Related papers: On the Complexity of BWT-runs Minimization via Alp…
Prior work inspired by compression algorithms has described how the Burrows Wheeler Transform can be used to create a distance measure for bioinformatics problems. We describe issues with this approach that were not widely known, and…
Large-alphabet strings are common in scenarios such as information retrieval and natural-language processing. The efficient storage and processing of such strings usually introduces several challenges that are not witnessed in…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
Mantaci et al. [TCS 2007] defined the eBWT to extend the definition of the BWT to a collection of strings, however, since this introduction, it has been used more generally to describe any BWT of a collection of strings and the fundamental…
Converting a compressed format of a string into another compressed format without an explicit decompression is one of the central research topics in string processing. We discuss the problem of converting the run-length Burrows-Wheeler…
Popular sequence alignment tools such as BWA convert a reference genome to an indexing data structure based on the Burrows-Wheeler Transform (BWT), from which matches to individual query sequences can be rapidly determined. However the…
The optimal transport (OT) problem has been used widely for machine learning. It is necessary for computation of an OT problem to solve linear programming with tight mass-conservation constraints. These constraints prevent its application…
Cartesian tree matching is a form of generalized pattern matching where a substring of the text matches with the pattern if they share the same Cartesian tree. This form of matching finds application for time series of stock prices and can…
Given a string $T$ on an alphabet of size $\sigma$, we describe a bidirectional Burrows-Wheeler index that takes $O(|T|\log{\sigma})$ bits of space, and that supports the addition \emph{and removal} of one character, on the left or right…
With the rapid growing of data and number of applications, there is a crucial need of dictionary based reversible transformation techniques to increase the efficiency of the compression algorithms and hence contribute towards the…
In this paper we investigate the problem of partitioning an input string T in such a way that compressing individually its parts via a base-compressor C gets a compressed output that is shorter than applying C over the entire T at once.…
The Positional Burrows-Wheeler Transform (PBWT) is a fundamental data structure for the efficient representation and analysis of large-scale haplotype panels. For a panel of $h$ sequences $\{S_1, \dots, S_h\}$ over $m$ sites, a key…
Wheeler nondeterministic finite automata (WNFAs) were introduced as a generalization of prefix sorting from strings to labeled graphs. WNFAs admit optimal solutions to classic hard problems on labeled graphs and languages. The problem of…
Sorting database tables before compressing them improves the compression rate. Can we do better than the lexicographical order? For minimizing the number of runs in a run-length encoding compression scheme, the best approaches to…
Recently, Holt and McMillan [Bionformatics 2014, ACM-BCB 2014] have proposed a simple and elegant algorithm to merge the Burrows-Wheeler transforms of a family of strings. In this paper we show that the H&M algorithm can be improved so…
We propose a new technique for creating a space-efficient index for large repetitive text collections, such as pangenomic databases containing sequences of many individuals from the same species. We combine two recent techniques from this…
In the reordering buffer problem (RBP), a server is asked to process a sequence of requests lying in a metric space. To process a request the server must move to the corresponding point in the metric. The requests can be processed slightly…
We present an $m^{4/3+o(1)}\log W$-time algorithm for solving the minimum cost flow problem in graphs with unit capacity, where $W$ is the maximum absolute value of any edge weight. For sparse graphs, this improves over the best known…
The notion of Wheeler languages is rooted in the Burrows-Wheeler transform (BWT), one of the most central concepts in data compression and indexing. The BWT has been generalized to finite automata, the so-called Wheeler automata, by Gagie…
We show how to merge two run-length compressed Burrows-Wheeler Transforms (RLBWTs) into a run-length compressed extended Burrows-Wheeler Transform (eBWT) in $O (r)$ space and $O ((r + L) \log (m + n))$ time, where $m$ and $n$ are the…