Related papers: BWT for string collections
The sort transform (ST) is a modification of the Burrows-Wheeler transform (BWT). Both transformations map an arbitrary word of length n to a pair consisting of a word of length n and an index between 1 and n. The BWT sorts all rotation…
In recent years, bundle recommendation systems have gained significant attention in both academia and industry due to their ability to enhance user experience and increase sales by recommending a set of items as a bundle rather than…
Behavior trees (BTs) are an optimally modular framework to assemble hierarchical hybrid control policies from a set of low-level control policies using a tree structure. Many robotic tasks are naturally decomposed into a hierarchy of…
The Burrows-Wheeler Transform (BWT) moves characters with similar contexts in a text together, where a character's context consists of the characters immediately following it. We say that a property has contextual locality if characters…
The positional Burrows-Wheeler Transform (PBWT) is commonly used to store haplotype panels compactly in such a way that, given a query haplotype, we can quickly find the set maximal exact matches (SMEMs) between the query and the haplotypes…
With the rapid advancement of Neural Machine Translation (NMT), enhancing translation efficiency and quality has become a focal point of research. Despite the commendable performance of general models such as the Transformer in various…
A standard format used for storing the output of high-throughput sequencing experiments is the FASTQ format. It comprises three main components: (i) headers, (ii) bases (nucleotide sequences), and (iii) quality scores. FASTQ files are…
Binary relations are commonly used in Computer Science for modeling data. In addition to classical representations using matrices or lists, some compressed data structures have recently been proposed to represent binary relations in compact…
We present a solver for a many-sorted first-order quantifier-free theory $T_{w,bv}$ of string equations, string length represented as bit-vectors, and bit-vector arithmetic aimed at formal verification, automated testing, and security…
We study optimal variance reduction solutions for count and ratio metrics in online controlled experiments. Our methods leverage flexible machine learning tools to incorporate covariates that are independent from the treatment but have…
Behavior Trees (BTs) were invented as a tool to enable modular AI in computer games, but have received an increasing amount of attention in the robotics community in the last decade. With rising demands on agent AI complexity, game…
In this paper, we consider the problem of compressing a trie while supporting the powerful \emph{locate} queries: to return the pre-order identifiers of all nodes reached by a path labeled with a given query pattern. Our result builds on…
We give a survey of a number of simple applications of renewal theory to problems on random strings and tries: insertion depth, size, insertion mode and imbalance of tries; variations for b-tries and Patricia tries; Khodak and Tunstall…
The notion of string attractor has been introduced in [Kempa and Prezza, 2018] in the context of Data Compression and it represents a set of positions of a finite word in which all of its factors can be "attracted". The smallest size…
We present a simple and effective pretraining strategy -- bidirectional training (BiT) for neural machine translation. Specifically, we bidirectionally update the model parameters at the early stage and then tune the model normally. To…
The Burrows-Wheeler transform (BWT) is used by the bzip2 family of compressors. In this paper, we present a hardware architecture that implements an inplace algorithm to compute the BWT. Our design does not have explicit storage for the…
DNA-based storage has emerged as a promising alternative to traditional data storage methods, offering unmatched advantages in data density, longevity, and sustainability. Two main approaches have developed: in-vitro storage, where…
Bayesian Optimization is ubiquitous in experimental design and black-box optimization for improving search efficiency. However, most existing approaches rely on regression models which are limited to fixed search spaces and structured,…
In this article we extend the elegant in-place Burrows-Wheeler transform (BWT) algorithm proposed by Crochemore et al. (Crochemore et al., 2015). Our extension is twofold: we first show how to compute simultaneously the longest common…
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…