Search results for "Computer and Information Science"
showing 10 items of 1335 documents
Sorting suffixes of a text via its Lyndon Factorization
2013
The process of sorting the suffixes of a text plays a fundamental role in Text Algorithms. They are used for instance in the constructions of the Burrows-Wheeler transform and the suffix array, widely used in several fields of Computer Science. For this reason, several recent researches have been devoted to finding new strategies to obtain effective methods for such a sorting. In this paper we introduce a new methodology in which an important role is played by the Lyndon factorization, so that the local suffixes inside factors detected by this factorization keep their mutual order when extended to the suffixes of the whole word. This property suggests a versatile technique that easily can b…
Helminth Microbiota Profiling Using Bacterial 16S rRNA Gene Amplicon Sequencing: From Sampling to Sequence Data Mining
2021
Symbiont microbial communities play important roles in animal biology and are thus considered integral components of metazoan organisms, including parasitic worms (helminths). Nevertheless, the study of helminth microbiomes has thus far been largely overlooked, and symbiotic relationships between helminths and their microbiomes have been only investigated in selected parasitic worms. Over the past decade, advances in next-generation sequencing technologies, coupled with their increased affordability, have spurred investigations of helminth-associated microbial communities aiming at enhancing current understanding of their fundamental biology and physiology, as well as of host-microbe intera…
Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases
2019
AbstractThe widespread occurrence of repetitive stretches of DNA in genomes of organisms across the tree of life imposes fundamental challenges for sequencing, genome assembly, and automated annotation of genes and proteins. This multi-level problem can lead to errors in genome and protein databases that are often not recognized or acknowledged. As a consequence, end users working with sequences with repetitive regions are faced with ‘ready-to-use’ deposited data whose trustworthiness is difficult to determine, let alone to quantify. Here, we provide a review of the problems associated with tandem repeat sequences that originate from different stages during the sequencing-assembly-annotatio…
Extending the Tsetlin Machine With Integer-Weighted Clauses for Increased Interpretability
2020
Despite significant effort, building models that are both interpretable and accurate is an unresolved challenge for many pattern recognition problems. In general, rule-based and linear models lack accuracy, while deep learning interpretability is based on rough approximations of the underlying inference. Using a linear combination of conjunctive clauses in propositional logic, Tsetlin Machines (TMs) have shown competitive performance on diverse benchmarks. However, to do so, many clauses are needed, which impacts interpretability. Here, we address the accuracy-interpretability challenge in machine learning by equipping the TM clauses with integer weights. The resulting Integer Weighted TM (…
Novel Results on the Number of Runs of the Burrows-Wheeler-Transform
2021
The Burrows-Wheeler-Transform (BWT), a reversible string transformation, is one of the fundamental components of many current data structures in string processing. It is central in data compression, as well as in efficient query algorithms for sequence data, such as webpages, genomic and other biological sequences, or indeed any textual data. The BWT lends itself well to compression because its number of equal-letter-runs (usually referred to as $r$) is often considerably lower than that of the original string; in particular, it is well suited for strings with many repeated factors. In fact, much attention has been paid to the $r$ parameter as measure of repetitiveness, especially to evalua…
Adaptive learning of compressible strings
2020
Suppose an oracle knows a string $S$ that is unknown to us and that we want to determine. The oracle can answer queries of the form "Is $s$ a substring of $S$?". In 1995, Skiena and Sundaram showed that, in the worst case, any algorithm needs to ask the oracle $\sigma n/4 -O(n)$ queries in order to be able to reconstruct the hidden string, where $\sigma$ is the size of the alphabet of $S$ and $n$ its length, and gave an algorithm that spends $(\sigma-1)n+O(\sigma \sqrt{n})$ queries to reconstruct $S$. The main contribution of our paper is to improve the above upper-bound in the context where the string is compressible. We first present a universal algorithm that, given a (computable) compre…
Adaptive Task Assignment in Online Learning Environments
2016
With the increasing popularity of online learning, intelligent tutoring systems are regaining increased attention. In this paper, we introduce adaptive algorithms for personalized assignment of learning tasks to student so that to improve his performance in online learning environments. As main contribution of this paper, we propose a a novel Skill-Based Task Selector (SBTS) algorithm which is able to approximate a student's skill level based on his performance and consequently suggest adequate assignments. The SBTS is inspired by the class of multi-armed bandit algorithms. However, in contrast to standard multi-armed bandit approaches, the SBTS aims at acquiring two criteria related to stu…
Popularity of patterns over $d$-equivalence classes of words and permutations
2020
Abstract Two same length words are d-equivalent if they have same descent set and same underlying alphabet. In particular, two same length permutations are d-equivalent if they have same descent set. The popularity of a pattern in a set of words is the overall number of copies of the pattern within the words of the set. We show the far-from-trivial fact that two patterns are d-equivalent if and only if they are equipopular over any d-equivalence class, and this equipopularity does not follow obviously from a trivial equidistribution.
Probabilistic entailment in the setting of coherence: The role of quasi conjunction and inclusion relation
2013
In this paper, by adopting a coherence-based probabilistic approach to default reasoning, we focus the study on the logical operation of quasi conjunction and the Goodman-Nguyen inclusion relation for conditional events. We recall that quasi conjunction is a basic notion for defining consistency of conditional knowledge bases. By deepening some results given in a previous paper we show that, given any finite family of conditional events F and any nonempty subset S of F, the family F p-entails the quasi conjunction C(S); then, given any conditional event E|H, we analyze the equivalence between p-entailment of E|H from F and p-entailment of E|H from C(S), where S is some nonempty subset of F.…
On the Number of Closed Factors in a Word
2015
A closed word (a.k.a. periodic-like word or complete first return) is a word whose longest border does not have internal occurrences, or, equivalently, whose longest repeated prefix is not right special. We investigate the structure of closed factors of words. We show that a word of length $n$ contains at least $n+1$ distinct closed factors, and characterize those words having exactly $n+1$ closed factors. Furthermore, we show that a word of length $n$ can contain $\Theta(n^{2})$ many distinct closed factors.