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The Tree-to-Tree Correction Problem

Kuo-Chung Tai
1979 Journal of the ACM  
The tree-to-tree correctmn problem Is to determine, for two labeled ordered trees T and T', the distance from T to T' as measured by the mlmmum cost sequence of edit operaUons needed to transform T into  ...  the similarity between trees, automatic error recovery and correction for programming languages, and determining the largest common substructure of two trees KEY WORDS AND PHRASES tree correction, tree  ...  Since each string can be considered a tree of depth two (with a vnrtual root added), the string-to-string correction problem is just a special case o f the tree-to-tree correction problem with L = L '  ... 
doi:10.1145/322139.322143 fatcat:637igsn5qrfl3oasee4uxixmeu

Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem

Pawel Górecki, Oliver Eulenstein
2012 BMC Bioinformatics  
Results: We introduce the problem of reconciling unrooted and erroneous gene trees by simultaneously rooting and error-correcting them, and describe an efficient algorithm for this problem.  ...  We introduce an effective heuristic for our error-corrected version of the gene duplication problem, given that the original version of this problem is NP-hard.  ...  This work was conducted in parts with support from the Gene Tree Reconciliation Working Group at NIMBioS through NSF award #EF-0832858.  ... 
doi:10.1186/1471-2105-13-s10-s14 pmid:22759419 pmcid:PMC3382441 fatcat:7jjnfyeavrb5pkoinqwfbezsky

TRACTION: Fast Non-Parametric Improvement of Estimated Gene Trees

Sarah Christensen, Erin K. Molloy, Pranjal Vachaspati, Tandy Warnow, Michael Wagner
2019 Workshop on Algorithms in Bioinformatics  
Here, we study the problem of gene tree correction where gene tree heterogeneity is instead due to incomplete lineage sorting (ILS, a common problem in eukaryotic phylogenetics) and horizontal gene transfer  ...  Gene tree correction aims to improve the accuracy of a gene tree by using computational techniques along with a reference tree (and in some cases available sequence data).  ...  Acknowledgements We thank Mike Steel for encouragement and the members of the Warnow lab for valuable feedback.  ... 
doi:10.4230/lipics.wabi.2019.4 dblp:conf/wabi/ChristensenMVW19 fatcat:y5dd2xv3v5b7fedd6ypbkbcvmu

Non-parametric correction of estimated gene trees using TRACTION

Sarah Christensen, Erin K. Molloy, Pranjal Vachaspati, Ananya Yammanuru, Tandy Warnow
2020 Algorithms for Molecular Biology  
Here, we study the problem of gene tree correction where gene tree heterogeneity is instead due to ILS and/or HGT.  ...  We also show that a naive generalization of the RF-OTRC problem to multi-labeled trees is possible, but can produce misleading results where gene tree heterogeneity is due to GDL.  ...  We also thank the anonymous reviewers of the WABI submission, which led to improvements in the manuscript.  ... 
doi:10.1186/s13015-019-0161-8 pmid:31911812 pmcid:PMC6942343 fatcat:qkc2dzjdivdq7bckd4y7pfsrrq

Polytomy refinement for the correction of dubious duplications in gene trees

Manuel Lafond, Cedric Chauve, Riccardo Dondi, Nadia El-Mabrouk
2014 Computer applications in the biosciences : CABIOS  
We apply our algorithm to a set of ray-finned fish gene trees from the Ensembl database to illustrate its ability to correct dubious duplications.  ...  Results: We introduce the problem of refining polytomies in a gene tree while minimizing the number of created non-apparent duplications in the resulting tree.  ...  GENE TREE CORRECTION The polytomy refinement problem is motivated by the problem of correcting gene trees.  ... 
doi:10.1093/bioinformatics/btu463 pmid:25161242 pmcid:PMC4147916 fatcat:w3tbt6b2kzb7fbvm3ieeuosx2y

Automatic Enhancement of LTAG Treebank

Farzaneh Zarei, Ali Basirat, Heshaam Faili, Maryam S. Mirian
2013 Recent Advances in Natural Language Processing  
The problem has been formulated as a classification problem and has been tackled by using several classifiers.  ...  The experiments show that by using this approach, about 95% of the errors could be detected and more than 77% of them could successfully be corrected in the case of using Adaboost classifier.  ...  Detecting the errors can be considered as a binary classification problem in which each word is classified correct or incorrect with respect to the XTAG elementary tree.  ... 
dblp:conf/ranlp/ZareiBFM13 fatcat:vnf4w3da35gvzatk4eioat7t5m

Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence

Ruchi Chaudhary, J Gordon Burleigh, Oliver Eulenstein
2012 BMC Bioinformatics  
Gene tree -species tree reconciliation problems infer the patterns and processes of gene evolution within a species tree.  ...  They provide a fast error correction protocol for ameliorating the effects of gene tree error by allowing small rearrangements in the topology to improve the reconciliation cost.  ...  JGB performed the experimental evaluation and the analysis of the results, and contributed to the writing of the paper.  ... 
doi:10.1186/1471-2105-13-s10-s11 pmid:22759416 pmcid:PMC3382437 fatcat:wfrpopwrqzh25f4es4nlbyno6a

