def setUp(self):
""""""
# Koller, Friedman 2009, p. 104
self.Bf = NumCatRVariable(
node_id="B",
input_data={"outcome-values": [10, 50]},
marginal_distribution=lambda x: 0.5,
)
self.Cf = NumCatRVariable(
node_id="C",
input_data={"outcome-values": [10, 50]},
marginal_distribution=lambda x: 0.5,
)
def phibc(scope_product):
""""""
sfs = set(scope_product)
if sfs == set([("B", 10), ("C", 10)]):
return 0.5
elif sfs == set([("B", 10), ("C", 50)]):
return 0.7
elif sfs == set([("B", 50), ("C", 10)]):
return 0.1
elif sfs == set([("B", 50), ("C", 50)]):
return 0.2
else:
raise ValueError("unknown arg")
self.bc = Factor(gid="bc",
scope_vars=set([self.Bf, self.Cf]),
factor_fn=phibc)
self.bc_b = BaseFactor(gid="bc",
scope_vars=set([self.Bf, self.Cf]),
factor_fn=phibc)
def test_from_scope_variables_with_fn(self):
""""""
A = NumCatRVariable(
"A",
input_data={"outcome-values": [True, False]},
marginal_distribution=lambda x: 0.6 if x else 0.4,
)
B = NumCatRVariable(
"B",
input_data={"outcome-values": [True, False]},
marginal_distribution=lambda x: 0.62 if x else 0.38,
)
def phi_ab(scope_product):
ss = set(scope_product)
if ss == set([("A", True), ("B", True)]):
return 0.9
elif ss == set([("A", True), ("B", False)]):
return 0.1
elif ss == set([("A", False), ("B", True)]):
return 0.2
elif ss == set([("A", False), ("B", False)]):
return 0.8
else:
raise ValueError("unknown argument")
f = Factor.from_scope_variables_with_fn(svars=set([A, B]), fn=phi_ab)
query = set([("A", True), ("B", True)])
ff = f.phi(query)
self.assertEqual(round(ff, 2), 0.9)
def data_2(self):
""""""
# Koller, Friedman 2009, p. 104
self.Af = NumCatRVariable(
node_id="A",
input_data={"outcome-values": [10, 50]},
marginal_distribution=lambda x: 0.5,
)
self.Bf = NumCatRVariable(
node_id="B",
input_data={"outcome-values": [10, 50]},
marginal_distribution=lambda x: 0.5,
)
self.Cf = NumCatRVariable(
node_id="C",
input_data={"outcome-values": [10, 50]},
marginal_distribution=lambda x: 0.5,
)
self.Df = NumCatRVariable(
node_id="D",
input_data={"outcome-values": [10, 50]},
marginal_distribution=lambda x: 0.5,
)
def phiAB(scope_product):
""""""
sfs = set(scope_product)
if sfs == set([("A", 10), ("B", 10)]):
return 30
elif sfs == set([("A", 10), ("B", 50)]):
return 5
elif sfs == set([("A", 50), ("B", 10)]):
return 1
elif sfs == set([("A", 50), ("B", 50)]):
return 10
else:
raise ValueError("unknown arg")
self.AB = Factor(gid="AB",
scope_vars=set([self.Af, self.Bf]),
factor_fn=phiAB)
def phiBC(scope_product):
""""""
sfs = set(scope_product)
if sfs == set([("B", 10), ("C", 10)]):
return 100
elif sfs == set([("B", 10), ("C", 50)]):
return 1
elif sfs == set([("B", 50), ("C", 10)]):
return 1
elif sfs == set([("B", 50), ("C", 50)]):
return 100
else:
raise ValueError("unknown arg")
self.BC = Factor(gid="BC",
scope_vars=set([self.Bf, self.Cf]),
factor_fn=phiBC)
def setUp(self):
""""""
self.data_1()
self.data_2()
# Koller, Friedman 2009 p. 107
self.af = NumCatRVariable(
node_id="A",
input_data={"outcome-values": [10, 50, 20]},
marginal_distribution=lambda x: 0.4 if x != 20 else 0.2,
)
def phiaB(scope_product):
""""""
sfs = set(scope_product)
if sfs == set([("A", 10), ("B", 10)]):
return 0.5
elif sfs == set([("A", 10), ("B", 50)]):
return 0.8
elif sfs == set([("A", 50), ("B", 10)]):
return 0.1
elif sfs == set([("A", 50), ("B", 50)]):
return 0
elif sfs == set([("A", 20), ("B", 10)]):
return 0.3
elif sfs == set([("A", 20), ("B", 50)]):
return 0.9
else:
raise ValueError("unknown arg")
self.aB = Factor(gid="ab",
scope_vars=set([self.af, self.Bf]),
factor_fn=phiaB)
self.aB_b = BaseFactor(gid="ab",
scope_vars=set([self.af, self.Bf]),
factor_fn=phiaB)
def phibc(scope_product):
""""""
sfs = set(scope_product)
if sfs == set([("B", 10), ("C", 10)]):
return 0.5
elif sfs == set([("B", 10), ("C", 50)]):
return 0.7
elif sfs == set([("B", 50), ("C", 10)]):
return 0.1
elif sfs == set([("B", 50), ("C", 50)]):
return 0.2
else:
raise ValueError("unknown arg")
self.bc = Factor(gid="bc",
scope_vars=set([self.Bf, self.Cf]),
factor_fn=phibc)
self.bc_b = BaseFactor(gid="bc",
scope_vars=set([self.Bf, self.Cf]),
factor_fn=phibc)
def data_1(self):
""""""
idata = {"outcome-values": [True, False]}
self.A = NumCatRVariable(node_id="A",
input_data=idata,
marginal_distribution=lambda x: 0.5)
self.B = NumCatRVariable(node_id="B",
input_data=idata,
marginal_distribution=lambda x: 0.5)
self.C = NumCatRVariable(node_id="C",
input_data=idata,
marginal_distribution=lambda x: 0.5)
self.D = NumCatRVariable(node_id="D",
input_data=idata,
marginal_distribution=lambda x: 0.5)
self.E = NumCatRVariable(node_id="E",
input_data=idata,
marginal_distribution=lambda x: 0.5)
self.F = NumCatRVariable(node_id="F",
input_data=idata,
marginal_distribution=lambda x: 0.5)
self.G = NumCatRVariable(node_id="G",
input_data=idata,
marginal_distribution=lambda x: 0.5)
self.H = NumCatRVariable(node_id="H",
input_data=idata,
marginal_distribution=lambda x: 0.5)
self.Irvar = NumCatRVariable(node_id="I",
input_data=idata,
marginal_distribution=lambda x: 0.5)
self.K = NumCatRVariable(node_id="K",
input_data=idata,
marginal_distribution=lambda x: 0.5)
self.L = NumCatRVariable(node_id="L",
input_data=idata,
marginal_distribution=lambda x: 0.5)
#
# Cowell 2005, p. 110
#
# A E---+
# | |
# +----+ F <-+
# | |
# B <--+---> C --> D <---+
# | |
# +---> H <--------+----> G
# | |
# +---> I
#
self.AB_c = Edge(
edge_id="AB",
start_node=self.A,
end_node=self.B,
edge_type=EdgeType.DIRECTED,
)
self.AC_c = Edge(
edge_id="AC",
start_node=self.A,
end_node=self.C,
edge_type=EdgeType.DIRECTED,
)
self.CD_c = Edge(
edge_id="CD",
start_node=self.C,
end_node=self.D,
edge_type=EdgeType.DIRECTED,
)
self.EF_c = Edge(
edge_id="EF",
start_node=self.E,
end_node=self.F,
edge_type=EdgeType.DIRECTED,
)
self.FD_c = Edge(
edge_id="FD",
start_node=self.F,
end_node=self.D,
edge_type=EdgeType.DIRECTED,
)
self.DG_c = Edge(
edge_id="DG",
start_node=self.D,
end_node=self.G,
edge_type=EdgeType.DIRECTED,
)
self.DH_c = Edge(
edge_id="DH",
start_node=self.D,
end_node=self.H,
edge_type=EdgeType.DIRECTED,
)
self.BH_c = Edge(
edge_id="BH",
start_node=self.B,
end_node=self.H,
edge_type=EdgeType.DIRECTED,
)
self.BI_c = Edge(
edge_id="BI",
start_node=self.B,
end_node=self.Irvar,
edge_type=EdgeType.DIRECTED,
)
self.HI_c = Edge(
edge_id="HI",
start_node=self.H,
end_node=self.Irvar,
edge_type=EdgeType.UNDIRECTED,
)
class LWFChainGraphTest(unittest.TestCase):
""""""
def data_1(self):
""""""
idata = {"outcome-values": [True, False]}
self.A = NumCatRVariable(node_id="A",
input_data=idata,
marginal_distribution=lambda x: 0.5)
self.B = NumCatRVariable(node_id="B",
input_data=idata,
marginal_distribution=lambda x: 0.5)
self.C = NumCatRVariable(node_id="C",
input_data=idata,
marginal_distribution=lambda x: 0.5)
self.D = NumCatRVariable(node_id="D",
input_data=idata,
marginal_distribution=lambda x: 0.5)
self.E = NumCatRVariable(node_id="E",
input_data=idata,
marginal_distribution=lambda x: 0.5)
self.F = NumCatRVariable(node_id="F",
input_data=idata,
marginal_distribution=lambda x: 0.5)
self.G = NumCatRVariable(node_id="G",
input_data=idata,
marginal_distribution=lambda x: 0.5)
self.H = NumCatRVariable(node_id="H",
input_data=idata,
marginal_distribution=lambda x: 0.5)
self.Irvar = NumCatRVariable(node_id="I",
input_data=idata,
marginal_distribution=lambda x: 0.5)
self.K = NumCatRVariable(node_id="K",
input_data=idata,
marginal_distribution=lambda x: 0.5)
self.L = NumCatRVariable(node_id="L",
input_data=idata,
marginal_distribution=lambda x: 0.5)
#
# Cowell 2005, p. 110
#
# A E---+
# | |
# +----+ F <-+
# | |
# B <--+---> C --> D <---+
# | |
# +---> H <--------+----> G
# | |
# +---> I
#
self.AB_c = Edge(
edge_id="AB",
start_node=self.A,
end_node=self.B,
edge_type=EdgeType.DIRECTED,
)
self.AC_c = Edge(
edge_id="AC",
start_node=self.A,
end_node=self.C,
edge_type=EdgeType.DIRECTED,
)
self.CD_c = Edge(
edge_id="CD",
start_node=self.C,
end_node=self.D,
edge_type=EdgeType.DIRECTED,
)
self.EF_c = Edge(
edge_id="EF",
start_node=self.E,
end_node=self.F,
edge_type=EdgeType.DIRECTED,
)
self.FD_c = Edge(
edge_id="FD",
start_node=self.F,
end_node=self.D,
edge_type=EdgeType.DIRECTED,
)
self.DG_c = Edge(
edge_id="DG",
start_node=self.D,
end_node=self.G,
edge_type=EdgeType.DIRECTED,
)
self.DH_c = Edge(
edge_id="DH",
start_node=self.D,
end_node=self.H,
edge_type=EdgeType.DIRECTED,
)
self.BH_c = Edge(
edge_id="BH",
start_node=self.B,
end_node=self.H,
edge_type=EdgeType.DIRECTED,
)
self.BI_c = Edge(
edge_id="BI",
start_node=self.B,
end_node=self.Irvar,
edge_type=EdgeType.DIRECTED,
)
self.HI_c = Edge(
edge_id="HI",
start_node=self.H,
end_node=self.Irvar,
edge_type=EdgeType.UNDIRECTED,
)
def data_2(self):
""""""
def phi_e(scope_product):
"""!
