Related papers: Distance Measures for Sequences
Measuring the distance between data points is fundamental to many statistical techniques, such as dimension reduction or clustering algorithms. However, improvements in data collection technologies has led to a growing versatility of…
Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realized by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free…
The Levenshtein distance is an important tool for the comparison of symbolic sequences, with many appearances in genome research, linguistics and other areas. For efficient applications, an approximation by a distance of smaller…
In this work, we consider the problem of synchronizing two sets of data where the size of the symmetric difference between the sets is small and, in addition, the elements in the symmetric difference are related through the Hamming distance…
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…
Sequence classification algorithms, such as SVM, require a definition of distance (similarity) measure between two sequences. A commonly used notion of similarity is the number of matches between $k$-mers ($k$-length subsequences) in the…
This paper proposes a novel similarity measure for clustering sequential data. We first construct a common state-space by training a single probabilistic model with all the sequences in order to get a unified representation for the dataset.…
This paper examines two methods for finding whether long-range correlations exist in DNA: a fractal measure and a mutual information technique. We evaluate the performance and implications of these methods in detail. In particular we…
Tools that effectively analyze and compare sequences are of great importance in various areas of applied computational research, especially in the framework of molecular biology. In the present paper, we introduce simple geometric criteria…
Correlation measure of order $k$ is an important measure of randomness in binary sequences. This measure tries to look for dependence between several shifted version of a sequence. We study the relation between the correlation measure of…
Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realised by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free…
This paper introduces the sequence covering similarity, that we formally define for evaluating the similarity between a symbolic sequence (string) and a set of symbolic sequences (strings). From this covering similarity we derive a…
Protein structures can be encoded into binary sequences, these are used to define a Hamming distance in conformational space: the distance between two different molecular conformations is the number of different bits in their sequences.…
In the recent past, binary similarity measures have been applied in solving biometric identification problems, including fingerprint, handwritten character detection, and in iris image recognition. The application of the relevant…
New lower bounds on the minimum average Hamming distance of binary codes are derived. The bounds are obtained using linear programming approach.
The most useful data mining primitives are distance measures. With an effective distance measure, it is possible to perform classification, clustering, anomaly detection, segmentation, etc. For single-event time series Euclidean Distance…
Traditional pairwise sequence alignment is based on matching individual samples from two sequences, under time monotonicity constraints. However, in many application settings matching subsequences (segments) instead of individual samples…
We define sequence patterns of length $n$ and level $\ell$ to be equivalence classes of sequences that have $n$ elements from the set of $\ell$ integer symbols $\{1,2,\ldots,\ell\}$ with no restriction on repetition, where the equivalence…
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…
When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…