Related papers: The Capacity of String-Replication Systems
This paper considers the problem of matching fragment to organism using its complete genome. Our method is based on the probability measure representation of a genome. We first demonstrate that these probability measures can be modelled as…
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…
DNA synthesis is considered as one of the most expensive components in current DNA storage systems. In this paper, focusing on a common synthesis machine, which generates multiple DNA strands in parallel following a fixed supersequence,we…
Fundamental to quantitative characterization of the B cell receptor repertoire is clonal diversity - the number of distinct somatically recombined receptors present in the repertoire and their relative abundances, defining the search space…
The T-cell (TCR) repertoire relies on the diversity of receptors composed of two chains, called $\alpha$ and $\beta$, to recognize pathogens. Using results of high throughput sequencing and computational chain-pairing experiments of human…
We present a new data structure called the \emph{Compressed Random Access Memory} (CRAM) that can store a dynamic string $T$ of characters, e.g., representing the memory of a computer, in compressed form while achieving asymptotically…
Motivated by studies of data retrieval in polymer-based storage systems, we consider the problem of reconstructing a multiset of binary strings that have the same length and the same weight from the compositions of their prefixes and…
Traditional studies of memory for meaningful narratives focus on specific stories and their semantic structures but do not address common quantitative features of recall across different narratives. We introduce a statistical ensemble of…
Generative models reliant on sequential autoregression have been at the forefront of language generation for an extensive period, particularly following the introduction of widely acclaimed transformers. Despite its excellent performance,…
We explore the large-scale behavior of nucleotide compositional strand asymmetries along human chromosomes. As we observe for 7 of 9 origins of replication experimentally identified so far, the (TA+GC) skew displays rather sharp upward…
Replication of genetic material is an important process for all living organisms. Origins of replication initiate the copying of DNA at many points on a chromosome, and it is the distribution of these points that is relevant here, as it…
We introduce a population dynamics model, where individual genomes are represented by bit-strings. Selection is described by death probabilities which depend on these genomes, and new individuals continuously replace the ones that die,…
This paper shows how Long Short-term Memory recurrent neural networks can be used to generate complex sequences with long-range structure, simply by predicting one data point at a time. The approach is demonstrated for text (where the data…
High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads…
This work uses a simple quantum computer model to discuss the randomness of bit strings originated from integer sequences. The considered quantum computer model has three elements: a processing unit responsible for a mathematical operation,…
The chain-structured long short-term memory (LSTM) has showed to be effective in a wide range of problems such as speech recognition and machine translation. In this paper, we propose to extend it to tree structures, in which a memory cell…
String barcoding is a recently introduced technique for genomic-based identification of microorganisms. In this paper we describe the engineering of highly scalable algorithms for robust string barcoding. Our methods enable distinguisher…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
In synchronous rewriting, the productions of two rewriting systems are paired and applied synchronously in the derivation of a pair of strings. We present a new synchronous rewriting system and argue that it can handle certain phenomena…
Out-of-distribution generalization capabilities of sequence-to-sequence models can be studied from the lens of two crucial forms of generalization: length generalization -- the ability to generalize to longer sequences than ones seen during…