Visit to Asia factor
p(a)
"""
ss = set(scope_product)
if ss == set([("E", True)]):
return 0.01
elif ss == set([("E", False)]):
return 0.99
else:
raise ValueError("Unknown scope product")
self.E_cf = Factor(gid="E_cf",
scope_vars=set([self.E]),
factor_fn=phi_e)
def phi_fe(scope_product):
"""!
Tuberculosis | Visit to Asia factor
p(t,a)
"""
ss = set(scope_product)
if ss == set([("F", True), ("E", True)]):
return 0.05
elif ss == set([("F", False), ("E", True)]):
return 0.95
elif ss == set([("F", True), ("E", False)]):
return 0.01
elif ss == set([("F", False), ("E", False)]):
return 0.99
else:
raise ValueError("Unknown scope product")
self.EF_cf = Factor(gid="EF_cf",
scope_vars=set([self.E, self.F]),
factor_fn=phi_fe)
def phi_dg(scope_product):
"""!
either tuberculosis or lung cancer | x ray
p(e,x)
"""
ss = set(scope_product)
if ss == set([("D", True), ("G", True)]):
return 0.98
elif ss == set([("D", False), ("G", True)]):
return 0.05
elif ss == set([("D", True), ("G", False)]):
return 0.02
elif ss == set([("D", False), ("G", False)]):
return 0.95
else:
raise ValueError("Unknown scope product")
self.DG_cf = Factor(gid="DG_cf",
scope_vars=set([self.D, self.G]),
factor_fn=phi_dg)
def data_3(self):
""""""
def phi_a(scope_product):
"""!
smoke factor
p(s)
"""
ss = set(scope_product)
if ss == set([("A", True)]):
return 0.5
elif ss == set([("A", False)]):
return 0.5
else:
raise ValueError("Unknown scope product")
self.A_cf = Factor(gid="A_cf",
scope_vars=set([self.A]),
factor_fn=phi_a)
def phi_ab(scope_product):
"""!
smoke given bronchitis
p(s,b)
"""
ss = set(scope_product)
if ss == set([("A", True), ("B", True)]):
return 0.6
elif ss == set([("A", False), ("B", True)]):
return 0.3
elif ss == set([("A", True), ("B", False)]):
return 0.4
elif ss == set([("A", False), ("B", False)]):
return 0.7
else:
raise ValueError("Unknown scope product")
self.AB_cf = Factor(gid="AB_cf",
scope_vars=set([self.A, self.B]),
factor_fn=phi_ab)
def phi_ac(scope_product):
"""!
lung cancer given smoke
p(s,l)
"""
ss = set(scope_product)
if ss == set([("A", True), ("C", True)]):
return 0.1
elif ss == set([("A", False), ("C", True)]):
return 0.01
elif ss == set([("A", True), ("C", False)]):
return 0.9
elif ss == set([("A", False), ("C", False)]):
return 0.99
else:
raise ValueError("Unknown scope product")
self.AC_cf = Factor(gid="AC_cf",
scope_vars=set([self.A, self.C]),
factor_fn=phi_ac)
def data_4(self):
""""""
# Factors
#
def phi_cdf(scope_product):
"""!
either tuberculosis or lung given lung cancer and tuberculosis
p(e, l, t)
"""
ss = set(scope_product)
if ss == set([("C", True), ("D", True), ("F", True)]):
return 1
elif ss == set([("C", True), ("D", False), ("F", True)]):
return 0
elif ss == set([("C", False), ("D", True), ("F", True)]):
return 1
elif ss == set([("C", False), ("D", False), ("F", True)]):
return 0
elif ss == set([("C", True), ("D", True), ("F", False)]):
return 1
elif ss == set([("C", True), ("D", False), ("F", False)]):
return 0
elif ss == set([("C", False), ("D", True), ("F", False)]):
return 0
elif ss == set([("C", False), ("D", False), ("F", False)]):
return 1
else:
raise ValueError("Unknown scope product")
self.CDF_cf = Factor(
gid="CDF_cf",
scope_vars=set([self.D, self.C, self.F]),
factor_fn=phi_cdf,
)
def phi_ihb(scope_product):
"""!
cough, dyspnoea, bronchitis
I, H, B
p(c,d,b)
"""
ss = set(scope_product)
if ss == set([("H", True), ("I", True), ("B", True)]):
return 16
elif ss == set([("H", True), ("I", False), ("B", True)]):
return 1
elif ss == set([("H", False), ("I", True), ("B", True)]):
return 4
elif ss == set([("H", False), ("I", False), ("B", True)]):
return 1
elif ss == set([("H", True), ("I", True), ("B", False)]):
return 2
elif ss == set([("H", True), ("I", False), ("B", False)]):
return 1
elif ss == set([("H", False), ("I", True), ("B", False)]):
return 1
elif ss == set([("H", False), ("I", False), ("B", False)]):
return 1
else:
raise ValueError("Unknown scope product")
self.IHB_cf = Factor(
gid="IHB_cf",
scope_vars=set([self.H, self.Irvar, self.B]),
factor_fn=phi_ihb,
)
def phi_hbd(scope_product):
"""!
cough, either tuberculosis or lung cancer, bronchitis
D, H, B
p(c,b,e)
"""
ss = set(scope_product)
if ss == set([("H", True), ("D", True), ("B", True)]):
return 5
elif ss == set([("H", True), ("D", False), ("B", True)]):
return 2
elif ss == set([("H", False), ("D", True), ("B", True)]):
return 1
elif ss == set([("H", False), ("D", False), ("B", True)]):
return 1
elif ss == set([("H", True), ("D", True), ("B", False)]):
return 3
elif ss == set([("H", True), ("D", False), ("B", False)]):
return 1
elif ss == set([("H", False), ("D", True), ("B", False)]):
return 1
elif ss == set([("H", False), ("D", False), ("B", False)]):
return 1
else:
raise ValueError("Unknown scope product")
self.HBD_cf = Factor(
gid="HBD_cf",
scope_vars=set([self.H, self.D, self.B]),
factor_fn=phi_hbd,
)
def phi_bd(scope_product):
"""!
bronchitis, either tuberculosis or lung cancer
B, D
p(b,e)
"""
ss = set(scope_product)
if ss == set([("B", True), ("D", True)]):
return 1 / 90
elif ss == set([("B", False), ("D", True)]):
return 1 / 11
elif ss == set([("B", True), ("D", False)]):
return 1 / 39
elif ss == set([("B", False), ("D", False)]):
return 1 / 5
else:
raise ValueError("Unknown scope product")
self.BD_cf = Factor(gid="BD_cf",
scope_vars=set([self.D, self.B]),
factor_fn=phi_bd)
def setUp(self):
""""""
self.data_1()
self.data_2()
self.data_3()
self.data_4()
#
self.cowell = LWFChainGraph(
gid="cowell",
nodes=set([
self.A,
self.B,
self.C,
self.D,
self.E,
self.F,
self.G,
self.H,
self.Irvar,
]),
edges=set([
self.AB_c,
self.AC_c,
self.CD_c,
self.EF_c,
self.FD_c,
self.DG_c,
self.DH_c,
self.BH_c,
self.BI_c,
self.HI_c,
]),
factors=set([
self.E_cf,
self.EF_cf,
self.DG_cf,
self.A_cf,
self.AB_cf,
self.AC_cf,
self.CDF_cf,
self.IHB_cf,
self.HBD_cf,
self.BD_cf,
]),
)
# Koller, Friedman 2009, p. 149
#
# +--------------+
# | |
# | A + B
# | | | |
# | +--> C -- D -- E <--+
# | | | |
# | +--+ | v
# | | +-------> I <---- H
# | F <-+
# | |
# | +----- G
# | ^
# | |
# +----------+
self.AC_k = Edge(
edge_id="AC",
start_node=self.A,
end_node=self.C,
edge_type=EdgeType.DIRECTED,
)
self.FG_k = Edge(
edge_id="FG",
start_node=self.F,
end_node=self.G,
edge_type=EdgeType.UNDIRECTED,
)
self.DG_k = Edge(
edge_id="DG",
start_node=self.D,
end_node=self.G,
edge_type=EdgeType.DIRECTED,
)
self.CF_k = Edge(
edge_id="CF",
start_node=self.C,
end_node=self.F,
edge_type=EdgeType.UNDIRECTED,
)
self.CD_k = Edge(
edge_id="CD",
start_node=self.C,
end_node=self.D,
edge_type=EdgeType.UNDIRECTED,
)
self.CI_k = Edge(
edge_id="CI",
start_node=self.C,
end_node=self.Irvar,
edge_type=EdgeType.DIRECTED,
)
self.DE_k = Edge(
edge_id="DE",
start_node=self.D,
end_node=self.E,
edge_type=EdgeType.UNDIRECTED,
)
self.EI_k = Edge(
edge_id="EI",
start_node=self.E,
end_node=self.Irvar,
edge_type=EdgeType.DIRECTED,
)
self.BE_k = Edge(
edge_id="BE",
start_node=self.B,
end_node=self.E,
edge_type=EdgeType.DIRECTED,
)
self.HI_k = Edge(
edge_id="HI",
start_node=self.H,
end_node=self.Irvar,
edge_type=EdgeType.DIRECTED,
)
self.koller = LWFChainGraph(
gid="koller",
nodes=set([
self.A,
self.C,
self.D,
self.E,
self.B,
self.Irvar,
self.F,
self.G,
]),
edges=set([
self.AC_k,
self.FG_k,
self.CF_k,
self.HI_k,
self.CD_k,
self.CI_k,
self.DE_k,
self.DG_k,
self.EI_k,
self.BE_k,
]),
factors=None,
)
# evidence values taken from
# Cowell 2005, p. 119, table 6.12
e_comp_val = [("E", True, 0.0096), ("E", False, 0.9904)]
h_comp_val = [("H", True, 0.7635), ("H", False, 0.2365)]
c_comp_val = [("C", True, 0.0025), ("C", False, 0.9975)]
i_comp_val = [("I", True, 0.7939), ("I", False, 0.2061)]
g_comp_val = [("G", True, 0.1849), ("G", False, 0.8151)]
a_comp_val = [("A", True, 0.4767), ("A", False, 0.5233)]
f_comp_val = [("F", True, 0.0012), ("F", False, 0.9988)]
d_comp_val = [("D", True, 0.0036), ("D", False, 0.9964)]
b_comp_val = [("B", True, 0.60), ("B", False, 0.40)]
self.evidences = set([("E", True), ("A", True), ("G", False)])
self.q_tsts = {
(self.E): e_comp_val, # asia
(self.Irvar): i_comp_val, # dyspnoea
(self.H): h_comp_val, # cough
(self.A): a_comp_val, # smoke
(self.B): b_comp_val, # bronchitis
(self.C): c_comp_val, # lung
(self.D): d_comp_val, # either
(self.F): f_comp_val, # tuberculosis
(self.G): g_comp_val, # x ray
}
def test_id(self):
""""""
self.assertEqual(self.cowell.id(), "cowell")
def test_nb_chain_components(self):
""""""
nb = self.cowell.nb_components
self.assertEqual(nb, 8)
def test_ccomponents(self):
""""""
ccomps_nds = set([
set(s).pop() for s in self.cowell.ccomponents
if isinstance(s, frozenset)
])
ccomps_undi = [
s for s in self.cowell.ccomponents if isinstance(s, UndiGraph)
].pop()
self.assertEqual(
ccomps_nds,
set([self.A, self.B, self.C, self.E, self.F, self.D, self.G]),
)
self.assertEqual(BaseGraphOps.nodes(ccomps_undi),
set([self.H, self.Irvar]))
def test_get_chain_dag(self):
""""""
dag_comps = self.cowell.dag_components
self.assertEqual(len(BaseGraphOps.nodes(dag_comps)), 8)
def test_parents_of_K(self):
""""""
ccomps_undi = [
s for s in enumerate(self.cowell.ccomponents)
if isinstance(s[1], UndiGraph)
].pop()
parents_k = self.cowell.parents_of_K(ccomps_undi[0])
self.assertEqual(parents_k, set([self.B, self.D]))
ccomps_undi = [
s for s in enumerate(self.koller.ccomponents)
if isinstance(s[1], frozenset)
]
parents = set()
for c in ccomps_undi:
obj = set(c[1]).pop()
parent = self.koller.parents_of_K(c[0])
parents.add(frozenset([obj, frozenset(parent)]))
self.assertEqual(
parents,
set([
frozenset([self.B, frozenset()]),
frozenset([self.A, frozenset()]),
frozenset([self.H, frozenset()]),
frozenset([self.Irvar,
frozenset([self.H, self.C, self.E])]),
]),
)
def test_K(self):
""""""
ccomps_undi = [
s for s in enumerate(self.cowell.ccomponents)
if isinstance(s[1], UndiGraph)
]
hi = self.cowell.K(ccomps_undi[0][0])
self.assertEqual(BaseGraphOps.nodes(hi), set([self.H, self.Irvar]))
def test_moralize(self):
"""!
