Related papers: Syntactic Phylogenetic Trees
The natural language generation (NLG) component of a spoken dialogue system (SDS) usually needs a substantial amount of handcrafting or a well-labeled dataset to be trained on. These limitations add significantly to development costs and…
Motivation: The construction of statistics for summarizing posterior samples returned by a Bayesian phylogenetic study has so far been hindered by the poor geometric insights available into the space of phylogenetic trees, and ad hoc…
Since the advent of modern bioinformatics, the challenging, multifaceted problem of reconstructing phylogenetic history from biological sequences has hatched perennial statistical and algorithmic innovation. Studies of the phylogenetic…
Synthetic tabular data are increasingly being used to replace real data, serving as an effective solution that simultaneously protects privacy and addresses data scarcity. However, in addition to preserving global statistical properties,…
Driven by the need for better models that allow one to shed light into the question how life's diversity has evolved, phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees,…
Binary trait data record the presence or absence of distinguishing traits in individuals. We treat the problem of estimating ancestral trees with time depth from binary trait data. Simple analysis of such data is problematic. Each homology…
The weighted ancestor problem on a rooted node-weighted tree $T$ is a generalization of the classic predecessor problem: construct a data structure for a set of integers that supports fast predecessor queries. Both problems are known to…
Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation…
The reconstruction of a species tree from genomic data faces a double hurdle. First, the (gene) tree describing the evolution of each gene may differ from the species tree, for instance, due to incomplete lineage sorting. Second, the…
Identifying undocumented or potential future interactions among species is a challenge facing modern ecologists. Recent link prediction methods rely on trait data, however large species interaction databases are typically sparse and…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes in a tree is computationally expensive. State-of-the-art…
As an alternative to parsimony analyses, stochastic models have been proposed (Lewis, 2001), (Nylander, et al., 2004) for morphological characters, so that maximum likelihood or Bayesian analyses may be used for phylogenetic inference. A…
Machine translation systems have been widely adopted in our daily life, making life easier and more convenient. Unfortunately, erroneous translations may result in severe consequences, such as financial losses. This requires to improve the…
Rare events have played an increasing role in molecular phylogenetics as potentially homoplasy-poor characters.In this contribution we analyze the phylogenetic information content from a combinatorial point of view by consid-ering the…
The use of linguistic typological resources in natural language processing has been steadily gaining more popularity. It has been observed that the use of typological information, often combined with distributed language representations,…
The identification of syllables within phonetic sequences is known as syllabification. This task is thought to play an important role in natural language understanding, speech production, and the development of speech recognition systems.…
Inference of phylogenetic networks is of increasing interest in the genomic era. However, the extent to which phylogenetic networks are identifiable from various types of data remains poorly understood, despite its crucial role in…
Originally formalized with symbolic representations, syntactic trees may also be effectively represented in the activations of large language models (LLMs). Indeed, a 'Structural Probe' can find a subspace of neural activations, where…
Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…