Related papers: FM-index of Alignment with Gaps
Orthogonal Matching Pursuit (OMP) has been a powerful method in sparse signal recovery and approximation. However, OMP suffers computational issues when the signal has a large number of non-zeros. This paper advances OMP and its extension…
We demonstrate that a graph-based search algorithm-relying on the construction of an approximate neighborhood graph-can directly work with challenging non-metric and/or non-symmetric distances without resorting to metric-space mapping…
We study a new variant of the string matching problem called cross-document string matching, which is the problem of indexing a collection of documents to support an efficient search for a pattern in a selected document, where the pattern…
The FM-index is a well-known compressed full-text index, based on the Burrows-Wheeler transform (BWT). During a pattern search, the BWT sequence is accessed at "random" locations, which is cache-unfriendly. In this paper, we are interested…
Music Structure Analysis (MSA) consists of representing a song in sections (such as ``chorus'', ``verse'', ``solo'' etc), and can be seen as the retrieval of a simplified organization of the song. This work presents a new algorithm, called…
Compressive sensing (CS) can effectively recover a signal when it is sparse in some discrete atoms. However, in some applications, signals are sparse in a continuous parameter space, e.g., frequency space, rather than discrete atoms.…
The suffix array is a classic full-text index, combining effectiveness with simplicity. We discuss three approaches aiming to improve its efficiency even more: changes to the navigation, data layout and adding extra data. In short, we show…
Multivariate time series alignment is critical for ensuring coherent analysis across variables, but missing values and timestamp inconsistencies make this task highly challenging. Existing approaches often rely on prior imputation, which…
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…
Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realised by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free…
Linear RNNs with gating recently demonstrated competitive performance compared to Transformers in language modeling. Although their linear compute scaling in sequence length offers theoretical runtime advantages over Transformers, realizing…
We introduce a new algorithm for constructing the generalized suffix array of a collection of highly similar strings. As a first step, we construct a compressed representation of the matching statistics of the collection with respect to a…
In this paper we investigate the \emph{approximate string matching problem} when the allowed edit operations are \emph{non-overlapping unbalanced translocations of adjacent factors}. Such kind of edit operations take place when two adjacent…
For taxonomic classification, we are asked to index the genomes in a phylogenetic tree such that later, given a DNA read, we can quickly choose a small subtree likely to contain the genome from which that read was drawn. Although popular…
The Fast Folding Algorithm (FFA) is a phase-coherent search technique for periodic signals. It has rarely been used in radio pulsar searches, having been historically supplanted by the less computationally expensive Fast Fourier Transform…
Matching statistics were introduced to solve the approximate string matching problem, which is a recurrent subroutine in bioinformatics applications. In 2010, Ohlebusch et al. [SPIRE 2010] proposed a time and space efficient algorithm for…
In this letter, a novel variation of sparse code multiple access (SCMA), called codeword position index based SCMA (CPI-SCMA), is proposed. In this scheme, the information is transmitted not only by the codewords in M point SCMA codebook,…
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…
Large Language Models (LLMs) have shown remarkable capabilities in natural language processing but exhibit significant performance gaps among different languages. Most existing approaches to address these disparities rely on pretraining or…
Time Series Alignment is a critical task in signal processing with numerous real-world applications. In practice, signals often exhibit temporal shifts and scaling, making classification on raw data prone to errors. This paper introduces a…