Test according to figure 4.15 in
Koller, Friedman 2009, p. 149
"""
moral = self.koller.moralize()
koller_moralized = set([
frozenset([self.A.id(), self.B.id()]),
frozenset([self.A.id(), self.C.id()]),
frozenset([self.C.id(), self.F.id()]),
frozenset([self.C.id(), self.D.id()]),
frozenset([self.C.id(), self.E.id()]),
frozenset([self.C.id(), self.Irvar.id()]),
frozenset([self.C.id(), self.H.id()]),
frozenset([self.D.id(), self.E.id()]),
frozenset([self.D.id(), self.G.id()]),
frozenset([self.F.id(), self.G.id()]),
frozenset([self.E.id(), self.Irvar.id()]),
frozenset([self.B.id(), self.E.id()]),
frozenset([self.E.id(), self.H.id()]),
frozenset([self.H.id(), self.Irvar.id()]),
])
medges = BaseGraphOps.edges(moral)
ms = set([frozenset([m.start().id(), m.end().id()]) for m in medges])
# [print(m) for m in ms]
self.assertEqual(
ms,
koller_moralized,
)
def test_cond_prod_by_variable_elimination_evidence(self):
"""!"""
qs = set([self.B])
evs = set([("E", True), ("A", True), ("G", False)])
moral = self.cowell
p, a = moral.cond_prod_by_variable_elimination(qs, evs)
# check if it is a valid distribution
s = 0
for ps in p.factor_domain():
pss = set(ps)
f = round(p.phi_normal(pss), 4)
s += f
if set([("A", True)]) == pss:
self.assertEqual(f, 0.01)
elif set([("A", False)]) == pss:
self.assertEqual(f, 0.99)
self.assertTrue(s, 1.0)
def test_cond_prod_by_variable_elimination(self):
"""!
Test values taken from
Cowell 2005, p. 116, table 6.9
"""
e_comp_val = [("E", True, 0.01), ("E", False, 0.99)]
i_comp_val = [("I", True, 0.7468), ("I", False, 0.2532)]
h_comp_val = [("H", True, 0.7312), ("H", False, 0.2688)]
c_comp_val = [("C", True, 0.055), ("C", False, 0.945)]
a_comp_val = [("A", True, 0.5), ("A", False, 0.5)]
b_comp_val = [("B", True, 0.45), ("B", False, 0.55)]
d_comp_val = [("D", True, 0.0648), ("D", False, 0.9352)]
f_comp_val = [("F", True, 0.0104), ("F", False, 0.9896)]
q_tsts = {
(self.E): e_comp_val,
(self.Irvar): i_comp_val, # dyspnoea
(self.H): h_comp_val, # cough
(self.A): a_comp_val, # smoke
(self.B): b_comp_val, # bronchitis
(self.C): c_comp_val, # lung
(self.D): d_comp_val, # either
(self.F): f_comp_val, # tuberculosis
}
evs = set()
for q, cvals in q_tsts.items():
final_factor, a = self.cowell.cond_prod_by_variable_elimination(
set([q]), evs)
s = 0
for cval in cvals:
cname = cval[0]
c_v = cval[1]
c_a = cval[2]
cs = set([(cname, c_v)])
f = round(final_factor.phi_normal(cs), 4)
s += f
self.assertEqual(c_a, f)
self.assertEqual(s, 1)
def test_cond_prod_by_variable_elimination_evidences_B(self):
"""!
Test values taken from
Cowell 2005, p. 119, table 6.12
"""
comp_vals = self.q_tsts[self.B]
final_factor, a = self.cowell.cond_prod_by_variable_elimination(
set([self.B]), self.evidences)
for e_val in comp_vals:
ename = e_val[0]
e_v = e_val[1]
f = round(final_factor.phi_normal(set([(ename, e_v)])), 4)
self.assertEqual(f, e_val[2])
def test_cond_prod_by_variable_elimination_evidences_I(self):
"""!
Test values taken from
Cowell 2005, p. 119, table 6.12
"""
comp_vals = self.q_tsts[self.Irvar]
final_factor, a = self.cowell.cond_prod_by_variable_elimination(
set([self.Irvar]), self.evidences)
for e_val in comp_vals:
ename = e_val[0]
e_v = e_val[1]
f = round(final_factor.phi_normal(set([(ename, e_v)])), 4)
self.assertEqual(f, e_val[2])
def test_cond_prod_by_variable_elimination_evidences_H(self):
"""!
Test values taken from
Cowell 2005, p. 119, table 6.12
"""
comp_vals = self.q_tsts[self.H]
final_factor, a = self.cowell.cond_prod_by_variable_elimination(
set([self.H]), self.evidences)
for e_val in comp_vals:
ename = e_val[0]
e_v = e_val[1]
f = round(final_factor.phi_normal(set([(ename, e_v)])), 4)
self.assertEqual(f, e_val[2])
def test_cond_prod_by_variable_elimination_evidences_C(self):
"""!
Test values taken from
Cowell 2005, p. 119, table 6.12
"""
comp_vals = self.q_tsts[self.C]
final_factor, a = self.cowell.cond_prod_by_variable_elimination(
set([self.C]), self.evidences)
for e_val in comp_vals:
ename = e_val[0]
e_v = e_val[1]
f = round(final_factor.phi_normal(set([(ename, e_v)])), 4)
self.assertEqual(f, e_val[2])
def test_cond_prod_by_variable_elimination_evidences_F(self):
"""!
Test values taken from
Cowell 2005, p. 119, table 6.12
"""
comp_vals = self.q_tsts[self.F]
final_factor, a = self.cowell.cond_prod_by_variable_elimination(
set([self.F]), self.evidences)
for e_val in comp_vals:
ename = e_val[0]
e_v = e_val[1]
f = round(final_factor.phi_normal(set([(ename, e_v)])), 4)
self.assertEqual(f, e_val[2])
@unittest.skip("unfinished test")
def test_most_probable_assignment(self):
"""!
From Cowell 2005, p. 119
"""
assignments, factors, z_phi = self.cowell.max_product_ve(set())
def test_mpe_prob_no_evidence(self):
"""!
From Cowell 2005, p. 119
"""
cval = 0.2063
prob = self.cowell.mpe_prob(set())
self.assertEqual(round(prob, 4), cval)
def test_mpe_prob_evidence(self):
"""!
From Cowell 2005, p. 119
"""
cval = 0.002
evs = set([("E", True), ("A", True), ("G", False)])
prob = self.cowell.mpe_prob(evs)
self.assertEqual(round(prob, 4), cval)
def test_max_product_ve_evidence(self):
"""!
