PNLtoGraphviz Package
LinkConnectionStrength Package

By Imme Ebert-Uphoff

The two packages below
are extensions for PNL (Intel's Open-Source Probabilistic Networks Library).

There are two components that are bundled together:
  1. PNLtoGraphviz Interface  (last updated Mar 11, 2006):
Short Description:
  1. LinkConnectionStrength Package  (last updated Mar 11, 2006)
Short Description:
See the documentation below for more details.

Documentation (all in PDF format, last updated January 21, 2006):
  1. PNLtoGraphviz and LinkConnectionStrength (Version 1.0) - Overview, Installation and Quick Command Reference.
  2. User's Guide for the PNLtoGraphviz Package (Version 1.0) Details of PNLtoGraphviz Package.
  3. User's Guide for the LinkConnectionStrength Package (Version 1.0) - Details of LinkConnectionStrength Package.

Related Publications and Research Reports:

Download of Version 1.01  (last updated March 11, 2006):

For installation instructions, see documentation above.
The two packages depend on each other, so you have to download all four files above, even if you only want to use one of the two packages.

Complete List of Changes Since Version 1.0 (Jan 20, 2006):
  1. Remedy for Numerical Error in Mutual Information or Link Strength:
Problem:  In theory, MI, LS_true and LS_blind are always positive, but in practice they can become slightly negative due to numerical error.  The negative values can create problems for choosing gray scale, etc., later on.
Changes: If any of the values MI, LS_true or LS_blind are between (- 0.0001) and 0, set it to zero.
  1. Deal with Degenerate Cases for Mutual Information Percentage and Link Strength Percentage
Problem: If MI=0, then MI% is undefined.  If LS=0, then LS% is undefined.  Division by zero would occur.
In calculation of MI and LS:
If MI<EPSILON, print warning on screen + set MI% to impossible value (-1).  
If LS<EPSILON, print warning on screen + set LS% to impossible value (-1).
In vizualization routines:
If MI% is undefined (i.e. value -1), write "(Undefined %)" as corresponding percentage value in graph.
If LS% is undefined (i.e. value -1), write "(Undefined %)" as corresponding percentage value in graph.
  1. Ensure the Sample Model AsiaModelCorrected is topologically sorted
Problem:  Previously Dyspnoea was defined before CancerOrTuberculosis, although CancerOrTuberculosis is a parent of Dyspnoea.  This can cause problems with SaveNet and other functions in PNL.
Changes: Switched order of definitions of nodes CancerOrTuberculosis and Dyspnoea


If you use the above packages in your work, please consider doing one of the following:
  1. Placing a link from your web page to the main page,  (This will help to increase use of the packages, which helps everyone using them.)
  2. Mentioning the packages in your publications, but only if they really made a difference for the work reported therein.
  3. Providing feedback and suggestions for improvements. 
When working on voluntary projects (such as these extensions) there is nothing as rewarding as hearing from people who actually use them!  Even constructive criticism is much better than no feedback at all... 
So, please send me your comments and questions!

This site and its content are maintained by Imme Ebert-Uphoff .

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Page last updated:  November, 2011