相关论文: Taxonomic Provenance: Two Influential Primate Clas…
Current comparisons of large reasoning models (LRMs) focus on macro-level statistics such as task accuracy or reasoning length. Whether different LRMs reason differently remains an open question. To address this gap, we introduce the…
Provenance information are essential for the traceability of scientific studies or experiments and thus crucial for ensuring the credibility and reproducibility of research findings. This paper discusses a comprehensive provenance framework…
Discovery of microRNAs (miRNAs) relies on predictive models for characteristic features from miRNA precursors (pre-miRNAs). The short length of miRNA genes and the lack of pronounced sequence features complicate this task. To accommodate…
Machine learning (ML) approaches are used more and more widely in biodiversity monitoring. In particular, an important application is the problem of predicting biodiversity indicators such as species abundance, species occurrence or species…
Divergence time estimation requires the reconciliation of two major sources of data. These are fossil and/or biogeographic evidence that give estimates of the absolute age of nodes (ancestors) and molecular estimates that give us estimates…
Leaf image recognition techniques have been actively researched for plant species identification. However it remains unclear whether leaf patterns can provide sufficient information for cultivar recognition. This paper reports the first…
Ecologists have long suspected that species are more likely to interact if their traits match in a particular way. For example, a pollination interaction may be more likely if the proportions of a bee's tongue fit a plant's flower shape.…
Computational phylogenetics has become an established tool in historical linguistics, with many language families now analyzed using likelihood-based inference. However, standard approaches rely on expert-annotated cognate sets, which are…
While Vision-Language Models (VLMs) excel at visual understanding, they often fail to grasp hierarchical knowledge. This leads to common errors where VLMs misclassify coarser taxonomic levels even when correctly identifying the most…
Botanical specimens are shared as long-term consultable research objects in a global network of specimen repositories. Multiple specimens are generated from a shared field collection event; generated specimens are then managed individually…
Within the field of phylogenetics there is growing interest in measures for summarising the dissimilarity, or 'incongruence', of two or more phylogenetic trees. Many of these measures are NP-hard to compute and this has stimulated a…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…
The preservation of soil health is a critical challenge in the 21st century due to its significant impact on agriculture, human health, and biodiversity. We provide the first deep investigation of the predictive potential of machine…
Reasoning and linguistic skills form the cornerstone of human intelligence, facilitating problem-solving and decision-making. Recent advances in Large Language Models (LLMs) have led to impressive linguistic capabilities and emergent…
Understanding the emergence of biodiversity patterns in nature is a central problem in biology. Theoretical models of speciation have addressed this question in the macroecological scale, but little has been investigated in the…
Large language models (LLMs) have achieved remarkable successes on various tasks. However, recent studies have found that there are still significant challenges to the logical reasoning abilities of LLMs, which can be categorized into the…
Ordinals can help prove termination for dependently typed programs. Brouwer trees are a particular ordinal notation that make it very easy to assign sizes to higher order data structures. They extend natural numbers with a limit…
Phylogenetic trees play a key role in the reconstruction of evolutionary relationships. Typically, they are derived from aligned sequence data (like DNA, RNA, or proteins) by using optimization criteria like, e.g., maximum parsimony (MP).…
The Provenance Ontology (PROV-O) is a World Wide Web Consortium (W3C) recommended ontology used to structure data about provenance across a wide variety of domains. Basic Formal Ontology (BFO) is a top-level ontology ISO/IEC standard used…