From Cowell 2005, p. 119
"""
cval = {
"B": True,
"A": True,
"C": False,
"D": False,
"F": False,
"H": True,
"G": False,
"I": True,
"E": True,
}
evs = set([("E", True), ("A", True), ("G", False)])
assignments, factors, z_phi = self.cowell.max_product_ve(evs)
self.assertEqual(assignments, cval)
def data_1(self):
""""""
input_data = {
"intelligence": {
"outcome-values": [0.1, 0.9],
"evidence": 0.9
},
"grade": {
"outcome-values": [0.2, 0.4, 0.6],
"evidence": 0.2
},
"dice": {
"outcome-values": [i for i in range(1, 7)],
"evidence": 1.0 / 6,
},
"fdice": {
"outcome-values": [i for i in range(1, 7)]
},
}
def intelligence_dist(intelligence_value: float):
if intelligence_value == 0.1:
return 0.7
elif intelligence_value == 0.9:
return 0.3
else:
return 0
def grade_dist(grade_value: float):
if grade_value == 0.2:
return 0.25
elif grade_value == 0.4:
return 0.37
elif grade_value == 0.6:
return 0.38
else:
return 0
def fair_dice_dist(dice_value: float):
if dice_value in [i for i in range(1, 7)]:
return 1.0 / 6.0
else:
return 0
def f_dice_dist(dice_value: float):
if dice_value in [i for i in range(1, 5)]:
return 0.2
else:
return 0.2
# intelligence
# grade
self.intelligence = NumCatRVariable(
node_id="int",
input_data=input_data["intelligence"],
marginal_distribution=intelligence_dist,
)
nid2 = "grade"
self.grade = NumCatRVariable(
node_id=nid2,
input_data=input_data["grade"],
marginal_distribution=grade_dist,
)
nid3 = "dice"
self.dice = NumCatRVariable(
node_id=nid3,
input_data=input_data["dice"],
marginal_distribution=fair_dice_dist,
)
nid4 = "fdice"
self.fdice = NumCatRVariable(
node_id=nid4,
input_data=input_data["fdice"],
marginal_distribution=f_dice_dist,
)
self.f = Factor(gid="f",
scope_vars=set(
[self.grade, self.dice, self.intelligence]))
self.f2 = Factor(gid="f2", scope_vars=set([self.grade, self.fdice]))
class TestFactor(unittest.TestCase):
"""!"""
def data_1(self):
""""""
input_data = {
"intelligence": {
"outcome-values": [0.1, 0.9],
"evidence": 0.9
},
"grade": {
"outcome-values": [0.2, 0.4, 0.6],
"evidence": 0.2
},
"dice": {
"outcome-values": [i for i in range(1, 7)],
"evidence": 1.0 / 6,
},
"fdice": {
"outcome-values": [i for i in range(1, 7)]
},
}
def intelligence_dist(intelligence_value: float):
if intelligence_value == 0.1:
return 0.7
elif intelligence_value == 0.9:
return 0.3
else:
return 0
def grade_dist(grade_value: float):
if grade_value == 0.2:
return 0.25
elif grade_value == 0.4:
return 0.37
elif grade_value == 0.6:
return 0.38
else:
return 0
def fair_dice_dist(dice_value: float):
if dice_value in [i for i in range(1, 7)]:
return 1.0 / 6.0
else:
return 0
def f_dice_dist(dice_value: float):
if dice_value in [i for i in range(1, 5)]:
return 0.2
else:
return 0.2
# intelligence
# grade
self.intelligence = NumCatRVariable(
node_id="int",
input_data=input_data["intelligence"],
marginal_distribution=intelligence_dist,
)
nid2 = "grade"
self.grade = NumCatRVariable(
node_id=nid2,
input_data=input_data["grade"],
marginal_distribution=grade_dist,
)
nid3 = "dice"
self.dice = NumCatRVariable(
node_id=nid3,
input_data=input_data["dice"],
marginal_distribution=fair_dice_dist,
)
nid4 = "fdice"
self.fdice = NumCatRVariable(
node_id=nid4,
input_data=input_data["fdice"],
marginal_distribution=f_dice_dist,
)
self.f = Factor(gid="f",
scope_vars=set(
[self.grade, self.dice, self.intelligence]))
self.f2 = Factor(gid="f2", scope_vars=set([self.grade, self.fdice]))
def data_2(self):
""""""
# Koller, Friedman 2009, p. 104
self.Af = NumCatRVariable(
node_id="A",
input_data={"outcome-values": [10, 50]},
marginal_distribution=lambda x: 0.5,
)
self.Bf = NumCatRVariable(
node_id="B",
input_data={"outcome-values": [10, 50]},
marginal_distribution=lambda x: 0.5,
)
self.Cf = NumCatRVariable(
node_id="C",
input_data={"outcome-values": [10, 50]},
marginal_distribution=lambda x: 0.5,
)
self.Df = NumCatRVariable(
node_id="D",
input_data={"outcome-values": [10, 50]},
marginal_distribution=lambda x: 0.5,
)
def phiAB(scope_product):
""""""
sfs = set(scope_product)
if sfs == set([("A", 10), ("B", 10)]):
return 30
elif sfs == set([("A", 10), ("B", 50)]):
return 5
elif sfs == set([("A", 50), ("B", 10)]):
return 1
elif sfs == set([("A", 50), ("B", 50)]):
return 10
else:
raise ValueError("unknown arg")
self.AB = Factor(gid="AB",
scope_vars=set([self.Af, self.Bf]),
factor_fn=phiAB)
def phiBC(scope_product):
""""""
sfs = set(scope_product)
if sfs == set([("B", 10), ("C", 10)]):
return 100
elif sfs == set([("B", 10), ("C", 50)]):
return 1
elif sfs == set([("B", 50), ("C", 10)]):
return 1
elif sfs == set([("B", 50), ("C", 50)]):
return 100
else:
raise ValueError("unknown arg")
self.BC = Factor(gid="BC",
scope_vars=set([self.Bf, self.Cf]),
factor_fn=phiBC)
def data_3(self):
""""""
def phiCD(scope_product):
""""""
sfs = set(scope_product)
if sfs == set([("C", 10), ("D", 10)]):
return 1
elif sfs == set([("C", 10), ("D", 50)]):
return 100
elif sfs == set([("C", 50), ("D", 10)]):
return 100
elif sfs == set([("C", 50), ("D", 50)]):
return 1
else:
raise ValueError("unknown arg")
self.CD = Factor(gid="CD",
scope_vars=set([self.Cf, self.Df]),
factor_fn=phiCD)
def phiDA(scope_product):
""""""
sfs = set(scope_product)
if sfs == set([("D", 10), ("A", 10)]):
return 100
elif sfs == set([("D", 10), ("A", 50)]):
return 1
elif sfs == set([("D", 50), ("A", 10)]):
return 1
elif sfs == set([("D", 50), ("A", 50)]):
return 100
else:
raise ValueError("unknown arg")
self.DA = Factor(gid="DA",
scope_vars=set([self.Df, self.Af]),
factor_fn=phiDA)
def setUp(self):
""""""
self.data_1()
self.data_2()
self.data_3()
# Koller, Friedman 2009 p. 107
self.af = NumCatRVariable(
node_id="A",
input_data={"outcome-values": [10, 50, 20]},
marginal_distribution=lambda x: 0.4 if x != 20 else 0.2,
)
def phiaB(scope_product):
""""""
sfs = set(scope_product)
if sfs == set([("A", 10), ("B", 10)]):
return 0.5
elif sfs == set([("A", 10), ("B", 50)]):
return 0.8
elif sfs == set([("A", 50), ("B", 10)]):
return 0.1
elif sfs == set([("A", 50), ("B", 50)]):
return 0
elif sfs == set([("A", 20), ("B", 10)]):
return 0.3
elif sfs == set([("A", 20), ("B", 50)]):
return 0.9
else:
raise ValueError("unknown arg")
self.aB = Factor(gid="ab",
scope_vars=set([self.af, self.Bf]),
factor_fn=phiaB)
def phibc(scope_product):
""""""
sfs = set(scope_product)
if sfs == set([("B", 10), ("C", 10)]):
return 0.5
elif sfs == set([("B", 10), ("C", 50)]):
return 0.7
elif sfs == set([("B", 50), ("C", 10)]):
return 0.1
elif sfs == set([("B", 50), ("C", 50)]):
return 0.2
else:
raise ValueError("unknown arg")
self.bc = Factor(gid="bc",
scope_vars=set([self.Bf, self.Cf]),
factor_fn=phibc)
def test_id(self):
""""""
self.assertEqual(self.f.id(), "f")
def test_domain_scope(self):
""""""
d = self.AB.domain_scope(
domain=[set([("A", 50), ("B", 50)]),
set([("A", 10), ("B", 10)])])
self.assertEqual(set(d), set([self.Af, self.Bf]))
def test_has_var(self):
""""""
intuple = self.f.has_var(ids="dice")
nottuple = self.f.has_var(ids="dice22")
self.assertTrue(intuple[0])
self.assertEqual(intuple[1], self.dice)
self.assertFalse(nottuple[0])
self.assertEqual(nottuple[1], None)
def test_in_scope_t_num(self):
self.assertTrue(self.dice in self.f)
def test_in_scope_t_str(self):
self.assertTrue(self.dice.id() in self.f)
def test_in_scope_f_str(self):
self.assertFalse("fdsfdsa" in self.f)
def test_scope_vars(self):
self.assertTrue(
self.f.scope_vars(),
set([self.dice, self.intelligence, self.grade]),
)
def test_marginal_joint(self):
""" """
mjoint = self.f.marginal_joint(
set([("int", 0.1), ("grade", 0.4), ("dice", 2)]))
dmarg = self.dice.marginal(2)
imarg = self.intelligence.marginal(0.1)
gmarg = self.grade.marginal(0.4)
self.assertTrue(mjoint, dmarg * imarg * gmarg)
def test_partition_value(self):
""""""
pval = self.f.partition_value(self.f.vars_domain())
self.assertTrue(pval, 1.0)
def test_phi(self):
""""""
mjoint = self.f.phi(set([("int", 0.1), ("grade", 0.4), ("dice", 2)]))
dmarg = self.dice.marginal(2)
imarg = self.intelligence.marginal(0.1)
gmarg = self.grade.marginal(0.4)
self.assertTrue(mjoint, dmarg * imarg * gmarg)
def test_phi_normalize(self):
mjoint = self.f.phi(set([("int", 0.1), ("grade", 0.4), ("dice", 2)]))
dmarg = self.dice.marginal(2)
imarg = self.intelligence.marginal(0.1)
gmarg = self.grade.marginal(0.4)
self.assertTrue(mjoint, (dmarg * imarg * gmarg) / self.f.zval())
def test_from_scope_variables_with_fn(self):
""""""
A = NumCatRVariable(
"A",
input_data={"outcome-values": [True, False]},
marginal_distribution=lambda x: 0.6 if x else 0.4,
)
B = NumCatRVariable(
"B",
input_data={"outcome-values": [True, False]},
marginal_distribution=lambda x: 0.62 if x else 0.38,
)
def phi_ab(scope_product):
ss = set(scope_product)
if ss == set([("A", True), ("B", True)]):
return 0.9
elif ss == set([("A", True), ("B", False)]):
return 0.1
elif ss == set([("A", False), ("B", True)]):
return 0.2
elif ss == set([("A", False), ("B", False)]):
return 0.8
else:
raise ValueError("unknown argument")
f = Factor.from_scope_variables_with_fn(svars=set([A, B]), fn=phi_ab)
query = set([("A", True), ("B", True)])
ff = f.phi(query)
self.assertEqual(round(ff, 2), 0.9)
@unittest.skip("Factor.from_conditional_vars not yet implemented")
def test_from_conditional_vars(self):
""""""
# A = NumCatRVariable(
# "A",
# input_data={"outcome-values": [True, False]},
# marginal_distribution=lambda x: 0.6 if x else 0.4,
# )
# B = NumCatRVariable(
# "B",
# input_data={"outcome-values": [True, False]},
# marginal_distribution=lambda x: 0.62 if x else 0.38,
# )
def phi_ab(scope_product):
ss = set(scope_product)
if ss == set([("A", True), ("B", True)]):
return 0.9
elif ss == set([("A", True), ("B", False)]):
return 0.1
elif ss == set([("A", False), ("B", True)]):
return 0.2
elif ss == set([("A", False), ("B", False)]):
return 0.8
else:
raise ValueError("unknown argument")
class TestFactorOps(unittest.TestCase):
"""!"""
