Related papers: Waiting for regulatory sequences to appear
Complex systems, such as life and languages, are governed by principles of evolution. The analogy and comparison between biology and linguistics\cite{alphafold2, RoseTTAFold, lang_virus, cell language, faculty1, language of gene, Protein…
In many growing networks, the age of the nodes plays an important role in deciding the attachment probability of the incoming nodes. For example, in a citation network, very old papers are seldom cited while recent papers are usually cited…
What is the productivity of Science? Can we measure an evolution of the production of mathematicians over history? Can we predict the waiting time till the proof of a challenging conjecture such as the P-versus-NP problem? Motivated by…
Perfect sorting by reversals, a problem originating in computational genomics, is the process of sorting a signed permutation to either the identity or to the reversed identity permutation, by a sequence of reversals that do not break any…
We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…
The role of positive selection in human evolution remains controversial. On the one hand, scans for positive selection have identified hundreds of candidate loci and the genome-wide patterns of polymorphism show signatures consistent with…
Gene expression is a cellular process that plays a fundamental role in human phenotypical variations and diseases. Despite advances of deep learning models for gene expression prediction, recent benchmarks have revealed their inability to…
Transcription factors (TFs) are key regulators of gene expression. Based on the classical scenario in which the TF search process switches between one-dimensional motion along the DNA molecule and free Brownian motion in the nucleus, we…
Human translators linger on some words and phrases more than others, and predicting this variation is a step towards explaining the underlying cognitive processes. Using data from the CRITT Translation Process Research Database, we evaluate…
The time required to transcribe genes with long primary transcripts may limit their ability to be expressed in cells with short mitotic cycles, a phenomenon termed intron delay. As such short cycles are a hallmark of the earliest stages of…
Though there is a strong consensus that word length and frequency are the most important single-word features determining visual-orthographic access to the mental lexicon, there is less agreement as how to best capture syntactic and…
Word order evolution has been hypothesized to be constrained by a word order permutation ring: transitions involving orders that are closer in the permutation ring are more likely. The hypothesis can be seen as a particular case of…
We collect and analyze the data for working time, life expectancy, and the pair output and infrastructure of industrializing nations. During S-functional recovery from disaster the pair's time shifts yield 25 years for the infrastructure's…
Adults vary greatly in how effectively they learn a new language, but the signals driving the learning processes and individual differences remain unclear. Over seven days, we tracked behavioral learning and collected fMRI data from 102…
Long-range correlations are found in symbolic sequences from human language, music and DNA. Determining the span of correlations in dolphin whistle sequences is crucial for shedding light on their communicative complexity. Dolphin whistles…
Given a text $T$ of length $n$ and a pattern $P$ of length $m$, the string matching problem is a task to find all occurrences of $P$ in $T$. In this study, we propose an algorithm that solves this problem in $O((n + m)q)$ time considering…
National research assessment exercises are conducted in different nations over varying periods. The choice of the publication period to be observed has to address often contrasting needs: it has to ensure the reliability of the results…
A standard measure of the influence of a research paper is the number of times it is cited. However, papers may be cited for many reasons, and citation count offers limited information about the extent to which a paper affected the content…
String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…
What insights can machine learning bring to understanding human language acquisition? Large language and multimodal models have achieved remarkable capabilities, but their reliance on massive training datasets creates a fundamental mismatch…