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Sci2ools

PR

2011

2011

This paper introduces a simple Sum-over-Paths (SoP) formulation of string edit distances accounting for all possible alignments between two sequences, and extends related previous work from bioinformatics to the case of graphs with cycles. Each alignment ℘, with a total cost C(℘), is assigned a probability of occurrence P(℘) = exp[−θC(℘)]/Z where Z is a normalization factor. Therefore, good alignments (having a low cost) are favoured over bad alignments (having a high cost). The expected cost, ℘∈P C(℘) exp [−θC(℘)] /Z, computed over all possible alignments ℘ ∈ P, deﬁnes the SoP edit distance. When θ → ∞, only the best alignments matter and the measure reduces to the standard edit distance. The rationale behind this deﬁnition is the following: for some applications, two sequences sharing many good alignments should be considered as more similar than two sequences having only one single good, optimal, alignment in common. In other words, sub-optimal al...

Added |
14 May 2011 |

Updated |
14 May 2011 |

Type |
Journal |

Year |
2011 |

Where |
PR |

Authors |
Silvia García-Díez, François Fouss, Masashi Shimbo, Marco Saerens |

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