Related papers: Efficient Quartet Representations of Trees and App…

Electromagnetic structure (EMS) design plays a critical role in developing advanced antennas and materials, but remains challenging due to high-dimensional design spaces and expensive evaluations. While existing methods commonly employ…

Test-time compute scaling has emerged as a new axis along which to improve model accuracy, where additional computation is used at inference time to allow the model to think longer for more challenging problems. One promising approach for…

The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we rather explore this framework for the sake of reconstructing a gene tree from a…

Phylogenetic trees (i.e. evolutionary trees, additive trees or X-trees) play a key role in the processes of modeling and representing species evolution. Genome evolution of a given group of species is usually modeled by a species…

Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. Existing methods are computationally expensive and can either handle only small numbers…

In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…

Estimating the effective sample size (ESS) is fundamental in Bayesian phylogenetic inference to properly account for autocorrelation in MCMC samples. While methods for continuous parameters are well established, the discrete and…

We present the phylogenetic quartet reconstruction method SAQ (Semi-algebraic quartet reconstruction). SAQ is consistent with the most general Markov model of nucleotide substitution and, in particular, it allows for rate heterogeneity…

Semantic segmentation with Convolutional Neural Networks is a memory-intensive task due to the high spatial resolution of feature maps and output predictions. In this paper, we present Quadtree Generating Networks (QGNs), a novel approach…

This work focuses on quantitative verification of fairness in tree ensembles. Unlike traditional verification approaches that merely return a single counterexample when the fairness is violated, quantitative verification estimates the ratio…

Generalized subtour elimination constraints (GSECs) are widely used in state-of-the-art exact algorithms for vehicle routing and network design problems, as their right-hand sides often capture problem-specific feasibility conditions of…

Tree covering is a technique for decomposing a tree into smaller-sized trees with desirable properties, and has been employed in various succinct data structures. However, significant hurdles stand in the way of a practical implementation…

We introduce new methods for phylogenetic tree quartet construction by using machine learning to optimize the power of phylogenetic invariants. Phylogenetic invariants are polynomials in the joint probabilities which vanish under a model of…

Real-world point sets tend to be clustered, so using a machine word for each point is wasteful. In this paper we first show how a compact representation of quadtrees using $\Oh{1}$ bits per node can break this bound on clustered point sets,…

Homogeneity across lineages is a common assumption in phylogenetics according to which nucleotide substitution rates remain constant in time and do not depend on lineages. This is a simplifying hypothesis which is often adopted to make the…

Traditional Quartet Puzzling algorithms use maximum likelihood methods to reconstruct quartet trees, and a puzzling algorithm to combine these quartets into a tree for the full collection of $n$ taxa. We propose a variation of Quartet…

Tree ensembles, such as random forests and boosted trees, are renowned for their high prediction performance. However, their interpretability is critically limited due to the enormous complexity. In this study, we present a method to make a…

The increasing complexity of data requires methods and models that can effectively handle intricate structures, as simplifying them would result in loss of information. While several analytical tools have been developed to work with complex…

Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into…

A metric phylogenetic tree relating a collection of taxa induces weighted rooted triples and weighted quartets for all subsets of three and four taxa, respectively. New intertaxon distances are defined that can be calculated from these…