Related papers: On Locating Paths in Compressed Tries
The positional Burrows-Wheeler Transform (PBWT) is commonly used to store haplotype panels compactly in such a way that, given a query haplotype, we can quickly find the set maximal exact matches (SMEMs) between the query and the haplotypes…
In this paper, we study the following problem: given $n$ subsets $S_1, \dots, S_n$ of an integer universe $U = \{0,\dots, u-1\}$, having total cardinality $N = \sum_{i=1}^n |S_i|$, find a prefix-free encoding $enc : U \rightarrow \{0,1\}^+$…
We show that the compressed suffix array and the compressed suffix tree for a string of length $n$ over an integer alphabet of size $\sigma\leq n$ can both be built in $O(n)$ (randomized) time using only $O(n\log\sigma)$ bits of working…
Suffix tree (and the closely related suffix array) are fundamental structures capturing all substrings of a given text essentially by storing all its suffixes in the lexicographical order. In some applications, we work with a subset of $b$…
Given a string of characters, the Burrows-Wheeler Transform rearranges the characters in it so as to produce another string of the same length which is more amenable to compression techniques such as move to front, run-length encoding, and…
We present a new universal source code for distributions of unlabeled binary and ordinal trees that achieves optimal compression to within lower order terms for all tree sources covered by existing universal codes. At the same time, it…
In this paper, we study the problem of map matching with travel time constraints. Given a sequence of $k$ spatio-temporal measurements and an embedded path graph with travel time costs, the goal is to snap each measurement to a close-by…
In order to avoid the reference bias introduced by mapping reads to a reference genome, bioinformaticians are investigating reference-free methods for analyzing sequenced genomes. With large projects sequencing thousands of individuals,…
We present linear-space data structures for several frequency queries on trees, namely: path mode, path least frequent element, and path $\alpha$-minority queries. We present the first linear-space data structures, requiring $O(n…
Given $d$ strings over the alphabet $\{0,1,\ldots,\sigma{-}1\}$, the classical Aho--Corasick data structure allows us to find all $occ$ occurrences of the strings in any text $T$ in $O(|T| + occ)$ time using $O(m\log m)$ bits of space,…
The run-length compressed Burrows-Wheeler transform (RLBWT) used in conjunction with the backward search introduced in the FM index is the centerpiece of most compressed indexes working on highly-repetitive data sets like biological…
The Burrows-Wheeler Transform (BWT) is often taught in undergraduate courses on algorithmic bioinformatics, because it underlies the FM-index and thus important tools such as Bowtie and BWA. Its admirers consider the BWT a thing of beauty…
This paper proposed a storing approach for trie structures, called coordinate hash trie. The basic idea is using a global hash table with a special hash function to store all edges of a trie. For a trie with $n$ nodes and an alphabet with…
We introduce a compressed suffix array representation that, on a text $T$ of length $n$ over an alphabet of size $\sigma$, can be built in $O(n)$ deterministic time, within $O(n\log\sigma)$ bits of working space, and counts the number of…
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 $T$…
The Burrows-Wheeler Transform (BWT) is an important technique both in data compression and in the design of compact indexing data structures. It has been generalized from single strings to collections of strings and some classes of labeled…
We first review how we can store a run-length compressed suffix array (RLCSA) for a text $T$ of length $n$ over an alphabet of size $\sigma$ whose Burrows-Wheeler Transform (BWT) consists of $r$ runs in $O \left( \rule{0ex}{2ex} r \log (n /…
``Algorithms with predictions'', or ``learning-augmented algorithms'', has proved to be an extremely useful paradigm for combining machine learning with traditional algorithms. One of the textbook settings for this is searching a sorted…
We consider the problem of querying a string (or, a database) of length $N$ bits to determine all the locations where a substring (query) of length $M$ appears either exactly or is within a Hamming distance of $K$ from the query. We assume…
We present a polynomial-time algorithm that discovers all maximal patterns in a point set, $D\subset\mathbb{R}^k$, that are related by transformations in a user-specified class, $F$, of bijections over $\mathbb{R}^k$. We also present a…