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*Junction Box: A free as in freedom implementation of Junction Tree Inference for Bayes Nets.

Milestone: Release 1

***Current Functionality: Perform Junction Tree inference on a Bayes Net with no evidence, specified in either C or Java Code

Release Targets:

Add simple evidence potentials [13/13]

  • [X] Add observations to JB_Model.h
  • [X] Add observations to JB_Model.c
    • [X] Observation_Create : Must initialize a potential based on variable pointer and value
      • Because of the tangledness of VariableSets, Orderings and Potentials, I am making Observation_Create take a VariableSet. It should be a singleton VariableSet. This necessitates a walk through the Variable Ordering[O(v) time], and will be done away with REFACTOR[0].
    • [X] Observation_Destroy
  • [X] Store Observations in BNet type
    • [X] Because of awkwardness with SWIG and ptrs to ptrs, I’m using Lists to initialize BNet Structures. [BNet_Create_List] .
    • [X] I’ll initially create a BNet_Create_List2 which will also take a list of observations.
      • [X] Modify bnet struct
      • [X] BNet_Create_List2
  • [X] Multiply the observations into potentials when initializing the JT Potentials.
  • [X] Test Observations in C
  • [X] Add Observations to SWIG
  • [X] Test Observations in Java

Add XML Parsing in Java Component, so as to attempt UAI benchmarks [7/7]

  • [X] Identify the easily passable benchmarks. Make a list in a linked file -Top Ten Easiest
  • [X] Set up XBIFParser based on Xerces-J2 SAX example
    • [X]Initial steps: Statistics about xbif file:
      • Number of Variables
      • Maximum number of values per variable
      • Maximum number of parents of any variable
      • Number of observations
  • [X] Build a JAR out of SWIG code
  • [X] See if it’s possible to tell swig to use packages instead of being so sloppy
    • It is, but it breaks the Void pointer typemap stuff.
  • [X] Include JAR in Parser
  • [X] Use JAR to construct Bayes Nets from UAI

****Testing

  • [X] Add a function which takes in a Bayes Net, and a list of variables and returns a list of all clique potentials containing all members of the list
  • [ ] Expose marginalization of potentials via SWIG
  • [ ] Verify that we are getting consistent marginals over each variable in all the places the variable occurs
  • [ ] Possibly contract the charge over the junction tree on some assignment, and verify that it is unchanged after each message pass

Merge SVN, or otherwise resolve somehow

****Memory Management

  • Key issue for memory management is potentials and their huge arrays of doubles.
  • Labels are sometimes shared. This saves memory, but makes deallocation problematic. This must be addresessed systematically

****General Refactoring

  • REFACTOR[0]The business about VariableSets and potentials and such in the creation of Conditional Probability Tables and observations should be moved into a factory method in order to make client code cleaner. This factory method could take a Variable List, and an array of doubles You’d probably want a factory object so as not to recreate VariableOrderings

rpm? deb?