Release v0.4.0

Updated code to use new API for Catlab.jl and Petri.jl

Release v0.3.0

Release v0.3.0

Release v0.3.0 is a major enhancement to the new model augmentation tools introduced the the last release. This includes a more robust design, easier model implementation, and more built in features to augment and compose models.

• New submodules
  • ModelTools
    • SemanticModels.ModelTools.CategoryTheory the main module that contains the category theory based building blocks for model augmentation
      • SemanticModels.ModelTools.CategoryTheory.AbstractMorph abstract type for representing morphisms
      • SemanticModels.ModelTools.CategoryTheory.FinSetMorph morphism in the category of finite sets
      • SemanticModels.ModelTools.CategoryTheory.GraphMorph morphism in the category of graphs
      • SemanticModels.ModelTools.CategoryTheory.⊔ get the union of two categorically defined models or morphisms
      • SemanticModels.ModelTools.CategoryTheory.Decorated a type representing a decoration applied to the objects of a morphism
      • SemanticModels.ModelTools.CategoryTheory.AbstractSpan an abstract type for representing spans
      • SemanticModels.ModelTools.CategoryTheory.Span general span of two morphisms
      • SemanticModels.ModelTools.CategoryTheory.AbstractCospan an abstract type for representing cospans
      • SemanticModels.ModelTools.CategoryTheory.Cospan general cospan of two morphisms
      • SemanticModels.ModelTools.CategoryTheory.pushout solve the pushout defined by a span
    • SemanticModels.ModelTools.PetriModels Extends ModelTools and the new CategoryTheory API to support models defined in Petri.jl
    • SemanticModels.ModelTools.OpenModels module for defining an open model where there are defined inputs and outputs, domain and codomain
    • SemanticModels.ModelTools.OpenPetris module for implementing the open petri model, and converting a PetriModel to an OpenPetri
      • SemanticModels.ModelTools.OpenPetris.otimes combine two open petri models in parallel
      • SemanticModels.ModelTools.OpenPetris.compose combine two open petri models in series
• New examples
  • decorations/graphs.jl example of using the new Category Theory based Morphism API to combine graphs and Petri models
  • petri/malaria.ipynb example of utilizing the new OpenModel API to combine a Lotka Volterra model and an Epidemiology model to simulate Malaria spreading between a population
  • petri/rewrite_demo.jl example of using rewrite rules to augment a Petri model
  • petri/rewrite.jl more detailed example of using rewrite rules to augment a Petri model and then solving the new models using both agent based models and differential equations
  • petri/wiring_petri.jl example of creating a model using wiring diagrams, converting that to a Petri model, and solving
• New docs pages
  • Removed Dubstep
  • Updates to ModelTools
  • Updates to Theory
  • Replaced Flu Model walkthrough with Malaria example

Release v0.2.0

Release v0.2.0

Release v0.2.0 include an inital version of our new model augmentation tools and program analysis features.

• New submodules

  • ModelTools
    • SemanticModels.ModelTools.model the main constructor for building model instances
    • Tools for accessing parts of expressions
      • SemanticModels.ModelTools.head gets the head of an Expr or nothing for LineNumberNodes
      • SemanticModels.ModelTools.bodyblock gets the body of the func
      • SemanticModels.ModelTools.argslist get the array of args representing the arguments of a defined function
      • SemanticModels.ModelTools.funcname get the function name from an expression object return :nothing for non function expressions
      • SemanticModels.ModelTools.callsites collects func calls
      • SemanticModels.ModelTools.structured extract the expressions that use structuring
    • Tools for modifying expressions
      • SemanticModels.ModelTools.pusharg! push a new argument onto the definition of a function.
      • SemanticModels.ModelTools.setarg! replace the argument in a function call
    • Predicates useful for manipulating expressions
      • SemanticModels.ModelTools.or or
      • SemanticModels.ModelTools.and and
      • SemanticModels.ModelTools.issome predicate for being neither missing or nothing
      • SemanticModels.ModelTools.isblock predicate for an expression being a block node
      • SemanticModels.ModelTools.isfunc predicate for an expression being a function
      • SemanticModels.ModelTools.isexpr checks if expr
      • SemanticModels.ModelTools.iscall checks if func call
      • SemanticModels.ModelTools.isusing checks for using statement
      • SemanticModels.ModelTools.isimport checks for import
    • Prebuilt model types
      • SemanticModels.ModelTools.AbstractModel the abstract type for generic models
      • SemanticModels.ModelTools.SimpleModels.SimpleModel represents generic models with just blocks and functions
      • SemanticModels.ModelTools.ExpStateModels.ExpStateModel represents a simple Agent Based Modeling (ABM) framework
      • SemanticModels.ModelTools.ExpStateModels.ExpStateTransition represents ABM transitions
      • SemanticModels.ModelTools.ExpODEModels.ExpODEModel represents ODEProblems as code expressions
    • Type Graphs
      • SemanticModels.ModelTools.typegraph annotate a code expression so that when you eval it, you get the typegraph
      • SemanticModels.ModelTools.@typegraph extract a typegraph from a block of code

