Related papers: Making mathematical online resources FAIR: at the …
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…
By providing a framework of accounting for the shared ancestry inherent to all life, phylogenetics is becoming the statistical foundation of biology. The importance of model choice continues to grow as phylogenetic models continue to…
Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…
Quality assessment of Research Software Engineering (RSE) plays an important role in all scientific fields. From the canonical three criteria (reliability, validity, and objectivity) previous research has focussed on reliability and the…
One of the foundations of science is that researchers must publish the methodology used to achieve their results so that others can attempt to reproduce them. This has the added benefit of allowing methods to be adopted and adapted for…
To fully exploit the potential of computational phylogenetic methods for cognate data one needs to leverage specific (complex) models an machine learning-based techniques. However, both approaches require datasets that are substantially…
The first step in a science project is the acquisition and understanding of the relevant data. This paper outlines the results of a project to design and test network tools specifically oriented at retrieving astronomical data. The tools…
With distributed computing and mobile applications, synchronizing diverging replicas of data structures is a more and more common problem. We use algebraic methods to reason about filesystem operations, and introduce a simplified definition…
Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources…
Motivation: The abundance of gene flow in the Tree of Life challenges the notion that evolution can be represented with a fully bifurcating process, as this process cannot capture important biological realities like hybridization,…
Computational workflows represent major investments of effort and expertise. As first-class, publishable research objects of their own, they are key to sharing methodological know-how for reuse, reproducibility, and transparency. Thus, the…
We consider the problem of online allocation (matching and assortments) of reusable resources where customers arrive sequentially in an adversarial fashion and allocated resources are used or rented for a stochastic duration that is drawn…
Although a standard in natural science, reproducibility has been only episodically applied in experimental computer science. Scientific papers often present a large number of tables, plots and pictures that summarize the obtained results,…
Phylogenetic trees are the fundamental mathematical representation of evolutionary processes in biology. They are also objects of interest in pure mathematics, such as algebraic geometry and combinatorics, due to their discrete geometry.…
Phylogenetic networks are a special type of graph which generalize phylogenetic trees and that are used to model non-treelike evolutionary processes such as recombination and hybridization. In this paper, we consider {\em unrooted}…
Comparative and evolutive ecologists are interested in the distribution of quantitative traits among related species. The classical framework for these distributions consists of a random process running along the branches of a phylogenetic…
It is essential for the advancement of science that scientists and researchers share, reuse and reproduce workflows and protocols used by others. The FAIR principles are a set of guidelines that aim to maximize the value and usefulness of…
The use of machine learning algorithms in finance, medicine, and criminal justice can deeply impact human lives. As a consequence, research into interpretable machine learning has rapidly grown in an attempt to better control and fix…
Scientific reasoning requires not only long-chain reasoning processes, but also knowledge of domain-specific terminologies and adaptation to updated findings. To deal with these challenges for scientific reasoning, we introduce RAISE, a…
The classical Fourier transform is, in essence, a way to take data and extract components (in the form of complex exponentials) which are invariant under cyclic shifts. We consider a case in which the components must instead be invariant…