Related papers: MARIA: Multiple-alignment $r$-index with aggregati…
The dictionary matching problem is to locate occurrences of any pattern among a set of patterns in a given text. Massive data sets abound and at the same time, there are many settings in which working space is extremely limited. We…
Graphs are extremely versatile and ubiquitous mathematical structures with potential to model a wide range of domains. For this reason, graph problems have been of interest since the early days of computer science. Some of these problems…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
Pattern matching is a powerful tool which is part of many functional programming languages as well as computer algebra systems such as Mathematica. Among the existing systems, Mathematica offers the most expressive pattern matching.…
The compact Merkle multiproof is a new and significantly more memory-efficient way to generate and verify sparse Merkle multiproofs. A standard sparse Merkle multiproof requires to store an index for every non-leaf hash in the multiproof.…
Acquiring genomes at single-cell resolution has many applications such as in the study of microbiota. However, deep sequencing and assembly of all of millions of cells in a sample is prohibitively costly. A property that can come to rescue…
We propose a multiple imputation method to deal with incomplete categorical data. This method imputes the missing entries using the principal components method dedicated to categorical data: multiple correspondence analysis (MCA). The…
We introduce a new metric of match, called Cartesian tree matching, which means that two strings match if they have the same Cartesian trees. Based on Cartesian tree matching, we define single pattern matching for a text of length n and a…
Discrete data such as counts of microbiome taxa resulting from next-generation sequencing are routinely encountered in bioinformatics. Taxa count data in microbiome studies are typically high-dimensional, over-dispersed, and can only reveal…
Cartesian tree matching is the problem of finding all substrings in a given text which have the same Cartesian trees as that of a given pattern. In this paper, we deal with Cartesian tree matching for the case of multiple patterns. We…
This work approaches human chromosome mapping by developing algorithms for ordering markers associated with radiation hybrid data. Motivated by recent work of Boehnke et al. [1], we formulate the ordering problem by developing stochastic…
Finding the model that best describes a high-dimensional dataset is a daunting task, even more so if one aims to consider all possible high-order patterns of the data, going beyond pairwise models. For binary data, we show that this task…
Recent technological advancements have led to the rapid generation of high-throughput biological data, which can be used to address novel scientific questions in broad areas of research. These data can be thought of as a large matrix with…
We consider the problem of enumeration of planar maps and revisit its one-matrix model solution in the light of recent combinatorial techniques involving conjugated trees. We adapt and generalize these techniques so as to give an…
MONI (Rossi et al., 2022) can store a pangenomic dataset T in small space and later, given a pattern P, quickly find the maximal exact matches (MEMs) of P with respect to T. In this paper we consider its one-pass version (Boucher et al.,…
The problem of monotone missing data has been broadly studied during the last two decades and has many applications in different fields such as bioinformatics or statistics. Commonly used imputation techniques require multiple iterations…
We analyze the grammar generation algorithm of the RePair compression algorithm and show the relation between a grammar generated by RePair and maximal repeats. We reveal that RePair replaces step by step the most frequent pairs within the…
We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…
In this article, we propose two classes of semiparametric mixture regression models with single-index for model based clustering. Unlike many semiparametric/nonparametric mixture regression models that can only be applied to low dimensional…
We present an exact algorithm for computing all common subgraphs with the maximum number of vertices across multiple graphs. Our approach is further extended to handle the connected Maximum Common Subgraph (MCS), identifying the largest…