 1
Efficient algorithms for substring near neighbor problem
 in ACMSIAM Symposium on Discrete Algorithms (SODA), 2006
, 2006
"... In this paper we consider the problem of finding the approximate nearest neighbor when the data set points are the substrings of a given text T. Specifically, for a string T of length n, we present a data structure which does the following: given a pattern P, if there is a substring of T within the ..."
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Cited by 12 (3 self)
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In this paper we consider the problem of finding the approximate nearest neighbor when the data set points are the substrings of a given text T. Specifically, for a string T of length n, we present a data structure which does the following: given a pattern P, if there is a substring of T within the distance R from P, it reports a (possibly different) substring of T within distance cR from P. The length of the pattern P, denoted by m, is not known in advance. For the case where the distances are measured using the Hamming distance, we present a data structure which uses Õ(n1+1/c) space 1 and with Õ � n 1/c + mn o(1) � query time. This essentially matches the earlier bounds of [Ind98], which assumed that the pattern length m is fixed in advance. In addition, our data structure can be constructed in time Õ � n 1+1/c + n 1+o(1) M 1/3 � , where M is an upper bound for m. This essentially matches the preprocessing bound of [Ind98] as long as the term Õ � n 1+1/c � dominates the running time, which is the case when, e.g., c < 3. We also extend our results to the case where the distances are measured according to the l1 distance. The query time and the space bound are essentially the same, while the preprocessing time becomes Õ � n 1+1/c + n 1+o(1) M 2/3 �. 1
Combinatorial and experimental methods for approximate point pattern matching
 Algorithmica
, 2003
"... Point pattern matching is an important problem in computational geometry, with applications in areas like computer vision, object recognition, molecular modelling, and image registration. Traditionally, it has been studied in an exact formulation, where the input point sets are given with arbitrary ..."
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Cited by 6 (0 self)
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Point pattern matching is an important problem in computational geometry, with applications in areas like computer vision, object recognition, molecular modelling, and image registration. Traditionally, it has been studied in an exact formulation, where the input point sets are given with arbitrary precision. This leads to algorithms that typically have running times of the order of high degree polynomials, and require robust calculations of intersection points of high degree surfaces. We study approximate point pattern matching, with the goal of developing algorithms that are more efficient and more practical than exact algorithms. Our work is motivated by the observation that in practice, data sets that form instances of pattern matching problems are noisy, and so approximate formulations are more appropriate. We present new and efficient algorithms for approximate point pattern matching in two and three dimensions, based on approximate combinatorial distance bounds on sets of points, and via the use of methods from combinatorial pattern matching. We also present an average case analysis and a detailed empirical study of our methods.
Tree Pattern Matching to Subset Matching in Linear Time
 IN SIAM J. ON COMPUTING
, 2000
"... This paper is the first of two papers describing an O (n polylog(m)) time algorithm for the Tree Pattern Matching problem on a pattern of size m and a text of size n. In this paper, we show an O(n+m) time Turing reduction from the Tree Pattern Matching problem to another problem called the Subset Ma ..."
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Cited by 5 (2 self)
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This paper is the first of two papers describing an O (n polylog(m)) time algorithm for the Tree Pattern Matching problem on a pattern of size m and a text of size n. In this paper, we show an O(n+m) time Turing reduction from the Tree Pattern Matching problem to another problem called the Subset Matching problem. The second paper will give efficient deterministic and randomized algorithms for the Subset Matching problem. Together,these two papers will imply an O(n log³ m + m)time deterministic algorithm and an O (n (log³m/log log m)+m) time randomized algorithm for the Tree Pattern Matching problem.
A Black Box for Online Approximate Pattern Matching
"... Abstract. We present a deterministic black box solution for online approximate matching. Given a pattern of length m and a streaming text of length n that arrives one character at a time, the task is to report the distance between the pattern and a sliding window of the text as soon as the new chara ..."
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Cited by 3 (2 self)
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Abstract. We present a deterministic black box solution for online approximate matching. Given a pattern of length m and a streaming text of length n that arrives one character at a time, the task is to report the distance between the pattern and a sliding window of the text as soon as the new character arrives. Our solution requires O(Σ log2 m j=1 T (n, 2j−1)/n) time for each input character, where T (n, m) is the total running time of the best offline algorithm. The types of approximation that are supported include exact matching with wildcards, matching under the Hamming norm, approximating the Hamming norm, kmismatch and numerical measures such as the L2 and L1 norms. For these examples, the resulting online algorithms take O(log 2 m), O ( √ m log m), O(log 2 m/ɛ 2), O ( √ k log k log m), O(log 2 m)andO ( √ m log m) time per character respectively. The space overhead is O(m) which we show is optimal. 1
From coding theory to efficient pattern matching
"... We consider the classic problem of pattern matching with few mismatches in the presence of promiscuously matching wildcard symbols. Given a text t of length n and a pattern p of length m with optional wildcard symbols and a bound k, our algorithm finds all the alignments for which the pattern matche ..."
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Cited by 2 (2 self)
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We consider the classic problem of pattern matching with few mismatches in the presence of promiscuously matching wildcard symbols. Given a text t of length n and a pattern p of length m with optional wildcard symbols and a bound k, our algorithm finds all the alignments for which the pattern matches the text with Hamming distance at most k and also returns the location and identity of each mismatch. The algorithm we present is deterministic and runs in Õ(kn) time, matching the best known randomised time complexity to within logarithmic factors. The solutions we develop borrow from the tool set of algebraic coding theory and provide a new framework in which to tackle approximate pattern matching problems. 1