Visualizing Model Architecture john.sekar@mssm.edu SASB `17 - PowerPoint PPT Presentation

Visualizing Model Architecture john.sekar@mssm.edu SASB `17

Kinetics ~ Reaction Rules Enz Sub Enz Sub sub enz sub enz p1 ~Y p1 ~pY Enz Sub Enz Sub sub enz sub enz Enz Sub Enz Sub p2 ~Y p2 ~pY sub enz sub enz BioNetGen Kappa Simmune SBML-multi 2

Causality Analysis Story Influence Diagram p1 ~Y Enz Sub p2 ~Y sub enz p1 ~pY Sub p2 ~pY 3

RINF of FceRI model with 24 rules 4

Goals 5

Structure Graph Representation Enz Sub p1 ~Y Enz Sub sub enz p1 p1 p2 ~pY sub enz ~Y ~pY 6

Correspondence Map Enz Sub Enz Sub sub enz sub enz Enz Enz Sub Sub sub sub enz enz 7

p1 ~Y p1 ~pY Enz Sub Enz Sub sub enz sub enz Sub Sub Enz Enz p1 p1 ~Y ~pY enz enz sub enz 8

Procedure • • • 9

p1 ~Y Rule consumes a pattern Sub ? Sub Sub Sub Enz Enz p1 p1 p1 ~Y ~Y ~pY enz enz sub enz 10

p1 ~pY Rule produces a pattern Sub Sub Sub Sub Enz Enz p1 p1 p1 ~pY ~Y ~pY enz enz sub enz ? 11

Rule requires a pattern Enz Sub sub enz Sub Sub Sub Sub Enz Enz Enz Enz p1 p1 ~Y ~pY enz enz enz enz sub sub sub enz 12

Atom-Rule Graph • – – – • – • 13

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AR of FceRI model with 24 rules 16

Compression Pipeline • – – • – – – – 17

Atom-Rule Graph Prioritization Grouping Structures Grouping Rules Compression System-specific complexity Universal principles 18

Full AR Graph 19

Prioritized Nodes 20

Grouping Structures 21

Grouping Rules 22

Compression 23

Larger Model 24

Relative Compactness 25

Future Tools 26

Future Tools 27

Summary • • • 28

Ac Acknow owledgem ledgements ents Ref efer erences ences 29