Related papers: Distance Measures for Sequences
Sequence classification has numerous applications in various fields. Despite extensive studies in the last decades, many challenges still exist, particularly in pattern-based methods. Existing pattern-based methods measure the…
Window profiles of amino acids in protein sequences are taken as a description of the amino acid environment. The relative entropy or Kullback-Leibler distance derived from profiles is used as a measure of dissimilarity for comparison of…
After a discussion of the Griesmer and Heller bound for the distance of a convolutional code we present several codes with various parameters, over various fields, and meeting the given distance bounds. Moreover, the Griesmer bound is used…
The detection of similarities between long DNA and protein sequences is studied using concepts of statistical physics. It is shown that mutual similarities can be detected by sequence alignment methods only if their amount exceeds a…
With recent advances in sensing and tracking technology, trajectory data is becoming increasingly pervasive and analysis of trajectory data is becoming exceedingly important. A fundamental problem in analyzing trajectory data is that of…
We provide, on an extensive dataset and using several different distances, confirmation of the hypothesis that CGR patterns are preserved along a genomic DNA sequence, and are different for DNA sequences originating from genomes of…
A new numerical characterization of symbolic sequences is proposed. The partition of sequence based on Ke and Tong algorithm is a starting point. Algorithm decomposes original sequence into set of distinct subsequences - a patterns. The set…
Every encoding has priori information if the encoding represents any semantic information of the unverse or object. Encoding means mapping from the unverse to the string or strings of digits. The semantic here is used in the model-theoretic…
Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly.…
Rotation distance measures the difference in shape between binary trees of the same size by counting the minimum number of rotations needed to transform one tree to the other. We describe several types of rotation distance where…
In a distributed information application an encoder compresses an arbitrary vector while a similar reference vector is available to the decoder as side information. For the Hamming-distance similarity measure, and when guaranteed perfect…
Generative models are invaluable in many fields of science because of their ability to capture high-dimensional and complicated distributions, such as photo-realistic images, protein structures, and connectomes. How do we evaluate the…
Distance queries are a basic tool in data analysis. They are used for detection and localization of change for the purpose of anomaly detection, monitoring, or planning. Distance queries are particularly useful when data sets such as…
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 work briefly explores the possibility of approximating spatial distance (alternatively, similarity) between data points using the Isolation Forest method envisioned for outlier detection. The logic is similar to that of isolation: the…
Color based re-identification methods usually rely on a distance function to measure the similarity between individuals. In this paper we study the behavior of several histogram distance measures in different color spaces. We wonder whether…
Distance measuring is a very important task in digital geometry and digital image processing. Due to our natural approach to geometry we think of the set of points that are equally far from a given point as a Euclidean circle. Using the…
We introduce a rigorous, physically appealing, and practical way to measure distances between exchange-only correlations of interacting many-electron systems, which works regardless of their size and inhomogeneity. We show that this…
Enormous volumes of short reads data from next-generation sequencing (NGS) technologies have posed new challenges to the area of genomic sequence comparison. The multiple sequence alignment approach is hardly applicable to NGS data due to…
The distribution function of a random distance in three dimensions is given and some new three-dimensional d2-tests of randomness are suggested. We show that our test statistics are not correlated with the usual test statistics and are…