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dc.contributor.authorSioson, Allan A.en_US
dc.date.accessioned2014-03-14T20:19:59Z
dc.date.available2014-03-14T20:19:59Z
dc.date.issued2005-11-29en_US
dc.identifier.otheretd-12082005-154559en_US
dc.identifier.urihttp://hdl.handle.net/10919/29995
dc.description.abstractA multimodal network (MMN) is a novel mathematical construct that captures the structure of biological networks, computational network models, and relationships from biological databases. An MMN subsumes the structure of graphs and hypergraphs, either undirected or directed. Formally, an MMN is a triple (V,E,M) where V is a set of vertices, E is a set of modal hyperedges, and M is a set of modes. A modal hyperedge e=(T,H,A,m) in E is an ordered 4-tuple, in which T,H,A are subsets of V and m is an element of M. The sets T, H, and A are the tail, head, and associate of e, while m is its mode. In the context of biology, each vertex is a biological entity, each hyperedge is a relationship, and each mode is a type of relationship (e.g., 'forms complex' and 'is a'). Within the space of multimodal networks, structural operations such as union, intersection, hyperedge contraction, subnetwork selection, and graph or hypergraph projections can be performed. A denotational semantics approach is used to specify the semantics of each hyperedge in MMN in terms of interaction among its vertices. This is done by mapping each hyperedge e to a hyperedge code algo:V(e), an algorithm that details how the vertices in V(e) get used and updated. A semantic MMN-based model is a function of a given schedule of evaluation of hyperedge codes and the current state of the model, a set of vertex-value pairs. An MMN-based computational system is implemented as a proof of concept to determine empirically the benefits of having it. This system consists of an MMN database populated by data from various biological databases, MMN operators implemented as database functions, graph operations implemented in C++ using LEDA, and mmnsh, a shell scripting language that provides a consistent interface to both data and operators. It is demonstrated that computational network models may enrich the MMN database and MMN data may be used as input to other computational tools and environments. A simulator is developed to compute from an initial state and a schedule of hyperedge codes the resulting state of a semantic MMN model.en_US
dc.publisherVirginia Techen_US
dc.relation.haspartdissertation.pdfen_US
dc.rightsI hereby certify that, if appropriate, I have obtained and attached hereto a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dissertation, or project report, allowing distribution as specified below. I certify that the version I submitted is the same as that approved by my advisory committee. I hereby grant to Virginia Tech or its agents the non-exclusive license to archive and make accessible, under the conditions specified below, my thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report.en_US
dc.subjectbiological network modelsen_US
dc.subjecthypergraphsen_US
dc.subjectMultimodal networksen_US
dc.subjectdenotational semanticsen_US
dc.titleMultimodal Networks in Biologyen_US
dc.typeDissertationen_US
dc.contributor.departmentComputer Scienceen_US
dc.description.degreePh. D.en_US
thesis.degree.namePh. D.en_US
thesis.degree.leveldoctoralen_US
thesis.degree.grantorVirginia Polytechnic Institute and State Universityen_US
thesis.degree.disciplineComputer Scienceen_US
dc.contributor.committeechairHeath, Lenwood S.en_US
dc.contributor.committeememberMurali, T. M.en_US
dc.contributor.committeememberGillaspy, Glenda E.en_US
dc.contributor.committeememberGrene, Ruthen_US
dc.contributor.committeememberRamakrishnan, Narenen_US
dc.identifier.sourceurlhttp://scholar.lib.vt.edu/theses/available/etd-12082005-154559/en_US
dc.date.sdate2005-12-08en_US
dc.date.rdate2005-12-14
dc.date.adate2005-12-14en_US


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