Related papers: A Practical Fixed-Parameter Algorithm for Construc…
We present a deterministic algorithm for solving a wide range of dynamic programming problems in trees in $O(\log D)$ rounds in the massively parallel computation model (MPC), with $O(n^\delta)$ words of local memory per machine, for any…
We present a linear programming based algorithm for computing a spanning tree $T$ of a set $P$ of $n$ points in $\Re^d$, such that its crossing number is $O(\min(t \log n, n^{1-1/d}))$, where $t$ the minimum crossing number of any spanning…
The first output-sensitive algorithm for the Maximal Clique Listing problem was given by Tsukiyama et.al. in 1977. As any algorithm falling within the Reverse Search paradigm, it performs a DFS visit of a directed tree (the RS-tree) having…
Phylogenetic networks provide a more general description of evolutionary relationships than rooted phylogenetic trees. One way to produce a phylogenetic network is to randomly place $k$ arcs between the edges of a rooted binary phylogenetic…
Recent work has proven the existence of extreme inbreeding in a European ancestry sample taken from the contemporary UK population \cite{nature_01}. This result brings our attention again to a math problem related to inbreeding family trees…
Linear model trees are regression trees that incorporate linear models in the leaf nodes. This preserves the intuitive interpretation of decision trees and at the same time enables them to better capture linear relationships, which is hard…
In this paper, we study the parallel query complexity of reconstructing biological and digital phylogenetic trees from simple queries involving their nodes. This is motivated from computational biology, data protection, and computer…
In this paper it is shown that for any network there is a uniquely determined network based on a structure tree that provides a convenient way of determining a minimal cut separating a pair $s, t$ where each of $s, t$ is either a vertex or…
In this paper, we present fixed-parameter tractability algorithms for both the undirected and directed versions of the Spanning Tree Isomorphism Problem, parameterized by the size $k$ of a redundant set. A redundant set is a collection of…
Phylogenetic trees are frequently used to model evolution. Such trees are typically reconstructed from data like DNA, RNA, or protein alignments using methods based on criteria like maximum parsimony (amongst others). Maximum parsimony has…
Motivation: Word-based or `alignment-free' methods for phylogeny reconstruction are much faster than traditional approaches, but they are generally less accurate. Most of these methods calculate pairwise distances for a set of input…
We present a randomized algorithm for reconstructing directed rooted trees of $n$ nodes and node degree at most $d$, by asking at most $O(dn\log^2 n)$ path queries. Each path query takes as input an origin node and a target node, and…
Phylogenetic networks are a flexible model of evolution that can represent reticulate evolution and handle complex data. Tree-based networks, which are phylogenetic networks that have a spanning tree with the same root and leaf-set as the…
Between the leaves and the nodes of a complete binary tree, a separate parent-child-sister hierarchy is employed independent of the parent-child-sister hierarchy used for the rest of the tree. Two different versions of such a local…
Without access to large compute clusters, building random forests on large datasets is still a challenging problem. This is, in particular, the case if fully-grown trees are desired. We propose a simple yet effective framework that allows…
Branchwidth determines how graphs, and more generally, arbitrary connectivity (basically symmetric and submodular) functions could be decomposed into a tree-like structure by specific cuts. We develop a general framework for designing…
Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…
We provide precise asymptotic estimates for the number of general phylogenetic networks by using analytic combinatorial methods. Recently, this approach is studied by Fuchs, Gittenberger, and the author himself (Australasian Journal of…
Gravitational $N$-body simulations calculate numerous interactions between particles. The tree algorithm reduces these calculations by constructing a hierarchical oct-tree structure and approximating gravitational forces on particles. Over…
In the study of rooted phylogenetic networks, analyzing the set of rooted phylogenetic trees that are embedded in such a network is a recurring task. From an algorithmic viewpoint, this analysis almost always requires an exhaustive search…