def __init__(self):
self.samples = np.array( [[0.82, 0.56, 0.08, 0.81],[0.34, 0.22, 0.37, 0.99],
[0.55, 0.61, 0.31, 0.66], [0.28, 1.00, 0.95, 0.71],
[0.14, 0.10, 1.00, 0.71], [0.10, 0.60, 0.64, 0.73],
[0.39, 0.03, 0.99, 1.00], [0.97, 0.54, 0.80, 0.97],
[0.07, 0.69, 0.43, 0.29], [0.61, 0.03, 0.13, 0.14],
[0.13, 0.40, 0.94, 0.19], [0.60, 0.68, 0.36, 0.67],
[0.12, 0.38, 0.42, 0.81], [0.00, 0.20, 0.85, 0.01],
[0.55, 0.30, 0.30, 0.11], [0.83, 0.96, 0.41, 0.65],
[0.29, 0.40, 0.54, 0.23], [0.74, 0.65, 0.38, 0.41],
[0.82, 0.08, 0.39, 0.97], [0.95, 0.01, 0.62, 0.32],
[0.56, 0.68, 0.32, 0.27], [0.77, 0.74, 0.79, 0.11],
[0.29, 0.69, 0.99, 0.79], [0.21, 0.20, 0.43, 0.81],
[0.90, 0.00, 0.91, 0.01]]);
# check self.samples is stored correctly
for i in self.samples:
printV(["given self.samples: ", i],0);
# Im not sure if this is how im supposed to use the given self.samples
# There are 4 nodes and 100 self.samples so there will be 25 complete iterations
self.cpt = {"cloudy":[0.5],"sprinkler":[0.1,0.5],"rain":[0.8,0.2],"wet":[0.99,0.90,0.90,0.00]}
self.dict_array = [];
# set the dictionary for each complete iteration and append
# to dict_array
for sample_temp in self.samples:
self.set_sample_dict(sample_temp)
self.dict_array = np.array(self.dict_array);
for i in range(0,25):
printV([i,": ",self.dict_array[i]],1);
def check_mark(self, check, mark):
printV(["check", check], 1)
printV(["mark", mark], 1)
if check <= mark:
return True
else:
return False
def setPrior(self,key,value):
if (key == 'P')is True:
self.marginal['p'] = value;
self.prior['p'] = value;
return ['p',self.marginal['p']];
elif(key == 'S')is True:
self.marginal['s'] = value;
self.prior['s'] = value;
return ['s',value];
else:
printV("ERROR: cant set prior to given key");
def prior_marginal_prob(self,key):
# calculate the number of entries where key is true
# divide by numnber of complete iterations (25)
true_count = 0;
false_count = 0;
for i in range(0,25):
if (self.dict_array[i][key])is True:
true_count = true_count + 1;
else:
false_count = false_count + 1;
printV(true_count,1);
printV(false_count,1);
return np.array([float(true_count)/25,float(false_count)/25]);
def main():
ps = prior_sampling();
# ready to start computing prob
printV("Problem 1: Prior sampling",2);
cloudy_marg = ps.prior_marginal_prob("cloudy");
printV(["a. P(c = True): ",cloudy_marg[0]],2);
cond_returned = ps.prior_conditional_prob({'cloudy':True,},[{'rain':True}]);
printV(["b. P(c = True | rain = True): ",cond_returned[0]],2);
cond_returned = ps.prior_conditional_prob({'sprinkler':True,},[{'wet':True}]);
printV(["c. P(s = True | w = True): ",cond_returned[0]],2);
cond_returned = ps.prior_conditional_prob({'sprinkler':True,},[{'cloudy':True},{'wet':True}]);
printV(["d. P(s = True | c = True, w = True): ",cond_returned[0]],2);
def calcJoint(self,key_list):
arg_list=self.get_arg_list(key_list);
printV(["arg_list: ",arg_list],1);
joint = 1;
for arg in arg_list:
printV(["arg: ",arg[0]],1);
if('~' is not arg[0]):
self.calcMarginal(arg[0]);
joint = joint * self.marginal[arg[0]];
else:
# case when there is ~
self.calcMarginal(arg[1]);
joint = joint * (1-self.marginal[arg[1]]);
return joint;
def add_temp_sample(self, sample, given_dict, name, cpt_val):
printV(["sample: ", sample, "given_dict: ", given_dict], 1)
printV(["self.cpt[name][cpt_val]", self.cpt[name][cpt_val]], 1)
name_val = self.check_mark(sample, self.cpt[name][cpt_val])
if (name in given_dict) is True:
# cloudy is in given
if (given_dict[name] == name_val) is True:
# no contradition
return name_val
else:
# cloudy is given and sample contradicts
return None
else:
# cloudy is not in given
return name_val
