Related papers: Succincter Text Indexing with Wildcards
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)…
Several biological problems require the identification of regions in a sequence where some feature occurs within a target density range: examples including the location of GC-rich regions, identification of CpG islands, and sequence…
Natural language text corpora are often available as sets of syntactically parsed trees. A wide range of expressive tree queries are possible over such parsed trees that open a new avenue in searching over natural language text. They not…
Text indexing is a classical algorithmic problem that has been studied for over four decades: given a text $T$, pre-process it off-line so that, later, we can quickly count and locate the occurrences of any string (the query pattern) in $T$…
Strings in the real world are often encoded with some level of uncertainty. In the character-level uncertainty model, an uncertain string $X$ of length $n$ on an alphabet $\Sigma$ is a sequence of $n$ probability distributions over…
Suffix arrays encode the lexicographical order of all suffixes of a text and are often combined with the Longest Common Prefix array (LCP) to simulate navigational queries on the suffix tree in reduced space. In space-critical applications…
It has been shown in the indexing literature that there is an essential difference between prefix/range searches on the one hand, and predecessor/rank searches on the other hand, in that the former provably allows faster query resolution.…
Many modern sequence alignment tools implement fast string matching using the space efficient data structure called FM-index. The succinct nature of this data structure presents unique challenges for the algorithm designers. In this paper,…
In this paper, we present a new data structure called the packed compact trie (packed c-trie) which stores a set $S$ of $k$ strings of total length $n$ in $n \log\sigma + O(k \log n)$ bits of space and supports fast pattern matching queries…
Text indexing is a fundamental and well-studied problem. Classic solutions either replace the original text with a compressed representation, e.g., the FM-index and its variants, or keep it uncompressed but attach some redundancy - an index…
Document listing on string collections is the task of finding all documents where a pattern appears. It is regarded as the most fundamental document retrieval problem, and is useful in various applications. Many of the fastest-growing…
In many real-world database systems, a large fraction of the data is represented by strings: sequences of letters over some alphabet. This is because strings can easily encode data arising from different sources. It is often crucial to…
We present a new algorithm for subsequence matching in grammar compressed strings. Given a grammar of size $n$ compressing a string of size $N$ and a pattern string of size $m$ over an alphabet of size $\sigma$, our algorithm uses…
We study the fundamental question of how efficiently suffix array entries can be accessed when the array cannot be stored explicitly. The suffix array $SA_T[1..n]$ of a text $T$ of length $n$ encodes the lexicographic order of its suffixes…
The classic string indexing problem is to preprocess a string S into a compact data structure that supports efficient pattern matching queries. Typical queries include existential queries (decide if the pattern occurs in S), reporting…
Let $\D = $$ \{d_1,d_2,...d_D\}$ be a given set of $D$ string documents of total length $n$, our task is to index $\D$, such that the $k$ most relevant documents for an online query pattern $P$ of length $p$ can be retrieved efficiently. We…
We study the Longest Common Extension (LCE) problem in a string containing wildcards. Wildcards (also called "don't cares" or "holes") are special characters that match any other character in the alphabet, similar to the character "?" in…
Compressed indexing is a powerful technique that enables efficient querying over data stored in compressed form, significantly reducing memory usage and often accelerating computation. While extensive progress has been made for…
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…
Given a partition of an n element set into equivalence classes, we consider time-space tradeoffs for representing it to support the query that asks whether two given elements are in the same equivalence class. This has various applications…