Filters








6,090 Hits in 4.2 sec

Algorithmic Aspects of Tree Amalgamation

Sebastian Böcker, David Bryant, Andreas W.M. Dress, Mike A. Steel
2000 Journal of Algorithms  
The amalgamation of leaf-labelled trees into a single (super)tree that "displays" each of the input trees is an important problem in classification.  ...  We discuss various approaches to this problem and show that a simple and well known polynomial-time algorithm can be used to solve this problem whenever the input set of trees contains a minimum size subset  ...  Amalgamating pairs of trees Our discussion on tree amalgamation begins with the simplest case: Amalgamating pairs of trees. L(T 1 ) ∩ L(T 2 ). 1.  ... 
doi:10.1006/jagm.2000.1116 fatcat:czowd7gcefflfag2ca5vn64ghy

Page 7709 of Mathematical Reviews Vol. , Issue 2001K [page]

2001 Mathematical Reviews  
(NZ-CANT-BM; Christchurch) Algorithmic aspects of tree amalgamation. (English summary) J. Algorithms 37 (2000), no. 2, 522-537.  ...  Given a collection of trees whose end vertices (vertices of degree one) are labelled by species names coming from a collection of names, it is an important problem in classification to amalgamate the trees  ... 

Principal Amalgamation Analysis for Microbiome Data [article]

Yan Li, Gen Li, Kun Chen
2022 arXiv   pre-print
To enable scalable computation, we develop a hierarchical PAA algorithm to trace the entire trajectory of successive simple amalgamations.  ...  We propose Principal Amalgamation Analysis (PAA), a novel amalgamation-based and taxonomy-guided dimension reduction paradigm for microbiome data.  ...  Here the length of branches may change with compositions at lower levels of taxonomic tree amalgamated to higher level.  ... 
arXiv:2205.05242v1 fatcat:4kphtibidvftnhikjra4q5wmfe

Principal Amalgamation Analysis for Microbiome Data

Yan Li, Gen Li, Kun Chen
2022 Genes  
To enable scalable computation, we develop a hierarchical PAA algorithm to trace the entire trajectory of successive simple amalgamations.  ...  We propose Principal Amalgamation Analysis (PAA), a novel amalgamation-based and taxonomy-guided dimension reduction paradigm for microbiome data.  ...  Restrictions apply to the availability of these data, which were used under license for this study.  ... 
doi:10.3390/genes13071139 pmid:35885922 pmcid:PMC9318429 fatcat:yorxynpjwvfzzgwyw4dwnl7dxu

Page 1111 of Mathematical Reviews Vol. 51, Issue 4 [page]

1976 Mathematical Reviews  
In the following three chapters aspects of orders in graphs, trees and rooted trees, incidence and cyclomatic matrices are treated.  ...  Ford’s algorithm, the Bellmann-Kalaba COMBINATORICS 51 #47911-7915 algorithm for finding the shortest paths in a graph, the branch and bound method and Little’s algorithm for the determination of the minimal  ... 

Joint amalgamation of most parsimonious reconciled gene trees

Celine Scornavacca, Edwin Jacox, Gergely J. Szöllősi
2014 Computer applications in the biosciences : CABIOS  
TERA explores all reconciled gene trees that can be amalgamated from a sample of gene trees.  ...  Results: Here, we present the Tree Estimation using Reconciliation (TERA) algorithm, a parsimony based, species tree aware method for gene tree reconstruction based on a scoring scheme combining duplication  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btu728 pmid:25380957 pmcid:PMC4380024 fatcat:urtdsh2qjrh4xm44kqasab5sea

GAP-Tree Extensions Based on Skeletons [chapter]

Tinghua Ai, Peter van Oosterom
2002 Advances in Spatial Data Handling  
The algorithm is given to construct the extended GAP-tree.  ...  The Generalized Area Partitioning tree (GAP-tree) is a model that supports onthe-fly generalisation of planar partitions of polygon objects.  ...  The algorithm of the GAP-tree construction, which is an iterative process, is described in Fig. 8 .  ... 
doi:10.1007/978-3-642-56094-1_37 fatcat:s2gmjlrmnbhg5ofy5fnoqi4qke

ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony: Table 1

Edwin Jacox, Cedric Chauve, Gergely J. Szöllősi, Yann Ponty, Celine Scornavacca
2016 Bioinformatics  
A gene tree-species tree reconciliation explains the evolution of a gene tree within the species tree given a model of gene-family evolution.  ...  Moreover, ecceTERA can estimate accurate species-tree aware gene trees using amalgamation. Availability and implementation: ecceTERA is freely available under  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btw105 pmid:27153713 fatcat:2cpgorlqynhohner54q5j4e6lu

Exploiting linkage information in real-valued optimization with the real-valued gene-pool optimal mixing evolutionary algorithm

Anton Bouter, Tanja Alderliesten, Cees Witteveen, Peter A. N. Bosman
2017 Proceedings of the Genetic and Evolutionary Computation Conference on - GECCO '17  
Comparisons of performance with state-of-the-art algorithms such as CMA-ES and AMaLGaM on a set of well-known benchmark problems show that RV-GOMEA achieves comparable, excellent scalability in case of  ...  Here, we introduce the Real-Valued GOMEA (RV-GOMEA), which incorporates several aspects of the real-valued EDA known as AMaLGaM into GOMEA in order to make GOMEA well-suited for real-valued optimization  ...  RV-GOMEA combines the Gene-pool Optimal Mixing (GOM) procedure of GOMEA with aspects of the Adapted Maximum-Likelihood Gaussian Model Iterated Density-Estimation Evolutionary Algorithm (AMaLGaM-IDEA or  ... 
doi:10.1145/3071178.3071272 dblp:conf/gecco/BouterAWB17 fatcat:xzukoavqxfdjfadsblscvcrv2m

