Related papers: Distance Measures for Sequences
The comparison of images is an important task in image processing. For a comparison of two images, a variety of measures has been suggested. However, applications such as dynamic imaging or serial sectioning provide a series of many images…
Alternative novel measures of the distance between any two partitions of a n-set are proposed and compared, together with a main existing one, namely 'partition-distance' D(.,.). The comparison achieves by checking their restriction to…
The study of the topological structure of complex networks has fascinated researchers for several decades, and today we have a fairly good understanding of the types and reoccurring characteristics of many different complex networks.…
This study is to review the approaches used for measuring sentences similarity. Measuring similarity between natural language sentences is a crucial task for many Natural Language Processing applications such as text classification,…
Multiple sequence alignment is increasingly important to bioinformatics, with several applications ranging from phylogenetic analyses to domain identification. There are several ways to perform multiple sequence alignment, an important way…
We consider a novel approach of measuring the homology of DNA sequences based of the variety of optimal alignments in the longest common subsequence sense. The proposed approach is compared with BLAST in measuring the homology of four…
We design a heuristic method, a genetic algorithm, for the computation of an upper bound of the minimum distance of a linear code over a finite field. By the use of the row reduced echelon form, we obtain a permutation encoding of the…
This work proposes a tentative model for the calculation of dimensionless distances between phonemes; sounds are described with binary distinctive features and distances show linear consistency in terms of such features. The model can be…
Conformational transitions are ubiquitous in biomolecular systems, have significant functional roles and are subject to evolutionary pressures. Here we provide a first theoretical framework for topological transition, i.e. conformational…
In this paper we exploit concepts of information theory to address the fundamental problem of identifying and defining the most suitable tools to extract, in a automatic and agnostic way, information from a generic string of characters. We…
We propose a computational method to measure and visualize interrelationships among any number of DNA sequences allowing, for example, the examination of hundreds or thousands of complete mitochondrial genomes. An "image distance" is…
Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of…
In this work we explore the dissimilarity between symmetric word pairs, by comparing the inter-word distance distribution of a word to that of its reversed complement. We propose a new measure of dissimilarity between such distributions.…
From longitudinal biomedical studies to social networks, graphs have emerged as a powerful framework for describing evolving interactions between agents in complex systems. In such studies, after pre-processing, the data can be represented…
We characterize the orderings of pairs of sets induced by several distances: Hamming, Jaccard, S\o rensen-Dice and Overlap. We also characterize these distances.
We present a powerful new loss function and training scheme for learning binary hash codes with any differentiable model and similarity function. Our loss function improves over prior methods by using log likelihood loss on top of an…
We present a framework for discriminative sequence classification where the learner works directly in the high dimensional predictor space of all subsequences in the training set. This is possible by employing a new coordinate-descent…
During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…
Dendrograms are a way to represent evolutionary relationships between organisms. Nowadays, these are inferred based on the comparison of genes or protein sequences by taking into account their differences and similarities. The genetic…
We consider DNA codes based on the nearest-neighbor (stem) similarity model which adequately reflects the "hybridization potential" of two DNA sequences. Our aim is to present a survey of bounds on the rate of DNA codes with respect to a…