Related papers: Alignment-free sequence comparison using absent wo…
In this work we present strategies for (optimal) measurement selection in model-based sequential diagnosis. In particular, assuming a set of leading diagnoses being given, we show how queries (sets of measurements) can be computed and…
Sequence segmentation is a well-studied problem, where given a sequence of elements, an integer K, and some measure of homogeneity, the task is to split the sequence into K contiguous segments that are maximally homogeneous. A classic…
Context-free grammars are not able to model cross-serial dependencies in natural languages. To overcome this issue, Seki et al. introduced a generalization called $m$-multiple context-free grammars ($m$-MCFGs), which deal with $m$-tuples of…
String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…
This paper deals with algorithms for producing and ordering lexical and nonlexical sequences of a given degree. The notion of "elementary operations" on positive integral sequences is introduced. Our main theorem answers the question of…
We propose novel algorithms for sequence prediction based on ideas from stringology. These algorithms are time and space efficient and satisfy mistake bounds related to particular stringological complexity measures of the sequence. In this…
This paper presents a novel approach to address the constrained coding challenge of generating almost-balanced sequences. While strictly balanced sequences have been well studied in the past, the problem of designing efficient algorithms…
We consider the problem of recognizing a vocabulary--a collection of words (sequences) over a finite alphabet--from a potential subsequence of one of its words. We assume the given subsequence is received through a deletion channel as a…
The statistical properties of local alignment algorithms with gaps are analyzed theoretically for uncorrelated and correlated DNA sequences. In the vicinity of the log-linear phase transition, the statistics of alignment with gaps is shown…
Genome-to-genome comparisons require designating anchor points, which are given by Maximum Exact Matches (MEMs) between their sequences. For large genomes this is a challenging problem and the performance of existing solutions, even in…
In this paper, we consider a variant of the classical algorithmic problem of checking whether a given word $v$ is a subsequence of another word $w$. More precisely, we consider the problem of deciding, given a number $p$ (defining a…
We study the problem of similarity detection by sequence alignment with gaps, using a recently established theoretical framework based on the morphology of alignment paths. Alignments of sequences without mutual correlations are found to…
Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…
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…
A new class of distances appropriate for measuring similarity relations between sequences, say one type of similarity per distance, is studied. We propose a new ``normalized information distance'', based on the noncomputable notion of…
We have developed an alignment-free method that calculates phylogenetic distances using a maximum likelihood approach for a model of sequence change on patterns that are discovered in unaligned sequences. To evaluate the phylogenetic…
The nature of the alignment with gaps corresponding to a longest common subsequence (LCS) of two independent iid random sequences drawn from a finite alphabet is investigated. It is shown that such an optimal alignment typically matches…
A string $w$ is called a minimal absent word (MAW) for a string $S$ if $w$ does not occur as a substring in $S$ and all proper substrings of $w$ occur in $S$. MAWs are well-studied combinatorial string objects that have potential…
Two objects are independent if they do not affect each other. Independence is well-understood in classical information theory, but less in algorithmic information theory. Working in the framework of algorithmic information theory, the paper…
Word segmentation is the task of inserting or deleting word boundary characters in order to separate character sequences that correspond to words in some language. In this article we propose an approach based on a beam search algorithm and…