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We address the problem of any-code completion - generating a missing piece of source code in a given program without any restriction on the vocabulary or structure. We introduce a new approach to any-code completion that leverages the…
In a recent study, Bryant, Francis and Steel investigated the concept of \enquote{future-proofing} consensus methods in phylogenetics. That is, they investigated if such methods can be robust against the introduction of additional data like…
Large language models (LLMs) achieve strong average performance yet remain unreliable at the instance level, with frequent hallucinations, brittle failures, and poorly calibrated confidence. We study reliability through the lens of…
The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…
Artificial Neural Networks (ANN) comprise important symmetry properties, which can influence the performance of Monte Carlo methods in Neuroevolution. The problem of the symmetries is also known as the competing conventions problem or…
The Maximum Agreement Forest (Maf) problem is a well-studied problem in evolutionary biology, which asks for a largest common subforest of a given collection of phylogenetic trees with identical leaf label-set. However, the previous work…
In the past several years a wide range of methods for the construction of regression trees and other estimators based on the recursive partitioning of samples have appeared in the statistics literature. Many applications involve data…
Tree-shaped graphical models are widely used for their tractability. However, they unfortunately lack expressive power as they require committing to a particular sparse dependency structure. We propose a novel class of generative models…
CRISPR technology has enabled large-scale cell lineage tracing for complex multicellular organisms by mutating synthetic genomic barcodes during organismal development. However, these sophisticated biological tools currently use ad-hoc and…
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…
Generating accurate digital tree models from scanned environments is invaluable for forestry, agriculture, and other outdoor industries in tasks such as identifying biomass, fall hazards and traversability, as well as digital applications…
Consider a Markov chain on an infinite tree T=(V,E) rooted at \rho. In such a chain, once the initial root state \sigma(\rho) is chosen, each vertex iteratively chooses its state from the one of its parent by an application of a Markov…
Distance-based approaches in phylogenetics such as Neighbor-Joining are a fast and popular approach for building trees. These methods take pairs of sequences from them construct a value that, in expectation, is additive under a stochastic…
Computer simulations of complex population genetic models are an essential tool for making sense of the large-scale datasets of multiple genome sequences from a single species that are becoming increasingly available. A widely used approach…
We present convincing empirical evidence for an effective and general strategy for building accurate small models. Such models are attractive for interpretability and also find use in resource-constrained environments. The strategy is to…
Background. The supertree problem, i.e., the task of finding a common refinement of a set of rooted trees is an important topic in mathematical phylogenetics. The special case of a common leaf set $L$ is known to be solvable in linear time.…
Many modified genetic codes are found in specific genomes in which one or more codons have been reassigned to a different amino acid from that in the canonical code. We present a model that unifies four possible mechanisms for reassignment,…
Reticulate evolutionary processes result in phylogenetic histories that cannot be modeled using a tree topology. Here, we apply methods from topological data analysis to molecular sequence data with reticulations. Using a simple example, we…
We answer two questions raised by Bryant, Francis and Steel in their work on consensus methods in phylogenetics. Consensus methods apply to every practical instance where it is desired to aggregate a set of given phylogenetic trees (say,…
We present a unified approach for learning the parameters of Sum-Product networks (SPNs). We prove that any complete and decomposable SPN is equivalent to a mixture of trees where each tree corresponds to a product of univariate…