Related papers: Segmenting DNA sequence into `words'
The typical process for classifying and submitting a newly sequenced virus to the NCBI database involves two steps. First, a BLAST search is performed to determine likely family candidates. That is followed by checking the candidate…
The genome sequence contains the blueprint for governing cellular processes. While the availability of genomes has vastly increased over the last decades, experimental annotation of the various functional, non-coding and regulatory elements…
Segmenting text into Elemental Discourse Units (EDUs) is a fundamental task in discourse parsing. We present a new simple method for identifying EDU boundaries, and hence segmenting them, based on lexical and character n-gram features,…
Using basic properties of p-adic numbers, we consider a simple new approach to describe main aspects of DNA sequence and genetic code. Central role in our investigation plays an ultrametric p-adic information space which basic elements are…
Nanopore sequencing is an emerging new technology for sequencing DNA, which can read long fragments of DNA (~50,000 bases) in contrast to most current short-read sequencing technologies which can only read hundreds of bases. While nanopore…
DNA language models are increasingly used to represent genomic sequence, yet their effectiveness depends critically on how raw nucleotides are converted into model inputs. Unlike natural language, DNA offers no canonical boundaries, making…
We propose a solution on the stopping criterion in segmenting inhomogeneous DNA sequences with complex statistical patterns. This new stopping criterion is based on Bayesian Information Criterion (BIC) in the model selection framework. When…
We introduce a protein language model for determining the complete sequence of a peptide based on measurement of a limited set of amino acids. To date, protein sequencing relies on mass spectrometry, with some novel edman degregation based…
The prevalent technique for DNA sequencing consists of two main steps: shotgun sequencing, where many randomly located fragments, called reads, are extracted from the overall sequence, followed by an assembly algorithm that aims to…
This paper presents a model-based, unsupervised algorithm for recovering word boundaries in a natural-language text from which they have been deleted. The algorithm is derived from a probability model of the source that generated the text.…
Data-driven subword segmentation has become the default strategy for open-vocabulary machine translation and other NLP tasks, but may not be sufficiently generic for optimal learning of non-concatenative morphology. We design a test suite…
DNA codes have many applications, such as in data storage, DNA computing, etc. Good DNA codes have large sizes and satisfy some certain constraints. In this paper, we present a new construction method for reversible DNA codes. We show that…
In this paper, we introduce an unsupervised approach for Speech Segmentation, which builds on previously researched approaches, e.g., Speaker Diarization, while being applicable to an inclusive set of acoustic-semantic distinctions, paving…
Most previous approaches to Chinese word segmentation can be roughly classified into character-based and word-based methods. The former regards this task as a sequence-labeling problem, while the latter directly segments character sequence…
Statistical analysis of bacteria genomes texts has been performed on the basis of 20 complete genomes origin from Genebank. It has been revealed that the word ranked distributions are quite well approximated by logarithmic law. Results…
Microbial clades modeling is a challenging problem in biology based on microarray genome sequences, especially in new species gene isolates discovery and category. Marker family genome sequences play important roles in describing specific…
In this paper, fundamental limits in sequencing of a set of closely related DNA molecules are addressed. This problem is called pooled-DNA sequencing which encompasses many interesting problems such as haplotype phasing, metageomics, and…
Complexity metrics and machine learning (ML) models have been utilized to analyze the lengths of segmental genomic entities like: exons, introns, intergenic and repeat/unique DNA sequences, in each of the 22 human chromosomes. The purpose…
In array-based DNA synthesis, multiple strands of DNA are synthesized in parallel to reduce the time cost from the sum of their lengths to the length their shortest common supersequences. To maximize the amount of information that can be…
Molecule generation is a challenging open problem in cheminformatics. Currently, deep generative approaches addressing the challenge belong to two broad categories, differing in how molecules are represented. One approach encodes molecular…