def data_1(self):
""""""
# Koller, Friedman 2009, p. 104
self.Af = NumCatRVariable(
node_id="A",
input_data={"outcome-values": [10, 50]},
marginal_distribution=lambda x: 0.5,
)
self.Bf = NumCatRVariable(
node_id="B",
input_data={"outcome-values": [10, 50]},
marginal_distribution=lambda x: 0.5,
)
self.Cf = NumCatRVariable(
node_id="C",
input_data={"outcome-values": [10, 50]},
marginal_distribution=lambda x: 0.5,
)
self.Df = NumCatRVariable(
node_id="D",
input_data={"outcome-values": [10, 50]},
marginal_distribution=lambda x: 0.5,
)
def phiAB(scope_product):
""""""
sfs = set(scope_product)
if sfs == set([("A", 10), ("B", 10)]):
return 30
elif sfs == set([("A", 10), ("B", 50)]):
return 5
elif sfs == set([("A", 50), ("B", 10)]):
return 1
elif sfs == set([("A", 50), ("B", 50)]):
return 10
else:
raise ValueError("unknown arg")
self.AB = Factor(gid="AB",
scope_vars=set([self.Af, self.Bf]),
factor_fn=phiAB)
self.AB_b = BaseFactor(gid="AB",
scope_vars=set([self.Af, self.Bf]),
factor_fn=phiAB)
def phiBC(scope_product):
""""""
sfs = set(scope_product)
if sfs == set([("B", 10), ("C", 10)]):
return 100
elif sfs == set([("B", 10), ("C", 50)]):
return 1
elif sfs == set([("B", 50), ("C", 10)]):
return 1
elif sfs == set([("B", 50), ("C", 50)]):
return 100
else:
raise ValueError("unknown arg")
self.BC = Factor(gid="BC",
scope_vars=set([self.Bf, self.Cf]),
factor_fn=phiBC)
self.BC_b = BaseFactor(gid="BC",
scope_vars=set([self.Bf, self.Cf]),
factor_fn=phiBC)
def data_2(self):
""""""
def phiCD(scope_product):
""""""
sfs = set(scope_product)
if sfs == set([("C", 10), ("D", 10)]):
return 1
elif sfs == set([("C", 10), ("D", 50)]):
return 100
elif sfs == set([("C", 50), ("D", 10)]):
return 100
elif sfs == set([("C", 50), ("D", 50)]):
return 1
else:
raise ValueError("unknown arg")
self.CD = Factor(gid="CD",
scope_vars=set([self.Cf, self.Df]),
factor_fn=phiCD)
self.CD_b = BaseFactor(gid="CD",
scope_vars=set([self.Cf, self.Df]),
factor_fn=phiCD)
def phiDA(scope_product):
""""""
sfs = set(scope_product)
if sfs == set([("D", 10), ("A", 10)]):
return 100
elif sfs == set([("D", 10), ("A", 50)]):
return 1
elif sfs == set([("D", 50), ("A", 10)]):
return 1
elif sfs == set([("D", 50), ("A", 50)]):
return 100
else:
raise ValueError("unknown arg")
self.DA = Factor(gid="DA",
scope_vars=set([self.Df, self.Af]),
factor_fn=phiDA)
self.DA_b = BaseFactor(gid="DA",
scope_vars=set([self.Df, self.Af]),
factor_fn=phiDA)
def setUp(self):
""""""
self.data_1()
self.data_2()
# Koller, Friedman 2009 p. 107
self.af = NumCatRVariable(
node_id="A",
input_data={"outcome-values": [10, 50, 20]},
marginal_distribution=lambda x: 0.4 if x != 20 else 0.2,
)
def phiaB(scope_product):
""""""
sfs = set(scope_product)
if sfs == set([("A", 10), ("B", 10)]):
return 0.5
elif sfs == set([("A", 10), ("B", 50)]):
return 0.8
elif sfs == set([("A", 50), ("B", 10)]):
return 0.1
elif sfs == set([("A", 50), ("B", 50)]):
return 0
elif sfs == set([("A", 20), ("B", 10)]):
return 0.3
elif sfs == set([("A", 20), ("B", 50)]):
return 0.9
else:
raise ValueError("unknown arg")
self.aB = Factor(gid="ab",
scope_vars=set([self.af, self.Bf]),
factor_fn=phiaB)
self.aB_b = BaseFactor(gid="ab",
scope_vars=set([self.af, self.Bf]),
factor_fn=phiaB)
def phibc(scope_product):
""""""
sfs = set(scope_product)
if sfs == set([("B", 10), ("C", 10)]):
return 0.5
elif sfs == set([("B", 10), ("C", 50)]):
return 0.7
elif sfs == set([("B", 50), ("C", 10)]):
return 0.1
elif sfs == set([("B", 50), ("C", 50)]):
return 0.2
else:
raise ValueError("unknown arg")
self.bc = Factor(gid="bc",
scope_vars=set([self.Bf, self.Cf]),
factor_fn=phibc)
self.bc_b = BaseFactor(gid="bc",
scope_vars=set([self.Bf, self.Cf]),
factor_fn=phibc)
def test_cls_factor_product(self):
"from Koller, Friedman 2009, p. 105, figure 4.2"
Ab_Bc, prod1 = FactorOps.cls_product(f=self.AB, other=self.BC)
Ab_Bc_Cd, prod2 = FactorOps.cls_product(f=Ab_Bc, other=self.CD)
result, prod3 = FactorOps.cls_product(f=Ab_Bc_Cd, other=self.DA)
for sm in result.scope_products:
sms = set(sm)
f = result.phi(sms)
ff = round(result.phi_normal(sms), 6)
if sms == set([("B", 50), ("C", 50), ("A", 50), ("D", 10)]):
self.assertEqual(f, 100000)
self.assertEqual(ff, 0.013885)
elif sms == set([("B", 50), ("C", 50), ("A", 50), ("D", 50)]):
self.assertEqual(f, 100000)
self.assertEqual(ff, 0.013885)
elif sms == set([("B", 50), ("C", 50), ("A", 10), ("D", 10)]):
self.assertEqual(f, 5000000)
self.assertEqual(ff, 0.694267)
elif sms == set([("B", 50), ("C", 50), ("A", 10), ("D", 50)]):
self.assertEqual(f, 500)
self.assertEqual(ff, 6.9e-05)
elif sms == set([("B", 50), ("C", 10), ("A", 50), ("D", 10)]):
self.assertEqual(f, 10)
self.assertEqual(ff, 1e-06)
elif sms == set([("B", 50), ("C", 10), ("A", 50), ("D", 50)]):
self.assertEqual(f, 100000)
self.assertEqual(ff, 0.013885)
elif sms == set([("B", 50), ("C", 10), ("A", 10), ("D", 10)]):
self.assertEqual(f, 500)
self.assertEqual(ff, 6.9e-05)
elif sms == set([("B", 50), ("C", 10), ("A", 10), ("D", 50)]):
self.assertEqual(f, 500)
self.assertEqual(ff, 6.9e-05)
elif sms == set([("B", 10), ("C", 50), ("A", 50), ("D", 10)]):
self.assertEqual(f, 100)
self.assertEqual(ff, 1.4e-05)
elif sms == set([("B", 10), ("C", 50), ("A", 50), ("D", 50)]):
self.assertEqual(f, 100)
self.assertEqual(ff, 1.4e-05)
elif sms == set([("B", 10), ("C", 50), ("A", 10), ("D", 10)]):
self.assertEqual(f, 300000)
self.assertEqual(ff, 0.041656)
elif sms == set([("B", 10), ("C", 50), ("A", 10), ("D", 50)]):
self.assertEqual(f, 30)
self.assertEqual(ff, 4e-06)
elif sms == set([("B", 10), ("C", 10), ("A", 50), ("D", 10)]):
self.assertEqual(f, 100)
self.assertEqual(ff, 1.4e-05)
elif sms == set([("B", 10), ("C", 10), ("A", 50), ("D", 50)]):
self.assertEqual(f, 1000000)
self.assertEqual(ff, 0.138853)
elif sms == set([("B", 10), ("C", 10), ("A", 10), ("D", 10)]):
self.assertEqual(f, 300000)
self.assertEqual(ff, 0.041656)
elif sms == set([("B", 10), ("C", 10), ("A", 10), ("D", 50)]):
self.assertEqual(f, 300000)
self.assertEqual(ff, 0.041656)
def test_cls_reduced_by_value(self):
"from Koller, Friedman 2009, p. 111 figure 4.5"
red = set([("C", 10)])
aB_c, prod = FactorOps.cls_product(f=self.aB, other=self.bc)
# print(aB_c.scope_products)
nf = FactorOps.cls_reduced_by_value(aB_c, assignments=red)
sps = set([frozenset(s) for s in nf.scope_products])
self.assertEqual(
sps,
set([
frozenset([("A", 10), ("B", 50), ("C", 10)]),
frozenset([("A", 10), ("B", 10), ("C", 10)]),
frozenset([("B", 50), ("A", 20), ("C", 10)]),
frozenset([("B", 10), ("A", 20), ("C", 10)]),
frozenset([("A", 50), ("B", 50), ("C", 10)]),
frozenset([("A", 50), ("B", 10), ("C", 10)]),
]),
)
for p in nf.scope_products:
ps = set(p)
f = round(nf.phi(ps), 5)
if ps == set([("A", 10), ("B", 50), ("C", 10)]):
self.assertEqual(f, 0.08)
elif ps == set([("A", 10), ("B", 10), ("C", 10)]):
self.assertEqual(f, 0.25)
elif ps == set([("B", 50), ("A", 20), ("C", 10)]):
self.assertEqual(f, 0.09)
elif ps == set([("B", 10), ("A", 20), ("C", 10)]):
self.assertEqual(f, 0.15)
elif ps == set([("A", 50), ("B", 50), ("C", 10)]):
self.assertEqual(f, 0.0)
elif ps == set([("A", 50), ("B", 10), ("C", 10)]):
self.assertEqual(f, 0.05)
def test_cls_reduce_by_vars(self):
""""""
evidence = set([("C", 10), ("D", 50)])
aB_c, prod = FactorOps.cls_product(f=self.aB, other=self.bc)
# print(aB_c.scope_products)
nf = FactorOps.cls_reduced_by_vars(aB_c, assignments=evidence)
sps = set([frozenset(s) for s in nf.scope_products])
self.assertEqual(
sps,
set([
frozenset([("A", 10), ("B", 50), ("C", 10)]),
frozenset([("A", 10), ("B", 10), ("C", 10)]),
frozenset([("B", 50), ("A", 20), ("C", 10)]),
frozenset([("B", 10), ("A", 20), ("C", 10)]),
frozenset([("A", 50), ("B", 50), ("C", 10)]),
frozenset([("A", 50), ("B", 10), ("C", 10)]),
]),
)
def test_cls_sumout_var(self):
"from Koller, Friedman 2009, p. 297 figure 9.7"
aB_c, prod = FactorOps.cls_product(f=self.aB, other=self.bc)
a_c = FactorOps.cls_sumout_var(aB_c, self.Bf)
dset = self.Bf.value_set()
for p in a_c.scope_products:
ps = set(p)
f = round(a_c.phi(ps), 4)
