相关论文: PhyloFrame: A DataFrame-based Library for Fast, Fl…

The Persistent-Phylogeny Model is an extension of the widely studied Perfect-Phylogeny Model, encompassing a broader range of evolutionary phenomena. Biological and algorithmic questions concerning persistent phylogeny have been intensely…

Deep learning-based vision is characterized by intricate frameworks that often necessitate a profound understanding, presenting a barrier to newcomers and limiting broad adoption. With many researchers grappling with the constraints of…

Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of…

The recomputability and reproducibility of results from scientific software requires access to both the source code and all associated input and output data. However, the full collection of these resources often does not accompany the key…

This paper proposes FREEtree, a tree-based method for high dimensional longitudinal data with correlated features. Popular machine learning approaches, like Random Forests, commonly used for variable selection do not perform well when there…

Pattern-based file access is a fundamental but often under-documented aspect of computational research. The Python glob module provides a simple yet powerful way to search, filter, and ingest files using wildcard patterns, enabling scalable…

Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…

Dataframes are a popular abstraction to represent, prepare, and analyze data. Despite the remarkable success of dataframe libraries in Rand Python, dataframes face performance issues even on moderately large datasets. Moreover, there is…

Machine learning has proved to be a useful tool for extracting knowledge from scientific data in numerous research fields, including astrophysics, genomics, and molecular dynamics. Often, data sets from these research areas need to be…

A large amount of data is produced every second from modern information systems such as mobile devices, the world wide web, Internet of Things, social media, etc. Analysis and mining of this massive data requires a lot of advanced tools and…

Since the advent of modern bioinformatics, the challenging, multifaceted problem of reconstructing phylogenetic history from biological sequences has hatched perennial statistical and algorithmic innovation. Studies of the phylogenetic…

Gradients of probabilistic model likelihoods with respect to their parameters are essential for modern computational statistics and machine learning. These calculations are readily available for arbitrary models via automatic…

Bibliometric analysis is a critical tool for understanding the structure, dynamics, and impact of scientific research. Traditional methods often fall short in capturing the intricate relationships and evolving trends within scientific…

Phylogenetic trees are widely used to display estimates of how groups of species evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees…

Machine learning solutions are very popular in the field of chemoinformatics, where they have numerous applications, such as novel drug discovery or molecular property prediction. Molecular fingerprints are algorithms commonly used for…

ProSper is a python library containing probabilistic algorithms to learn dictionaries. Given a set of data points, the implemented algorithms seek to learn the elementary components that have generated the data. The library widens the scope…

The data science community today has embraced the concept of Dataframes as the de facto standard for data representation and manipulation. Ease of use, massive operator coverage, and popularization of R and Python languages have heavily…

Taxonomies represent an arborescence hierarchical structure that establishes relationships among entities to convey knowledge within a specific domain. Each edge in the taxonomy signifies a hypernym-hyponym relationship. Taxonomies find…

Agent-based simulation platforms play a key role in enabling fast-to-run evolution experiments that can be precisely controlled and observed in detail. Availability of high-resolution snapshots of lineage ancestries from digital…

Phylogenomic approaches developed thus far are either too time-consuming or lack a solid evolutionary basis. Moreover, no phylogenomic approach is capable of constructing a tree directly from unassembled raw sequencing data. A new…