Related papers: Comparing reverse complementary genomic words base…
This study aims to publish a novel similarity metric to increase the speed of comparison operations. Also the new metric is suitable for distance-based operations among strings. Most of the simple calculation methods, such as string length…
Human similarity judgments are a powerful supervision signal for machine learning applications based on techniques such as contrastive learning, information retrieval, and model alignment, but classical methods for collecting human…
The analysis of correlations of amino acid occurrences in globular proteins has led to the development of statistical tools that can identify native contacts -- portions of the chains that come to close distance in folded structural…
By using the random interchanging algorithm, we investigate the relations between average distance, standard deviation of degree distribution and synchronizability of complex networks. We find that both increasing the average distance and…
Motivation: Alignment-free (AF) distance/similarity functions are a key tool for sequence analysis. Experimental studies on real datasets abound and, to some extent, there are also studies regarding their control of false positive rate…
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…
We demonstrate that the frequency distribution of phonemes across languages can be explained at both macroscopic and microscopic levels. Macroscopically, phoneme rank-frequency distributions closely follow the order statistics of a…
We study hypothesis testing under communication constraints, where each sample is quantized before being revealed to a statistician. Without communication constraints, it is well known that the sample complexity of simple binary hypothesis…
Recently, diffusion probabilistic models (DPMs) have achieved promising results in diverse generative tasks. A typical DPM framework includes a forward process that gradually diffuses the data distribution and a reverse process that…
Many of the commonly used methods for orthology detection start from mutually most similar pairs of genes (reciprocal best hits) as an approximation for evolutionary most closely related pairs of genes (reciprocal best matches). This…
Word similarity has many applications to social science and cultural analytics tasks like measuring meaning change over time and making sense of contested terms. Yet traditional similarity methods based on cosine similarity between word…
We survey the emerging area of compression-based, parameter-free, similarity distance measures useful in data-mining, pattern recognition, learning and automatic semantics extraction. Given a family of distances on a set of objects, a…
The text-length-dependence of real word-frequency distributions can be connected to the general properties of a random book. It is pointed out that this finding has strong implications, when deciding between two conceptually different views…
The normalized edit distance is one of the distances derived from the edit distance. It is useful in some applications because it takes into account the lengths of the two strings compared. The normalized edit distance is not defined in…
Language models that are trained on the next-word prediction task have been shown to accurately model human behavior in word prediction and reading speed. In contrast with these findings, we present a scenario in which the performance of…
Motivation: Recombination rates vary considerably at the fine scale within mammalian genomes, with the majority of recombination occurring within hotspots of ~2 kb in width. We present a method for inferring the location of recombination…
Understanding the population structure and patterns of gene flow within species is of fundamental importance to the study of evolution. In the fields of population and evolutionary genetics, measures of genetic differentiation are commonly…
The paper considers various formalisms based on Automata, Temporal Logic and Regular Expressions for specifying queries over sequences. Unlike traditional binary semantics, the paper presents a similarity based semantics for thse…
In this study, we investigate the problem of comparing gene trees reconciled with the same species tree using a novel semi-metric, called the Path-Label Reconciliation (PLR) dissimilarity measure. This approach not only quantifies…
Measuring the relatedness between scientific publications has important applications in many areas of bibliometrics and science policy. Controlled vocabularies provide a promising basis for measuring relatedness because they address issues…