diff = ps.difference(dset)
if diff == set([("C", 10), ("A", 10)]):
self.assertEqual(f, 0.33)
elif diff == set([("C", 50), ("A", 10)]):
self.assertEqual(f, 0.51)
elif diff == set([("C", 10), ("A", 50)]):
self.assertEqual(f, 0.05)
elif diff == set([("C", 50), ("A", 50)]):
self.assertEqual(f, 0.07)
elif diff == set([("C", 10), ("A", 20)]):
self.assertEqual(f, 0.24)
elif diff == set([("C", 50), ("A", 20)]):
self.assertEqual(f, 0.39)
def test_cls_maxout_var(self):
"from Koller, Friedman 2009, p. 555 figure 13.1"
aB_c, prod = FactorOps.cls_product(f=self.aB, other=self.bc)
a_c = FactorOps.cls_maxout_var(aB_c, self.Bf)
dset = self.Bf.value_set()
for p in a_c.scope_products:
ps = set(p)
f = round(a_c.phi(ps), 4)
diff = ps.difference(dset)
if diff == set([("C", 10), ("A", 10)]):
self.assertEqual(f, 0.25)
elif diff == set([("C", 50), ("A", 10)]):
self.assertEqual(f, 0.35)
elif diff == set([("C", 10), ("A", 50)]):
self.assertEqual(f, 0.05)
elif diff == set([("C", 50), ("A", 50)]):
self.assertEqual(f, 0.07)
elif diff == set([("C", 10), ("A", 20)]):
self.assertEqual(f, 0.15)
elif diff == set([("C", 50), ("A", 20)]):
self.assertEqual(f, 0.21)
def setUp(self):
nid1 = "rvar1"
input_data = {
"intelligence": {
"outcome-values": [0.1, 0.9],
"evidence": 0.9
},
"grade": {
"outcome-values": [0.2, 0.4, 0.6],
"evidence": 0.2
},
"dice": {
"outcome-values": [i for i in range(1, 7)],
"evidence": 1.0 / 6,
},
}
def intelligence_dist(intelligence_value: float):
if intelligence_value == 0.1:
return 0.7
elif intelligence_value == 0.9:
return 0.3
else:
raise ValueError(
"intelligence_value does not belong to possible outcomes")
def grade_dist(grade_value: float):
if grade_value == 0.2:
return 0.25
elif grade_value == 0.4:
return 0.37
elif grade_value == 0.6:
return 0.38
else:
raise ValueError("unknown grade value")
def fair_dice_dist(dice_value: float):
if dice_value in [i for i in range(1, 7)]:
return 1.0 / 6.0
else:
raise ValueError("dice value")
# intelligence
# grade
self.intelligence = NumCatRVariable(
node_id=nid1,
input_data=input_data["intelligence"],
marginal_distribution=intelligence_dist,
)
nid2 = "rvar2"
self.grade = NumCatRVariable(
node_id=nid2,
input_data=input_data["grade"],
marginal_distribution=grade_dist,
)
nid3 = "rvar3"
self.dice = NumCatRVariable(
node_id=nid3,
input_data=input_data["dice"],
marginal_distribution=fair_dice_dist,
)
#
students = PossibleOutcomes(frozenset(["student_1", "student_2"]))
def grade_f(x):
return "F" if x == "student_1" else "A"
def grade_distribution(x):
return 0.1 if x == "F" else 0.9
indata = {"possible-outcomes": students}
self.rvar = CatRandomVariable(
input_data=indata,
node_id="myrandomvar",
f=grade_f,
marginal_distribution=grade_distribution,
)
def setUp(self):
""""""
idata = {
"A": {"outcome-values": [True, False]},
"B": {"outcome-values": [True, False]},
"C": {"outcome-values": [True, False]},
"D": {"outcome-values": [True, False]},
}
# misconception example: Koller, Friedman, 2009 p. 104
self.A = NumCatRVariable(
node_id="A",
input_data=idata["A"],
marginal_distribution=lambda x: 0.5,
)
self.B = NumCatRVariable(
node_id="B",
input_data=idata["B"],
marginal_distribution=lambda x: 0.5,
)
self.C = NumCatRVariable(
node_id="C",
input_data=idata["C"],
marginal_distribution=lambda x: 0.5,
)
self.D = NumCatRVariable(
node_id="D",
input_data=idata["D"],
marginal_distribution=lambda x: 0.5,
)
self.AB = Edge(
edge_id="AB",
edge_type=EdgeType.UNDIRECTED,
start_node=self.A,
end_node=self.B,
)
self.AD = Edge(
edge_id="AD",
edge_type=EdgeType.UNDIRECTED,
start_node=self.A,
end_node=self.D,
)
self.DC = Edge(
edge_id="DC",
edge_type=EdgeType.UNDIRECTED,
start_node=self.D,
end_node=self.C,
)
self.BC = Edge(
edge_id="BC",
edge_type=EdgeType.UNDIRECTED,
start_node=self.B,
end_node=self.C,
)
def phi_AB(scope_product):
""""""
ss = frozenset(scope_product)
if ss == frozenset([("A", False), ("B", False)]):
return 30.0
elif ss == frozenset([("A", False), ("B", True)]):
return 5.0
elif ss == frozenset([("A", True), ("B", False)]):
return 1.0
elif ss == frozenset([("A", True), ("B", True)]):
return 10.0
else:
raise ValueError("product error")
def phi_BC(scope_product):
""""""
ss = frozenset(scope_product)
if ss == frozenset([("B", False), ("C", False)]):
return 100.0
elif ss == frozenset([("B", False), ("C", True)]):
return 1.0
elif ss == frozenset([("B", True), ("C", False)]):
return 1.0
elif ss == frozenset([("B", True), ("C", True)]):
return 100.0
else:
raise ValueError("product error")
def phi_CD(scope_product):
""""""
ss = frozenset(scope_product)
if ss == frozenset([("C", False), ("D", False)]):
return 1.0
elif ss == frozenset([("C", False), ("D", True)]):
return 100.0
elif ss == frozenset([("C", True), ("D", False)]):
return 100.0
elif ss == frozenset([("C", True), ("D", True)]):
return 1.0
else:
raise ValueError("product error")
def phi_DA(scope_product):
""""""
ss = frozenset(scope_product)
if ss == frozenset([("D", False), ("A", False)]):
return 100.0
elif ss == frozenset([("D", False), ("A", True)]):
return 1.0
elif ss == frozenset([("D", True), ("A", False)]):
return 1.0
elif ss == frozenset([("D", True), ("A", True)]):
return 100.0
else:
raise ValueError("product error")
self.AB_f = Factor(
gid="ab_f", scope_vars=set([self.A, self.B]), factor_fn=phi_AB
)
self.BC_f = Factor(
gid="bc_f", scope_vars=set([self.B, self.C]), factor_fn=phi_BC
)
self.CD_f = Factor(
gid="cd_f", scope_vars=set([self.C, self.D]), factor_fn=phi_CD
)
self.DA_f = Factor(
gid="da_f", scope_vars=set([self.D, self.A]), factor_fn=phi_DA
)
self.mnetwork = MarkovNetwork(
gid="mnet",
nodes=set([self.A, self.B, self.C, self.D]),
edges=set([self.AB, self.AD, self.BC, self.DC]),
factors=set([self.DA_f, self.CD_f, self.BC_f, self.AB_f]),
)
# CH-Asia values from Cowell 2005, p. 116 table 6.9
self.a = NumCatRVariable(
node_id="a",
input_data=idata["A"],
marginal_distribution=lambda x: 0.01 if x else 0.99,
)
self.b = NumCatRVariable(
node_id="b",
input_data=idata["B"],
marginal_distribution=lambda x: 0.5,
)
self.d = NumCatRVariable(
node_id="d",
input_data=idata["A"],
marginal_distribution=lambda x: 0.7468 if x else 0.2532,
)
self.c = NumCatRVariable(
node_id="c",
input_data=idata["A"],
marginal_distribution=lambda x: 0.7312 if x else 0.2688,
)
self.ab = Edge(
"ab",
start_node=self.a,
end_node=self.b,
edge_type=EdgeType.UNDIRECTED,
)
self.ad = Edge(
"ad",
start_node=self.a,
end_node=self.d,
edge_type=EdgeType.UNDIRECTED,
)
self.bc = Edge(
"bc",
start_node=self.b,
end_node=self.c,
edge_type=EdgeType.UNDIRECTED,
)
self.dc = Edge(
"dc",
start_node=self.d,
end_node=self.c,
edge_type=EdgeType.UNDIRECTED,
)
self.ugraph = UndiGraph(
"ug1",
data={"m": "f"},
nodes=set([self.a, self.b, self.c, self.d]),
edges=set([self.ab, self.ad, self.bc, self.dc]),
)
#
# Conditional Random Field test
# from Koller, Friedman 2009, p. 144-145, example 4.20
self.X_1 = NumCatRVariable(
node_id="X_1",
input_data=idata["A"],
marginal_distribution=lambda x: 0.5,
)
self.X_2 = NumCatRVariable(
node_id="X_2",
input_data=idata["A"],
marginal_distribution=lambda x: 0.5,
)
self.X_3 = NumCatRVariable(
node_id="X_3",
input_data=idata["A"],
marginal_distribution=lambda x: 0.5,
)
self.Y_1 = NumCatRVariable(
node_id="Y_1",
input_data=idata["A"],
marginal_distribution=lambda x: 0.5,
)
self.X1_Y1 = Edge(
edge_id="X1_Y1",
edge_type=EdgeType.UNDIRECTED,
start_node=self.X_1,
end_node=self.Y_1,
)
self.X2_Y1 = Edge(
edge_id="X2_Y1",
edge_type=EdgeType.UNDIRECTED,
start_node=self.X_2,
end_node=self.Y_1,
)
self.X3_Y1 = Edge(
edge_id="X3_Y1",
edge_type=EdgeType.UNDIRECTED,
start_node=self.X_3,
end_node=self.Y_1,
)
def phi_X1_Y1(scope_product):
""""""
w = 0.5
ss = frozenset(scope_product)
if ss == frozenset([("X_1", True), ("Y_1", True)]):
return math.exp(1.0 * w)
else:
return math.exp(0.0)
def phi_X2_Y1(scope_product):
""""""
w = 5.0
ss = frozenset(scope_product)
if ss == frozenset([("X_2", True), ("Y_1", True)]):
return math.exp(1.0 * w)
else:
return math.exp(0.0)
def phi_X3_Y1(scope_product):
""""""
w = 9.4
ss = frozenset(scope_product)
