Related papers: Computing maximal palindromes in non-standard matc…
The stochastic block model (SBM) is a generalization of the Erd\H{o}s--R\'enyi model of random graphs that describes the interaction of a finite number of distinct communities. In sparse Erd\H{o}s--R\'enyi graphs, it is known that a…
Exact pattern matching in labeled graphs is the problem of searching paths of a graph $G=(V,E)$ that spell the same string as the pattern $P[1..m]$. This basic problem can be found at the heart of more complex operations on variation graphs…
The study of approximate matching in the Massively Parallel Computations (MPC) model has recently seen a burst of breakthroughs. Despite this progress, however, we still have a far more limited understanding of maximal matching which is one…
Finding an Approximate Longest Common Substring (ALCS) within a given set $S=\{s_1,s_2,\ldots,s_m\}$ of $m \ge 2$ strings is a key problem in computational biology, such as identifying related mutations across multiple genetic sequences. We…
A palintiple is a natural number which is an integer multiple of its digit reversal. A previous paper partitions all palintiples into three distinct classes according to patterns in the carries and then determines all palintiples belonging…
We present an algorithm for approximating the edit distance $\operatorname{ed}(x, y)$ between two strings $x$ and $y$ in time parameterized by the degree to which one of the strings $x$ satisfies a natural pseudorandomness property. The…
Supertree methods are tree reconstruction techniques that combine several smaller gene trees (possibly on different sets of species) to build a larger species tree. The question of interest is whether the reconstructed supertree converges…
Computing string or sequence alignments is a classical method of comparing strings and has applications in many areas of computing, such as signal processing and bioinformatics. Semi-local string alignment is a recent generalisation of this…
Word alignments identify translational correspondences between words in a parallel sentence pair and is used, for instance, to learn bilingual dictionaries, to train statistical machine translation systems , or to perform quality…
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…
We study the online variant of the language distance problem for two classical formal languages, the language of palindromes and the language of squares, and for the two most fundamental distances, the Hamming distance and the edit…
Factor complexity $\mathcal{C}$ and palindromic complexity $\mathcal{P}$ of infinite words with language closed under reversal are known to be related by the inequality $\mathcal{P}(n) + \mathcal{P}(n+1) \leq 2 +…
Long Short-Term Memory (LSTM) networks, a type of recurrent neural network with a more complex computational unit, have been successfully applied to a variety of sequence modeling tasks. In this paper we develop Tree Long Short-Term Memory…
This paper presents an efficient algorithm for retrieving from a database of trees, all trees that match a given query tree approximately, that is, within a certain error tolerance. It has natural language processing applications in…
Frequent pattern mining is widely used to find ``important'' or ``interesting'' patterns in data. While it is not easy to mathematically define such patterns, maximal frequent patterns are promising candidates, as frequency is a natural…
We study distributed algorithms for string matching problem in presence of wildcard characters. Given a string T (a text), we look for all occurrences of another string P (a pattern) as a substring of string T . Each wildcard character in…
Kernel methods are used frequently in various applications of machine learning. For large-scale high dimensional applications, the success of kernel methods hinges on the ability to operate certain large dense kernel matrix K. An enormous…
We report (to our knowledge) the first evaluation of Constraint Satisfaction as a computational framework for solving closest string problems. We show that careful consideration of symbol occurrences can provide search heuristics that…
Two results on palindromicity of bi-infinite words in a finite alphabet are presented. The first is a simple, but efficient criterion to exclude palindromicity of minimal sequences and applies, in particular, to the Rudin-Shapiro sequence.…
Distribution matching is the process of invertibly mapping a uniformly distributed input sequence onto sequences that approximate the output of a desired discrete memoryless source. The special case of a binary output alphabet and…