Related papers: FM-index of Alignment with Gaps
The matched filter (MF) is widely used to detect signals hidden within the noise. If the noise is Gaussian, its performances are well-known and describable in an elegant analytical form. The treatment of non-Gaussian noises is often…
We present an online algorithm to deal with pattern matching in strings. The problem we investigate is commonly known as string matching with mismatches in which the objective is to report the number of characters that match when a pattern…
The task of calculating similarities between strings held by different organizations without revealing these strings is an increasingly important problem in areas such as health informatics, national censuses, genomics, and fraud detection.…
We propose a new alignment-free algorithm by constructing a compact vector representation on $\mathbb{R}^{24}$ of a DNA sequence of arbitrary length. Each component of this vector is obtained from a representative sequence, the elements of…
Pattern matching is the most central task for text indices. Most recent indices leverage compression techniques to make pattern matching feasible for massive but highly-compressible datasets. Within this kind of indices, we propose a new…
It has been shown in the indexing literature that there is an essential difference between prefix/range searches on the one hand, and predecessor/rank searches on the other hand, in that the former provably allows faster query resolution.…
The problem of finding factors of a text string which are identical or similar to a given pattern string is a central problem in computer science. A generalised version of this problem consists in implementing an index over the text to…
Forced alignment (FA) predicts start and end timestamps for words or characters in speech, but existing methods are language-specific and prone to cumulative temporal shifts. The multilingual speech understanding and long-sequence…
We study strategies of approximate pattern matching that exploit bidirectional text indexes, extending and generalizing ideas of Lam et al. We introduce a formalism, called search schemes, to specify search strategies of this type, then…
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 /…
In this paper, we propose a new type of array antenna, termed the Random Frequency Diverse Array (RFDA), for an uncoupled indication of target direction and range with low system complexity. In RFDA, each array element has a narrow…
The rise of repetitive datasets has lately generated a lot of interest in compressed self-indexes based on dictionary compression, a rich and heterogeneous family that exploits text repetitions in different ways. For each such compression…
In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount…
Sound correspondence patterns form the basis of cognate detection and phonological reconstruction in historical language comparison. Methods for the automatic inference of correspondence patterns from phonetically aligned cognate sets have…
Next Generation Sequencing (NGS) platforms and, more generally, high-throughput technologies are giving rise to an exponential growth in the size of nucleotide sequence databases. Moreover, many emerging applications of nucleotide datasets…
Spaced seeds are important tools for similarity search in bioinformatics, and using several seeds together often significantly improves their performance. With existing approaches, however, for each seed we keep a separate linear-size data…
We introduce a compact pangenome representation based on an optimal segmentation concept that aims to reconstruct founder sequences from a multiple sequence alignment (MSA). Such founder sequences have the feature that each row of the MSA…
Future wireless networks, deploying thousands of antenna elements, may operate in the radiative near-field (NF), enabling spatial multiplexing across both angle and range domains. Sparse arrays have the potential to achieve comparable…
We present a novel compressed dynamic self-index for highly repetitive text collections. Signature encoding is a compressed dynamic self-index for highly repetitive texts and has a large disadvantage that the pattern search for short…
This paper is an effort to evaluate the numerical indices for the assessment of the frequency response analysis (FRA) to provide a deeper understanding of their characteristics. The study introduces the indices in the literature and…