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Bayesian Network Models in PyMC3 and NetworkX
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@madHatter106
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madHatter106 commented Mar 20, 2018

This is really cool. Thanks!

@Nilavro
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Nilavro commented Sep 16, 2018

How do you make a query ? For example P(C3 |C2 = 12)

@dynaryu
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dynaryu commented Nov 13, 2018

I've got the following error message when I tried the Networkx with PyMC3:


TypeError Traceback (most recent call last)
in
8 BN.node['D2']['dist_obj'] = pm.Categorical('D2',p=BN.node['D2']['prob'])
9
---> 10 BN.node['C1']['dist_obj'] = pm.Normal('C1', mu=10+4*gpm(BN,'C1'),
11 tau = (1./2)*2)
12 BN.node['C2']['dist_obj'] = pm.Normal('C2', mu=6+2
(gpm(BN,'C2'))**2,

in gpm(BN, node, num)
1 # utily to quickly access the parent nodes' pymc3 objects
2 def gpm(BN, node, num=0):
----> 3 return BN.node[BN.predecessors(node)[num]]['dist_obj']
4
5 with pm.Model() as mod2:

TypeError: 'dict_keyiterator' object is not subscriptable

I'm currently using networkx 2.2, pymc3 3.5, and python 3.5 on OS X

@Fangwq
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Fangwq commented Jan 2, 2019

I got the following error message:

Traceback (most recent call last):
File "./pmml_test.py", line 126, in
BN.node['C1']['dist_obj'] = pm.Normal('C1', mu=10+4*gpm(BN,'C1'),tau = (1./2)**2)
File "./pmml_test.py", line 118, in gpm
return BN.node[BN.predecessors(node)[num]]['dist_obj']
TypeError: 'dictionary-keyiterator' object has no attribute 'getitem'

I'm currently using networkx 2.2, pymc3 3.5, and python 2.7 on OS X. Can you help me?

@DanielaLaura
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DanielaLaura commented Jan 4, 2019

I got the following error message:

Traceback (most recent call last):
File "./pmml_test.py", line 126, in
BN.node['C1']['dist_obj'] = pm.Normal('C1', mu=10+4*gpm(BN,'C1'),tau = (1./2)**2)
File "./pmml_test.py", line 118, in gpm
return BN.node[BN.predecessors(node)[num]]['dist_obj']
TypeError: 'dictionary-keyiterator' object has no attribute 'getitem'

I'm currently using networkx 2.2, pymc3 3.5, and python 2.7 on OS X. Can you help me?

Here, he is using network 1.x. Here is the Migration guide :https://networkx.github.io/documentation/stable/release/migration_guide_from_1.x_to_2.0.html

In :
"# utily to quickly access the parent nodes' pymc3 objects
def gpm(BN, node, num=0):
return BN.node[BN.predecessors(node)[num]]['dist_obj'] "
you have to change BN.predecessors(node) to list(BN.predecessors(node)).

That is why you might get that keyiterator error.

Edit: aslo, you might want to change BN.node to BN.nodes
Hope it helps!

@DanielaLaura
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DanielaLaura commented Jan 4, 2019

I've got the following error message when I tried the Networkx with PyMC3:

TypeError Traceback (most recent call last)
in
8 BN.node['D2']['dist_obj'] = pm.Categorical('D2',p=BN.node['D2']['prob'])
9
---> 10 BN.node['C1']['dist_obj'] = pm.Normal('C1', mu=10+4gpm(BN,'C1'),
11 tau = (1./2)
2) 12 BN.node['C2']['dist_obj'] = pm.Normal('C2', mu=6+2(gpm(BN,'C2'))**2,

in gpm(BN, node, num)
1 # utily to quickly access the parent nodes' pymc3 objects
2 def gpm(BN, node, num=0):
----> 3 return BN.node[BN.predecessors(node)[num]]['dist_obj']
4
5 with pm.Model() as mod2:

TypeError: 'dict_keyiterator' object is not subscriptable

I'm currently using networkx 2.2, pymc3 3.5, and python 3.5 on OS X

Here, he is using network 1.x. Here is the Migration guide :https://networkx.github.io/documentation/stable/release/migration_guide_from_1.x_to_2.0.html

In :
"# utily to quickly access the parent nodes' pymc3 objects
def gpm(BN, node, num=0):
return BN.node[BN.predecessors(node)[num]]['dist_obj'] "
you have to change BN.predecessors(node) to list(BN.predecessors(node)).

That is why you might get that keyiterator error.

Edit: aslo, you might want to change BN.node to BN.nodes
Hope it helps!

@tomkovna
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tomkovna commented Jan 7, 2019

How do you make a query such as: P(C1_a<C1<C1_b | C3_a<C3<C3_b, D4 = 1)?

@13charliebrown
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13charliebrown commented Feb 9, 2019

I am getting the following error:

Traceback (most recent call last):

File "", line 30, in
BN.edge['C3']['D4']['bin']], observed=BN.node['D4']['observe'])

File "C:\Users\Andrea\Anaconda3\lib\site-packages\theano\tensor\var.py", line 544, in getitem
theano.tensor.subtensor.Subtensor.convert(arg)

File "C:\Users\Andrea\Anaconda3\lib\site-packages\theano\tensor\subtensor.py", line 354, in convert
raise TypeError("Expected an integer")

TypeError: Expected an integer

Any help, please? Thanks!

@Fangwq
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Fangwq commented Mar 7, 2019

I get the same error with pymc3 3.6 and python3.

Traceback (most recent call last):
File "pmml_test.py", line 147, in
[gpm(BN,'D4', num=1),BN.adj['C3']['D4']['bin']], observed=BN.node['D4']['observe'])
File "/Users/fangwq/Library/Python/3.6/lib/python/site-packages/theano/tensor/var.py", line 544, in getitem
theano.tensor.subtensor.Subtensor.convert(arg)
File "/Users/fangwq/Library/Python/3.6/lib/python/site-packages/theano/tensor/subtensor.py", line 354, in convert
raise TypeError("Expected an integer")
TypeError: Expected an integer

Any help, please? Thanks!

@NelisW
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NelisW commented Jul 1, 2019

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!

@tbsexton
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tbsexton 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
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NelisW commented Jul 1, 2019

@tbsexton
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tbsexton commented Jul 1, 2019

@NelisW certainly, and like I said, feel free to open an issue if something works unexpectedly on that repo (as I said, it's been a while).

@eHonnef
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eHonnef commented Nov 22, 2019

If you are having issues with BN.edges['C3']['D4']['bin'], substitute for BN.edges['C3','D4']['bin'].

As described in the migration guide mentioned before

G.edge have been removed in favor of using G.nodes[n] and G.edges[u, v]

@rezaaskary
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rezaaskary commented Oct 1, 2020

Do you have any example for dynamic BN simulated on PYMC3?

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