24 papers · ranked by Valyu relevance
Xiaowei Wu, Hongxiao Zhu
We propose a new approach to test associations between binary trees and covariates. In this approach, binary-tree structured data are treated as sample paths of binary fission Markov branching processes (bMBP). We propose a generalized linear regression model and developed inference procedures for association testing…
Shalosh B. Ekhad, Doron Zeilberger
Fabrice Rouillier and Paul Zimmermann [RZ] proposed a unified and very efficient algorithm for finding real roots of univariate polynomials based on the good-old Descartes' rule of signs. It improved previous algorithms due to George Collins and Alkiviadis G. Akritas, Jeremy Johnson, and Werner Krandick (see [RZ] for…
Matthew J Penn, Neil Scheidwasser, Mark P Khurana, David A Duchêne + 3 more
'Christl A Donnelly' 'Samir Bhatt' 'Stephen Smith'] Title: Abstract Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes in a tree is computationally expensive. State-of-the-art methods rely on…
Luc Devroye, Michael R. Doboli, Noah A. Rosenberg, Stephan Wagner
The Colijn-Plazzotta ranking is a bijective encoding of the unlabeled binary rooted trees with positive integers. We show that the rank f(t) of a tree t is closely related to its height h, the maximal path length from a leaf to the root. We consider the rank $f\tau _n$ of a random n-leaf tree $\tau _n$ under each of…
Kou Hamada, Sankardeep Chakraborty, Seungbum Jo, Takuto Koriyama + 2 more
and Efficient Implementation of Average-Case Optimal RMQs Authors: ['Kou Hamada' 'Sankardeep Chakraborty' 'Seungbum Jo' 'Takuto Koriyama' 'Kunihiko Sadakane' 'Srinivasa Rao Satti'] Tree covering is a technique for decomposing a tree into smaller-sized trees with desirable properties, and has been employed in various…
François Bienvenu, Mike Steel
In a recent paper, the question of determining the fraction of binary trees that contain a fixed pattern known as the snowflake was posed. We show that this fraction goes to 1, providing two very different proofs: a purely combinatorial one that is quantitative and specific to this problem; and a proof using branching…
Sandip Das, Sk Samim Islam, Ritam M Mitra, Sanchita Paul
Graph burning is a graph process that models the spread of social contagion. Initially, all the vertices of a graph G are unburnt. At each step, an unburnt vertex is put on fire and the fire from burnt vertices of the previous step spreads to their adjacent unburnt vertices. This process continues till all the vertices…
Xi He, Max A. Little
In this paper, we introduce a generic data structure called decision trees, which integrates several well-known data structures, including binary search trees, -D trees, binary space partition trees, and decision tree models from machine learning. We provide the first axiomatic definition of decision trees. These…
Svante Janson
We study the distribution of fringe trees in Patricia tries and compressed binary search trees; both cases are random binary trees that have been compressed by deleting vertices of outdegree 1 so that they are random full binary trees. The main results are central limit theorems for the number of fringe trees of a…
Sean Cleary, Mareike Fischer, Katherine St. John
Tree balance plays an important role in various research areas in phylogenetics and computer science. Typically, it is measured with the help of a balance index or imbalance index. There are more than 25 such indices available, recently surveyed in a book by Fischer et al. They are used to rank rooted binary trees on a…
Mathieu Gascon, Nadia El-Mabrouk
Reconciling a non-binary gene tree with a binary species tree can be done efficiently in the absence of horizontal gene transfers, but becomes NP-hard in the presence of gene transfers. Here, we focus on the special case of endosymbiotic gene transfers (EGT), i.e. transfers between the mitochondrial and nuclear genome…
Michael Goodrich, Yan Gu, Ryuto Kitagawa, Yihan Sun
Balanced search trees are widely used in computer science to efficiently maintain dynamic ordered data. To support efficient set operations (e.g., union, intersection, difference) using trees, the join-based framework is widely studied. This framework has received particular attention in the parallel setting, and has…
Baqiao Liu, Tandy Warnow
Species tree inference under the multi-species coalescent (MSC) model is a basic step in biological discovery. Despite the developments in recent years of methods that are proven statistically consistent and that have high accuracy, large datasets create computational challenges. Although there is generally some…
Andrew Francis, Mike Steel
Phylogenetic networks are mathematical representations of evolutionary history that are able to capture both tree-like evolutionary processes (speciations), and non-tree-like “reticulate” processes such as hybridization or horizontal gene transfer. The additional complexity that comes with this capacity, however, makes…
Songpeng Liu
As data volumes continue to grow rapidly, traditional search algorithms, like the red-black tree and B+ Tree, face increasing challenges in performance, especially in big data scenarios with intensive storage access. This paper presents the Linked Array Tree (LAT), a novel data structure designed to achieve…
Vincent Moulton, Andreas Spillner
Ranked tree-child networks are a recently introduced class of rooted phylogenetic networks in which the evolutionary events represented by the network are ordered so as to respect the flow of time. This class includes the well-studied ranked phylogenetic trees (also known as ranked genealogies). An important problem in…
Wei Wei, David Koslicki
Distance-guided tree construction with unknown tree topology and branch lengths has been a long studied problem. In contrast, distance-guided branch lengths assignment with fixed tree topology has not yet been systematically investigated, despite having significant applications. In this paper, we provide a formal…
Authors not listed
We present a simple yet efficient random (brute-force) algorithm for constructing solvated molecular systems. By placing solvent molecules at random positions and orientations within a simulation box, we circumvent the complexities typically associated with more sophisticated packing algorithms. The main computational…
Yuki Takazawa, Atsushi Takeda, Momoko Hayamizu, Olivier Gascuel
Phylogenetic analyses often require the summarization of multiple trees, e.g., in Bayesian analyses to obtain the centroid of the posterior distribution of trees, or to determine the consensus of a set of bootstrap trees. The majority-rule consensus tree is the most commonly used. It is easy to compute and minimizes…
Palash Sashittal, Henri Schmidt, Michelle Chan, Benjamin J. Raphael
CRISPR-Cas9 based genome editing combined with single-cell sequencing enables the tracing of the history of cell divisions, or cellular lineage, in tissues and whole organisms. While standard phylogenetic approaches may be applied to reconstruct cellular lineage trees from this data, the unique features of the…
Richard Apodaca
Despite its widespread use, Simplified Molecular Input Line Entry System (SMILES) remains underspecified. The lack of a detailed specification encourages improvisation by software developers, complicates data standardization efforts, and undermines extension development. Balsa, a reformulation of SMILES, addresses…
Aviva K. Englander, Martin Frohn, Elizabeth Gross, Niels Holtgrefe + 3 more
We consider the fundamental question of which evolutionary histories can potentially be reconstructed from sufficiently long DNA sequences, by studying the identifiability of phylogenetic networks from data generated under Markov models of DNA evolution. This topic has previously been studied for phylogenetic trees and…
Jonas Schaub, Julian Zander, Achim Zielesny, Christoph Steinbeck
The concept of molecular scaffolds as defining core structures of organic molecules is utilised in many areas of chemistry and cheminformatics, e.g. drug design, chemical classification, or the analysis of high-throughput screening data. Here, we present Scaffold Generator, a comprehensive open library for the…
Itamar Borges Jr, Júlio César Duarte, Romulo Dias da Rocha
We decomposed density functional theory charge densities of 53 nitroaromatic molecules into atom-centered electric multipoles using the distributed multipole analysis that provides a detailed picture of the molecular electronic structure. Three electric multipoles, ∑▒〖Q_0 (NO_2)〗 (the charge of the nitro groups)…