Related papers: Fast Circular Pattern Matching
Concurrent pattern calculus (CPC) drives interaction between processes by comparing data structures, just as sequential pattern calculus drives computation. By generalising from pattern matching to pattern unification, interaction becomes…
Early literature on genome rearrangement modelling views the problem of computing evolutionary distances as an inherently combinatorial one. In particular, attention was given to estimating distances using the minimum number of events…
Disease progression modeling (DPM) involves using mathematical frameworks to quantitatively measure the severity of how certain disease progresses. DPM is useful in many ways such as predicting health state, categorizing disease stages, and…
Considering a 2D matrix of positive and negative numbers, how might one draw a rectangle within it whose contents sum higher than all other rectangles'? This fundamental problem, commonly known the maximum rectangle problem or subwindow…
Given a pattern x of length m and a text y of length n, both over an ordered alphabet, the order-preserving pattern matching problem consists in finding all substrings of the text with the same relative order as the pattern. It is an…
Fast matching of regular expressions with bounded repetition, aka counting, such as (ab){50,100}, i.e., matching linear in the length of the text and independent of the repetition bounds, has been an open problem for at least two decades.…
We introduce a new approach to a linear-circular regression problem that relates multiple linear predictors to a circular response. We follow a modeling approach of a wrapped normal distribution that describes angular variables and angular…
Many researches have been working on the protein folding problem from more than half century. Protein folding is indeed one of the major unsolved problems in science. In this work, we discuss a model for the simulation of protein…
The fundamental question considered in algorithms on strings is that of indexing, that is, preprocessing a given string for specific queries. By now we have a number of efficient solutions for this problem when the queries ask for an exact…
The last decade has seen a flurry of research on all-pairs-similarity-search (or, self-join) for text, DNA, and a handful of other datatypes, and these systems have been applied to many diverse data mining problems. Surprisingly, however,…
This paper presents a new, parallel implementation of clustering and demonstrates its utility in greatly speeding up the process of identifying homologous proteins. Clustering is a technique to reduce the number of comparison needed to find…
Packing optimization is a prevalent problem that necessitates robust and efficient algorithms that are also simple to implement. One group of approaches is the raster methods, which rely on approximating the objects with pixelated…
We investigate the symmetry of circular genome rearrangement models, discuss the implementation of a new representation-theoretic method of calculating evolutionary distances between circular genomes, and give the results of some initial…
We propose a new problem called coordinated topic modeling that imitates human behavior while describing a text corpus. It considers a set of well-defined topics like the axes of a semantic space with a reference representation. It then…
There is a growing interest in characterizing circular data found in biological systems. Such data are wide ranging and varied, from signal phase in neural recordings to nucleotide sequences in round genomes. Traditional clustering…
Sequential pattern mining (SPM) is an important technique of pattern mining, which has many applications in reality. Although many efficient sequential pattern mining algorithms have been proposed, there are few studies can focus on target…
Previous partial permutation synchronization (PPS) algorithms, which are commonly used for multi-object matching, often involve computation-intensive and memory-demanding matrix operations. These operations become intractable for large…
In the last years, different types of patterns in permutations have been studied: vincular, bivincular and mesh patterns, just to name a few. Every type of permutation pattern naturally defines a corresponding computational problem: Given a…
Finding patterns in data is one of the most challenging open questions in information science. The number of possible relationships scales combinatorially with the size of the dataset, overwhelming the exponential increase in availability…
Large-scale proteomic analysis is emerging as a powerful technique in biology and relies heavily on data acquired by state-of-the-art mass spectrometers. As with any other field in Systems Biology, computational tools are required to deal…