tableTPG: Valid configurations for hidden variable nodes in a Forney...
In fspetale/fgga: Hierarchical ensemble method based on factor graph
tableTPG R Documentation
Valid configurations for hidden variable nodes in a Forney Factor Graph
Description
tableTPG provides valid configurations of hidden variable nodes at logical function nodes in a Forney Factor Graph under the True Path Graph (TPG) constraint.
Usage
tableTPG(att)
Arguments
att
An integer indicating the number of cross-Ontology nodes involved
Details
Valid configurations of hidden variable nodes at logical function nodes enable messaging passing across the Forney Factor Graph. The TPG constraint is defined as: “If the child Ontology node describes the protein, then all its parent terms must also apply to that protein; and if a Ontology node does not describe a protein, then all its descendant Ontology nodes must not describe it”. The TPG constraint governs the structure of the Ontology-DAG and the inference process in the associated Forney Factor Graph.
Value
A binary matrix with (n-1)^2+1 rows by n+1 columns where n = attr
Author(s)
Flavio E. Spetale, Pilar Bulacio and Javier Murillo <spetale@cifasis-conicet.gov.ar>
References
Tanoue J, Yoshikawa M, Uemura S (2012). The Gene Around GO viewer. Bioinformatics 18(12): 1705–1706.
Spetale FE, Tapia E, Krsticevic F, Roda F, Bulacio P (2016). A Factor Graph Approach to Automated GO Annotation. PLOS ONE 11(1): e0146986
Examples
tableTPG(3)
fspetale/fgga documentation built on Jan. 29, 2024, 6:53 p.m.
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| tableTPG | R Documentation |
Valid configurations for hidden variable nodes in a Forney Factor Graph
Description
tableTPG provides valid configurations of hidden variable nodes at logical function nodes in a Forney Factor Graph under the True Path Graph (TPG) constraint.
Usage
tableTPG(att)
Arguments
att |
An integer indicating the number of cross-Ontology nodes involved |
Details
Valid configurations of hidden variable nodes at logical function nodes enable messaging passing across the Forney Factor Graph. The TPG constraint is defined as: “If the child Ontology node describes the protein, then all its parent terms must also apply to that protein; and if a Ontology node does not describe a protein, then all its descendant Ontology nodes must not describe it”. The TPG constraint governs the structure of the Ontology-DAG and the inference process in the associated Forney Factor Graph.
Value
A binary matrix with (n-1)^2+1 rows by n+1 columns where n = attr
Author(s)
Flavio E. Spetale, Pilar Bulacio and Javier Murillo <spetale@cifasis-conicet.gov.ar>
References
Tanoue J, Yoshikawa M, Uemura S (2012). The Gene Around GO viewer. Bioinformatics 18(12): 1705–1706.
Spetale FE, Tapia E, Krsticevic F, Roda F, Bulacio P (2016). A Factor Graph Approach to Automated GO Annotation. PLOS ONE 11(1): e0146986
Examples
tableTPG(3)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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