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Journal of Computational Biology
Article . 2012 . Peer-reviewed
License: Mary Ann Liebert TDM
Data sources: Crossref
https://dx.doi.org/10.48550/ar...
Article . 2010
License: arXiv Non-Exclusive Distribution
Data sources: Datacite
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Comparing Pedigree Graphs

Authors: Kirkpatrick, Bonnie; Reshef, Yakir; Finucane, Hilary; Jiang, Haitao; Zhu, Binhai; Karp, Richard M.;

Comparing Pedigree Graphs

Abstract

Pedigree graphs, or family trees, are typically constructed by an expensive process of examining genealogical records to determine which pairs of individuals are parent and child. New methods to automate this process take as input genetic data from a set of extant individuals and reconstruct ancestral individuals. There is a great need to evaluate the quality of these methods by comparing the estimated pedigree to the true pedigree. In this paper, we consider two main pedigree comparison problems. The first is the pedigree isomorphism problem, for which we present a linear-time algorithm for leaf-labeled pedigrees. The second is the pedigree edit distance problem, for which we present 1) several algorithms that are fast and exact in various special cases, and 2) a general, randomized heuristic algorithm. In the negative direction, we first prove that the pedigree isomorphism problem is as hard as the general graph isomorphism problem, and that the sub-pedigree isomorphism problem is NP-hard. We then show that the pedigree edit distance problem is APX-hard in general and NP-hard on leaf-labeled pedigrees. We use simulated pedigrees to compare our edit-distance algorithms to each other as well as to a branch-and-bound algorithm that always finds an optimal solution.

Keywords

FOS: Computer and information sciences, Models, Genetic, Artificial Intelligence, Computer Science - Data Structures and Algorithms, Humans, Computer Simulation, Data Structures and Algorithms (cs.DS), Algorithms, Pedigree

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
11
Average
Top 10%
Average
Green
bronze