• Examples

  • agentbased.jl we define a modeling microframework for Agent Based Modeling (ABM)
  • agentbased2.jl a more refined version of agentbased.jl that uses singleton types
  • agentgraft.jl an example of model augmentation for ABM
  • agenttype.jl example of how to reverse engineer a model structure with the typegraph function
  • defintions.jl
  • diffeq.jl
  • macromodel.jl example of using modeltools as a macro
  • regression.jl basic regression script
  • monomial_regression.jl transformations on linear regression build nonlinear regression
  • multivariate_regression.jl product group to manipulate a multivariate regression model
  • odegraft.jl updated version of our old graft.jl script
  • pseudo_polynomial_regression.jl transforms linear regression into a 1 degree of freedom polynomial regression
  • polynomial_regression.jl manipulate a univariate linear regression model into polynomial regression
  • workflow.jl model synthesis with a pipeline of agentgraft.jl and polynomial_regression.jl

• New docs pages

  • ModelTools
  • Updates to Theory
  • Updated examples

• Removed Functionality

  • SemanticModels.Graph, replaced by SemanticModels.ModelTools.typegraph
  • Parsers.edges, replaces by typegraph and MetaGraphs.edges(g)

v0.2.0-rc1

A release candidate for v0.2.0

v0.1.2 Initial METADATA release

Initial Release on Metadata

v0.1.1

Fixed some documentation bugs and deployment for github pages and GT hosting.

v0.1.0

News

Release v0.1

Release v0.1 includes an initial version of every step in the SemanticModels pipeline.
Users can now extract information, build knowledge graphs, and generate new models.

The following is a summary of the most important new features and updates:

• New submodules

  • Dubstep
    • SemanticModels.Dubstep.TraceCtx builds dynamic analysis traces of a model for information extraction.
    • SemanticModels.Dubstep.LPCtx allows you to modify the norms used in a model.
    • SemanticModels.Dubstep.GraftCtx allows grafting components of one model onto another.
  • Parsers
    • Parsers.parsefile reads in a julia source file as an expression.
    • Parsers.defs extracts all of the code definitions from a module definition expression.
    • Parsers.edges extracts edges for the knowledge graph from code.
  • Graphs
    • A knowledge graph schema Knowledge Graphs.
    • Graphs.insert_edges_from_jl builds a knowledge graph from extracted edges.

• Examples

  • test/transform/ode.jl shows how to perturb an ODE with overdub.
  • test/transform/varextract.jl shows how to use a compiler pass to extract dynamic analysis information.

• Scripts

  • bin/extract.jl extracts knowledge elements from parsed markdown and source code files.
  • bin/graft.jl performs metamodeling by grafting a component of one model onto another.

• New docs pages

  • Intended Use Cases
  • Dubstep
  • Knowledge Graphs
  • Knowledge Extraction
  • Model Validation with Dynamic Analysis
  • Semantic Modeling Theory
  • Developer Guidelines

Release v0.0.1

Initial release with documentation and some examples designed to illustrate the inteded scope of the software.

Initial Report to DARPA

This release is our first submission to our sponsor DARPA. There is an initial prototype of the modeling system and the documentation of our initial approach.