Related papers: A Self-Index on Block Trees
We introduce a cluster evaluation technique called Tree Index. Our Tree Index algorithm aims at describing the structural information of the clustering rather than the quantitative format of cluster-quality indexes (where the representation…
The compressed indexing problem is to preprocess a string $S$ of length $n$ into a compressed representation that supports pattern matching queries. That is, given a string $P$ of length $m$ report all occurrences of $P$ in $S$. We present…
Given a string $S$, the \emph{compressed indexing problem} is to preprocess $S$ into a compressed representation that supports fast \emph{substring queries}. The goal is to use little space relative to the compressed size of $S$ while…
We consider document listing on string collections, that is, finding in which strings a given pattern appears. In particular, we focus on repetitive collections: a collection of size $N$ over alphabet $[1,\sigma]$ is composed of $D$ copies…
A compressed self-index stores a string in compressed form while supporting locate queries without decompression. For highly repetitive strings (arising in web crawls, versioned documents, and genomic collections), static self-indexes can…
We present a scalable approach for range and $k$ nearest neighbor queries under computationally expensive metrics, like the continuous Fr\'echet distance on trajectory data. Based on clustering for metric indexes, we obtain a dynamic tree…
We introduce the zip tree, a form of randomized binary search tree that integrates previous ideas into one practical, performant, and pleasant-to-implement package. A zip tree is a binary search tree in which each node has a numeric rank…
We consider strategies to organize easily updatable associative arrays in external memory. These arrays are used for full-text search. We study indexes with different keys: single word form, two word forms, and sequences of word forms. The…
We present a new on-line algorithm for computing the Lempel-Ziv factorization of a string that runs in $O(N\log N)$ time and uses only $O(N\log\sigma)$ bits of working space, where $N$ is the length of the string and $\sigma$ is the size of…
Indexing highly repetitive collections has become a relevant problem with the emergence of large repositories of versioned documents, among other applications. These collections may reach huge sizes, but are formed mostly of documents that…
Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…
XML document markup is highly repetitive and therefore well compressible using dictionary-based methods such as DAGs or grammars. In the context of selectivity estimation, grammar-compressed trees were used before as synopsis for structural…
A central task in string processing is text indexing, where the goal is to preprocess a text (a string of length $n$) into an efficient index (a data structure) supporting queries about the text. Cole, Gottlieb, and Lewenstein (STOC 2004)…
Random access to highly compressed strings -- represented by straight-line programs or Lempel-Ziv parses, for example -- is a well-studied topic. Random access to such strings in strongly sublogarithmic time is impossible in the worst case,…
Binary jumbled pattern matching asks to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of length $i$ and has exactly $j$ 1-bits. This problem naturally generalizes to…
A classic data structure problem is to preprocess a string T of length $n$ so that, given a query $q$, we can quickly find all substrings of T with Hamming distance at most $k$ from the query string. Variants of this problem have seen…
We introduce data structures answering queries concerning the occurrences of patterns from a given dictionary $\mathcal{D}$ in fragments of a given string $T$ of length $n$. The dictionary is internal in the sense that each pattern in…
The problem of finding factors of a text string which are identical or similar to a given pattern string is a central problem in computer science. A generalised version of this problem consists in implementing an index over the text to…
Despite consistently yielding the best compression on repetitive text collections, the Lempel-Ziv parsing has resisted all attempts at offering relevant guarantees on the cost to access an arbitrary symbol. This makes it less attractive for…
We consider several types of internal queries, that is, questions about fragments of a given text $T$ specified in constant space by their locations in $T$. Our main result is an optimal data structure for Internal Pattern Matching (IPM)…