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REPRESENTING A SET OF RECONCILIATIONS IN A COMPACT WAY

CELINE SCORNAVACCA, WOJCIECH PAPROTNY, VINCENT BERRY, VINCENT RANWEZ
2013 Journal of Bioinformatics and Computational Biology  
In this paper we describe a polynomial space and time algorithm to build a minimum reconciliation graph -a graph that summarizes the set of all most parsimonious reconciliations.  ...  The resulting complexity is masked by the fact that a majority of reconciliation software pick up a random optimal solution that is returned to the end-user.  ...  This publication is the contribution no. 2012-147 of the Institut des Sciences de l'Evolution de Montpellier (ISE-M, UMR 5554).  ... 
doi:10.1142/s0219720012500254 pmid:23600816 fatcat:a734n3somne3dnnpedmdyfsg7q

Inferring gene duplications, transfers and losses can be done in a discrete framework

Vincent Ranwez, Celine Scornavacca, Jean-Philippe Doyon, Vincent Berry
2015 Journal of Mathematical Biology  
In the field of phylogenetics, the evolutionary history of a set of organisms is commonly depicted by a species tree -whose internal nodes represent speciation events -while the evolutionary history of  ...  This is done by embedding the gene tree inside the species tree and hence providing a reconciliation of those trees.  ...  This publication is contribution no. 2015-098 of the Institut des Sciences de l'Evolution de Montpellier (ISEM, UMR 5554).  ... 
doi:10.1007/s00285-015-0930-z pmid:26337177 fatcat:6q7i7gpbqfauzbcuuecu4bfnfa

Reconciliation of metabolites and biochemical reactions for metabolic networks

T. Bernard, A. Bridge, A. Morgat, S. Moretti, I. Xenarios, M. Pagni
2012 Briefings in Bioinformatics  
Each of these resources provides a pre-compiled reconciliation of many of the most commonly used metabolic resources.  ...  The reconciliation of discrepancies between data from these sources generally requires significant manual curation, which constitutes a major obstacle in efforts to develop and apply genome-scale metabolic  ...  Acknowledgements We thank Mathias Ganter for his useful feedback on the MNXref reconciliation.  ... 
doi:10.1093/bib/bbs058 pmid:23172809 pmcid:PMC3896926 fatcat:ztz6xxdddnc5xkcnfcjy7bxsai

Using Permuted States and Validated Simulation to Analyze Conflict Rates in Optimistic Replication

An-I Andy Wang, Geoff Kuenning, Peter Reiher
2007 Simulation (San Diego, Calif.)  
However, a theoretical result in the database literature suggests that the proliferation of conflicts will prevent optimistic replication from scaling  ...  Optimistic replication provides high data availability in the presence of network outages.  ...  XY is in conflict with Z, YZ, and XZ). Effectively, the original three-way conflict has evolved into a four-way conflict due to conflict resolutions.  ... 
doi:10.1177/0037549707085073 fatcat:ph6xspcnkngglbhqgs5mhkwdu4

KD2R: A Key Discovery Method for Semantic Reference Reconciliation [chapter]

Danai Symeonidou, Nathalie Pernelle, Fatiha Saïs
2011 Lecture Notes in Computer Science  
Some existing reference reconciliation approaches use key constraints to infer reconciliation decisions. In the context of the Linked Open Data, this knowledge is not available.  ...  KD2R has been tested on data sets of the international contest OAEI and obtains promising results.  ...  KD2R uses a compact representation of RDF data expressed in a prefix-tree in order to compute the complete set of maximal undermined keys and maximal non keys and then the complete set of minimal keys.  ... 
doi:10.1007/978-3-642-25126-9_51 fatcat:cot4yh7iljdxjbxdzmv4ujajc4

DTL-RnB: Algorithms and Tools for Summarizing the Space of DTL Reconciliations

W. Ma, D. Smirnov, J. Forman, A. Schweickart, C. Slocum, S. Srinivasan, R. Libeskind-Hadas
2018 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
Reconciliation is typically performed in a maximum parsimony framework and the number of optimal reconciliations can grow exponentially with the size of the trees, making it difficult to understand the  ...  This paper demonstrates how a small number of reconciliations can be found that collectively contain the most highly supported events in the solution space.  ...  Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.  ... 
doi:10.1109/tcbb.2016.2537319 pmid:26955051 fatcat:pdx6mxzg3bfpvn56es5g3s26uq

Hierarchical clustering of maximum parsimony reconciliations

Ross Mawhorter, Ran Libeskind-Hadas
2019 BMC Bioinformatics  
The hierarchical clustering algorithm method proposed here provides a new approach to find a set of representative reconciliations in the potentially vast and diverse space of maximum parsimony reconciliations  ...  Therefore, there is a need to find small sets of best representative reconciliations when the space of solutions is large and diverse.  ...  A fundamental problem, therefore, is that of identifying a set of best representative reconciliations.  ... 
doi:10.1186/s12859-019-3223-5 pmid:31775628 pmcid:PMC6882150 fatcat:eitxxb5n4ze6pm44ta6u6g7xfi

primetv: a viewer for reconciled trees

Bengt Sennblad, Eva Schreil, Ann-Charlotte Berglund Sonnhammer, Jens Lagergren, Lars Arvestad
2007 BMC Bioinformatics  
illustrations in an educational setting. primetv is available at http://prime.sbc.su.se/primetv, both as a standalone command-line tool and as a web service.  ...  It is a simple and compact visualization program that is the first automatic tool for illustrating general tree reconciliations.  ...  indeed represent a duplication.  ... 
doi:10.1186/1471-2105-8-148 pmid:17484781 pmcid:PMC1891116 fatcat:3rak4w4mkzdp3e2ssziilnritq

