Related papers: Comparing reverse complementary genomic words base…
Divergent word usages reflect differences among people. In this paper, we present a novel angle for studying word usage divergence -- word interpretations. We propose an approach that quantifies semantic differences in interpretations among…
There have been several efforts to extend distributional semantics beyond individual words, to measure the similarity of word pairs, phrases, and sentences (briefly, tuples; ordered sets of words, contiguous or noncontiguous). One way to…
In the human genomes, recombination frequency between homologous chromosomes during meiosis is highly correlated with their physical length while it differs significantly when their coding density is considered. Furthermore, it has been…
Tandem duplication in DNA is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain {\em et al.} (2016) proposed the study of codes that…
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 article, we propose a new three parameter distribution by compounding negative binomial with reciprocal inverse Gaussian model called negative binomial-reciprocal inverse Gaussian distribution. This model is tractable with some…
Sentence similarity is considered the basis of many natural language tasks such as information retrieval, question answering and text summarization. The semantic meaning between compared text fragments is based on the words semantic…
Genome and metagenome comparisons based on large amounts of next-generation sequencing (NGS) data pose significant challenges for alignment-based approaches due to the huge data size and the relatively short length of the reads.…
Using recent results on the occurrence times of a string of symbols in a stochastic process with mixing properties, we present a new method for the search of rare words in biological sequences generally modelled by a Markov chain. We obtain…
A central problem in comparative genomics consists in computing a (dis-)similarity measure between two genomes, e.g. in order to construct a phylogeny. All the existing measures are defined on genomes without duplicates. However, we know…
Lexical resemblances among a group of languages indicate that the languages could be genetically related, i.e., they could have descended from a common ancestral language. However, such resemblances can arise by chance and, hence, need not…
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…
In forensic DNA calculations of relatedness of individuals and in DNA mixture analyses, two sources of uncertainty are present concerning the allele frequencies used for evaluating genotype probabilities when evaluating likelihoods. They…
The so called long range correlation properties of DNA sequences are studied using the variance analyses of the density distribution of a single or a group of nucleotides in a model independent way. This new method which was suggested…
Since the completion of the human genome sequencing project in 2001, significant progress has been made in areas such as gene regulation editing and protein structure prediction. However, given the vast amount of genomic data, the segments…
Genomes may be analyzed from an information viewpoint as very long strings, containing functional elements of variable length, which have been assembled by evolution. In this work an innovative information theory based algorithm is…
This paper presents a new approach for measuring semantic similarity/distance between words and concepts. It combines a lexical taxonomy structure with corpus statistical information so that the semantic distance between nodes in the…
This work presents a mathematical model that establishes an interesting connection between nucleotide frequencies in human single-stranded DNA and the famous Fibonacci's numbers. The model relies on two assumptions. First, Chargaff's second…
The inverse relationship between the length of a word and the frequency of its use, first identified by G.K. Zipf in 1935, is a classic empirical law that holds across a wide range of human languages. We demonstrate that length is one…
Assessing the significance of alignment scores of optimally aligned DNA or amino acid sequences can be achieved via the knowledge of the score distribution of random sequences. But this requires obtaining the distribution in the…