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The software program BAMM has been widely used to study the dynamics of speciation, extinction, and phenotypic evolution on phylogenetic trees. The program implements a model-based clustering algorithm to identify clades that share common…
The inability to resolve deep node relationships of highly divergent/rapidly evolving protein families is a major factor that stymies evolutionary studies. In this manuscript, we propose a Multiple Sequence Alignment (MSA) independent…
By retracing my scientific journey that began 20 years ago, I highlight in this thesis the need to consider the organization of the brain, which is certainly globally hierarchical, but also highly distributed and mixed in the neuronal…
Ground beetles are a highly sensitive and speciose biological indicator, making them vital for monitoring biodiversity. However, they are currently an underutilized resource due to the manual effort required by taxonomic experts to perform…
Large Language Models (LLMs) are accelerating scientific idea generation, but rigorously evaluating these numerous, often superficial, AI-generated propositions for novelty and factual accuracy is a critical bottleneck; manual verification…
Classification aids software development activities by organizing requirements in classes for easier access and retrieval. The majority of requirements classification research has, so far, focused on binary or multi-class classification.…
The theory of evolution states that the diversity of species can be explained by descent with modification. Therefore, all living beings are related through a common ancestor. This evolutionary process must have left traces in our molecular…
Understanding the meaning of words is crucial for many tasks that involve human-machine interaction. This has been tackled by research in Word Sense Disambiguation (WSD) in the Natural Language Processing (NLP) field. Recently, WSD and many…
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…
Clear and effective explanations are essential for human understanding and knowledge dissemination. The scope of scientific research aiming to understand the essence of explanations has recently expanded from the social sciences to machine…
Large language models are often assumed to acquire increasingly structured, generalizable internal representations simply by scaling data and parameters. We interrogate this assumption by introducing a Clinical Trial Natural Language…
When studying ecosystems, hierarchical trees are often used to organize entities based on proximity criteria, such as the taxonomy in microbiology, social classes in geography, or product types in retail businesses, offering valuable…
In computational biology and bioinformatics, the manner to understand evolution processes within various related organisms paid a lot of attention these last decades. However, accurate methodologies are still needed to discover genes…
Large Language Models (LLMs) have demonstrated remarkable capabilities across various domains. Math Word Problems (MWPs) serve as a crucial benchmark for evaluating LLMs' reasoning abilities. While most research primarily focuses on…
Motivation: Word-based or `alignment-free' methods for phylogeny reconstruction are much faster than traditional approaches, but they are generally less accurate. Most of these methods calculate pairwise distances for a set of input…
Taxonomies represent hierarchical relations between entities, frequently applied in various software modeling and natural language processing (NLP) activities. They are typically subject to a set of structural constraints restricting their…
Identifying a subset of taxa that maximizes Phylogenetic Diversity (PD) is a cornerstone of quantitative conservation planning. Traditionally, PD is defined over a phylogenetic tree in which leaves resemble present-day taxa and the branch…
Humans and animals exhibit a range of interesting behaviors in dynamic environments, and it is unclear how our brains actively reformat this dense sensory information to enable these behaviors. Experimental neuroscience is undergoing a…
We consider the problem of the extraction of semantic attributes, supervised only with classification labels. For example, when learning to classify images of birds into species, we would like to observe the emergence of features that…
Bayesian inference is now a leading technique for reconstructing phylogenetic trees from aligned sequence data. In this short note, we formally show that the maximum posterior tree topology provides a statistically consistent estimate of a…