9 papers · ranked by Valyu relevance
Erik S. Parker, Lilian Golzarri-Arroyo, Stephanie Dickinson, Beate Henschel + 6 more
Clustering effects, such as those introduced by housing animals in shared cages, are often overlooked in preclinical lifespan studies, despite their potential to distort variance estimates and inflate Type I error rates, leading to misleading conclusions. This methodological oversight reduces statistical rigor and may…
Isaac Virshup, Sergei Rybakov, Fabian J. Theis, Philipp Angerer + 1 more
anndata is a Python package for handling annotated data matrices in memory and on disk (github.com/theislab/anndata), positioned between pandas and xarray. anndata offers a broad range of computationally efficient features including, among others, sparse data support, lazy operations, and a PyTorch interface.…
Phillip P. A. Staniczenko, Debabrata Panja
Nestedness is a common property of communication, finance, trade, and ecological networks. In networks with high levels of nestedness, the link positions of low-degree nodes (those with few links) form nested subsets of the link positions of high-degree nodes (those with many links), leading to matrix representations…
Thi Minh Thao Le, Sten Madec, Erida Gjini
How does coexistence of multiple species or pathogen strains arise in a system? What do coexistence patterns in time and space reveal about the epidemiology, ecology and evolution of such systems? Species abundance patterns often defy fully mechanistic explanations, especially when compositional variation and relative…
Ehsan Zangene, Veit Schwämmle, Mohieddin Jafari
Missing data is often treated as a nuisance, routinely imputed or excluded from statistical analyses, especially in nominal datasets where its structure cannot be easily modeled. However, the form of missingness itself can reveal hidden relationships, substructures, and biological or operational constraints within a…
Connor Bernard, Gabriel Silva Santos, Jacques Deere, Roberto Rodriguez-Caro + 5 more
The ecological sciences have joined the big data revolution. However, despite exponential growth in data availability, broader interoperability amongst datasets is still needed to unlock the potential of open access. The interface of demography and functional traits is well-positioned to benefit from said…
Elizabeth Wenk, Payal Bal, David Coleman, Rachael Gallagher + 2 more
Trait databases have proliferated over the past decades, facilitating research on the ecology, evolution, and conservation of taxa across the Tree of Life. Typically, teams of independent researchers build these databases, and each must develop their own workflow and output structure. This divests research hours from…
Felix Wiegand, David Lähnemann, Felix Mölder, Hamdiye Uzuner + 3 more
Tabular data, often scattered across multiple tables, is the primary output of data analyses in virtually all scientific fields. Exchange and communication of tabular data is therefore a central challenge. We present Datavzrd, a tool for creating portable, visually rich, interactive reports from tabular data in any…
Patrick Scheibe, Jana Schor
Scientific knowledge is increasingly captured in structured formats, such as knowledge graphs, yet it remains largely inaccessible to non-technical users. We present EcoToxFred, a prototype conversational AI agent that enables intuitive, natural language access to curated environmental toxicology data. Designed to…