Related papers: Computing the optimal BWT of very large string col…
Motivated by challenges in pangenomic read alignment, we propose a generalization of Wheeler graphs that we call Wheeler maps. A Wheeler map stores a text $T[1..n]$ and an assignment of tags to the characters of $T$ such that we can…
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 /…
String kernels are typically used to compare genome-scale sequences whose length makes alignment impractical, yet their computation is based on data structures that are either space-inefficient, or incur large slowdowns. We show that a…
Two simple yet powerful optimization algorithms, named the Best-Mean-Random (BMR) and Best-Worst-Random (BWR) algorithms, are developed and presented in this paper to handle both constrained and unconstrained optimization problems. These…
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…
In this paper we present an algorithm to compute the Lyndon array of a string $T$ of length $n$ as a byproduct of the inversion of the Burrows-Wheeler transform of $T$. Our algorithm runs in linear time using only a stack in addition to the…
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…
The size and complexity of software and hardware systems have significantly increased in the past years. As a result, it is harder to guarantee their correct behavior. One of the most successful methods for automated verification of…
In this paper, we show that the LZ77 factorization of a text T {\in\Sigma^n} can be computed in O(R log n) bits of working space and O(n log R) time, R being the number of runs in the Burrows-Wheeler transform of T reversed. For extremely…
A degenerate or indeterminate string on an alphabet $\Sigma$ is a sequence of non-empty subsets of $\Sigma$. Given a degenerate string $t$ of length $n$, we present a new method based on the Burrows--Wheeler transform for searching for a…
Transforming an input sequence into its constituent k-mers is a fundamental operation in computational genomics. To reduce storage costs associated with k-mer datasets, we introduce and formally analyze MCTR, a novel two-stage algorithm for…
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…
The minimizers sampling mechanism is a popular mechanism for string sampling introduced independently by Schleimer et al. [SIGMOD 2003] and by Roberts et al. [Bioinf. 2004]. Given two positive integers $w$ and $k$, it selects the…
Despite the recent advancements in offline reinforcement learning via supervised learning (RvS) and the success of the decision transformer (DT) architecture in various domains, DTs have fallen short in several challenging benchmarks. The…
The Best-Worst Method (BWM) is a well-known Multi-Criteria Decision-Making (MCDM) method. This article deals with the multiplicative model of BWM. We first formulate an optimization model that is equivalent to the existing multiplicative…
The Extended Burrows Wheeler transform (EBWT) helps to find the distance between two sequences. Implementation of an existing algorithm takes considerable amount of time for small size sequences. In this paper, we give a parallel…
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…
Ultra low-bit quantization brings substantial efficiency for Transformer-based models, but the accuracy degradation and limited GPU support hinder its wide usage. In this paper, we analyze zero-point distortion in binarization and propose a…
The Continuous Wavelet Transform (CWT) is an effective tool for feature extraction in acoustic recognition using Convolutional Neural Networks (CNNs), particularly when applied to non-stationary audio. However, its high computational cost…
In order to better understand and analyze the currently widely used population-based metaheuristic optimization algorithms, , this paper proposes a novel computational intelligence algorithm called bare bones grey wolf optimizer (BBGWO)…