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Ontology & Graphical Representations

Ontology & Graphical Representations. NET Meeting – Ottawa – July 7, 2010 Subproject report By Anya Okhmatovskaia. Current strategy. Build the ontology bottom-up: Examine existing POHEM models Identify common concepts, principles, relations

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Ontology & Graphical Representations

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  1. Ontology & Graphical Representations NET Meeting – Ottawa – July 7, 2010 Subproject report By Anya Okhmatovskaia

  2. Current strategy • Build the ontology bottom-up: • Examine existing POHEM models • Identify common concepts, principles, relations • Create a POHEM-specific ontology, later extend it • Sources of knowledge on POHEM models: • Existing model diagrams • POHEM code • “Data items” spreadsheets for Cancer models

  3. Graphical representation • Helpful exercise in organizing POHEM concepts: leverages ontology development • Progress since first version: • Attempted to separate causal view from temporal • More explicit and (hopefully) more consistent • Web-interactive • Prototype of automatic generator under way • Diagrams are descriptive: we do not intend to do reasoning over graphs

  4. Causal view Health Determinants Diseases Mortality Interventions RF interventions, Treatment Health Utility Costs Direct, Indirect Notation: Nodes = random vars Arcs = causal effect

  5. Causal view: Nodes • Nodes = random variables • Define an agent’s state* • Have an associated function used to compute the node’s value • regression model • look-up table • probabilistic mapping • Input nodes: • have no parent nodes • initialized from data • Different colors = categories of variables in POHEM * There’s no “system state in POHEM, but possible for other simulation models

  6. Causal view: Links • Links = causal effects • Have associated data • directly used in a function to compute a node • used in analysis to derive parameters • used for calibration • Suggested diagrams are not DAGs • Cycles in the graph reflect flattening temporal aspect Disease t1 Disease t2 Intervention t1 Intervention t1

  7. Encoding time Important dimensions: • constant vs. changing over time • time between updates • regular change: fixed intervals (e.g. BMI, Smoking) • dynamically computed time to event (e.g. AMI) • restrictions on temporal dynamics • unconstrained (e.g. BMI?) • monotonic increase/decrease (e.g. Age, Costs) • restricted state transitions (e.g. Disease progression, Death)

  8. Encoding time • State transitions is the most elaborate/detailed way to specify change over time • state diagrams define restrictions on transitions • for each state causal view can be different • It is possible to cast different kinds of temporal change to state transitions • not necessarily the best solution • Node’s temporal dynamics representation is related to variable type • continuous variables would have to be discretized to apply state transition restriction • parameterized functions are a more compact and complete specification

  9. Encoding time Health Determinants (regular change): categorical, logical, rank, numeric (discrete, continuous) etc … Diseases (restricted transitions): categorical Mortality (restricted transitions): logical (T/F) Interventions (possibly constant): logical (?) Health Utility: numeric (continuous) Costs (monotonic increase): numeric (continuous)

  10. Automatic diagrams So far for causal view only Ontology (OWL) Formatted graph (SVG) Java SVG translator or XSLT Protégé plug-in Graph definition file (DOT) GraphViz dot utility Graph image (GIF) Interactive diagram (HTML)

  11. Future work plan Goals & timeline

  12. Goals: Development 1. Ontology development • Refine POHEM-specific ontology • Encode existing POHEM models • Review literature and terminology • Extend/generalize ontology • Encode non-POHEM model(s) • Formally evaluate the ontology 2. Ontology applications • Automatic model documentation • Diagram generator ? Model consistency checking ? Literature search aid

  13. Goals: Training & KT 3. Training • Ontology development and evaluation:CS/Epi Master Thesis • Applications development:CS Master summer Project (1-2) 4. Publications • Conference papers: • initial version of generalized ontology • ontology evaluation • application(s) • Journal paper: Putting everything together

  14. Diagraming application summer project Onto-based documentation summer project Ontology evaluation complete Hire a student for ontology thesis (optimistic scenario) Terminology review done, 1st version of generalized ontology POHEM ontology refinement & model encoding complete Generalized ontology refinement, encoding of non-POHEM model(s) complete Timeline

  15. Conf. paper:initial description of ontology + POHEM examples Conf. paper:ontology application Conf. paper:ontology evaluation Timeline: Publications Diagraming application summer project Onto-based documentation summer project Ontology evaluation complete Hire a student for ontology thesis (optimistic scenario) Submission deadlines: AIME: January AMIA: March EKAW: April ISWC: June Terminology review done, 1st version of generalized ontology POHEM ontology refinement & model encoding complete Generalized ontology refinement, encoding of non-POHEM model(s) complete Journal paper:generalized ontology, examples, evaluation, applications

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