Related papers: Invariant Based Quartet Puzzling
We consider the reconciliation problem, in which the task is to find a mapping of a gene tree into a species tree, so as to maximize the likelihood of such fitting, given the available data. We describe a model for the evolution of the…
Vine copulas are pair-copula constructions enabling multivariate dependence modeling in terms of bivariate building blocks. One of the main tasks of fitting a vine copula is the selection of a suitable tree structure. For this the prevalent…
When hybridization or other forms of lateral gene transfer have occurred, evolutionary relationships of species are better represented by phylogenetic networks than by trees. While inference of such networks remains challenging, several…
The maximum parsimony phylogenetic tree reconstruction problem is NP-hard, presenting a computational bottleneck for classical computing and motivating the exploration of emerging paradigms like quantum computing. To this end, we design…
Variable selection in cluster analysis is important yet challenging. It can be achieved by regularization methods, which realize a trade-off between the clustering accuracy and the number of selected variables by using a lasso-type penalty.…
A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree…
In this paper we provide a novel mathematical optimization based methodology to perturb the features of a given observation to be re-classified, by a tree ensemble classification rule, to a certain desired class. The method is based on…
The Binary Search Tree (BST) is average in computer science which supports a compact data structure in memory and oneself even conducts a row of quick algorithms, by which people often apply it in dynamical circumstance. Besides these…
Based on decision trees, many fields have arguably made tremendous progress in recent years. In simple words, decision trees use the strategy of "divide-and-conquer" to divide the complex problem on the dependency between input features and…
In this paper, we consider the problem of lifted inference in the context of Prism-like probabilistic logic programming languages. Traditional inference in such languages involves the construction of an explanation graph for the query and…
The concept of trustworthy AI has gained widespread attention lately. One of the aspects relevant to trustworthy AI is robustness of ML models. In this study, we show how to probabilistically quantify robustness against naturally occurring…
In this article we propose a new method, which we name 'quartet neighbor joining', or 'quartet-NJ', to infer an unrooted species tree on a given set of taxa T from empirical distributions of unrooted quartet gene trees on all four-taxon…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
Balanced knockout tournaments are ubiquitous in sports competitions and are also used in decision-making and elections. The traditional computational question, that asks to compute a draw (optimal draw) that maximizes the winning…
Research in reinforcement learning has produced algorithms for optimal decision making under uncertainty that fall within two main types. The first employs a Bayesian framework, where optimality improves with increased computational time.…
Reasoning with defeasible and conflicting knowledge in an argumentative form is a key research field in computational argumentation. Reasoning under various forms of uncertainty is both a key feature and a challenging barrier for automated…
We investigate sampling laws for particle algorithms and the influence of these laws on the efficiency of particle approximations of marginal likelihoods in hidden Markov models. Among a broad class of candidates we characterize the…
In this paper we consider two aspects of the inverse problem of how to construct merge trees realizing a given barcode. Much of our investigation exploits a recently discovered connection between the symmetric group and barcodes in general…
A random jigsaw puzzle is constructed by arranging $n^2$ square pieces into an $n \times n$ grid and assigning to each edge of a piece one of $q$ available colours uniformly at random, with the restriction that touching edges receive the…
This paper presents several new tractability results for planning based on macros. We describe an algorithm that optimally solves planning problems in a class that we call inverted tree reducible, and is provably tractable for several…