def isCausal(self,key,E_list):
E_list=self.get_arg_list(E_list);
r_val = 1;
# recursive check
for ch_key in self.children[key]:
self.isCausal(ch_key,self.children[ch_key]);
for E in E_list:
if '~' is not E[0]:
for ch_key in self.children[key]:
if E[0] is ch_key:
printV(["found evidence",E[0],"is not a parent of",key],1);
r_val=0;
else:
for ch_key in self.children[key]:
if E[1] is ch_key:
printV(["found evidence",E[1],"is not a parent of",key],1);
r_val=0;
return r_val;
def calcProb_given_E(self,key):
if (key == 'p')is True or (key == 's')is True:
return self.prior[key];
# update_pi with no evidence is same as marginal
parent = self.parents[key];
key_cpt = self.cpt[key];
printV(["inside calcMarginal key: ",key],1);
printV(["key_cpt:",key_cpt[0]],1);
for index_parent in parent:
self.calcProb_given_E(index_parent);
# FIXME: matt
# change this to work for any node with two parents
# p --> pollution = low
# given p, prior(p)--> 1
# if prior[parent]_0 (pollution) = 0 then pollution = h
if (key == 'c')is True:
self.prior[key] = (
(1-self.prior[parent[0]]) *
(self.prior[parent[1]]) *
(key_cpt[0]) +
(1-self.prior[parent[0]]) *
(1-self.prior[parent[1]]) *
(key_cpt[1]) +
(self.prior[parent[0]]) *
(self.prior[parent[1]]) *
(key_cpt[2]) +
(self.prior[parent[0]]) *
(1-self.prior[parent[1]]) *
(key_cpt[3])
);
printV(self.prior[key],1);
return self.prior[key];
else :
self.prior[key] = (
(self.prior[parent[0]]) *
(key_cpt[0]) +
(1-self.prior[parent[0]]) *
(key_cpt[1])
);
printV(self.prior[key],1);
return self.prior[key];
def calcMarginal(self,key):
if (key == 'p')is True or (key == 's')is True:
return self.marginal[key];
# update_pi with no evidence is same as marginal
parent = self.parents[key];
key_cpt = self.cpt[key];
printV(["inside calcMarginal key: ",key],1);
printV(["key_cpt:",key_cpt[0]],1);
# recursinve call update_pi for parents
for index_parent in parent:
self.calcMarginal(index_parent);
# FIXME: matt
# change this to work for any node with two parents
if (key == 'c')is True:
self.marginal[key] = (
(1-self.marginal[parent[0]]) *
(self.marginal[parent[1]]) *
(key_cpt[0]) +
(1-self.marginal[parent[0]]) *
(1-self.marginal[parent[1]]) *
(key_cpt[1]) +
(self.marginal[parent[0]]) *
(self.marginal[parent[1]]) *
(key_cpt[2]) +
(self.marginal[parent[0]]) *
(1-self.marginal[parent[1]]) *
(key_cpt[3])
);
printV(self.marginal[key],1);
return self.marginal[key];
else :
self.marginal[key] = (
(self.marginal[parent[0]]) *
(key_cpt[0]) +
(1-self.marginal[parent[0]]) *
(key_cpt[1])
);
printV(self.marginal[key],1);
return self.marginal[key];
def make_valid_array(self, given_dict):
return_val = 1
while return_val:
printV("********************************************", 1)
return_val = self.set_sample_dict(given_dict)
printV(self.valid_array, 1)
for i in range(len(self.valid_array)):
printV([i, ": ", self.valid_array[i]], 1)
def main():
rs = rejection_sampling()
printV("Problem 2: Rejection sampling", 2)
return_val = rs.rejection_prob("cloudy", {})
printV(["a. P(c = True): ", return_val[0]], 2)
rs.sample_cnt = 0
rs.valid_array = []
return_val = rs.rejection_prob("cloudy", {"rain": True})
printV(["b. P(c = True | rain = True): ", return_val[0]], 2)
rs.sample_cnt = 0
rs.valid_array = []
return_val = rs.rejection_prob("sprinkler", {"wet": True})
printV(["c. P(s = True | wet = True): ", return_val[0]], 2)
rs.sample_cnt = 0
rs.valid_array = []
return_val = rs.rejection_prob("sprinkler", {"wet": True, "cloudy": True})
printV(["d. P(s = True | wet = True, cloudy = True): ", return_val[0]], 2)
rs.sample_cnt = 0
rs.valid_array = []
def set_sample_dict(self,sample_array):
temp_dict = {};
#check cloudy
