Related papers: Indexing Finite Language Representation of Populat…
The aim of this paper is to provide a resampling technique that allows us to make inference on superpopulation parameters in finite population setting. Under complex sampling designs, it is often difficult to obtain explicit results about…
Automaton models are often seen as interpretable models. Interpretability itself is not well defined: it remains unclear what interpretability means without first explicitly specifying objectives or desired attributes. In this paper, we…
Index structures are a building block of query processing and computer science in general. Since the dawn of computer technology there have been index structures. And since then, a myriad of index structures are being invented and published…
Sequence discriminative training is a great tool to improve the performance of an automatic speech recognition system. It does, however, necessitate a sum over all possible word sequences, which is intractable to compute in practice.…
The deterministic selection-recombination equation describes the evolution of the genetic type composition of a population under selection and recombination in a law of large numbers regime. So far, an explicit solution has seemed out of…
The linking genotype to phenotype is the fundamental aim of modern genetics. We focus on study of links between gene expression data and phenotype data through integrative analysis. We propose three approaches. 1) The inherent complexity of…
Relation of genome sizes to organisms complexity is still described rather equivocally. Neither the number of genes (G-value), nor the total amount of DNA (C-value) correlates consistently with phenotype complexity. Using information theory…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
The complex correlation structure of a collection of orthologous DNA sequences is uniquely captured by the "ancestral recombination graph" (ARG), a complete record of coalescence and recombination events in the history of the sample.…
Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical…
Modern biological techniques enable very dense genetic sampling of unfolding evolutionary histories, and thus frequently sample some genotypes multiple times. This motivates strategies to incorporate genotype abundance information in…
Populations evolving under the joint influence of recombination and resampling (traditionally known as genetic drift) are investigated. First, we summarise and adapt a deterministic approach, as valid for infinite populations, which assumes…
There now exist compact indexes that can efficiently list all the occurrences of a pattern in a dataset consisting of thousands of genomes, or even all the occurrences of all the pattern's maximal exact matches (MEMs) with respect to the…
Exact string matching has been a fundamental problem in computer science for decades because of many practical applications. Some are related to common procedures, such as searching in files and text editors, or, more recently, to more…
Accurate identification of haplotypes in sequenced human genomes can provide invaluable information about population demography and fine-scale correlations along the genome, thus empowering both population genomic and medical association…
Generative models, widely utilized in various applications, can often struggle with prompts corresponding to partial tokens. This struggle stems from tokenization, where partial tokens fall out of distribution during inference, leading to…
Repetitive elements are important in genomic structures, functions and regulations, yet effective methods in precisely identifying repetitive elements in DNA sequences are not fully accessible, and the relationship between repetitive…
We obtain an index of the complexity of a random sequence by allowing the role of the measure in classical probability theory to be played by a function we call the generating mechanism. Typically, this generating mechanism will be a finite…
Clinical adoption of human genome sequencing requires methods with known accuracy of genotype calls at millions or billions of positions across a genome. Previous work showing discordance amongst sequencing methods and algorithms has made…
An approach based on using the idea of distinguished coding phase in explicit form for identification of protein-coding regions (exons) in whole genome has been proposed. For several genomes an optimal window length for averaging GC-content…