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Network Motifs

Network Motifs. Zach Saul CS 289 Network Motifs: Simple Building Blocks of Complex Networks R. Milo et al. Network Models. Interactions are represented as directed nodes (as presented in class)

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Network Motifs

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  1. Network Motifs Zach Saul CS 289 Network Motifs: Simple Building Blocks of Complex Networks R. Milo et al.

  2. Network Models • Interactions are represented as directed nodes (as presented in class) • Example problems include gene networks, neural nets, ecological models and computer networking models

  3. Network Motifs • Patterns that appear more often in real networks than in randomly generated networks • Many notions of a random network • Naïve algorithm • Erdos-Renyi random graphs • Scale free networks • Even more specialized?

  4. Random Graphs • Three node motifs • Preserve degree for each node • Four node motifs • Preserve degree for each node • Preserve the number of three node motifs

  5. Example Motif

  6. Method • Using brute force, searched target network for every possible subgraph, counting results • Similarly, searched random network • Motifs are patterns that occur greater or equal number of times in random networks more than 1% of the time.

  7. Results

  8. Results (cont.)

  9. Gene/Neural Net Analysis • The nematode neural net and the gene net both contain similar structures • Feed forward • Bi-fan • Both are information processing networks with sensory and acting components • Sensory neurons/transcription factors regulated by biochemical signals • Motor neurons/structural genes

  10. Food Web Analysis • Food Webs do not show feed-forward motifs • Suggests that direct interaction between species at a separation of two layers selected against (e.g. Omnivores) • Bi-parallel suggests that prey of same predator share prey

  11. Electronic Circuit Analysis • Circuits can be classified by function using network motifs • Circuits from benchmark set showed different motifs for each functional class • Some info processing circuits show similar motifs to biological info processing circuits

  12. Web Analysis • Network of hyperlinks • Many more bidirectional links • Motifs indicate a design that allows the shortest path among sets of related pages

  13. Conclusions • Technique robust to data errors • Motifs can indicate common function • ..or could indicate similar evolutionary constraints • Scalability to other types of networks possible • Scalability to larger subgraphs difficult

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