if ss == frozenset([("X_3", True), ("Y_1", True)]):
return math.exp(1.0 * w)
else:
return math.exp(0.0)
def phi_Y1(scope_product):
""""""
w = 0.6
ss = frozenset(scope_product)
if ss == frozenset([("Y_1", True)]):
return math.exp(1.0 * w)
else:
return math.exp(0.0)
self.X1_Y1_f = Factor(
gid="x1_y1_f",
scope_vars=set([self.X_1, self.Y_1]),
factor_fn=phi_X1_Y1,
)
self.X2_Y1_f = Factor(
gid="x2_y1_f",
scope_vars=set([self.X_2, self.Y_1]),
factor_fn=phi_X2_Y1,
)
self.X3_Y1_f = Factor(
gid="x3_y1_f",
scope_vars=set([self.X_3, self.Y_1]),
factor_fn=phi_X3_Y1,
)
self.Y1_f = Factor(
gid="y1_f", scope_vars=set([self.Y_1]), factor_fn=phi_Y1
)
self.crf_koller = ConditionalRandomField(
"crf",
observed_vars=set([self.X_1, self.X_2, self.X_3]),
target_vars=set([self.Y_1]),
edges=set([self.X1_Y1, self.X2_Y1, self.X3_Y1]),
factors=set([self.X1_Y1_f, self.X2_Y1_f, self.X3_Y1_f, self.Y1_f]),
)
class NumCatRVariableTest(unittest.TestCase):
def setUp(self):
nid1 = "rvar1"
input_data = {
"intelligence": {
"outcome-values": [0.1, 0.9],
"evidence": 0.9
},
"grade": {
"outcome-values": [0.2, 0.4, 0.6],
"evidence": 0.2
},
"dice": {
"outcome-values": [i for i in range(1, 7)],
"evidence": 1.0 / 6,
},
}
def intelligence_dist(intelligence_value: float):
if intelligence_value == 0.1:
return 0.7
elif intelligence_value == 0.9:
return 0.3
else:
raise ValueError(
"intelligence_value does not belong to possible outcomes")
def grade_dist(grade_value: float):
if grade_value == 0.2:
return 0.25
elif grade_value == 0.4:
return 0.37
elif grade_value == 0.6:
return 0.38
else:
raise ValueError("unknown grade value")
def fair_dice_dist(dice_value: float):
if dice_value in [i for i in range(1, 7)]:
return 1.0 / 6.0
else:
raise ValueError("dice value")
# intelligence
# grade
self.intelligence = NumCatRVariable(
node_id=nid1,
input_data=input_data["intelligence"],
marginal_distribution=intelligence_dist,
)
nid2 = "rvar2"
self.grade = NumCatRVariable(
node_id=nid2,
input_data=input_data["grade"],
marginal_distribution=grade_dist,
)
nid3 = "rvar3"
self.dice = NumCatRVariable(
node_id=nid3,
input_data=input_data["dice"],
marginal_distribution=fair_dice_dist,
)
#
students = PossibleOutcomes(frozenset(["student_1", "student_2"]))
def grade_f(x):
return "F" if x == "student_1" else "A"
def grade_distribution(x):
return 0.1 if x == "F" else 0.9
indata = {"possible-outcomes": students}
self.rvar = CatRandomVariable(
input_data=indata,
node_id="myrandomvar",
f=grade_f,
marginal_distribution=grade_distribution,
)
def test_id(self):
""""""
self.assertEqual(self.grade.id(), "rvar2")
def test_values(self):
self.assertEqual(self.rvar.values(), frozenset(["A", "F"]))
def test_value_set(self):
self.assertEqual(
self.rvar.value_set(
value_transform=lambda x: x.lower(),
value_filter=lambda x: x != "A",
),
frozenset([("myrandomvar", "f")]),
)
def test_max_marginal_value(self):
self.assertEqual(self.intelligence.max_marginal_value(), 0.1)
def test_max(self):
self.assertEqual(self.intelligence.max(), 0.7)
def test_min(self):
self.assertEqual(self.intelligence.min(), 0.3)
def test_min_marginal_value(self):
self.assertEqual(self.intelligence.min_marginal_value(), 0.9)
def test_expected_value(self):
""""""
self.assertEqual(self.dice.expected_value(), 3.5)
def test_marginal_with_known_value(self):
""""""
self.assertEqual(self.grade.marginal(0.4), 0.37)
def test_p_x_known_value(self):
""""""
self.assertEqual(self.grade.p(0.4), 0.37)
def test_P_X_e(self):
""""""
self.assertEqual(self.grade.P_X_e(), 0.25)
def test_max_marginal_e(self):
""""""
self.assertEqual(self.grade.max_marginal_e(), 0.25)
def test_min_marginal_e(self):
""""""
self.assertEqual(self.grade.min_marginal_e(), 0.25)
def test_marginal_over(self):
""""""
eval_value = 0.2
margover = self.grade.marginal_over(eval_value, self.dice)
self.assertEqual(margover, 3.5 * 0.25)
def test_marginal_over_evidence_key(self):
""""""
margover = self.grade.marginal_over_evidence_key(self.dice)
self.assertEqual(margover, 3.5 * 0.25)
def test_joint_without_evidence(self):
dice = self.dice
dice.pop_evidence()
self.assertEqual(dice.joint(dice), 3.5 * 3.5)
def test_variance(self):
self.assertEqual(round(self.dice.variance(), 3), 2.917)
def test_standard_deviation(self):
""""""
self.assertEqual(
round(self.dice.standard_deviation(), 3),
round(math.sqrt(2.917), 3),
)
def cls_nodes_1(cls):
""""""
idata = {
"a": {
"outcome-values": [True, False]
},
"b": {
"outcome-values": [True, False]
},
"c": {
"outcome-values": [True, False]
},
}
cls.a = NumCatRVariable(
node_id="a",
input_data=idata["a"],
marginal_distribution=lambda x: 0.6 if x else 0.4,
)
cls.b = NumCatRVariable(
node_id="b",
input_data=idata["b"],
marginal_distribution=lambda x: 0.5 if x else 0.5,
)
cls.c = NumCatRVariable(
node_id="c",
input_data=idata["c"],
marginal_distribution=lambda x: 0.5 if x else 0.5,
)
cls.ab = Edge(
edge_id="ab",
edge_type=EdgeType.UNDIRECTED,
start_node=cls.a,
end_node=cls.b,
)
cls.bc = Edge(
edge_id="bc",
edge_type=EdgeType.UNDIRECTED,
start_node=cls.b,
end_node=cls.c,
)
def phi_ba(scope_product):
""""""
ss = set(scope_product)
if ss == set([("a", True), ("b", True)]):
return 0.9
elif ss == set([("a", True), ("b", False)]):
return 0.1
elif ss == set([("a", False), ("b", True)]):
return 0.2
elif ss == set([("a", False), ("b", False)]):
return 0.8
else:
raise ValueError("product error")
def phi_cb(scope_product):
""""""
ss = set(scope_product)
if ss == set([("c", True), ("b", True)]):
return 0.3
elif ss == set([("c", True), ("b", False)]):
return 0.5
elif ss == set([("c", False), ("b", True)]):
return 0.7
elif ss == set([("c", False), ("b", False)]):
return 0.5
else:
raise ValueError("product error")
def phi_a(scope_product):
s = set(scope_product)
if s == set([("a", True)]):
return 0.6
elif s == set([("a", False)]):
return 0.4
else:
raise ValueError("product error")
cls.ba_f = Factor(gid="ba",
scope_vars=set([cls.b, cls.a]),
factor_fn=phi_ba)
cls.cb_f = Factor(gid="cb",
scope_vars=set([cls.c, cls.b]),
factor_fn=phi_cb)
cls.a_f = Factor(gid="a", scope_vars=set([cls.a]), factor_fn=phi_a)
def cls_nodes_2(cls):
""""""
odata = {"outcome-values": [True, False]}
cls.J = NumCatRVariable(node_id="J",
input_data=odata,
marginal_distribution=lambda x: 0.5)
cls.Irvar = NumCatRVariable(node_id="I",
input_data=odata,
marginal_distribution=lambda x: 0.5)
cls.X = NumCatRVariable(node_id="X",
input_data=odata,
marginal_distribution=lambda x: 0.5)
cls.Y = NumCatRVariable(node_id="Y",
input_data=odata,
marginal_distribution=lambda x: 0.5)
cls.Orvar = NumCatRVariable(node_id="O",
input_data=odata,
marginal_distribution=lambda x: 0.5)
cls.JX = Edge(
edge_id="JX",
edge_type=EdgeType.DIRECTED,
start_node=cls.J,
end_node=cls.X,
)
cls.JY = Edge(
edge_id="JY",
edge_type=EdgeType.DIRECTED,
start_node=cls.J,
end_node=cls.Y,
)
cls.IX = Edge(
edge_id="IX",
edge_type=EdgeType.DIRECTED,
start_node=cls.Irvar,
end_node=cls.X,
)
cls.XO = Edge(
edge_id="XO",
edge_type=EdgeType.DIRECTED,
start_node=cls.X,
end_node=cls.Orvar,
)
cls.YO = Edge(
edge_id="YO",
edge_type=EdgeType.DIRECTED,
start_node=cls.Y,
end_node=cls.Orvar,
)
def phi_ij(scope_product, i: str):
""""""
ss = set(scope_product)
if ss == set([(i, True)]):
return 0.5
elif ss == set([(i, False)]):
return 0.5
else:
raise ValueError("unknown scope product")
def phi_i(scope_product):
""""""
return phi_ij(scope_product, i="I")
cls.I_f = Factor(gid="I_f",
scope_vars=set([cls.Irvar]),
factor_fn=phi_i)
def phi_j(scope_product):
""""""
return phi_ij(scope_product, i="J")
cls.J_f = Factor(gid="J_f", scope_vars=set([cls.J]), factor_fn=phi_j)
def phi_jy(scope_product):
""""""
ss = set(scope_product)
if ss == set([("J", True), ("Y", True)]):
return 0.01
elif ss == set([("J", True), ("Y", False)]):
return 0.99
elif ss == set([("J", False), ("Y", True)]):
return 0.99
elif ss == set([("J", False), ("Y", False)]):
return 0.01
else:
raise ValueError("scope product unknown")
cls.JY_f = Factor(gid="JY_f",
scope_vars=set([cls.J, cls.Y]),
factor_fn=phi_jy)
def test_from_digraph_with_factors(self):
"""!
