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AlignmentGenerator: PhaseTab Algorithm

Developers: ​Björn Endres and ​Malte Kiesel

Description

The PhaseTab algorithm is a generic algorithm that employs an arbitrary number of SimilarityMeasures to generate an alignment. The algorithm was originally developed by ​Malte Kiesel and ​Ludger van Elst and has been presented in the paper referenced here. It was then adapted for the PhaseLibs project.

The basic principle of the algorithm is the iterative confirmation of the best ranked relation proposals. This approach makes use of a feature of some SimilarityMeasures, especially the SimilarityFlooding, which increase their precision when given higher confidences on correct relations.

In order to archieve a robust and fair ranking, a BordaCount alogrithm is used to identify the n best rated realtion of all SimilarityMeasures involved.

An iteration cycle now consists of three phases:

1) Generate the SimilarityMatrix for all SimilarityMeasures involved, using the current alignment as an input; the current alignment being empty in the first iteration. If the SimilarityMeasure is independent of such input, e.g. with a frame name based comparison measure, the matrix should not be recalculated. This is, however, up to the measure to decide. 2) Copy all 1.0 rated realtions, i.e. "confirmed ones", into a new and empty alignment. 3) Rank the remaining relations and identify the n best. These are also confirmed by setting their confidence to 1.0. 4) Finally append all other relations with the confidences given by the BordaCount algorithm.

Characteristics

Evaluation/Performance

Specification

Intitialisation

Parameters

none

Dependencies

none

License Issues

TODO