def setUp(self):
reader = XMLBIFReader(string=TEST_FILE)
self.expected_model = reader.get_model()
self.writer = XMLBIFWriter(self.expected_model)
self.model_stateless = BayesianModel([('D', 'G'), ('I', 'G'), ('G', 'L'), ('I', 'S')])
self.cpd_d = TabularCPD(variable='D', variable_card=2, values=[[0.6, 0.4]])
self.cpd_i = TabularCPD(variable='I', variable_card=2, values=[[0.7, 0.3]])
self.cpd_g = TabularCPD(variable='G', variable_card=3,
values=[[0.3, 0.05, 0.9, 0.5],
[0.4, 0.25, 0.08, 0.3],
[0.3, 0.7, 0.02, 0.2]],
evidence=['I', 'D'],
evidence_card=[2, 2])
self.cpd_l = TabularCPD(variable='L', variable_card=2,
values=[[0.1, 0.4, 0.99],
[0.9, 0.6, 0.01]],
evidence=['G'],
evidence_card=[3])
self.cpd_s = TabularCPD(variable='S', variable_card=2,
values=[[0.95, 0.2],
[0.05, 0.8]],
evidence=['I'],
evidence_card=[2])
self.model_stateless.add_cpds(self.cpd_d, self.cpd_i, self.cpd_g, self.cpd_l, self.cpd_s)
self.writer_stateless = XMLBIFWriter(self.model_stateless)
def test_write_xmlbif_statefull(self):
self.writer.write_xmlbif("dog_problem_output.xbif")
with open("dog_problem_output.xbif", "r") as f:
file_text = f.read()
reader = XMLBIFReader(string=file_text)
model = reader.get_model()
self.assert_models_equivelent(self.expected_model, model)
os.remove("dog_problem_output.xbif")
def loadXMLBIF(path):
reader = XMLBIFReader(path)
model = reader.get_model()
print("LOADMODEL: "+str(path))
"""
for cpd in model.get_cpds():
#if(cpd.variable == "SENSOR1"):
print("CPD of {variable}:".format(variable=cpd.variable))
print(cpd)
"""
return model
def test_write_xmlbif_stateless(self):
self.writer_stateless.write_xmlbif("grade_problem_output.xbif")
with open("grade_problem_output.xbif", 'r') as f:
reader = XMLBIFReader(f)
model = reader.get_model()
self.assert_models_equivelent(self.model_stateless, model)
self.assertDictEqual({'G': ['state0', 'state1', 'state2'],
'I': ['state0', 'state1'],
'D': ['state0', 'state1'],
'S': ['state0', 'state1'],
'L': ['state0', 'state1']},
model.get_cpds('D').state_names)
os.remove("grade_problem_output.xbif")
def test_write_xmlbif_stateless(self):
self.writer_stateless.write_xmlbif("grade_problem_output.xbif")
with open("grade_problem_output.xbif", "r") as f:
reader = XMLBIFReader(f)
model = reader.get_model()
self.assert_models_equivelent(self.model_stateless, model)
self.assertDictEqual(
{
"G": ["state0", "state1", "state2"],
"I": ["state0", "state1"],
"D": ["state0", "state1"],
"S": ["state0", "state1"],
"L": ["state0", "state1"],
},
model.get_cpds("D").state_names,
)
os.remove("grade_problem_output.xbif")
def setUp(self):
reader = XMLBIFReader(string=TEST_FILE)
self.expected_model = reader.get_model()
self.writer = XMLBIFWriter(self.expected_model)
self.model_stateless = BayesianModel([("D", "G"), ("I", "G"),
("G", "L"), ("I", "S")])
self.cpd_d = TabularCPD(variable="D",
variable_card=2,
values=[[0.6, 0.4]])
self.cpd_i = TabularCPD(variable="I",
variable_card=2,
values=[[0.7, 0.3]])
self.cpd_g = TabularCPD(
variable="G",
variable_card=3,
values=[
[0.3, 0.05, 0.9, 0.5],
[0.4, 0.25, 0.08, 0.3],
[0.3, 0.7, 0.02, 0.2],
],
