相关论文: KGP: An R Package with Metadata from the 1000 Geno…
Current Y chromosome research is limited in the poor resolution of Y chromosome phylogenetic tree. Entirely sequenced Y chromosomes in numerous human individuals have only recently become available by the advent of next-generation…
Recent interest in building foundation models for KGs has highlighted a fundamental challenge: knowledge-graph data is relatively scarce. The best-known KGs are primarily human-labeled, created by pattern-matching, or extracted using early…
This paper introduces Multi-population Ensemble Genetic Programming (MEGP), a computational intelligence framework that integrates cooperative coevolution and the multiview learning paradigm to address classification challenges in…
Summary: BGT is a compact format, a fast command line tool and a simple web application for efficient and convenient query of whole-genome genotypes and frequencies across tens to hundreds of thousands of samples. On real data, it encodes…
Processing high-throughput DNA sequencing data of individuals or populations requires stringing together independent software tools with many parameters, often leading to non-reproducible pipelines and datasets. We developed grenepipe to…
This paper reviews strategies for solving problems encountered when analyzing large genomic data sets and describes the implementation of those strategies in R by packages from the Bioconductor project. We treat the scalable processing,…
Genetic Programming, a kind of evolutionary computation and machine learning algorithm, is shown to benefit significantly from the application of vectorized data and the TensorFlow numerical computation library on both CPU and GPU…
In this research, we present a comprehensive, longitudinal empirical summary of the R package ecosystem, including not just CRAN, but also Bioconductor and GitHub. We analyze more than 25,000 packages, 150,000 releases, and 15 million files…
We introduce TurboGP, a Genetic Programming (GP) library fully written in Python and specifically designed for machine learning tasks. TurboGP implements modern features not available in other GP implementations, such as island and cellular…
Building high-quality knowledge graphs (KGs) from diverse sources requires combining methods for information extraction, data transformation, ontology mapping, entity matching, and data fusion. Numerous methods and tools exist for each of…
Research done using model organisms has been fundamental to the biological understanding of human genes, diseases and phenotypes. Model organisms provide tractable systems for experiments to enhance understanding of biological mechanisms…
Rgbp is an R package that provides estimates and verifiable confidence intervals for random effects in two-level conjugate hierarchical models for overdispersed Gaussian, Poisson, and Binomial data. Rgbp models aggregate data from k…
We present SemRepo, an RDF knowledge graph comprising over 81 million triples describing nearly 200,000 GitHub repositories associated with scientific research. SemRepo captures repository-level metadata, such as contributors, issues, and…
The Genographic Project is an international effort using genetic data to chart human migratory history. The project is non-profit and non-medical, and through its Legacy Fund supports locally led efforts to preserve indigenous and…
Detecting changepoints in a time series of length $N$ entails evaluating up to $2^{N-1}$ possible changepoint models, making exhaustive enumeration computationally infeasible. Genetic algorithms (GAs) provide a stochastic way to identify…
Being able to store and transmit human genome sequences is an important part in genomic research and industrial applications. The complete human genome has 3.1 billion base pairs (haploid), and storing the entire genome naively takes about…
The usefulness of a `total-evidence' approach to human population genetics was assessed through a clustering analysis of combined genome-wide SNP datasets. The combination contained only 3146 SNPs. Detailed examination of the results…
Population size estimation is a major challenge in official statistics, social sciences, and natural sciences. The problem can be tackled by applying capture-recapture methods, which vary depending on the number of sources used,…
Since the arrival of next-generation sequencing technologies the amount of genetic sequencing data has increased dramatically. This has has fueled an increase in human genetics research. At the same time, with the recent advent of…
RNA-KG is a recently developed knowledge graph that integrates the interactions involving coding and non-coding RNA molecules extracted from public data sources. It can be used to support the classification of new molecules, identify new…