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Sorting is a fundamental algorithmic pre-processing technique which often allows to represent data more compactly and, at the same time, speeds up search queries on it. In this paper, we focus on the well-studied problem of sorting and…
The longest common prefix array is a very advantageous data structure that, combined with the suffix array and the Burrows-Wheeler transform, allows to efficiently compute some combinatorial properties of a string useful in several…
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…
When building Burrows-Wheeler Transforms (BWTs) of truly huge datasets, prefix-free parsing (PFP) can use an unreasonable amount of memory. In this paper we show how if a dataset can be broken down into small datasets that are not very…
Recently, Cenzato et al.\ proposed a new text index, called the \emph{suffixient array}, which is a subset of the suffix array and supports locating a single pattern occurrence or finding its maximal exact matches (MEMs), assuming random…
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…
This paper introduces the de Bruijn graph edge minimization problem, which is related to the compression of de Bruijn graphs: find the order-k de Bruijn graph with minimum edge count among all orders. We describe an efficient algorithm that…
In the last decades, the necessity to process massive amounts of textual data fueled the development of compressed text indexes: data structures efficiently answering queries on a given text while occupying space proportional to the…
The k-spectrum of a string is the set of all distinct substrings of length k occurring in the string. K-spectra have many applications in bioinformatics including pseudoalignment and genome assembly. The Spectral Burrows-Wheeler Transform…
A parameterized string (p-string) is a string over an alphabet $(\Sigma_{s} \cup \Sigma_{p})$, where $\Sigma_{s}$ and $\Sigma_{p}$ are disjoint alphabets for static symbols (s-symbols) and for parameter symbols (p-symbols), respectively.…
Binary neural networks (BNNs) have been widely adopted to reduce the computational cost and memory storage on edge-computing devices by using one-bit representation for activations and weights. However, as neural networks become…
Compression algorithms and streaming algorithms are both powerful tools for dealing with massive data sets, but many of the best compression algorithms -- e.g., those based on the Burrows-Wheeler Transform -- at first seem incompatible with…
The box-constrained integer least squares problem (BILS) arises in MIMO wireless communications applications. Typically a sphere decoding algorithm (a tree search algorithm) is used to solve the problem. In order to make the search…
Nishimoto and Tabei [CPM, 2021] proposed r-enum, an algorithm to enumerate various characteristic substrings, including maximal repeats, in a string $T$ of length $n$ in $O(r)$ words of compressed working space, where $r \le n$ is the…
Wheeler DFAs (WDFAs) are a sub-class of finite-state automata which is playing an important role in the emerging field of compressed data structures: as opposed to general automata, WDFAs can be stored in just $\log\sigma + O(1)$ bits per…
We develop fast approximation algorithms for the minimum-cost version of the Bounded-Degree MST problem (BD-MST) and its generalization the Crossing Spanning Tree problem (Crossing-ST). We solve the underlying LP to within a $(1+\epsilon)$…
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…
Highly-repetitive collections of strings are increasingly being amassed by genome sequencing and genetic variation experiments, as well as by storing all versions of human-generated files, like webpages and source code. Existing indexes for…
The purpose of this report is to explain how the textbook breadth-first search algorithm (BFS) can be modified in order to also create a compact representation of all shortest paths connecting a single source node to all the nodes reachable…
Optimal transport (OT), which provides a distance between two probability distributions by considering their spatial locations, has been applied to widely diverse applications. Computing an OT problem requires solution of linear programming…