Related papers: Segmenting DNA sequence into `words'
Subwords have become the standard units of text in NLP, enabling efficient open-vocabulary models. With algorithms like byte-pair encoding (BPE), subword segmentation is viewed as a preprocessing step applied to the corpus before training.…
DNA microarray experiments, a well-established experimental technique, aim at understanding the function of genes in some biological processes. One of the most common experiments in functional genomics research is to compare two groups of…
Background: The inception of next generations sequencing technologies have exponentially increased the volume of biological sequence data. Protein sequences, being quoted as the `language of life', has been analyzed for a multitude of…
We study statistical properties of DNA chains of thirteen microbial complete genomes. We find that the power spectrum of several of the sequences studied flattens off in the low frequency limit. This implies that the correlation length in…
A rapid and low-cost method to sequence DNA would usher in a revolution in medicine. We propose and theoretically show the feasibility of a protocol for sequencing based on the distributions of transverse electrical currents of…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
Sequence segmentation is a well-studied problem, where given a sequence of elements, an integer K, and some measure of homogeneity, the task is to split the sequence into K contiguous segments that are maximally homogeneous. A classic…
Motivation: Array Comparative Genomic Hybridization (aCGH) is used to scan the entire genome for variations in DNA copy number. A central task in the analysis of aCGH data is the segmentation into groups of probes sharing the same DNA copy…
The frequency distributions of DNA k-mers are shaped by fundamental biological processes and offer a window into genome structure and evolution. Inspired by analogies to natural language, prior studies have attempted to model genomic k-mer…
Recent work on unsupervised speech segmentation has used self-supervised models with phone and word segmentation modules that are trained jointly. This paper instead revisits an older approach to word segmentation: bottom-up phone-like unit…
In this paper we treat some fractal and statistical features of the DNA sequences. First, a fractal record model of DNA sequence is proposed by mapping DNA sequences to integer sequences, followed by R/S analysis of the model and…
In this article, we investigate the properties of phoneme N-grams across half of the world's languages. We investigate if the sizes of three different N-gram distributions of the world's language families obey a power law. Further, the…
We analyze the structure of DNA molecules of different organisms by using the additive Markov chain approach. Transforming nucleotide sequences into binary strings, we perform statistical analysis of the corresponding "texts". We develop…
The DNA storage channel is considered, in which a codeword is comprised of $M$ unordered DNA molecules. At reading time, $N$ molecules are sampled with replacement, and then each molecule is sequenced. A coded-index concatenated-coding…
We study the amount of reliable information that can be stored in a DNA-based storage system composed of short DNA molecules. In this regime, Shomorony and Heckel (2022) put forward a conjecture on the scaling of the number of information…
We propose a novel semantic segmentation algorithm by learning a deconvolution network. We learn the network on top of the convolutional layers adopted from VGG 16-layer net. The deconvolution network is composed of deconvolution and…
Chinese word segmentation and part-of-speech tagging are necessary tasks in terms of computational linguistics and application of natural language processing. Many re-searchers still debate the demand for Chinese word segmentation and…
DNA sequences are prone to creating secondary structures by folding back on themselves by non-specific hybridization among its nucleotides. The formation of secondary structures makes the sequences chemically inactive towards synthesis and…
Speech Segmentation is the process change point detection for partitioning an input audio stream into regions each of which corresponds to only one audio source or one speaker. One application of this system is in Speaker Diarization…
Recent studies on direct speech translation show continuous improvements by means of data augmentation techniques and bigger deep learning models. While these methods are helping to close the gap between this new approach and the more…