Related papers: Distance Measures for Sequences
Graphs are used in almost every scientific discipline to express relations among a set of objects. Algorithms that compare graphs, and output a closeness score, or a correspondence among their nodes, are thus extremely important. Despite…
A flat membrane with given shape is displayed; two points in the membrane are randomly selected; the probability that the separation between the points have a specified value is sought. A simple method to evaluate the probability density is…
We model long range correlations of nucleotides in the human DNA sequence using the long range one dimensional Ising model. We show that for distances between $10^3$ and $10^6$ bp the correlations show an universal behaviour and may be…
An important problem in geometric computing is defining and computing similarity between two geometric shapes, e.g. point sets, curves and surfaces, etc. Important geometric and topological information of many shapes can be captured by…
Clustering of motion trajectories is highly relevant for human-robot interactions as it allows the anticipation of human motions, fast reaction to those, as well as the recognition of explicit gestures. Further, it allows automated analysis…
This commentary discusses a recently proposed measure of heterogeneity of DNA sequences and compares with the measures of complexity.
Finite mixture models that allow for a broad range of potentially non-elliptical cluster distributions is an emerging methodological field. Such methods allow for the shape of the clusters to match the natural heterogeneity of the data,…
We consider a random tree and introduce a metric in the space of trees to define the ``mean tree'' as the tree minimizing the average distance to the random tree. When the resulting metric space is compact we have laws of large numbers and…
Similarity distance measure between two trajectories is an essential tool to understand patterns in motion, for example, in Human-Robot Interaction or Imitation Learning. The problem has been faced in many fields, from Signal Processing,…
Data of sequential nature arise in many application domains in forms of, e.g. textual data, DNA sequences, and software execution traces. Different research disciplines have developed methods to learn sequence models from such datasets: (i)…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
Graphs are interesting structures: extremely useful to depict real-life problems, extremely easy to understand given a sketch, extremely complicated to represent formally, extremely complicated to compare. Phylogeny is the study of the…
Distance-based clustering and classification are widely used in various fields to group mixed numeric and categorical data. In many algorithms, a predefined distance measurement is used to cluster data points based on their dissimilarity.…
The Universal Similarity Metric (USM) has been demonstrated to give practically useful measures of "similarity" between sequence data. Here we have used the USM as an alternative distance metric in a K-Nearest Neighbours (K-NN) learner to…
In comparative genomics, the rearrangement distance between two genomes (equal the minimal number of genome rearrangements required to transform them into a single genome) is often used for measuring their evolutionary remoteness.…
Time series are ubiquitous, and a measure to assess their similarity is a core part of many computational systems. In particular, the similarity measure is the most essential ingredient of time series clustering and classification systems.…
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…
Temporal graphs are commonly used to represent time-resolved relations between entities in many natural and artificial systems. Many techniques were devised to investigate the evolution of temporal graphs by comparing their state at…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…