if (self.check_mark(sample_array[0],self.cpt['cloudy'][0]))is True:
printV("it is cloudy",1);
# set the cloudy value in
temp_dict['cloudy'] = True;
else:
printV("it is not cloudy",1);
# set the cloudy value in
temp_dict['cloudy'] = False;
# check sprinkler
if (temp_dict['cloudy']) is True:
# cloudy is true so look at sprinkler[0]
if (self.check_mark(sample_array[1],self.cpt['sprinkler'][0]))is True:
printV("cloudy is true and sprinkler is true",1);
temp_dict['sprinkler'] = True;
else:
printV("cloudy is true and sprinkler is false",1);
temp_dict['sprinkler'] = False;
else:
# cloudy is false so look at sprinkler[1]
if (self.check_mark(sample_array[1],self.cpt['sprinkler'][1]))is True:
printV("cloudy is false and sprinkler is true",1);
temp_dict['sprinkler'] = True;
else:
printV("cloudy is false and sprinkler is false",1);
temp_dict['sprinkler'] = False;
# check rain
if (temp_dict['cloudy']) is True:
# cloudy is true so look at rain[0]
if (self.check_mark(sample_array[2],self.cpt['rain'][0]))is True:
printV("cloudy is true and rain is true",1);
temp_dict['rain'] = True;
else:
printV("cloudy is true and rain is false",1);
temp_dict['rain'] = False;
else:
# cloudy is false so look at rain[1]
if (self.check_mark(sample_array[2],self.cpt['rain'][1]))is True:
printV("cloudy is false and rain is true",1);
temp_dict['rain'] = True;
else:
printV("cloudy is false and rain is false",1);
temp_dict['rain'] = False;
#check wet grass
if ((temp_dict['sprinkler'])is True and (temp_dict['rain'])is True):
printV("true true",1);
# use wet[0]
if (self.check_mark(sample_array[3],self.cpt['wet'][0]))is True:
printV("cloudy is false and wet is true",1);
temp_dict['wet'] = True;
else:
printV("cloudy is false and wet is false",1);
temp_dict['wet'] = False;
elif ((temp_dict['sprinkler'])is True and (temp_dict['rain'])is False):
printV("true false",1);
# use wet[1]
if (self.check_mark(sample_array[3],self.cpt['wet'][1]))is True:
printV("cloudy is false and wet is true",1);
temp_dict['wet'] = True;
else:
printV("cloudy is false and wet is false",1);
temp_dict['wet'] = False;
elif ((temp_dict['sprinkler'])is False and (temp_dict['rain'])is True):
printV("false true",1);
# use wet[2]
if (self.check_mark(sample_array[3],self.cpt['wet'][2]))is True:
printV("cloudy is false and wet is true",1);
temp_dict['wet'] = True;
else:
printV("cloudy is false and wet is false",1);
temp_dict['wet'] = False;
elif ((temp_dict['sprinkler'])is False and (temp_dict['rain'])is False):
printV("false false",1);
# use wet[3]
if (self.check_mark(sample_array[3],self.cpt['wet'][3]))is True:
printV("cloudy is false and wet is true",1);
temp_dict['wet'] = True;
else:
printV("cloudy is false and wet is false",1);
temp_dict['wet'] = False;
self.dict_array.append(temp_dict);
def check_mark(self,check,mark):
printV(["check",check],1);
printV(["mark",mark],1);
if (check <= mark):
return True;
else: return False;
def set_sample_dict(self, given_dict):
# This is where you will call each node
# Each node will return true to keep going
# will return false to start a new iteration
temp_dict = {}
# cloudy
if (self.sample_cnt < len(self.samples)) is True:
cloudy_sample = self.get_sample()
printV(["cloudy sample: ", cloudy_sample], 1)
cloudy_ret = self.add_temp_sample(cloudy_sample, given_dict, "cloudy", 0)
# if false start a new iteration
if (cloudy_ret == None) is True:
return True
else:
temp_dict["cloudy"] = cloudy_ret
else:
return False
printV(["temp_dict after cloudy check", temp_dict], 1)
# sprinkler
# set cpt_val for sprinkler based on cloudy_val
if (temp_dict["cloudy"] == False) is True:
cpt_s = 1
else:
cpt_s = 0
if (self.sample_cnt < len(self.samples)) is True:
