Related papers: Making mathematical online resources FAIR: at the …
The idea that all life on earth traces back to a common beginning dates back at least to Charles Darwin's {\em Origin of Species}. Ever since, biologists have tried to piece together parts of this `tree of life' based on what we can observe…
The FAIR (Findable, Accessible, Interoperable, Reusable) data principles are fundamental for climate researchers and all stakeholders in the current digital ecosystem. In this paper, we demonstrate how relational climate data can be "FAIR"…
Academic literature retrieval is concerned with the selection of papers that are most likely to match a user's information needs. Most of the retrieval systems are limited to list-output models, in which the retrieval results are isolated…
Phylogenetic inference, the task of reconstructing how related sequences evolved from common ancestors, is a central objective in evolutionary genomics. The current state-of-the-art methods exploit probabilistic models of sequence evolution…
The FAIR Principles are a set of good practices to improve the reproducibility and quality of data in an Open Science context. Different sets of indicators have been proposed to evaluate the FAIRness of digital objects, including datasets…
The aim of this review is to present and analyze the probabilistic models of mathematical phylogenetics which have been intensively used in recent years in biology as the cornerstone of attempts to infer and reconstruct the ancestral…
In the last decade, some algebraic tools have been successfully applied to phylogenetic reconstruction. These tools are mainly based on the knowledge of equations describing algebraic varieties associated to phylogenetic trees evolving…
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…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, like recombination between genes, hybridization between lineages, and lateral gene…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
Phylogenetics begins with reconstructing biological family trees from genetic data. Since Nature is not limited to tree-like histories, we use networks to organize our data, and have discovered new polytopes, metric spaces, and simplicial…
The prosperity and lifestyle of our society are very much governed by achievements in condensed matter physics, chemistry and materials science, because new products for sectors such as energy, the environment, health, mobility and…
Despite much creative work on methods and tools, reproducibility -- the ability to repeat the computational steps used to obtain a research result -- remains elusive. One reason for these difficulties is that extant tools for capturing…
We are facing a real challenge when coping with the continuous acceleration of scientific production and the increasingly changing nature of science. In this article, we extend the classical framework of co-word analysis to the study of…
Based on decision trees, many fields have arguably made tremendous progress in recent years. In simple words, decision trees use the strategy of "divide-and-conquer" to divide the complex problem on the dependency between input features and…
A foundational set of findable, accessible, interoperable, and reusable (FAIR) principles were proposed in 2016 as prerequisites for proper data management and stewardship, with the goal of enabling the reusability of scholarly data. The…
This chapter addresses the forth paradigm of materials research -- big-data driven materials science. Its concepts and state-of-the-art are described, and its challenges and chances are discussed. For furthering the field, Open Data and an…
In the last years, algebraic tools have been proven useful in phylogenetic reconstruction and model selection through the study of phylogenetic invariants. However, up to now, the models studied from an algebraic viewpoint are either too…
We present the first sub-quadratic time algorithm that with high probability correctly reconstructs phylogenetic trees for short sequences generated by a Markov model of evolution. Due to rapid expansion in sequence databases, such very…
In this paper, I summarize our work on online fair division. In particular, I present two models for online fair division: (1) one existing model for fair division in food banks and (2) one new model for fair division of deceased organs to…