相关论文: Detecting Mutations by eBWT

Some recent results have introduced external-memory algorithms to compute self-indexes of a set of strings, mainly via computing the Burrows-Wheeler Transform (BWT) of the input strings. The motivations for those results stem from…

Genome Wide Association Studies (GWAS) and eQTL analyses have produced a large and growing number of genetic associations linked to a wide range of human phenotypes. As of 2013, there were more than 11,000 SNPs associated with a trait as…

Humans have $23$ pairs of homologous chromosomes. The homologous pairs are almost identical pairs of chromosomes. For the most part, differences in homologous chromosome occur at certain documented positions called single nucleotide…

Constructing the Burrows-Wheeler transform (BWT) for long strings poses significant challenges regarding construction time and memory usage. We use a prefix of the suffix array to partition a long string into shorter substrings, thereby…

Finite mixture models are frequently used to uncover latent structures in high-dimensional datasets (e.g.\ identifying clusters of patients in electronic health records). The inference of such structures can be performed in a Bayesian…

Several modern genomic technologies, such as DNA-Methylation arrays, measure spatially registered probes that number in the hundreds of thousands across multiplechromosomes. The measured probes are by themselves less interesting…

DNA sequence classification requires not only high predictive accuracy but also the ability to uncover latent site interactions, combinatorial regulation, and epistasis-like higher-order dependencies. Although the standard Transformer…

Computational methods for discovering patterns of local correlations in sequences are important in computational biology. Here we show how to determine the optimal partitioning of aligned sequences into non-overlapping segments such that…

In this study we map out the large-scale structure of citation networks of science journals and follow their evolution in time by using stochastic block models (SBMs). The SBM fitting procedures are principled methods that can be used to…

Machine learning is becoming an increasingly valuable tool in mathematics, enabling one to identify subtle patterns across collections of examples so vast that they would be impossible for a single researcher to feasibly review and analyze.…

We propose a deep and interpretable probabilistic generative model to analyze glyph shapes in printed Early Modern documents. We focus on clustering extracted glyph images into underlying templates in the presence of multiple confounding…

This paper presents a new approach to non-parametric cluster analysis called Adaptive Weights Clustering (AWC). The idea is to identify the clustering structure by checking at different points and for different scales on departure from…

We study how the application of injective morphisms affects the number $r$ of equal-letter runs in the Burrows-Wheeler Transform (BWT). This parameter has emerged as a key repetitiveness measure in compressed indexing. We focus on the…

The paramount importance of replicating associations is well recognized in the genome-wide associaton (GWA) research community, yet methods for assessing replicability of associations are scarce. Published GWA studies often combine…

The Positional Burrows--Wheeler Transform (PBWT) is a data structure designed for efficiently representing and querying large collections of sequences, such as haplotype panels in genomics. Forward and backward stepping operations --…

Methods that generate networks sharing a given degree distribution and global clustering can induce changes in structural properties other than that controlled for. Diversity in structural properties, in turn, can affect the outcomes of…

DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…

The detailed analysis of molecular structures and properties holds great potential for drug development discovery through machine learning. Developing an emergent property in the model to understand molecules would broaden the horizons for…

Genome-Wide Association Studies (GWAS) help identify genetic variations in people with diseases such as Parkinson's disease (PD), which are less common in those without the disease. Thus, GWAS data can be used to identify genetic variations…

The k-spectrum of a string is the set of all distinct substrings of length k occurring in the string. K-spectra have many applications in bioinformatics including pseudoalignment and genome assembly. The Spectral Burrows-Wheeler Transform…