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A new method to identify all sufficiently long repeating substrings in one or several symbol sequences is proposed. The method is based on a specific gauge applied to symbol sequences that guarantees identification of the repeating…
Fast radio bursts (FRBs) are bright, millisecond-duration radio pulses whose origins are unknown. To date, only one (FRB 121102) out of several dozen has been seen to repeat, though the extent to which it is exceptional remains unclear. We…
In computational biology and bioinformatics, the manner to understand evolution processes within various related organisms paid a lot of attention these last decades. However, accurate methodologies are still needed to discover genes…
When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…
We consider the problem of identifying whether findings replicate from one study of high dimension to another, when the primary study guides the selection of hypotheses to be examined in the follow-up study as well as when there is no…
We analyze the convergence rate of a simplified version of a popular Gibbs sampling method used for statistical discovery of gene regulatory binding motifs in DNA sequences. This sampler satisfies a very strong form of ergodicity (uniform).…
Large-scale biobanks are being collected around the world in efforts to better understand human health and risk factors for disease. They often survey hundreds of thousands of individuals, combining questionnaires with clinical, genetic,…
Sequence comparison is a widely used computational technique in modern molecular biology. In spite of the frequent use of sequence comparisons the important problem of assigning statistical significance to a given degree of similarity is…
In this paper, a novel method for automatic planogram compliance checking in retail chains is proposed without requiring product template images for training. Product layout is extracted from an input image by means of unsupervised…
Genome wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene by gene basis that need to be clustered into regulons. Using the assumption that regulatory sites can be represented as…
Leveraging the disparity information from both left and right views is crucial for stereo disparity estimation. Left-right consistency check is an effective way to enhance the disparity estimation by referring to the information from the…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
A fundamental property of DNA is that the reverse complement (RC) of a sequence often carries identical biological meaning. However, state-of-the-art DNA language models frequently fail to capture this symmetry, producing inconsistent…
Background: The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required…
Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…
Generative techniques continue to evolve at an impressively high rate, driven by the hype about these technologies. This rapid advancement severely limits the application of deepfake detectors, which, despite numerous efforts by the…
Tandem repeats in proteins identification, classification and curation is a complex process that requires manual processing from experts, processing power and time. There are recent and relevant advances applying machine learning for…
This paper focuses on pattern matching in the DNA sequence. It was inspired by a previously reported method that proposes encoding both pattern and sequence using prime numbers. Although fast, the method is limited to rather small pattern…
Subgraph matching is a fundamental problem in graph analysis with a wide range of applications. However, due to its inherent NP-hardness, enumerating subgraph matches efficiently on large real-world graphs remains highly challenging. Most…
Purpose: In many clinical MRI scenarios, existing imaging information can be used to significantly shorten acquisition time or to improve Signal to Noise Ratio (SNR). In this paper the authors present a framework for fast MRI by exploiting…