相关论文: Principal Component Analysis as a Sanity Check for…
This paper presents a novel approach to functional principal component analysis (FPCA) in Bayes spaces in the setting where densities are the object of analysis, but only few individual samples from each density are observed. We use the…
A unified theory of language combines a Bayesian cognitive linguistic model of language processing, with the proposal that language evolved by sexual selection for the display of intelligence. The theory accounts for the major facts of…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
Fixed tree topologies are widely used in phylodynamic analyses to reduce computational burden, yet the consequences of this assumption remain insufficiently understood. Here, we systematically assess the impact of various fixed-topology…
A method for conducting Bayesian elicitation and learning in risk assessment is presented. It assumes that the risk process can be described as a fault tree. This is viewed as a belief network, for which prior distributions on primary event…
We consider the problem of estimating the evolutionary history of a set of species (phylogeny or species tree) from several genes. It is known that the evolutionary history of individual genes (gene trees) might be topologically distinct…
We describe algorithms for symbolic reasoning about executable models of type systems, supporting three queries intended for designers of type systems. First, we check for type soundness bugs and synthesize a counterexample program if such…
Arguments are a fundamental aspect of human reasoning, in which claims are supported, challenged, and weighed against one another. We present an end-to-end large language model (LLM)-based system for reconstructing arguments from natural…
A gene's rate of sequence evolution is among the most fundamental evolutionary quantities in common use, but what determines evolutionary rates has remained unclear. Here, we show that the two most commonly used methods to disentangle the…
Language models have primarily been evaluated with perplexity. While perplexity quantifies the most comprehensible prediction performance, it does not provide qualitative information on the success or failure of models. Another approach for…
In settings from fact-checking to question answering, we frequently want to know whether a collection of evidence (premises) entails a hypothesis. Existing methods primarily focus on the end-to-end discriminative version of this task, but…
The Bayesian method is noted to produce spuriously high posterior probabilities for phylogenetic trees in analysis of large datasets, but the precise reasons for this over-confidence are unknown. In general, the performance of Bayesian…
The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data.…
Bayesian model selection is premised on the assumption that the data are generated from one of the postulated models. However, in many applications, all of these models are incorrect (that is, there is misspecification). When the models are…
Dictionaries are often developed using tools that save to Extensible Markup Language (XML)-based standards. These standards often allow high-level repeating elements to represent lexical entries, and utilize descendants of these repeating…
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…
Evolutionary models of languages are usually considered to take the form of trees. With the development of so-called tree constraints the plausibility of the tree model assumptions can be addressed by checking whether the moments of…
Testing the validity of probabilistic models containing unmeasured (hidden) variables is shown to be a hard task. We show that the task of testing whether models are structurally incompatible with the data at hand, requires an exponential…
Traversals are commonly seen in tree data structures, and performance-enhancing transformations between tree traversals are critical for many applications. Existing approaches to reasoning about tree traversals and their transformations are…
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…