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Generating Biological Network Motifs

Generating Biological Network Motifs. Sai Badey. Biological Networks. What are they? Biological vs Regular Networks* Terminology Motifs Vertices Edges. Overall Scope. Focus on efficiency Large networks Network generation. Project Aim. Random Network Generation

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Generating Biological Network Motifs

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  1. Generating Biological Network Motifs Sai Badey

  2. Biological Networks • What are they? • Biological vs Regular Networks* • Terminology • Motifs • Vertices • Edges

  3. Overall Scope • Focus on efficiency • Large networks • Network generation

  4. 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

  5. Potential Results • No difference • Compare efficiencies of generation methods • Create a standard for network generation • Significant Difference • Determine which is more accurate

  6. Steps • AmalaGhandi’s work • Looks through existing network • Determines motif • Expansion • Determine motif across several networks • Compare different networks & performance • Network Generation

  7. 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)

  8. To Do • Function implementation • Combine with AmalaGhandi’s work • Learning • Vectors • Hash tables

  9. Issues • Lots of research

  10. Sources • AmalaGhandi’s paper • SahandKhakabimamaghani, ImanSharafuddin, Norbert Dichter, Ina Koch,  Ali Masoudi-Nejad • QuateXelero: An Accelerated Exact Network Motif Detection Algorithm (Article) • Joseph Blitzstein and PersiDiaconis • A SEQUENTIAL IMPORTANCE SAMPLING ALGORITHM FOR GENERATING RANDOM GRAPHS WITH PRESCRIBED DEGREES (Article) • Bjorn H. Junker & Falk Schreiber • Analysis of Biological Networks (Book)

  11. Questions? • Take node, change the order of the vertices

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