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.  ...  We describe ecceTERA, a program that implements a generic parsimony reconciliation algorithm, which accounts for gene duplication, loss and transfer (DTL) as well as speciation, involving sampled and unsampled  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btw105 pmid:27153713 fatcat:2cpgorlqynhohner54q5j4e6lu

A framework for reconciliating data clusters from a fleet of nuclear power plants turbines for fault diagnosis

Sameer Al-Dahidi, Francesco Di Maio, Piero Baraldi, Enrico Zio, Redouane Seraoui
2018 Applied Soft Computing  
Acknowledgements The participation of Sameer Al-Dahidi and Piero Baraldi to  ...  The goodness of the final reconciliated clustering is quantified in terms of clusters separation and compactness.  ...  In this way, each entry of the similarity matrix has a value in [0, 1], which is proportional to how likely a pair of data is, when grouped together. Step Step 4: Clustering algorithm.  ... 
doi:10.1016/j.asoc.2018.04.044 fatcat:djstsw65ijhplmh7gqeyozcf7e

Informed Content Delivery Across Adaptive Overlay Networks

J.W. Byers, J. Considine, M. Mitzenmacher, S. Rost
2004 IEEE/ACM Transactions on Networking  
Our main contribution is a collection of useful algorithmic tools for efficient summarization and approximate reconciliation of sets of symbols between pairs of collaborating peers, all of which keep message  ...  Using the digital fountain encoding approach, end hosts can efficiently reconstruct the original content of size from a subset of any symbols drawn from a large universe of encoding symbols.  ...  A Bloom filter is used to represent a set of elements from a universe of size , and consists of an array of bits, initially all set to 0.  ... 
doi:10.1109/tnet.2004.836103 fatcat:ciy5cbsx75ggzkc5bhdzsqne24

Informed content delivery across adaptive overlay networks

John Byers, Jeffrey Considine, Michael Mitzenmacher, Stanislav Rost
2002 Proceedings of the 2002 conference on Applications, technologies, architectures, and protocols for computer communications - SIGCOMM '02  
Our main contribution is a collection of useful algorithmic tools for efficient summarization and approximate reconciliation of sets of symbols between pairs of collaborating peers, all of which keep message  ...  Using the digital fountain encoding approach, end hosts can efficiently reconstruct the original content of size from a subset of any symbols drawn from a large universe of encoding symbols.  ...  A Bloom filter is used to represent a set of elements from a universe of size , and consists of an array of bits, initially all set to 0.  ... 
doi:10.1145/633025.633031 dblp:conf/sigcomm/ByersCMR02 fatcat:25ny6vf7inb37acghjlrsqffsa

Informed content delivery across adaptive overlay networks

John Byers, Jeffrey Considine, Michael Mitzenmacher, Stanislav Rost
2002 Proceedings of the 2002 conference on Applications, technologies, architectures, and protocols for computer communications - SIGCOMM '02  
Our main contribution is a collection of useful algorithmic tools for efficient summarization and approximate reconciliation of sets of symbols between pairs of collaborating peers, all of which keep message  ...  Using the digital fountain encoding approach, end hosts can efficiently reconstruct the original content of size from a subset of any symbols drawn from a large universe of encoding symbols.  ...  A Bloom filter is used to represent a set of elements from a universe of size , and consists of an array of bits, initially all set to 0.  ... 
doi:10.1145/633030.633031 fatcat:vgxn6littzglviau2yy72nm2py

Visualizing Co-Phylogenetic Reconciliations [article]

Tiziana Calamoneri and Valentino Di Donato and Diego Mariottini and Maurizio Patrignani
2017 arXiv   pre-print
The typical application is the visualization of the co-evolution of hosts and parasites in biology. Our strategy combines a space-filling and a node-link approach.  ...  We introduce a hybrid metaphor for the visualization of the reconciliations of co-phylogenetic trees, that are mappings among the nodes of two trees.  ...  Acknowledgments We thank Riccardo Paparozzi for first experiments on the visualization of cophylogenetic trees.  ... 
arXiv:1708.09691v1 fatcat:g3ufkpjd7zho3pudscyceaal34

Page 380 of British and Foreign Evangelical Review Vol. 31, Issue 120 [page]

1882 British and Foreign Evangelical Review  
If a correct solution of the effect of the sacrifice toward God has been reached, its effect toward man, the other party in the reconciliation, is easily apprehended, and can be stated in few words.  ...  Second, His relation to men is essentially representative, i.c. not by authoritative selection, nor by compact, as a “ federal head,” which would be arbitrary, but by His original connection, as the actual  ... 
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