Related papers: Making mathematical online resources FAIR: at the …

Phylogenetic trees are pervasively used to depict evolutionary relationships. Increasingly, researchers need to visualize large trees and compare multiple large trees inferred for the same set of taxa (reflecting uncertainty in the tree…

This paper addresses the issue of making legacy information (that material held in paper format only) electronically searchable and retrievable. We used proprietary software and commercial hardware to create a process for scanning,…

From the era of big science we are back to the "do it yourself", where you do not have any money to buy clusters or subscribe to grids but still have algorithms that crave many computing nodes and need them to measure scalability.…

This work proposes an algebraic model for classical information theory. We first give an algebraic model of probability theory. Information theoretic constructs are based on this model. In addition to theoretical insights provided by our…

Inferring evolutionary histories (phylogenetic trees) has important applications in biology, criminology and public health. However, phylogenetic trees are complex mathematical objects that reside in a non-Euclidean space, which complicates…

While extensive guidance exists for ensuring the reproducibility of one's own study, there is little discussion regarding the reproduction and replication of external studies within one's own research. To initiate this discussion, drawing…

MathRepo, located at https://mathrepo.mis.mpg.de, is an online repository for mathematical research data. In mathematics, research data comes in many different flavours. For instance, in computer algebra it most often takes the form of…

Data analytics often involves hypothetical reasoning: repeatedly modifying the data and observing the induced effect on the computation result of a data-centric application. Previous work has shown that fine-grained data provenance can help…

Reconstructing pathogen dynamics from genetic data as they become available during an outbreak or epidemic represents an important statistical scenario in which observations arrive sequentially in time and one is interested in performing…

Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…

We introduce a boosting algorithm to pre-process data for fairness. Starting from an initial fair but inaccurate distribution, our approach shifts towards better data fitting while still ensuring a minimal fairness guarantee. To do so, it…

The ubiquity of computation in modern scientific research inflicts new challenges for reproducibility. While most journals now require code and data be made available, the standards for organization, annotation, and validation remain lax,…

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…

Context: Mining software repositories is a popular means to gain insights into a software project's evolution, monitor project health, support decisions and derive best practices. Tools supporting the mining process are commonly applied by…

Accessing research data at any time is what FAIR (Findable Accessible Interoperable Reusable) data sharing aims to achieve at scale. Yet, we argue that it is not sustainable to keep accumulating and maintaining all datasets for rapid…

Polyploidization is an important evolutionary process which affects organisms ranging from plants to fish and fungi. The signal left behind by it is in the form of a species' ploidy level (number of complete chromosome sets found in a cell)…

Open science represents a transformative research approach essential for enhancing sustainability and impact. Data generation encompasses various methods, from automated processes to human-driven inputs, creating a rich and diverse…

Obtaining a relevant dataset is central to conducting empirical studies in software engineering. However, in the context of mining software repositories, the lack of appropriate tooling for large scale mining tasks hinders the creation of…

The amount of completely sequenced chloroplast genomes increases rapidly every day, leading to the possibility to build large scale phylogenetic trees of plant species. Considering a subset of close plant species defined according to their…

An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…