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A New Perspective on the Tree Edit Distance [chapter]

Stefan Schwarz, Mateusz Pawlik, Nikolaus Augsten
2017 Lecture Notes in Computer Science  
In this paper we fill the gap and revisit Chen's TED algorithm. We analyse the recursion by Chen and compare it to Zhang's recursion.  ...  Moreover, we revise the runtime complexity of Chen's algorithm and develop a new traversal strategy to reduce its memory complexity.  ...  We thank Willi Mann and Daniel Kocher for valuable discussions.  ... 
doi:10.1007/978-3-319-68474-1_11 fatcat:3ihpe33ypfctzc4zeiey3dchom

On the top-down evaluation of tree inclusion problem

Yangjun Chen, Yibin Chen
2011 International Journal of Information Technology, Communications and Convergence  
P), and D T (resp. D P ) for the height of T (resp. P). In this paper, we present a new algorithm that requires O(|T|·|leaves(P)|) time but only O(|T| + |P|) space.  ...  We consider the following tree-matching problem: Given labelled, ordered trees P and T, can P be obtained from T by deleting nodes.  ...  The time complexity of the new one is bounded by O(|T|⋅|leaves(P)|). It is the same as Chen's algorithm (Chen, 1998) . But the space requirement remains O(|T| + |P|).  ... 
doi:10.1504/ijitcc.2011.042124 fatcat:lrxo4i4sdfdq3pdfyozyatqjz4

Page 2674 of Mathematical Reviews Vol. , Issue 82f [page]

1982 Mathematical Reviews  
Chen. IEEE Trans. Circuits and Systems 28 (1981), no. 7, 747-748. Authors’ summary: “The problem of efficient generation of all trees has been considered in the paper by Chen.  ...  Max Dauchet (Villeneuve d’Ascq) Saisyu, Kazuo [Saishu, Kazuo]; Sato, Kimio; Onodera, Rikio Comments on: ‘Computer generation of trees and co-trees in a cascade of multiterminal networks” [IEEE Trans.  ... 

A new tree inclusion algorithm

Yangjun Chen, Yibin Chen
2006 Information Processing Letters  
In this paper, we present a new algorithm that requires O(|T | min{D P , | leaves(P )|}) time and no extra space, where D P represents the height of P .  ...  We consider the following tree-matching problem: Given labeled, ordered trees P and T , can P be obtained from T by deleting nodes?  ...  Conclusion In this paper, a new algorithm for checking the inclusion of a pattern tree P in a target tree T is discussed.  ... 
doi:10.1016/j.ipl.2005.11.022 fatcat:5wczcyptgvejngkc5n4mtgmhui

Matching subsequences in trees

Philip Bille, Inge Li Gørtz
2009 Journal of Discrete Algorithms  
In this paper we propose this problem as a useful query primitive for XML data, and provide new algorithms improving the previously best known time and space bounds.  ...  Given two rooted, labeled trees P and T the tree path subsequence problem is to determine which paths in P are subsequences of which paths in T . Here a path begins at the root and ends at a leaf.  ...  At a high level, the algorithms are essentially identical and therefore the bounds should be regarded as an improved analysis of Chen's algorithm.  ... 
doi:10.1016/j.jda.2008.11.005 fatcat:7zqaak5nkbh2vb4meyqyrk5y2a

Matching Subsequences in Trees [chapter]

Philip Bille, Inge Li Gørtz
2006 Lecture Notes in Computer Science  
In this paper we propose this problem as a useful query primitive for XML data, and provide new algorithms improving the previously best known time and space bounds.  ...  Given two rooted, labeled trees P and T the tree path subsequence problem is to determine which paths in P are subsequences of which paths in T . Here a path begins at the root and ends at a leaf.  ...  At a high level, the algorithms are essentially identical and therefore the bounds should be regarded as an improved analysis of Chen's algorithm.  ... 
doi:10.1007/11758471_25 fatcat:mvvuzfsuwza7vcg3ud5akaho5i

Stratified Sampling for Even Workload Partitioning Applied to IDA* and Delaunay Algorithms

Jeeva Paudel, Levi H. S. Lelis, Jose Nelson Amaral
2015 2015 IEEE International Parallel and Distributed Processing Symposium  
This work presents Workload Partitioning and Scheduling (WPS), a novel algorithm for evenly partitioning the computational workload of large implicitly-defined worklist-based applications on distributed  ...  An empirical evaluation on large applications -Iterative-Deepening A* (IDA*) applied to (4×4)-and (5×5)-Sliding-Tile Puzzles, Delaunay Mesh Generation, and Delaunay Mesh Refinement -shows that WPS is applicable  ...  CHEN'S STRATIFIED SAMPLING Knuth [10] presents a technique to estimate the size of the tree expanded by a search algorithm such as chronological backtracking.  ... 
doi:10.1109/ipdps.2015.63 dblp:conf/ipps/PaudelLA15 fatcat:hlnzaa2fr5arddok6acz6z3t3m

Memory-Efficient Tree Size Prediction for Depth-First Search in Graphical Models [chapter]

