Related papers: The Capacity of String-Replication Systems
The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain detailed information concerning this process through…
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…
We investigate the problem of generating common randomness (CR) from finite compound sources aided by unidirectional communication over rate-limited perfect channels. The two communicating parties, often referred to as terminals, observe…
We observe the propagation of information in a system of self-replicating strings of code (``Artificial Life'') as a function of fitness and mutation rate. Comparison with theoretical predictions based on the reaction-diffusion equation…
When considering binary strings, it's natural to wonder how many distinct subsequences might exist in a given string. Given that there is an existing algorithm which provides a straightforward way to compute the number of distinct…
Each human genome is a 3 billion base pair set of encoding instructions. Decoding the genome using deep learning fundamentally differs from most tasks, as we do not know the full structure of the data and therefore cannot design…
Labeled infinite trees provide combinatorial interpretations for many integer sequences generated by nested recurrence relations. Typically, such sequences are monotone increasing. Several of these sequences also have straightforward…
The study of regenerating codes has advanced tremendously in recent years. However, most known constructions require large field size, and hence may be hard to implement in practice. By using notions from the theory of extension fields, we…
In this paper we present a model containing modifications to the Signal-passing Tile Assembly Model (STAM), a tile-based self-assembly model whose tiles are capable of activating and deactivating glues based on the binding of other glues.…
In modern neuroscience, memory has been postulated to stored in neural circuits as sequential spike train and Reverberation is one of the specific example.Former research has made much progress on phenomenon description. However, the…
Motivation: Gene regulatory interactions are of fundamental importance to various biological functions and processes. However, only a few previous computational studies have claimed success in revealing genome-wide regulatory landscapes…
DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes, and DNA…
P systems with active membranes were used to generate languages, in the sense of languages associated with the structure of membrane systems. Here, we analyze the power of P systems with membrane creation and dissolution restricted to…
Reproducibility of modeling is a problem that exists for any machine learning practitioner, whether in industry or academia. The consequences of an irreproducible model can include significant financial costs, lost time, and even loss of…
It takes several years for the developing brain of a baby to fully master word repetition-the task of hearing a word and repeating it aloud. Repeating a new word, such as from a new language, can be a challenging task also for adults.…
In the trace reconstruction problem, the goal is to reconstruct an unknown string $x$ of length $n$ from multiple traces obtained by passing $x$ through the deletion channel. In the relaxed problem of $approximate$ trace reconstruction, the…
Computer simulations of complex population genetic models are an essential tool for making sense of the large-scale datasets of multiple genome sequences from a single species that are becoming increasingly available. A widely used approach…
In this work we seek clusters of genomic words in human DNA by studying their inter-word lag distributions. Due to the particularly spiked nature of these histograms, a clustering procedure is proposed that first decomposes each…
We study the complexity of the problem of searching for a set of patterns that separate two given sets of strings. This problem has applications in a wide variety of areas, most notably in data mining, computational biology, and in…
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…