Related papers: Checking Phylogenetic Decisiveness in Theory and i…

Phylogenetic analyses of gene expression have great potential for addressing a wide range of questions. These analyses will, for example, identify genes that have evolutionary shifts in expression that are correlated with evolutionary…

Statistical consistency in phylogenetics has traditionally referred to the accuracy of estimating phylogenetic parameters for a fixed number of species as we increase the number of characters. However, as sequences are often of fixed length…

Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…

A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…

Given a classification model and a prediction for some input, there are heuristic strategies for ranking features according to their importance in regard to the prediction. One common approach to this task is rooted in propositional logic…

We present a formulation of the problem of probabilistic model checking as one of query evaluation over probabilistic logic programs. To the best of our knowledge, our formulation is the first of its kind, and it covers a rich class of…

We find surprisingly simple formulas for the limiting probability that the rank of a randomly selected vertex in a randomly selected phylogenetic tree or generalized phylogenetic tree is a given integer.

In medical imaging, particularly in early disease detection and prognosis tasks, discerning the rationale behind an AI model's predictions is crucial for evaluating the reliability of its decisions. Conventional explanation methods face…

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 $X$…

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…

In classification and forecasting with tabular data, one often utilizes tree-based models. Those can be competitive with deep neural networks on tabular data and, under some conditions, explainable. The explainability depends on the depth…

During the last decade, deep neural networks (DNN) have demonstrated impressive performances solving a wide range of problems in various domains such as medicine, finance, law, etc. Despite their great performances, they have long been…

We survey the problem of deciding the stability or stabilizability of uncertain linear systems whose region of uncertainty is a polytope. This natural setting has applications in many fields of applied science, from Control Theory to…

Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…

Local explanation frameworks aim to rationalize particular decisions made by a black-box prediction model. Existing techniques are often restricted to a specific type of predictor or based on input saliency, which may be undesirably…

One challenge in fact checking is the ability to improve the transparency of the decision. We present a fact checking method that uses reference information in knowledge graphs (KGs) to assess claims and explain its decisions. KGs contain a…

Some genes can change their relative locations in a genome. Thus for different individuals of the same species, the orders of genes might be different. Such jumping genes are called transposons. A practical problem is to determine…

Over the past 30 years numerous algorithms have been designed for symmetry breaking problems in the LOCAL model, such as maximal matching, MIS, vertex coloring, and edge-coloring. For most problems the best randomized algorithm is at least…

Models like support vector machines or Gaussian process regression often require positive semi-definite kernels. These kernels may be based on distance functions. While definiteness is proven for common distances and kernels, a proof for a…