Bayesian Network Models in PyMC3 and NetworkX

NelisW commented Jul 1, 2019 •

edited

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Thanks to all above!
I have about four hours experience in pymc3, so the above comments are much appreciated.

Using networkx 2.3 and pyMC3 3.7, cpu on Windows.
Fixed the dict_keyiterator problem.

    32     BN.edge['C3']['D4']['bin'] = T.switch(T.lt(gpm(BN,'D4'),9), 0, 
---> 33                                           T.switch(T.gt(gpm(BN,'D4'), 9) & T.lt(gpm(BN,'D4'),11), 1, 2))

AttributeError: 'DiGraph' object has no attribute 'edge'

When print(BN.__dict__) I see no edge attribute.
The edges seem to be embedded in _adj, _pred and _succ.

BN = nx.DiGraph()
BN.add_node('D1', dtype='Discrete', prob=d1_prob, pos=(2, 4))
BN.add_node('D2', dtype='Discrete', prob=d2_prob, pos=(4, 4))
BN.add_node('C1', dtype='Continuous', mu=c1_mu, sd=c1_sd, pos=(1,3))
BN.add_edge('D1', 'C1')
print(BN.__dict__)
-----------------------------------------------
{
'graph_attr_dict_factory': <class 'dict'>, 'node_dict_factory': <class 'dict'>, 
'node_attr_dict_factory': <class 'dict'>, 'adjlist_outer_dict_factory': <class 'dict'>, 
'adjlist_inner_dict_factory': <class 'dict'>, 'edge_attr_dict_factory': <class 'dict'>, 
'graph': {}, 
'_node': {
  'D1': {'dtype': 'Discrete', 'prob': array([0.3, 0.7]), 'pos': (2, 4)}, 
  'D2': {'dtype': 'Discrete', 'prob': array([0.6, 0.3, 0.1]), 'pos': (4, 4)}, 
  'C1': {'dtype': 'Continuous', 'mu': array([10, 14]), 'sd': array([2, 2]), 'pos': (1, 3)}
  }, 
'_adj': {'D1': {'C1': {}}, 'D2': {}, 'C1': {}},
'_pred': {'D1': {}, 'D2': {}, 'C1': {'D1': {}}}, 
'_succ': {'D1': {'C1': {}}, 'D2': {}, 'C1': {}}
}

D1 is a predecessor for C1.
C1 is a successor for D1.
But C1 is also adjacent to D1?

My bigger issue is what to do with the error on line 32/33 above.

I have no idea how to handle this. Any help will be appreciated!

Author

rtbs-dev commented Jul 1, 2019

Wow, I had no idea there were comments here! Thanks to all for checking out the example. For those of you with issues/ideas (especially networkx v2 problems), check out the repository that automates a lot of the underlying mechanical/boilerplate code in this example. This notebook was really just a proof-of-concept for that repository.

I haven't gone back to the code for a while, but if there's interest I would be happy to update things to newer pymc3 features. Please see if your above issues persist in the more mature repository. Thanks!

NelisW commented Jul 1, 2019 via email

Hi Tbsexton thanks for your prompt reply! Much appreciated

…

On Mon, 1 Jul 2019 at 15:52, Thurston Sexton ***@***.***> wrote: Wow, I had no idea there were comments here! Thanks to all for checking out the example. For those of you with issues/ideas (especially networkx v2 problems), check out the repository <https://github.com/usnistgov/pmml_pymcBN> that automates a lot of the underlying mechanical/boilerplate code in this example. This notebook was really just a proof-of-concept for that repository. I haven't gone back to the code for a while, but if there's interest I would be happy to update things to newer pymc3 features. Please see if your above issues persist in the more mature repository. Thanks! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://gist.github.com/1349864212b25cce91dbe5e336d794b4?email_source=notifications&email_token=ABOR6SK332I4ZSCQAXDB63TP5ID3NA5CNFSM4H4SQIM2YY3PNVWWK3TUL52HS4DFVNDWS43UINXW23LFNZ2KUY3PNVWWK3TUL5UWJTQAFUS4U#gistcomment-2958794>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABOR6SJMJ2QGVZ5CUMO4BCLP5ID3NANCNFSM4H4SQIMQ> .