Levi H. S. Lelis, Lars Otten, Rina Dechter
2014 Lecture Notes in Computer Science  
We address the problem of predicting the size of the search tree explored by Depth-First Branch and Bound (DFBnB) while solving optimization problems over graphical models.  ...  Using empirical evaluation on optimization problems over probabilistic graphical models we show impressive prediction power that is far superior to both TSS and to earlier competing schemes.  ...  Acknowledgements This work was sponsored by FAPEMIG, in part by NSF grants IIS-1065618 and IIS-1254071, and in part by the United States Air Force under Contract No.  ... 
doi:10.1007/978-3-319-10428-7_36 fatcat:xl2ocmdjrve4lgjofnqi3wcmfi

Molecular systematics of the Cyprinoidea (Teleostei: Cypriniformes), the world's largest clade of freshwater fishes: Further evidence from six nuclear genes

Wei-Jen Chen, Richard L. Mayden
2009 Molecular Phylogenetics and Evolution  
This research is part of an ongoing international Tree of Life initiative on the order Cypriniformes USA NSF awards EF 0431326.  ...  Conway for providing valuable comments for this work and for manuscript-improvement. We thank Maski Miya, Tetsuya Sado, and Shunping He for the specimens.  ...  Methods for collecting new DNA data from the specimens and/or gene loci followed the procedures outlined in Chen et al. (2008) .  ... 
doi:10.1016/j.ympev.2009.01.006 pmid:19489125 fatcat:oj4wck5fu5eaxjsynfp5gibfvu

Comparative Performance of Supertree Algorithms in Large Data Sets Using the Soapberry Family (Sapindaceae) as a Case Study

Sven Buerki, Félix Forest, Nicolas Salamin, Nadir Alvarez
2010 Systematic Biology  
and computational time required by the algorithm.  ...  Based on our results, two main groups of supertree methods were identified: on one hand, the matrix representation with parsimony (MRP), MinFlip, and MinCut methods performed well according to our criteria  ...  We are grateful to the associate editor Olaf Bininda-Emonds, Mark Wilkinson, Francois-Joseph Lapointe, Chris Creevey, and one anonymous reviewer for their comments that greatly improved our manuscript.  ... 
doi:10.1093/sysbio/syq057 pmid:21068445 fatcat:lh2ucrwprnbljgiwlayrsitpue

Aggregation convergecast scheduling in wireless sensor networks

Baljeet Malhotra, Ioanis Nikolaidis, Mario A. Nascimento
2010 Wireless networks  
Following a similar approach, we propose two new improvements, one to each of the two phases. Starting with a new lower bound on the schedule length, we make use of it in the tree construction step.  ...  The scheduling step is a weight-based priority scheme that obeys dependency (tree) and interference constraints.  ...  Within this category, there are those algorithms that retain the tree constructed in the first phase, and others that do not. In the latter category we find SDA by Chen et al.  ... 
doi:10.1007/s11276-010-0282-y fatcat:lajfmrt2qbfvxb6z5w4cfb5egi

Resolving Cypriniformes relationships using an anchored enrichment approach

Carla C. Stout, Milton Tan, Alan R. Lemmon, Emily Moriarty Lemmon, Jonathan W. Armbruster
2016 BMC Evolutionary Biology  
Species tree analysis was highly congruent with the concatenation analysis with only two major differences: monophyly of Cobitoidei and placement of Danionidae.  ...  Results: Concatenation analysis establishes a robust tree with 97 % of nodes at 100 % bootstrap support.  ...  Susana Schonhuth and Richard Mayden at St. Louis University, Gabriela M. Hogue at North Carolina Museum of Natural Sciences, and Frank's Aquarium and Wet Spot Tropical Fish.  ... 
doi:10.1186/s12862-016-0819-5 pmid:27829363 pmcid:PMC5103605 fatcat:xft7wetmrnc57gc6y3tscj4uk4

Lossless Compression Algorithms [chapter]

Ze-Nian Li, Mark S. Drew, Jiangchuan Liu
2014 Texts in Computer Science  
Recently, new algorithms have been introduced specifically for this purpose.  ...  In this paper, we comparatively survey the main ideas and results of lossless compression algorithms that have been developed for DNA sequences.  ...  Bao et al. introduced a new algorithm based on fixed length LUT and LZ77 [44] .  ... 
doi:10.1007/978-3-319-05290-8_7 fatcat:vyv2p3xwcvbe3oz32bnmjuvray

Iterated Integrals and Population Time Series Analysis [article]

Chad Giusti, Darrick Lee
2019 arXiv   pre-print
Here, we describe such a semantic structure on Chen's classical iterated integral cochain model for paths in Euclidean space.  ...  Along the way, we survey recent results and applications, review the current standard methods for causality inference, and briefly provide our outlook on generalizations to go beyond time series data.  ...  algorithms.  ... 
arXiv:1811.03558v2 fatcat:rvalniuezng37eqjqwqocwblti

Pattern Matching in Trees and Strings [article]

Philip Bille
2007 arXiv   pre-print
We study the design of efficient algorithms for combinatorial pattern matching. More concretely, we study algorithms for tree matching, string matching, and string matching in compressed texts.  ...  A Faster Tree Inclusion Algorithm In this section we present a new tree inclusion algorithm which has a worst-case subquadratic running time.  ...  Complexity of the Tree Inclusion Algorithm Using the node list implementation of the set procedures we get: Theorem 6 For trees P and T the tree inclusion problem can be solved in O(l P n T ) time and  ... 
arXiv:0708.4288v1 fatcat:55quki3onrfa3cqvmvsbfsavwq
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