pomegranate dependency

[ivaxi0s]

Hi authors,

I am trying to reproduce the work and it seems to have pomegranate==0.14.8 dependency but currently, there is no wheel present to install that version of pomegranate and seems to fail with newer versions of pomegranate.

AttributeError: module 'pomegranate' has no attribute 'DiscreteDistribution'

[felixludos]

Currently, you will need pomegranate==0.14.8 which is available through pip here (install from source if need be). We are looking into refactoring to use pomegranate 1.0 or torchegranate, but I can't make any promises yet (that depends on how PyTorch-dependent our extension is).

[jameszhou-gl]

Hi authors, thanks for your great work.
Same problem: causalbenchmark.queries.base.QueryFailedError: module 'pomegranate' has no attribute 'DiscreteDistribution' with pomegranate==0.14.8.
When would you like to update the code?
Many thanks.

========================================================================= short test summary info ==========================================================================
FAILED causalbenchmark/test/test_bayes.py::test_conditional - AttributeError: module 'pomegranate' has no attribute 'DiscreteDistribution'
FAILED causalbenchmark/test/test_bayes.py::test_marginals - AttributeError: module 'pomegranate' has no attribute 'DiscreteDistribution'
FAILED causalbenchmark/test/test_bayes.py::test_ate - AttributeError: module 'pomegranate' has no attribute 'DiscreteDistribution'
FAILED causalbenchmark/test/test_builder.py::test_ensemble - AttributeError: module 'pomegranate' has no attribute 'DiscreteDistribution'
FAILED causalbenchmark/test/test_builder.py::test_correlation - AttributeError: module 'pomegranate' has no attribute 'DiscreteDistribution'
FAILED causalbenchmark/test/test_generation.py::test_generate_questions - assert 0 == 10
FAILED causalbenchmark/test/test_generation.py::test_full_generator - IndexError: list index out of range
FAILED causalbenchmark/test/test_generation.py::test_extract_summary - assert 0 == 10
FAILED causalbenchmark/test/test_generation.py::test_summary - IndexError: list index out of range
FAILED causalbenchmark/test/test_generation.py::test_cleanup_temp_data - AssertionError: assert False
FAILED causalbenchmark/test/test_queries.py::test_collider_bias - AttributeError: module 'pomegranate' has no attribute 'DiscreteDistribution'
FAILED causalbenchmark/test/test_queries.py::test_exp_away - AttributeError: module 'pomegranate' has no attribute 'DiscreteDistribution'
FAILED causalbenchmark/test/test_queries.py::test_ate - causalbenchmark.queries.base.QueryFailedError: module 'pomegranate' has no attribute 'DiscreteDistribution'
FAILED causalbenchmark/test/test_queries.py::test_ett - causalbenchmark.queries.base.QueryFailedError: module 'pomegranate' has no attribute 'DiscreteDistribution'
FAILED causalbenchmark/test/test_queries.py::test_nde - causalbenchmark.queries.base.QueryFailedError: module 'pomegranate' has no attribute 'DiscreteDistribution'
FAILED causalbenchmark/test/test_queries.py::test_nie - causalbenchmark.queries.base.QueryFailedError: module 'pomegranate' has no attribute 'DiscreteDistribution'
FAILED causalbenchmark/test/test_queries.py::test_marginals - AttributeError: module 'pomegranate' has no attribute 'DiscreteDistribution'
FAILED causalbenchmark/test/test_queries.py::test_correlations - AttributeError: module 'pomegranate' has no attribute 'DiscreteDistribution'
FAILED causalbenchmark/test/test_solver.py::test_constrained - AttributeError: module 'pomegranate' has no attribute 'DiscreteDistribution'
====================================================================== 19 failed, 22 passed in 2.38s =======================================================================

[ivaxi0s]

Thank you @felixludos. I was able to download the earlier version of pomegranate. I have a followup question, since the pytest fails and gives one error.

==================================================================================== test session starts ====================================================================================
platform linux -- Python 3.9.6, pytest-7.4.0, pluggy-1.3.0
rootdir: /lustre04/scratch/ivsh/projects/cladder
collected 41 items                                                                                                                                                                          

test/test_alpha.py ..                                                                                                                                                                 [  4%]
test/test_bayes.py .......                                                                                                                                                            [ 21%]
test/test_builder.py .......                                                                                                                                                          [ 39%]
test/test_data.py .                                                                                                                                                                   [ 41%]
test/test_generation.py ......                                                                                                                                                        [ 56%]
test/test_graphs.py .....                                                                                                                                                             [ 68%]
test/test_queries.py ...........                                                                                                                                                      [ 95%]
test/test_solver.py F                                                                                                                                                                 [ 97%]
test/test_unified.py .                                                                                                                                                                [100%]

========================================================================================= FAILURES ==========================================================================================
_____________________________________________________________________________________ test_constrained ______________________________________________________________________________________

    def test_constrained():
    
        graph_id = 'example-confounding'
    
        builder = MechanismCorrelationBuilder(seed=11)
    
        specs = list(builder.spawn_specs(graph_id))
        specs = np.random.choice(specs, size=5)
        specs = [{'Z': 1, 'X': {'Z': 1}, 'Y': {'X': 0, 'Z': -1}}]
    
        ana_time = 0.
        mc_time = 0.
    
        ana = []
        mc = []
    
        size = 10
    
        print()
        for spec in specs:
                tick = time.time()
>               scm_ana = builder.generate_constrained_scm(graph_id, spec)#, method='slsqp')

test/test_solver.py:33: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
graphs/builders.py:101: in generate_constrained_scm
    constraints=self.generate_scm_constraints(story, spec), **scm_kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <causalbenchmark.graphs.builders.MechanismCorrelationBuilder object at 0x2b77876c7790>, story = 'example-confounding', spec = {'X': {'Z': 1}, 'Y': {'X': 0, 'Z': -1}, 'Z': 1}

    def generate_scm_constraints(self, story: Dict[str, Any], spec: JSONABLE):
        base = self._find_graph_type(story)
        n = base.dof()
    
        constraints = [opt.LinearConstraint(np.eye(n),
                                            self.limit + self.epsilon,
                                            1 - self.limit - self.epsilon,
                                            keep_feasible=False)] # TODO: find method where this can be true
    
        b = []
        A = []
    
        for node in base.static_variables():
                if node.name in spec:
                        if len(node.parents):
                                corrs = {parent: val for parent, val in spec[node.name].items() if val != 0}
                                if len(corrs):
                                        Anew, bnew = self._correlation_to_constraint(base, node, corrs)
                                        b.extend(bnew)
                                        A.extend(Anew)
                        else:
                                Anew, bnew = self._source_to_constraint(base, node, spec[node.name])
                                b.extend(bnew)
                                A.extend(Anew)
    
        if len(A):
>               constraints.append(opt.LinearConstraint(np.stack(A), np.asarray(b), keep_feasible=False))
E     TypeError: __init__() missing 1 required positional argument: 'ub'

graphs/builders.py:653: TypeError
----------------------------------------------------------------------------------- Captured stdout call ------------------------------------------------------------------------------------

================================================================================== short test summary info ==================================================================================
FAILED test/test_solver.py::test_constrained - TypeError: __init__() missing 1 required positional argument: 'ub'
=============================================================================== 1 failed, 40 passed in 6.18s ================================================================================