Niching an estimation-of-distribution algorithm by hierarchical Gaussian mixture learning

S. C. Maree, T. Alderliesten, D. Thierens, P. A. N. Bosman
2017 Proceedings of the Genetic and Evolutionary Computation Conference on - GECCO '17  
Estimation-of-Distribution Algorithms (EDAs) have been applied with quite some success when solving real-valued optimization problems, especially in the case of Black Box Optimization (BBO).  ...  We test the performance of a combination of this niching approach with AMaLGaM on both new and well-known niching benchmark problems and nd that the new approach properly identi es multiple landscape modes  ...  When testing the niching capacities of CAMaLGaM, a number of interesting aspects can be noted.  ... 
doi:10.1145/3071178.3071283 dblp:conf/gecco/MareeATB17 fatcat:hhi6b5qblbb45pwt7h3mazktva

Finding Branch-Decompositions and Rank-Decompositions

Petr Hliněný, Sang-il Oum
2008 SIAM journal on computing (Print)  
We present a new algorithm that can output the rankdecomposition of width at most k of a graph if such exists.  ...  Both these algorithms are fixed-parameter tractable, that is, they run in time O(n 3 ) for each fixed value of k where n is the number of vertices / elements of the input.  ...  We are left with (IV), an immediate extension of [14, Algorithm 4.9] computing λ M1 (W ). Algorithm 5. 3 . 3 Computing an amalgam with a uniform matroid on the parse tree.  ... 
doi:10.1137/070685920 fatcat:ybfpvrma5vbofhyzpqvcr4otrq

Implementation of Machine Learning Classification Regarding Hemiplegic Gait Using an Assortment of Machine Learning Algorithms with Quantification from Conformal Wearable and Wireless Inertial Sensor System

Robert LeMoyne, Timothy Mastroianni
2021 Journal of Biomedical Science and Engineering  
The achievements of this research endeavor demonstrate the utility of amalgamating the conformal wearable and wireless inertial sensor with machine learning algorithms for distinguishing the hemiplegic  ...  An assortment of machine learning algorithms, such as the multilayer perceptron neural network, J48 decision tree, random forest, K-nearest neighbors, logistic regression, and naïve Bayes, were evaluated  ...  the BioStamp nPoint and an assortment of machine learning algorithms, such as the multilayer perceptron neural network, J48 decision tree, random forest, K-nearest neighbors, logistic regression, and  ... 
doi:10.4236/jbise.2021.1412035 fatcat:7rkudqg5uvhjfmapjzwp6gc6xu

Dynamic Choropleth Maps – Using Amalgamation to Increase Area Perceivability

Liam McNabb, Robert S Laramee, Richard Fry
2018 2018 22nd International Conference Information Visualisation (IV)  
We break down each step of the algorithm and provide pseudo-code to enable reproducibility.  ...  We also discuss unique test cases that challenge the robustness of the algorithm with 30,000 polygons and 4,652,800 vertices as well as the performance.  ...  Knowledge Economy Skills Scholarships (KESS) is a pan-Wales higher level skills initiative led by Bangor University on behalf of the HE sector in Wales.  ... 
doi:10.1109/iv.2018.00056 dblp:conf/iv/McNabbLF18 fatcat:duucbwtcurdf5ac7hghumbilwq

An Efficient Gravitational Search Decision Forest Approach for Fingerprint Recognition

Mahesh Kumar, Department of Computer Science and Engineering, Baba Mastnath University, Asthal Bohar, Sector-29, Rohtak, India, Devender Kumar, Department of Computer Science and Engineering, Baba Mastnath University, Asthal Bohar, Sector-29, Rohtak, India
2022 Maǧallaẗ Al-Kuwayt li-l-ʿulūm  
The current work proposes an efficient Gravitational Search Decision Forest (GSDF) method, which is a combination of the gravitational search algorithm (GSA) and the random forest (RF) method.  ...  In the proposed GSDF approach, the mass agent of GSA determines the solution by constructing decision trees in accordance with the random forest hypothesis.  ...  The amalgamation of the machine learning based RF algorithm with the GSA algorithm is owing to the stability of the GSA method, which is theoretically modeled using Newton's laws.  ... 
doi:10.48129/kjs.20635 fatcat:y2iplyvcezdcvbfwfafcpnqquu

Short Quartet Puzzling: A New Quartet-Based Phylogeny Reconstruction Algorithm

Sagi Snir, Tandy Warnow, Satish Rao
2008 Journal of Computational Biology  
In particular, Ranwez and Gascuel, the developers of one of the best quartet methods, conjecture that quartet-based methods have inherent limitations that make them unable to produce trees as accurate  ...  In this paper, we present Short Quartet Puzzling, a new quartet-based phylogeny reconstruction algorithm, and we demonstrate the improved topological accuracy of the new method over maximum parsimony and  ...  Both these aspects of the algorithm would need to be modified for SQP to become computationally fast enough for use on large datasets.  ... 
doi:10.1089/cmb.2007.0103 pmid:18199023 fatcat:ll2pzvza5nbbvotg4uafbaouuy
« Previous Showing results 1 — 15 out of 6,090 results