Related papers: Comparing reverse complementary genomic words base…
The evolution of languages closely resembles the evolution of haploid organisms. This similarity has been recently exploited \cite{GA,GJ} to construct language trees. The key point is the definition of a distance among all pairs of…
Recursive processing in sentence comprehension is considered a hallmark of human linguistic abilities. However, its underlying neural mechanisms remain largely unknown. We studied whether a modern artificial neural network trained with…
Heaps' or Herdan's law is a linguistic law describing the relationship between the vocabulary/dictionary size (type) and word counts (token) to be a power-law function. Its existence in genomes with certain definition of DNA words is…
A minimal absent word of a sequence x, is a sequence yt hat is not a factorof x, but all of its proper factors are factors of x as well. The set of minimal absent words uniquely defines the sequence itself. In recent times minimal absent…
The field of computational linguistics constantly presents new challenges and topics for research. Whether it be analyzing word usage changes over time or identifying relationships between pairs of seemingly unrelated words. To this point,…
Cosine similarity of contextual embeddings is used in many NLP tasks (e.g., QA, IR, MT) and metrics (e.g., BERTScore). Here, we uncover systematic ways in which word similarities estimated by cosine over BERT embeddings are understated and…
The nature of the quantitative distribution of the 64 DNA codons in the human genome has been an issue of debate for over a decade. Some groups have proposed that the quantitative distribution of the DNA codons ordered as a rank-frequency…
Several characteristics of written texts have been inferred from statistical analysis derived from networked models. Even though many network measurements have been adapted to study textual properties at several levels of complexity, some…
We propose a Likelihood Matching approach for training diffusion models by first establishing an equivalence between the likelihood of the target data distribution and a likelihood along the sample path of the reverse diffusion. To…
The distribution of frequency counts of distinct words by length in a language's vocabulary will be analyzed using two methods. The first, will look at the empirical distributions of several languages and derive a distribution that…
In a population with haploid reproduction any individual has a single parent in the previous generation. If all genealogical distances among pairs of individuals (generations from the closest common ancestor) are known it is possible to…
A tandem duplication denotes the process of inserting a copy of a segment of DNA adjacent to its original position. More formally, a tandem duplication can be thought of as an operation that converts a string $S = AXB$ into a string $T =…
Calculating the semantic similarity between sentences is a long dealt problem in the area of natural language processing. The semantic analysis field has a crucial role to play in the research related to the text analytics. The semantic…
The distances between words calculated in word units are studied and compared with the distributions of the Random Matrix Theory (RMT). It is found that the distribution of distance between the same words can be well described by the…
The length of coding sequence series in microbial genomes were regarded as a fluctuating system and characterized by the methods of statistical physics. The distribution and the correlatin properties of 50 genomes including bacteria and…
A correlation is a binary vector that encodes all possible positions of overlaps of two words, where an overlap for an ordered pair of words (u,v) occurs if a suffix of word u matches a prefix of word v. As multiple pairs can have the same…
We introduce the diffusion and superposition distances as two metrics to compare signals supported in the nodes of a network. Both metrics consider the given vectors as initial temperature distributions and diffuse heat trough the edges of…
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…
Sorting by reversals is an important problem in inferring the evolutionary relationship between two genomes. The problem of sorting unsigned permutation has been proven to be NP-hard. The best guaranteed error bounded is the 3/2-…
The distributions of the number of occurrences of words (the distributions of words for short) play key roles in information theory, statistics, probability theory, ergodic theory, computer science, and DNA analysis. Bassino et al. 2010 and…