project.org~

*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
   -[[~/Documents/Academic/Masters_Thesis/code/JunctionBox_noGraphviz/res/UAI/results/pe/sorted_pe_topTen.txt][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?