evidence=["I", "D"],
evidence_card=[2, 2],
)
self.cpd_l = TabularCPD(
variable="L",
variable_card=2,
values=[[0.1, 0.4, 0.99], [0.9, 0.6, 0.01]],
evidence=["G"],
evidence_card=[3],
)
self.cpd_s = TabularCPD(
variable="S",
variable_card=2,
values=[[0.95, 0.2], [0.05, 0.8]],
evidence=["I"],
evidence_card=[2],
)
self.model_stateless.add_cpds(self.cpd_d, self.cpd_i, self.cpd_g,
self.cpd_l, self.cpd_s)
self.writer_stateless = XMLBIFWriter(self.model_stateless)
def setUp(self):
with open("dog_problem.xml", 'w') as fout:
fout.write(TEST_FILE)
self.reader = XMLBIFReader("dog_problem.xml")
def setUp(self):
self.reader = XMLBIFReader(string=TEST_FILE)
def setUp(self):
self.reader = XMLBIFReader(string="""
<BIF VERSION="0.3">
<NETWORK>
<NAME>Dog-Problem</NAME>
<VARIABLE TYPE="nature">
<NAME>light-on</NAME>
<OUTCOME>true</OUTCOME>
<OUTCOME>false</OUTCOME>
<PROPERTY>position = (73, 165)</PROPERTY>
</VARIABLE>
<VARIABLE TYPE="nature">
<NAME>bowel-problem</NAME>
<OUTCOME>true</OUTCOME>
<OUTCOME>false</OUTCOME>
<PROPERTY>position = (190, 69)</PROPERTY>
</VARIABLE>
<VARIABLE TYPE="nature">
<NAME>dog-out</NAME>
<OUTCOME>true</OUTCOME>
<OUTCOME>false</OUTCOME>
<PROPERTY>position = (155, 165)</PROPERTY>
</VARIABLE>
<VARIABLE TYPE="nature">
<NAME>hear-bark</NAME>
<OUTCOME>true</OUTCOME>
<OUTCOME>false</OUTCOME>
<PROPERTY>position = (154, 241)</PROPERTY>
</VARIABLE>
<VARIABLE TYPE="nature">
<NAME>family-out</NAME>
<OUTCOME>true</OUTCOME>
<OUTCOME>false</OUTCOME>
<PROPERTY>position = (112, 69)</PROPERTY>
</VARIABLE>
<DEFINITION>
<FOR>light-on</FOR>
<GIVEN>family-out</GIVEN>
<TABLE>0.6 0.4 0.05 0.95 </TABLE>
</DEFINITION>
<DEFINITION>
<FOR>bowel-problem</FOR>
<TABLE>0.01 0.99 </TABLE>
</DEFINITION>
<DEFINITION>
<FOR>dog-out</FOR>
<GIVEN>bowel-problem</GIVEN>
<GIVEN>family-out</GIVEN>
<TABLE>0.99 0.01 0.97 0.03 0.9 0.1 0.3 0.7 </TABLE>
</DEFINITION>
<DEFINITION>
<FOR>hear-bark</FOR>
<GIVEN>dog-out</GIVEN>
<TABLE>0.7 0.3 0.01 0.99 </TABLE>
</DEFINITION>
<DEFINITION>
<FOR>family-out</FOR>
<TABLE>0.15 0.85 </TABLE>
</DEFINITION>
</NETWORK>
</BIF>
""")
#!/usr/bin/env python
import sys
sys.path.insert(0, 'lib') # this line is necessary for the rest
import os # of the imports to work!
import web
import sqlitedb
from jinja2 import Environment, FileSystemLoader
import json
from pgmpy.models import BayesianModel
from pgmpy.inference import VariableElimination
from pgmpy.readwrite import XMLBIFReader
MODEL_FILE = 'bayes453.bif.xml'
model = XMLBIFReader(MODEL_FILE).get_model()
infer = VariableElimination(model)
baseline_result = {}
for node in model.nodes():
baseline_result[node] = infer.query([node])[node].values[1]
###########################################################################################
##########################DO NOT CHANGE ANYTHING ABOVE THIS LINE!##########################
###########################################################################################
######################BEGIN HELPER METHODS######################
# helper method to render a template in the templates/ directory
#
# `template_name': name of template file to render
#