Related papers: Alignment-free sequence comparison using absent wo…
Identifying palindromes in sequences has been an interesting line of research in combinatorics on words and also in computational biology, after the discovery of the relation of palindromes in the DNA sequence with the HIV virus. Efficient…
Within bioinformatics, the textual alignment of amino acid sequences has long dominated the determination of similarity between proteins, with all that implies for shared structure, function and evolutionary descent. Despite the relative…
Linear regression without correspondences is the problem of performing a linear regression fit to a dataset for which the correspondences between the independent samples and the observations are unknown. Such a problem naturally arises in…
Conformance checking encompasses a body of process mining techniques which aim to find and describe the differences between a process model capturing the expected process behavior and a corresponding event log recording the observed…
Minimal-interval semantics associates with each query over a document a set of intervals, called witnesses, that are incomparable with respect to inclusion (i.e., they form an antichain): witnesses define the minimal regions of the document…
Given a sequence composed of a limit number of characters, we try to "read" it as a "text". This involves to segment the sequence into "words". The difficulty is to distinguish good segmentation from enormous number of random ones.Aiming at…
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…
We propose a metric for the space of multiple sequence alignments that can be used to compare two alignments to each other. In the case where one of the alignments is a reference alignment, the resulting accuracy measure improves upon…
Pattern matching is a fundamental process in almost every scientific domain. The problem involves finding the positions of a given pattern (usually of short length) in a reference stream of data (usually of large length). The matching can…
Since Bahdanau et al. [1] first introduced attention for neural machine translation, most sequence-to-sequence models made use of attention mechanisms [2, 3, 4]. While they produce soft-alignment matrices that could be interpreted as…
We investigate how to determine whether the states of a set of quantum systems are identical or not. This paper treats both error-free comparison, and comparison where errors in the result are allowed. Error-free comparison means that we…
A word $x$ that is absent from a word $y$ is called minimal if all its proper factors occur in $y$. Given a collection of $k$ words $y_1,y_2,\ldots,y_k$ over an alphabet $\Sigma$, we are asked to compute the set…
We show a new simple algorithm that checks whether a given higher-order grammar generates a nonempty language of trees. The algorithm amounts to a procedure that transforms a grammar of order n to a grammar of order n-1, preserving…
We consider the problem of identifying tandem scattered subsequences within a string. Our algorithm identifies a longest subsequence which occurs twice without overlap in a string. This algorithm is based on the Hunt-Szymanski algorithm,…
Automatic segmentation of text into minimal content-bearing units is an unsolved problem even for languages like English. Spaces between words offer an easy first approximation, but this approximation is not good enough for machine…
The paper surveys the evolution of main algorithmic techniques to compare and search biological sequences. We highlight key algorithmic ideas emerged in response to several interconnected factors: shifts of biological analytical paradigm,…
Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between two input sequences. Haubold {\em et al.} (2009) showed how the average number of substitutions between two DNA…
The paper considers various formalisms based on Automata, Temporal Logic and Regular Expressions for specifying queries over sequences. Unlike traditional binary semantics, the paper presents a similarity based semantics for thse…
Common intervals have been defined as a modelisation of gene clusters in genomes represented either as permutations or as sequences. Whereas optimal algorithms for finding common intervals in permutations exist even for an arbitrary number…
We design alignment-free techniques for comparing a sequence or word, called a target, against a set of words, called a reference. A target-specific factor of a target $T$ against a reference $R$ is a factor $w$ of a word in $T$ which is…