Related papers: Invariant Based Quartet Puzzling
One approach to estimating a species tree from a collection of gene trees is to first estimate probabilities of clades from the gene trees, and then to construct the species tree from the estimated clade probabilities. While a greedy…
We describe a method that will reconstruct an unrooted binary phylogenetic level-1 network on n taxa from the set of all quartets containing a certain fixed taxon, in O(n^3) time. We also present a more general method which can handle more…
Many interesting computational problems can be reformulated in terms of decision trees. A natural classical algorithm is to then run a random walk on the tree, starting at the root, to see if the tree contains a node n levels from the root.…
A binary tanglegram is a pair <S,T> of binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example in phylogenetics or software engineering, it is required…
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…
Sorting is a foundational problem in computer science that is typically employed on sequences or total orders. More recently, a more general form of sorting on partially ordered sets (or posets), where some pairs of elements are…
Biclustering is a class of techniques that simultaneously clusters the rows and columns of a matrix to sort heterogeneous data into homogeneous blocks. Although many algorithms have been proposed to find biclusters, existing methods suffer…
Covariance selection seeks to estimate a covariance matrix by maximum likelihood while restricting the number of nonzero inverse covariance matrix coefficients. A single penalty parameter usually controls the tradeoff between log likelihood…
We propose a new methodology to develop heuristic algorithms using tree decompositions. Traditionally, such algorithms construct an optimal solution of the given problem instance through a dynamic programming approach. We modify this…
We present a bijective algorithm with which an arbitrary permutation decomposes canonically into elementary blocks which we call families, which are sets with a specified number of ascents and descents. We show that families, arranged in an…
Probabilistic circuits (PCs) are a unifying representation for probabilistic models that support tractable inference. Numerous applications of PCs like controllable text generation depend on the ability to efficiently multiply two circuits.…
Dual-tree algorithms are a widely used class of branch-and-bound algorithms. Unfortunately, developing dual-tree algorithms for use with different trees and problems is often complex and burdensome. We introduce a four-part logical split:…
Trees or rooted trees have been generously studied in the literature. A forest is a set of trees or rooted trees. Here we give recurrence relations between the number of some kind of rooted forest with $k$ roots and that with $k+1$ roots on…
Ensembling can improve the performance of Neural Networks, but existing approaches struggle when the architecture likelihood surface has dispersed, narrow peaks. Furthermore, existing methods construct equally weighted ensembles, and this…
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 present a simple yet powerful and applicable quadrature based scheme for constructing optimal iterative methods. According to the, still unproved, Kung-Traub conjecture an optimal iterative method based on $n+1$ evaluations could achieve…
Recursive partitioning is the core of several statistical methods including CART, random forest, and boosted trees. Despite the popularity of tree based methods, to date, there did not exist methods for combining multiple trees into a…
Probability estimation is one of the fundamental tasks in statistics and machine learning. However, standard methods for probability estimation on discrete objects do not handle object structure in a satisfactory manner. In this paper, we…
This paper presents a new kind of self-balancing ternary search trie that uses a randomized balancing strategy adapted from Aragon and Seidel's randomized binary search trees ("treaps"). After any sequence of insertions and deletions of…
The purpose of this paper is to analyze certain statistics of a recently introduced non-uniform random tree model, biased recursive trees. This model is based on constructing a random tree by establishing a correspondence with non-uniform…