相关论文: Efficient Quartet Representations of Trees and App…
Topological phylogenetic trees can be assigned edge weights in several natural ways, highlighting different aspects of the tree. Here the rooted triple and quartet metrizations are introduced, and applied to formulate novel fast methods of…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
An attempt to use phylogenetic invariants for tree reconstruction was made at the end of the 80s and the beginning of the 90s by several authors (the initial idea due to Lake and Cavender and Felsenstein in 1987. However, the efficiency of…
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…
Tree ensembles (TEs) find a multitude of practical applications. They represent one of the most general and accurate classes of machine learning methods. While they are typically quite concise in representation, their operation remains…
The forest matrix plays a crucial role in network science, opinion dynamics, and machine learning, offering deep insights into the structure of and dynamics on networks. In this paper, we study the problem of querying entries of the forest…
Quantum simulations constructing probability tensors of biological multi-taxa in phylogenetic trees are proposed, in terms of positive trace preserving maps, describing evolving systems of quantum walks with multiple walkers. Basic…
We propose a novel "tree-averaging" model that utilizes the ensemble of classification and regression trees (CART). Each constituent tree is estimated with a subset of similar data. We treat this grouping of subsets as Bayesian ensemble…
Among the distance based algorithms in phylogenetic tree reconstruction, the neighbor-joining algorithm has been a widely used and effective method. We propose a new algorithm which counts the number of consistent quartets for cherry…
Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for…
Connected acyclic graphs (trees) are data objects that hierarchically organize categories. Collections of trees arise in a diverse variety of fields, including evolutionary biology, public health, machine learning, social sciences and…
Effective feature selection is essential for enhancing the performance of artificial intelligence models. It involves identifying feature combinations that optimize a given metric, but this is a challenging task due to the problem's…
Quantum network communication is challenging, as the No-cloning theorem in quantum regime makes many classical techniques inapplicable. For long-distance communication, the only viable communication approach is teleportation of quantum…
Recently there has been renewed interest in phylogenetic inference methods based on phylogenetic invariants, alongside the related Markov invariants. Broadly speaking, both these approaches give rise to polynomial functions of sequence site…
How can we identify the training examples that contribute most to the prediction of a tree ensemble? In this paper, we introduce TREX, an explanation system that provides instance-attribution explanations for tree ensembles, such as random…
Motion planning problems can be simplified by admissible projections of the configuration space to sequences of lower-dimensional quotient-spaces, called sequential simplifications. To exploit sequential simplifications, we present the…
In evolutionary studies it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or other genetic information between the species or their ancestors has…
Argument mining involves multiple sub-tasks that automatically identify argumentative elements, such as claim detection, evidence extraction, stance classification, etc. However, each subtask alone is insufficient for a thorough…
Wavelet trees are widely used in the representation of sequences, permutations, text collections, binary relations, discrete points, and other succinct data structures. We show, however, that this still falls short of exploiting all of the…
A classical problem in phylogenetic tree analysis is to decide whether there is a phylogenetic tree $T$ that contains all information of a given collection $\cP$ of phylogenetic trees. If the answer is "yes" we say that $\cP$ is compatible…