Related papers: Segmenting DNA sequence into `words'
Large language models (LLMs) have notably enhanced the fluency and diversity of machine-generated text. However, this progress also presents a significant challenge in detecting the origin of a given text, and current research on detection…
Recent work on segmentation-free word embedding(sembei) developed a new pipeline of word embedding for unsegmentated language while avoiding segmentation as a preprocessing step. However, too many noisy n-grams existing in the embedding…
This thesis investigates how the sub-structure of words can be accounted for in probabilistic models of language. Such models play an important role in natural language processing tasks such as translation or speech recognition, but often…
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…
A number of bioinformatic or biostatistical methods are available for analyzing DNA copy number profiles measured from microarray or sequencing technologies. In the absence of rich enough gold standard data sets, the performance of these…
The statistical methods derived and described in this thesis provide new ways to elucidate the structural properties of text and other symbolic sequences. Generically, these methods allow detection of a difference in the frequency of a…
Objectives: The vast and complex nature of human genomic sequencing data presents challenges for effective analysis. This review aims to investigate the application of Natural Language Processing (NLP) techniques, particularly Large…
The codons, sixtyfour in number, are distributed over the coding parts of DNA sequences. The distribution function is the plot of frequency-versus-rank of the codons. These distributions are characterised by parameters that are almost…
We introduce and test a method to predict the sequence of DNA molecules from in silico unzipping experiments. The method is based on Bayesian inference and on the Viterbi decoding algorithm. The probability of misprediction decreases…
In this letter we present a very general method to extract information from a generic string of characters, e.g. a text, a DNA sequence or a time series. Based on data-compression techniques, its key point is the computation of a suitable…
Learning word representations has recently seen much success in computational linguistics. However, assuming sequences of word tokens as input to linguistic analysis is often unjustified. For many languages word segmentation is a…
Tools that effectively analyze and compare sequences are of great importance in various areas of applied computational research, especially in the framework of molecular biology. In the present paper, we introduce simple geometric criteria…
Gene regulation involves a hierarchy of events that extend from specific protein-DNA interactions to the combinatorial assembly of nucleoprotein complexes. The effects of DNA sequence on these processes have typically been studied based…
Given the lack of word delimiters in written Japanese, word segmentation is generally considered a crucial first step in processing Japanese texts. Typical Japanese segmentation algorithms rely either on a lexicon and syntactic analysis or…
We classify twenty-one Indo-European languages starting from written text. We use neural networks in order to define a distance among different languages, construct a dendrogram and analyze the ultrametric structure that emerges. Four or…
The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to…
With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, we need a revolutionary sequencing method for the…
Genomic (DNA) sequences encode an enormous amount of information for gene regulation and protein synthesis. Similar to natural language models, researchers have proposed foundation models in genomics to learn generalizable features from…
A common approach to quantifying DNA involves repeated cycles of DNA amplification. This approach, employed by the polymerase chain reaction (PCR), produces outputs that are corrupted by amplification noise, making it challenging to…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…