Symbols and Motifs How to identify symbols and motifs in literature.
Generating Biological Network Motifs
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Transcript of Generating Biological Network Motifs
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Generating Biological Network Motifs
Sai Badey
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Biological Networks What are they?
Biological vs Regular Networks*
Terminology Motifs Vertices Edges
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Overall Scope Focus on efficiency
Large networks Network generation
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Project Aim Random Network Generation
functions (keep # vertices & # edges constant) Swap the edges between outer-vertices Completely random generation Swap node degrees
Analysis & Comparisons Run z-testing on the generations for small to
extremely large graphs
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Potential Results No difference
Compare efficiencies of generation methods Create a standard for network generation
Significant Difference Determine which is more accurate
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Steps Amala Ghandi’s work
Looks through existing network Determines motif
Expansion Determine motif across several networks Compare different networks & performance Network Generation
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Current Status Class Design
Network Class Jung Library Constructor, Copy constructor Network generation Analysis (z-test, motif searching, data collection)
Compare Networks Class Equals Comparison (highest degree node, motif comparison) Analysis (significant difference, etc)
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To Do Function implementation
Combine with Amala Ghandi’s work
Learning Vectors Hash tables
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Issues Lots of research
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Sources Amala Ghandi’s paper
Sahand Khakabimamaghani, Iman Sharafuddin, Norbert Dichter, Ina Koch, Ali Masoudi-Nejad
QuateXelero: An Accelerated Exact Network Motif Detection Algorithm (Article)
Joseph Blitzstein and Persi Diaconis A SEQUENTIAL IMPORTANCE SAMPLING ALGORITHM FOR GENERATING RANDOM
GRAPHS WITH PRESCRIBED DEGREES (Article)
Bjorn H. Junker & Falk Schreiber Analysis of Biological Networks (Book)
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Questions?
Take node, change the order of the vertices