Related papers: Solving Non-homogeneous Nested Recursions Using Tr…
In this paper we present novel algorithmic techniques with a O(H(N)+N/H(N)) time complexity for performing several types of queries and updates on general rooted trees, binary search trees and lists of size N. For rooted trees we introduce…
Counting non-isomorphic tree-like multigraphs that include self-loops and multiple edges is an important problem in combinatorial enumeration, with applications in chemical graph theory, polymer science, and network modeling. Traditional…
This paper presents a novel nonlinear regression model for estimating heterogeneous treatment effects from observational data, geared specifically towards situations with small effect sizes, heterogeneous effects, and strong confounding.…
A consensus tree is a phylogenetic tree that captures the similarity between a set of conflicting phylogenetic trees. The problem of computing a consensus tree is a major step in phylogenetic tree reconstruction. It also finds applications…
Cartesian tree matching is the problem of finding all substrings of a given text which have the same Cartesian trees as that of a given pattern. So far there is one linear-time solution for Cartesian tree matching, which is based on the KMP…
Given a data set with many features observed in a large number of conditions, it is desirable to fuse and aggregate conditions which are similar to ease the interpretation and extract the main characteristics of the data. This paper…
In this paper, we address the problem of enumerating all induced subtrees in an input k-degenerate graph, where an induced subtree is an acyclic and connected induced subgraph. A graph G = (V, E) is a k-degenerate graph if for any its…
A $k$-plane tree is a plane tree whose vertices are assigned labels between $1$ and $k$ in such a way that the sum of the labels along any edge is no greater than $k+1$. These trees are known to be related to $(k+1)$-ary trees, and they are…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
Several computational problems in phylogenetic reconstruction can be formulated as restrictions of the following general problem: given a formula in conjunctive normal form where the literals are rooted triples, is there a rooted binary…
In this paper we consider the variational approach to cactus trees (Husimi trees) and the more common recursive approach, that are in principle equivalent for finite systems. We discuss in detail the conditions under which the two methods…
We consider the genealogy tree for a critical branching process conditioned on non-extinction. We enumerate vertices in each generation of the tree so that for each two generations one can define a monotone map describing the…
A fringe subtree of a rooted tree is a subtree consisting of one of the nodes and all its descendants. In this paper, we are specifically interested in the number of non-isomorphic trees that appear in the collection of all fringe subtrees…
We introduce a graph partitioning problem motivated by computational topology and propose two algorithms that produce approximate solutions. Specifically, given a weighted, undirected graph $G$ and a positive integer $k$, we desire to find…
Given a gene tree and a species tree, ancestral configurations represent the combinatorially distinct sets of gene lineages that can reach a given node of the species tree. They have been introduced as a data structure for use in the…
Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…
Convolution trees, loopy belief propagation, and fast numerical p-convolution are combined for the first time to efficiently solve networks with several additive constraints between random variables. An implementation of this "convolution…
We prove a new formula for the generating function of multitype Cayley trees counted according to their degree distribution. Using this formula we recover and extend several enumerative results about trees. In particular, we extend some…
A tree with at most k leaves is called k-ended tree, and a tree with exactly k leaves is called k-end tree, where a leaf is a vertex of degree one. Contraction of a graph G along the edge e means deleting the edge e and identifying its end…
For any real-valued $k > 1$, we consider the tree rooted at 0, where each positive integer $n$ has parent $\lfloor\frac{n}{k}\rfloor$. The average number of children per node is $k$, thus this definition gives a natural way to extend…