Gene tree correction guided by orthology

Manuel Lafond, Magali Semeria, Krister M Swenson, Eric Tannier, Nadia El-Mabrouk
2013 BMC Bioinformatics  
We assess the validity of the modifications we propose by computing the likelihood ratio between initial and modified trees according to sequence alignments on Ensembl trees, showing that often the two  ...  is as close as possible to the original one according to the Robinson-Foulds distance.  ...  The Gene Orthology Correction Problem Notice that for any instance of the GOC problem, a corrected tree satisfying P always exists.  ... 
doi:10.1186/1471-2105-14-s15-s5 pmid:24564227 pmcid:PMC3851885 fatcat:qwgdmtik4neqxczpdjvkbtyeuy

Grade 12 Students' Proficiency in Solving Probability Problems Involving Contingency Tables and Tree Diagrams

Francis K. Awuah, Institute for Science and Technology Education, University of South Africa, Pretoria, South Africa, awuahfrancis@yahoo.com, Ugorji I. Ogbonnaya, Department of Science, Maths and Technology Education, University of Pretoria, Pretoria, South Africa, ugorji.ogbonnaya@up.ac.za
2020 International Journal of Instruction  
The findings show that the students were not proficient in the use of tree diagrams and contingency tables to solve probability problems.  ...  The study revealed that most of the students (97% and 91%) scored below 50% in solving probability problems involving the use of tree diagrams and contingency tables respectively.  ...  In Figure 2c , the student got the question completely wrong because he/she was unable to draw a correct tree diagram.  ... 
doi:10.29333/iji.2020.13255a fatcat:jokk5rq5lfblzgrdpriqnrmwim

Gene Tree Construction and Correction using SuperTree and Reconciliation [article]

Manuel Lafond, Cédric Chauve, Nadia El-Mabrouk, Aïda Ouangraoua
2016 arXiv   pre-print
A dynamic programming supertree algorithm for constructing or correcting gene trees, exponential in the number of input trees, is first developed for the less constrained version of the problem.  ...  By applying these algorithms to the set of Ensembl gene trees, we show that this new correction framework is particularly useful to correct weaklysupported duplication nodes.  ...  This new gene tree construction and correction paradigm leads to many new open problems.  ... 
arXiv:1610.05068v2 fatcat:wcc2n7rjr5ekjasoszeao2jyi4

Visiting Byzantine Agreement underlying Ad Hoc environment

K. -Q. Yan, S. -C. Wang
2007 Journal of computer & systems sciences international  
In this study, the BA problem is visited in a MANET, in which the components are subject to a malicious fault.  ...  Each fault-free node can reach a common agreement value for the BA problem in a MANET.  ...  Since MAHAP can solve the BA problem, the correctness of MAHAP should be examined using the following two terms. (1) Correct vertex: Vertex αi of a tree is qualified as a correct vertex if node i (the  ... 
doi:10.1134/s1064230707010157 fatcat:2oopmrugt5hr5p36nbph24psp4

Obtaining Calibrated Probabilities from Boosting [article]

Alexandru Niculescu-Mizil, Richard A. Caruana
2012 arXiv   pre-print
decision trees.  ...  Boosted decision trees typically yield good accuracy, precision, and ROC area.  ...  Acknowledgments Thanks to Bianca Zadrozny and Charles Elkan for use of their Isotonic Regression code. Thanks to Charles Young et al. at SLAC (Stanford Linear Accelerator) for the SLAC data set.  ... 
arXiv:1207.1403v1 fatcat:plnina3ubfd7jeefd6szgdoriu

TreeSolve: Rapid Error-Correction of Microbial Gene Trees [chapter]

Misagh Kordi, Mukul S. Bansal
2020 Lecture Notes in Computer Science  
To overcome this limitation, the best gene tree reconstruction methods use a known species tree topology to guide the reconstruction of the gene tree.  ...  Gene tree reconstruction is an important problem in phylogenetics. However, gene sequences often lack sufficient information to confidently distinguish between competing gene tree topologies.  ...  To address the problem of gene tree error, many species-tree-aware methods have been developed for reconstructing or error-correcting gene trees.  ... 
doi:10.1007/978-3-030-42266-0_10 fatcat:yqzmxiny5zcixlfhqddahfsv5q

Parallel implementation of a quartet-based algorithm for phylogenetic analysis

B.B. Zhou, D. Chu, M. Tarawneh, P. Wang, C. Wang, A.Y. Zomaya, R.P. Brent
2006 Proceedings 20th IEEE International Parallel & Distributed Processing Symposium  
This collective network connects all the compute nodes in the shape of a tree and any node can be the tree root (originating point).  ...  This algorithm constructs evolutionary trees for a given set of DNA or protein sequences based on the topological information of every possible quartet trees.  ...  This research was partially funded by Discovery Grants (DP0557909) from the Australian Research Council. It was also partially supported by IBM, Australia.  ... 
doi:10.1109/ipdps.2006.1639534 dblp:conf/ipps/ZhouCTWWZB06 fatcat:ybwmxjol2nbsvjv7hizuii33yy

Correcting Syntactic Annotation Errors Using a Synchronous Tree Substitution Grammar

Yoshihide KATO, Shigeki MATSUBARA
2010 IEICE transactions on information and systems  
By using a synchronous grammar, the method transforms parse trees containing annotation errors into the ones whose errors are corrected.  ...  The synchronous grammar is automatically induced from the treebank. We report an experimental result of applying our method to the Penn Treebank.  ...  Acknowledgments This research was partially supported by the Grant-in-Aid for Scientific Research (B) (No. 20300058) of JSPS and by the Kayamori Foundation of Informational Science Advancement.  ... 
doi:10.1587/transinf.e93.d.2660 fatcat:a3izwqotdngr7oz426sr46hyji
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