Average running time of Boyer-Moore-Horspool algorithm

Projet ICSL

Matching Subsequences in Trees

Given two rooted, labeled trees $P$ and $T$ the tree path subsequence problem is to determine which paths in $P$ are subsequences of which paths in $T$. Here a path begins at the root and ends at a leaf. In this paper we propose this problem as a useful query primitive for XML data, and provide new algorithms improving the previously best known time and space bounds.Comment: Minor correction of typos, et

Structured Text Retrieval Models

Structured text retrieval models provide a formal definition or mathematical framework for querying semistructured textual databases. A textual database contains both content and structure. The content is the text itself, and the structure divides the database into separate textual parts and relates those textual parts by some criterion. Often, textual databases can be represented as marked up text, for instance as XML, where the XML elements define the structure on the text content. Retrieval models for textual databases should comprise three parts: 1) a model of the text, 2) a model of the structure, and 3) a query language [4]: The model of the text defines a tokenization into words or other semantic units, as well as stop words, stemming, synonyms, etc. The model of the structure defines parts of the text, typically a contiguous portion of the text called element, region, or segment, which is defined on top of the text modelâ\u80\u99s word tokens. The query language typically defines a number of operators on content and structure such as set operators and operators like â\u80\u9ccontaining â\u80\u9d and â\u80\u9ccontained-by â\u80\u9d to model relations between content and structure, as well as relations between the structural elements themselves. Using such a query language, the (expert) user can for instance formulate requests like â\u80\u9cI want a paragraph discussing formal models near to a table discussing the differences between databases and information retrievalâ\u80\u9d. Here, â\u80\u9cformal models â\u80\u9d and â\u80\u9cdifferences between databases and information retrieval â\u80\u9d should match the content that needs to be retrieved from the database, whereas â\u80\u9cparagraph â\u80\u9d and â\u80\u9ctable â\u80\u9d refer to structural constraints on the units to retrieve. The features, structuring power, and the expressiveness of the query languages of several models for structured text retrieval are discussed below. HISTORICAL BACKGROUND The STAIRS system (Storage and Information Retrieval System), which was developed at IBM already in the late 1950â\u80\u99s allowed querying both content and structure. Much like todayâ\u80\u99s On-line Public Access Catalogues, it wa

Fast Searching in Packed Strings

Given strings $P$ and $Q$ the (exact) string matching problem is to find all positions of substrings in $Q$ matching $P$. The classical Knuth-Morris-Pratt algorithm [SIAM J. Comput., 1977] solves the string matching problem in linear time which is optimal if we can only read one character at the time. However, most strings are stored in a computer in a packed representation with several characters in a single word, giving us the opportunity to read multiple characters simultaneously. In this paper we study the worst-case complexity of string matching on strings given in packed representation. Let $m \leq n$ be the lengths $P$ and $Q$, respectively, and let $\sigma$ denote the size of the alphabet. On a standard unit-cost word-RAM with logarithmic word size we present an algorithm using time O\left(\frac{n}{\log_\sigma n} + m + \occ\right). Here \occ is the number of occurrences of $P$ in $Q$. For $m = o(n)$ this improves the $O(n)$ bound of the Knuth-Morris-Pratt algorithm. Furthermore, if $m = O(n/\log_\sigma n)$ our algorithm is optimal since any algorithm must spend at least \Omega(\frac{(n+m)\log \sigma}{\log n} + \occ) = \Omega(\frac{n}{\log_\sigma n} + \occ) time to read the input and report all occurrences. The result is obtained by a novel automaton construction based on the Knuth-Morris-Pratt algorithm combined with a new compact representation of subautomata allowing an optimal tabulation-based simulation.Comment: To appear in Journal of Discrete Algorithms. Special Issue on CPM 200

Revisiting the Problem of Searching on a Line

We revisit the problem of searching for a target at an unknown location on a line when given upper and lower bounds on the distance D that separates the initial position of the searcher from the target. Prior to this work, only asymptotic bounds were known for the optimal competitive ratio achievable by any search strategy in the worst case. We present the first tight bounds on the exact optimal competitive ratio achievable, parameterized in terms of the given bounds on D, along with an optimal search strategy that achieves this competitive ratio. We prove that this optimal strategy is unique. We characterize the conditions under which an optimal strategy can be computed exactly and, when it cannot, we explain how numerical methods can be used efficiently. In addition, we answer several related open questions, including the maximal reach problem, and we discuss how to generalize these results to m rays, for any m >= 2

Faster Approximate String Matching for Short Patterns

We study the classical approximate string matching problem, that is, given strings $P$ and $Q$ and an error threshold $k$, find all ending positions of substrings of $Q$ whose edit distance to $P$ is at most $k$. Let $P$ and $Q$ have lengths $m$ and $n$, respectively. On a standard unit-cost word RAM with word size $w \geq \log n$ we present an algorithm using time $$O(nk \cdot \min(\frac{\log^2 m}{\log n},\frac{\log^2 m\log w}{w}) + n)$$ When $P$ is short, namely, $m = 2^{o(\sqrt{\log n})}$ or $m = 2^{o(\sqrt{w/\log w})}$ this improves the previously best known time bounds for the problem. The result is achieved using a novel implementation of the Landau-Vishkin algorithm based on tabulation and word-level parallelism.Comment: To appear in Theory of Computing System

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 $A$ and $B$ is a compacted trie representing all suffixes in $A$ and $B$. It has $|A|+|B|$ leaves and can be constructed in $O(|A|+|B|)$ 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 $A$ and $B$. 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 $A$ and $B$ has $|A| + l_d + l_1$ leaves where $l_d$ is the sum of the lengths of all parts of $B$ different from $A$ and $l_1$ is the sum of the lengths of some common parts of $A$ and $B$. We did not compromise the pattern search to reduce the space. Our suffix tree can be searched for a pattern $P$ in $O(|P|+occ)$ time where $occ$ is the number of occurrences of $P$ in $A$ and $B$. We also present an efficient algorithm to construct the suffix tree of alignment. When the suffix tree is constructed from scratch, the algorithm requires $O(|A| + l_d + l_1 + l_2)$ time where $l_2$ is the sum of the lengths of other common substrings of $A$ and $B$. When the suffix tree of $A$ is already given, it requires $O(l_d + l_1 + l_2)$ time.Comment: 12 page

Efficient exact pattern-matching in proteomic sequences

This paper proposes a novel algorithm for complete exact pattern-matching focusing the specificities of protein sequences (alphabet of 20 symbols) but, also highly efficient considering larger alphabets. The searching strategy uses large search windows allowing multiple alignments per iteration. A new filtering heuristic, named compatibility rule, contributed decisively to the efficiency improvement. The new algorithm’s performance is, on average, superior in comparison with its best-rated competitors