Related papers: Comparing reverse complementary genomic words base…
The problem addressed concerns the determination of the average number of successive attempts of guessing a word of a certain length consisting of letters with given probabilities of occurrence. Both first- and second-order approximations…
Correlation of gene histories in the human genome determines the patterns of genetic variation (haplotype structure) and is crucial to understanding genetic factors in common diseases. We derive closed analytical expressions for the…
Four-term word analogies (A:B::C:D) are classically modeled geometrically as ''parallelograms,'' yet recent work suggests this model poorly captures how humans produce analogies, with simple local-similarity heuristics often providing a…
A new class of distances appropriate for measuring similarity relations between sequences, say one type of similarity per distance, is studied. We propose a new ``normalized information distance'', based on the noncomputable notion of…
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…
The human genome contains repetitive DNA at different level of sequence length, number and dispersion. Highly repetitive DNA is particularly rich in homo-- and di--nucleotide repeats, while middle repetitive DNA is rich of families of…
In this work, we consider the problem of pattern matching under the dynamic time warping (DTW) distance motivated by potential applications in the analysis of biological data produced by the third generation sequencing. To measure the DTW…
In this paper we propose a Bayesian answer to testing problems when the hypotheses are not well separated. The idea of the method is to study the posterior distribution of a discrepancy measure between the parameter and the model we want to…
How do two distributions of texts differ? Humans are slow at answering this, since discovering patterns might require tediously reading through hundreds of samples. We propose to automatically summarize the differences by "learning a…
In this article, we investigate the properties of phoneme N-grams across half of the world's languages. We investigate if the sizes of three different N-gram distributions of the world's language families obey a power law. Further, the…
It is known that humans can easily read words where the letters have been jumbled in a certain way. This paper examines this problem by associating a distance measure with the jumbling process. Modifications to text were generated according…
Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…
Statistical properties of the taxonomic classification of human languages are studied. It is shown that, at the highest levels of the taxonomic hierarchy, the frequency of taxon members as a function of the number of languages belonging to…
Mixtures of high dimensional Gaussian distributions have been studied extensively in statistics and learning theory. While the total variation distance appears naturally in the sample complexity of distribution learning, it is analytically…
The distance standard deviation, which arises in distance correlation analysis of multivariate data, is studied as a measure of spread. The asymptotic distribution of the empirical distance standard deviation is derived under the assumption…
Recent observations in the theory of verse and empirical metrics have suggested that constructing a verse line involves a pattern-matching search through a source text, and that the number of found elements (complete words totaling a…
Recent studies have shown that as Transformer-based language models become larger and are trained on very large amounts of data, the fit of their surprisal estimates to naturalistic human reading times degrades. The current work presents a…
We show how generalized Gibbs-Shannon entropies can provide new insights on the statistical properties of texts. The universal distribution of word frequencies (Zipf's law) implies that the generalized entropies, computed at the word level,…
Palindromes are popular and important objects in textual data processing, bioinformatics, and combinatorics on words. Let $S = XaY$ be a string where $X$ and $Y$ are of the same length, and $a$ is either a single character or the empty…
Adaptations of features commonly applied in the field of visual computing, co-occurrence matrix (COM) and run-length matrix (RLM), are proposed for the similarity computation of strings in general (words, phrases, codes and texts). The…