相关论文: A note on efficient computation of hybridization n…

Phylogenetic reconciliation seeks to explain host-symbiont co-evolution by mapping parasite trees onto host trees through events such as cospeciation, duplication, host switching, and loss. Finding an optimal reconciliation that ensures…

We propose to prune a random forest (RF) for resource-constrained prediction. We first construct a RF and then prune it to optimize expected feature cost & accuracy. We pose pruning RFs as a novel 0-1 integer program with linear constraints…

Peca suggested in a recent paper on the arxiv to consider binary butterfly trees and their Horton-Strahler numbers. The trees are obtained by glueing two binary trees together in a special way; the results are again binary trees but with a…

Extreme classification problems are multiclass and multilabel classification problems where the number of outputs is so large that straightforward strategies are neither statistically nor computationally viable. One strategy for dealing…

Clustering serves as a vital tool for uncovering latent data structures, and achieving both high accuracy and interpretability is essential. To this end, existing methods typically construct binary decision trees by solving mixed-integer…

We investigate active learning by pairwise similarity over the leaves of trees originating from hierarchical clustering procedures. In the realizable setting, we provide a full characterization of the number of queries needed to achieve…

Rooted phylogenetic networks are often constructed by combining trees, clusters, triplets or characters into a single network that in some well-defined sense simultaneously represents them all. We review these four models and investigate…

We herein introduce a new method of interpretable clustering that uses unsupervised binary trees. It is a three-stage procedure, the first stage of which entails a series of recursive binary splits to reduce the heterogeneity of the data…

Phylogenetic networks are important for the study of evolution. The number of methods to find such networks is increasing, but most such methods can only reconstruct small networks. To find bigger networks, one can attempt to combine small…

We herein introduce a new method of interpretable clustering that uses unsupervised binary trees. It is a three-stage procedure, the first stage of which entails a series of recursive binary splits to reduce the heterogeneity of the data…

We give an explicit algorithm and source code for computing optimal weights for combining a large number N of alphas. This algorithm does not cost O(N^3) or even O(N^2) operations but is much cheaper, in fact, the number of required…

Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…

The amount of completely sequenced chloroplast genomes increases rapidly every day, leading to the possibility to build large-scale phylogenetic trees of plant species. Considering a subset of close plant species defined according to their…

In this paper, we describe a new hybrid algorithm for computing all singular triplets above a given threshold and provide its implementation in MATLAB/Octave and R. The high performance of our codes and ease at which they can be used,…

Holonomic equations are recursive equations which allow computing efficiently numbers of combinatoric objects. R{\'e}my showed that the holonomic equation associated with binary trees yields an efficient linear random generator of binary…

We define a new balance index for rooted phylogenetic trees based on the symmetry of the evolutive history of every set of 4 leaves. This index makes sense for multifurcating trees and it can be computed in time linear in the number of…

We describe a combinatorial approach for investigating properties of rational numbers. The overall approach rests on structural bijections between rational numbers and familiar combinatorial objects, namely rooted trees. We emphasize that…

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…

Let $F(z)$ be an arbitrary complex polynomial. We introduce the local root clustering problem, to compute a set of natural $\varepsilon$-clusters of roots of $F(z)$ in some box region $B_0$ in the complex plane. This may be viewed as an…

We suggest a new non-recursive algorithm for constructing a binary search tree given an array of numbers. The algorithm has $O(N)$ time and $O(1)$ memory complexity if the given array of $N$ numbers is sorted. The resulting tree is of…