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Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names.…
Query evaluation in monadic second-order logic (MSO) is tractable on trees and treelike instances, even though it is hard for arbitrary instances. This tractability result has been extended to several tasks related to query evaluation, such…
Automatic phylogenetic inference plays an increasingly important role in computational historical linguistics. Most pertinent work is currently based on expert cognate judgments. This limits the scope of this approach to a small number of…
Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees…
In the field of wildlife observation and conservation, approaches involving machine learning on audio recordings are becoming increasingly popular. Unfortunately, available datasets from this field of research are often not optimal learning…
The PHASE software package allows phylogenetic tree construction with a number of evolutionary models designed specifically for use with RNA sequences that have conserved secondary structure. Evolution in the paired regions of RNAs occurs…
In recent years, bio-inspired optimization methods, which mimic biological processes to solve complex problems, have gained popularity in recent literature. The proliferation of proposals prove the growing interest in this field. The…
Long-term data-driven studies have become indispensable in many areas of science. Often, the data formats, structures and semantics of data change over time, the data sets evolve. Therefore, studies over several decades in particular have…
Scientific names of organisms consist of a genus name and a species epithet, with the latter often reflecting aspects such as morphology, ecology, distribution, and cultural background. Traditionally, researchers have manually labeled…
Category fluency is a widely studied cognitive phenomenon, yet two conflicting accounts have been proposed as the underlying retrieval mechanism -- an optimal foraging process deliberately searching through memory (Hills et al., 2012) and a…
Provenance, or information about the origin or derivation of data, is important for assessing the trustworthiness of data and identifying and correcting mistakes. Most prior implementations of data provenance have involved heavyweight…
Multi-label classification consists in classifying an instance into two or more classes simultaneously. It is a very challenging task present in many real-world applications, such as classification of biology, image, video, audio, and text.…
Having a unified, coherent taxonomy is essential for effective knowledge representation in domain-specific applications as diverse terminologies need to be mapped to underlying concepts. Traditional manual approaches to taxonomy alignment…
Biological and artificial information processing systems form representations of the world that they can use to categorize, reason, plan, navigate, and make decisions. How can we measure the similarity between the representations formed by…
Multimodal large language models increasingly solve vision-centric tasks by calling external tools for visual inspection, OCR, retrieval, calculation, and multi-step reasoning. Current tool-using agents usually expose the executed tool…
Phylogeny can be inferred using two sources of data from an organism: morphological data and molecular data. Historically, phylogenies were usually inferred using morphological characters, but some morphological features may not necessarily…
The inference of new information on the relatedness of species by phylogenetic trees based on DNA data is one of the main challenges of modern biology. But despite all technological advances, DNA sequencing is still a time-consuming and…
Sound correspondence patterns form the basis of cognate detection and phonological reconstruction in historical language comparison. Methods for the automatic inference of correspondence patterns from phonetically aligned cognate sets have…
Machine Learning (ML) has already fundamentally changed several businesses. More recently, it has also been profoundly impacting the computational science and engineering domains, like geoscience, climate science, and health science. In…
Free associations have been extensively used in cognitive psychology and linguistics for studying how conceptual knowledge is organized. Recently, the potential of applying a similar approach for investigating the knowledge encoded in LLMs…