Skip to content


Folders and files

Last commit message
Last commit date

Latest commit


Repository files navigation

These scripts demonstrate the use of bayesian metamodeling of complex biological systems across varying representations.

Authors: Liping Sun, Barak Raveh




  • matlab: The scripts are built upon and work with Matlab.
  • bnt: Bayes Net Toolbox for Matlab.

To get started:

  • Either use the bnt version here (under bnt_master/), or download a recent version of bnt here:

  • If downloaded, apply two minor bugfixes on bnt:

    • Disable line 132 of /Your-Path-To/bnt-master/BNT/learning/learn_params_dbn_em.m.
     125- loglik = 0;
     126- for l=1:length(cases)
     127-   evidence = cases{l};
     128-   if ~iscell(evidence)
     129-     error('training data must be a cell array of cell arrays')
     130-   end
     131-   [engine, ll] = enter_evidence(engine, evidence);
     132-   % assert(~isnan(ll))
     133-   loglik = loglik + ll;
     134-   T = size(evidence, 2);
    • Wrap line 85 with the following if statement in /Your-Path-To/bnt-master/BNT/general/mk_bnet.m.
     85-  if length(mems)>=1
     86-    bnet.rep_of_eclass(e) = mems(1);
     87-  end
  • Add the path of the bnt package:

1- addpath(genpathKPM('/Your-Path-To/bnt-master'))

List of files and directories:

  • data contains the data of six input models and the metamodel including:
    • JSON files with the values of model parameters and variables:
    • GI.dat with the observed values for the glucose intake after a meal
    • Gb_kt_input_err101.dat and Gb_kt_input_sigma101.dat with the input values for different accuracy and precision of model variables G_B and kt
    • 072919-INS1e-30min-Enrichment-analysis-cleaned-summary.xlsx with the data for the metabolism model
  • scripts contains all the bnet scripts for metamodeling, please refer to in scripts for more details
  • bnt_master contains Bayes Net Toolbox for Matlab with the bugfixes.