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

Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…

This paper describes PlinyCompute, a system for development of high-performance, data-intensive, distributed computing tools and libraries. In the large, PlinyCompute presents the programmer with a very high-level, declarative interface,…

Analyzing the increasingly large volumes of data that are available today, possibly including the application of custom machine learning models, requires the utilization of distributed frameworks. This can result in serious productivity…

To facilitate flexible and efficient structural bioinformatics analyses, new functionality for three-dimensional structure processing and analysis has been introduced into PyCogent -- a popular feature-rich framework for sequence-based…

Data preparation is a trial-and-error process that typically involves countless iterations over the data to define the best pipeline of operators for a given task. With tabular data, practitioners often perform that burdensome activity on…

The advent of modern data processing has led to an increasing tendency towards interdisciplinarity, which frequently involves the importation of different technical approaches. Consequently, there is an urgent need for a unified data…

Fast algorithms for the computation of $N$-body problems can be broadly classified into mesh-based interpolation methods, and hierarchical or multiresolution methods. To this last class belongs the well-known fast multipole method (FMM),…

In this work we present the development of a workflow based on Taverna which is going to be implemented for calculations in Phylogeny by means of the MrBayes tool. It has a friendly interface developed with the Gridsphere framework. The…

A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…

With the advancement of natural language generation (NLG) technologies, creative story generation systems have gained increasing attention. However, current systems often fail to accurately translate user intent into satisfactory story…

ControlBurn is a Python package to construct feature-sparse tree ensembles that support nonlinear feature selection and interpretable machine learning. The algorithms in this package first build large tree ensembles that prioritize basis…

Partial differential equations describing the dynamics of physical systems rarely have closed-form solutions. Fourier spectral methods, which use Fast Fourier Transforms (FFTs) to approximate solutions, are a common approach to solving…

In recent years, tree tensor network methods have proven capable of simulating quantum many-body and other high-dimensional systems. This work is a user guide to our Python library PyTreeNet. It includes code examples and exercises to…

Phylogenetic trees represent evolutionary relationships among sets of organisms. Popular phylogenetic reconstruction approaches typically yield hundreds to thousands of trees on a common leafset. Storing and sharing such large collection of…

The increasing risk of epidemics and a fast-growing world population has contributed to a great investment in phylogenetic analysis, in order to track numerous diseases and conceive effective medication and treatments. Phylogenetic analysis…

Evolutionary computation is an important component within various fields such as artificial intelligence research, reinforcement learning, robotics, industrial automation and/or optimization, engineering design, etc. Considering the…

Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…

In computational phylogenetics, the problem of constructing a supertree of a given set of rooted input trees can be formalized in different ways, to cope with contradictory information in the input. We consider the Minimum Flip Supertree…

Radio astronomy observatories with high throughput back end instruments require real-time data processing. While computing hardware continues to advance rapidly, development of real-time processing pipelines remains difficult and…

In this paper, we present a new Python library called mPyPl, which is intended to simplify complex data processing tasks using functional approach. This library defines operations on lazy data streams of named dictionaries represented as…