Values from Darwiche 2009, p. 132, figure 6.4
"""
A = NumCatRVariable(
"A",
input_data={"outcome-values": [True, False]},
marginal_distribution=lambda x: 0.6 if x else 0.4,
)
B = NumCatRVariable(
"B",
input_data={"outcome-values": [True, False]},
marginal_distribution=lambda x: 0.62 if x else 0.38,
)
C = NumCatRVariable(
"C",
input_data={"outcome-values": [True, False]},
marginal_distribution=lambda x: 0.624 if x else 0.376,
)
AB_Edge = Edge(
edge_id="ab_edge",
start_node=A,
end_node=B,
edge_type=EdgeType.DIRECTED,
)
BC_Edge = Edge(
edge_id="bc_edge",
start_node=B,
end_node=C,
edge_type=EdgeType.DIRECTED,
)
def phi_a(scope_product):
""""""
ss = set(scope_product)
if ss == set([("A", True)]):
return 0.6
elif ss == set([("A", False)]):
return 0.4
else:
raise ValueError("unknown argument")
def phi_ab(scope_product):
ss = set(scope_product)
if ss == set([("A", True), ("B", True)]):
return 0.9
elif ss == set([("A", True), ("B", False)]):
return 0.1
elif ss == set([("A", False), ("B", True)]):
return 0.2
elif ss == set([("A", False), ("B", False)]):
return 0.8
else:
raise ValueError("unknown argument")
def phi_bc(scope_product):
ss = set(scope_product)
if ss == set([("C", True), ("B", True)]):
return 0.3
elif ss == set([("C", True), ("B", False)]):
return 0.5
elif ss == set([("C", False), ("B", True)]):
return 0.7
elif ss == set([("C", False), ("B", False)]):
return 0.5
else:
raise ValueError("unknown argument")
A_f = Factor(gid="A_f", scope_vars=set([A]), factor_fn=phi_a)
AB_f = Factor(gid="AB_f", scope_vars=set([A, B]), factor_fn=phi_ab)
BC_f = Factor(gid="BC_f", scope_vars=set([C, B]), factor_fn=phi_bc)
dig = DiGraph(gid="temp",
nodes=set([A, B, C]),
edges=set([AB_Edge, BC_Edge]))
factors = set([A_f, AB_f, BC_f])
bn = BayesianNetwork(
gid="temp",
nodes=set([A, B, C]),
edges=set([AB_Edge, BC_Edge]),
factors=set([A_f, AB_f, BC_f]),
)
q = set([B])
evidence = set([])
foo, a = bn.cond_prod_by_variable_elimination(queries=q,
evidences=evidence)
bayes = BayesianNetwork.from_digraph(dig, factors)
foo2, a2 = bayes.cond_prod_by_variable_elimination(queries=q,
evidences=evidence)
f1 = set([("B", False)])
self.assertEqual(foo.phi(f1), foo2.phi(f1))
f1 = set([("B", True)])
self.assertEqual(foo.phi(f1), foo2.phi(f1))
def setUp(self):
""""""
idata = {
"rain": {
"outcome-values": [True, False]
},
"sprink": {
"outcome-values": [True, False]
},
"wet": {
"outcome-values": [True, False]
},
"road": {
"outcome-values": [True, False]
},
"winter": {
"outcome-values": [True, False]
},
"earthquake": {
"outcome-values": [True, False]
},
"burglary": {
"outcome-values": [True, False]
},
"alarm": {
"outcome-values": [True, False]
},
}
self.rain = NumCatRVariable(
input_data=idata["rain"],
node_id="rain",
marginal_distribution=lambda x: 0.2 if x is True else 0.8,
)
self.sprink = NumCatRVariable(
node_id="sprink",
input_data=idata["sprink"],
marginal_distribution=lambda x: 0.6 if x is True else 0.4,
)
self.wet = NumCatRVariable(
node_id="wet",
input_data=idata["wet"],
marginal_distribution=lambda x: 0.7 if x is True else 0.3,
)
self.rain_wet = Edge(
edge_id="rain_wet",
start_node=self.rain,
end_node=self.wet,
edge_type=EdgeType.DIRECTED,
)
self.rain_sprink = Edge(
edge_id="rain_sprink",
start_node=self.rain,
end_node=self.sprink,
edge_type=EdgeType.DIRECTED,
)
self.sprink_wet = Edge(
edge_id="sprink_wet",
start_node=self.sprink,
end_node=self.wet,
edge_type=EdgeType.DIRECTED,
)
def sprink_rain_factor(scope_product):
""""""
sfs = set(scope_product)
if sfs == set([("rain", True), ("sprink", True)]):
return 0.01
elif sfs == set([("rain", True), ("sprink", False)]):
return 0.99
elif sfs == set([("rain", False), ("sprink", True)]):
return 0.4
elif sfs == set([("rain", False), ("sprink", False)]):
return 0.6
else:
raise ValueError("unknown product")
self.rain_sprink_f = Factor.from_scope_variables_with_fn(
svars=set([self.rain, self.sprink]), fn=sprink_rain_factor)
def grass_wet_factor(scope_product):
""""""
sfs = set(scope_product)
if sfs == set([("rain", False), ("sprink", False), ("wet", True)]):
return 0.0
elif sfs == set([("rain", False), ("sprink", False),
("wet", False)]):
return 1.0
elif sfs == set([("rain", False), ("sprink", True),
("wet", True)]):
return 0.8
elif sfs == set([("rain", False), ("sprink", True),
("wet", False)]):
return 0.2
elif sfs == set([("rain", True), ("sprink", False),
("wet", True)]):
return 0.9
elif sfs == set([("rain", True), ("sprink", False),
("wet", False)]):
return 0.1
elif sfs == set([("rain", True), ("sprink", True), ("wet", True)]):
return 0.99
elif sfs == set([("rain", True), ("sprink", True),
("wet", False)]):
return 0.01
else:
raise ValueError("unknown product")
self.grass_wet_f = Factor.from_scope_variables_with_fn(
svars=set([self.rain, self.sprink, self.wet]), fn=grass_wet_factor)
self.bayes = BayesianNetwork(
gid="b",
nodes=set([self.rain, self.sprink, self.wet]),
edges=set([self.rain_wet, self.rain_sprink, self.sprink_wet]),
factors=set([self.grass_wet_f, self.rain_sprink_f]),
)
#
# Darwiche 2009, p. 30
#
# Earthquake Burglary
# \ /
# \ /
# Alarm
#
self.EarthquakeN = NumCatRVariable(
input_data=idata["earthquake"],
node_id="EarthquakeN",
marginal_distribution=lambda x: 0.1 if x is True else 0.9,
)
self.BurglaryN = NumCatRVariable(
input_data=idata["burglary"],
node_id="BurglaryN",
marginal_distribution=lambda x: 0.2 if x is True else 0.8,
)
self.AlarmN = NumCatRVariable(
input_data=idata["alarm"],
node_id="AlarmN",
marginal_distribution=lambda x: 0.2442 if x is True else 0.7558,
)
self.burglar_alarm = Edge(
edge_id="burglar_alarm",
start_node=self.BurglaryN,
end_node=self.AlarmN,
edge_type=EdgeType.DIRECTED,
)
self.earthquake_alarm = Edge(
edge_id="earthquake_alarm",
start_node=self.EarthquakeN,
end_node=self.AlarmN,
edge_type=EdgeType.DIRECTED,
)
idata = {"outcome-values": [True, False]}
self.C = NumCatRVariable(node_id="C",
input_data=idata,
marginal_distribution=lambda x: 0.5)
self.E = NumCatRVariable(node_id="E",
input_data=idata,
marginal_distribution=lambda x: 0.5)
self.F = NumCatRVariable(node_id="F",
input_data=idata,
marginal_distribution=lambda x: 0.5)
self.D = NumCatRVariable(node_id="D",
input_data=idata,
marginal_distribution=lambda x: 0.5)
self.CE = Edge(
edge_id="CE",
start_node=self.C,
end_node=self.E,
edge_type=EdgeType.DIRECTED,
)
self.ED = Edge(
edge_id="ED",
start_node=self.E,
end_node=self.D,
edge_type=EdgeType.DIRECTED,
)
self.EF = Edge(
edge_id="EF",
start_node=self.E,
end_node=self.F,
edge_type=EdgeType.DIRECTED,
)
def phi_c(scope_product):
ss = set(scope_product)
if ss == set([("C", True)]):
return 0.8
elif ss == set([("C", False)]):
return 0.2
else:
raise ValueError("scope product unknown")
def phi_ec(scope_product):
ss = set(scope_product)
if ss == set([("C", True), ("E", True)]):
return 0.9
elif ss == set([("C", True), ("E", False)]):
return 0.1
elif ss == set([("C", False), ("E", True)]):
return 0.7
elif ss == set([("C", False), ("E", False)]):
return 0.3
else:
raise ValueError("scope product unknown")
def phi_fe(scope_product):
ss = set(scope_product)
if ss == set([("E", True), ("F", True)]):
return 0.9
elif ss == set([("E", True), ("F", False)]):
return 0.1
elif ss == set([("E", False), ("F", True)]):
return 0.5
elif ss == set([("E", False), ("F", False)]):
return 0.5
else:
raise ValueError("scope product unknown")
def phi_de(scope_product):
ss = set(scope_product)
if ss == set([("E", True), ("D", True)]):
return 0.7
elif ss == set([("E", True), ("D", False)]):
return 0.3
elif ss == set([("E", False), ("D", True)]):
return 0.4
elif ss == set([("E", False), ("D", False)]):
return 0.6
else:
raise ValueError("scope product unknown")
self.CE_f = Factor(gid="CE_f",
scope_vars=set([self.C, self.E]),
factor_fn=phi_ec)
self.C_f = Factor(gid="C_f", scope_vars=set([self.C]), factor_fn=phi_c)
self.FE_f = Factor(gid="FE_f",
scope_vars=set([self.F, self.E]),
factor_fn=phi_fe)
self.DE_f = Factor(gid="DE_f",
scope_vars=set([self.D, self.E]),
factor_fn=phi_de)
self.bayes_n = BayesianNetwork(
gid="ba",
nodes=set([self.C, self.E, self.D, self.F]),
edges=set([self.EF, self.CE, self.ED]),
factors=set([self.C_f, self.DE_f, self.CE_f, self.FE_f]),
)