sprinkler_sample = self.get_sample()
printV(["sprinkler sample: ", sprinkler_sample], 1)
sprinkler_ret = self.add_temp_sample(sprinkler_sample, given_dict, "sprinkler", cpt_s)
# if false start a new iteration
if (sprinkler_ret == None) is True:
return True
else:
temp_dict["sprinkler"] = sprinkler_ret
else:
return False
printV(["temp_dict after sprinkler check", temp_dict], 1)
# rain
# set cpt_val for rain based on cloudy_val
if (self.sample_cnt < len(self.samples)) is True:
rain_sample = self.get_sample()
printV(["rain sample: ", rain_sample], 1)
rain_ret = self.add_temp_sample(rain_sample, given_dict, "rain", cpt_s)
# if false start a new iteration
if (rain_ret == None) is True:
return True
else:
temp_dict["rain"] = rain_ret
else:
return False
printV(["temp_dict after rain check", temp_dict], 1)
# wet
# set cpt_val for wet based on sprinkler_val and rain_val
if (temp_dict["sprinkler"] == True) is True and (temp_dict["rain"] == True) is True:
cpt_w = 0
elif (temp_dict["sprinkler"] == True) is True and (temp_dict["rain"] == False) is True:
cpt_w = 1
elif (temp_dict["sprinkler"] == False) is True and (temp_dict["rain"] == True) is True:
cpt_w = 2
elif (temp_dict["sprinkler"] == False) is True and (temp_dict["rain"] == False) is True:
cpt_w = 3
printV(["cpt_w value:", cpt_w], 1)
if (self.sample_cnt < len(self.samples)) is True:
wet_sample = self.get_sample()
printV(["wet sample: ", wet_sample], 1)
wet_ret = self.add_temp_sample(wet_sample, given_dict, "wet", cpt_w)
# if false start a new iteration
if (wet_ret == None) is True:
return True
else:
temp_dict["wet"] = wet_ret
else:
return False
printV(["temp_dict after wet check", temp_dict], 1)
printV("----- Iteration satisfies all given values -----", 1)
self.valid_array.append(temp_dict)
return True
def prior_conditional_prob(self,find_val,given_list):
printV(["find value",find_val],1);
printV(["given list",given_list],1);
# need to calculate the total number of eqations that satisfy the
# given list
cond_array = [];
[(find_key,find_value)] = find_val.items();
printV(["find_key: ",find_key," find_value: ",find_value],1);
# valid array is the array of currently valid complete samples
valid_array = self.dict_array;
# find all complete samples which satisfy all of the givens
for given_temp in given_list:
given_sample_number = 0;
[(given_key, given_value)] = given_temp.items();
# temp_array stores complete samples from valid array that
# satisfy the new given
temp_array = [];
printV(["given_key: ",given_key," given_value: ",given_value],1);
for i in range(len(valid_array)):
if (valid_array[i][given_key] == given_value)is True:
given_sample_number = given_sample_number + 1;
temp_array.append(valid_array[i]);
valid_array = temp_array;
cond_array = np.array(valid_array);
printV(["given_sample_number: ",given_sample_number],1);
for i in range(0,given_sample_number):
printV([i," :",cond_array[i]],1);
# calculate the number of equations where find_value is <true,false> from within the
# above list and divide by the total number of eq in the above list
find_value_cnt = 0;
not_find_value_cnt = 0;
for i in range(0,given_sample_number):
if (cond_array[i][find_key] == find_value)is True:
find_value_cnt = find_value_cnt + 1;
else:
not_find_value_cnt = not_find_value_cnt +1;
return np.array([float(find_value_cnt)/given_sample_number,
float(not_find_value_cnt)/given_sample_number]);
def __init__(self):
self.samples = np.array(
[
0.82,
0.56,
0.08,
0.81,
0.34,
0.22,
0.37,
0.99,
0.55,
0.61,
0.31,
0.66,
0.28,
1.00,
0.95,
0.71,
0.14,
0.10,
1.00,
0.71,
0.10,
0.60,
0.64,
0.73,
0.39,
0.03,
0.99,
1.00,
0.97,
0.54,
0.80,
0.97,
0.07,
0.69,
0.43,
0.29,
0.61,
0.03,
0.13,
0.14,
0.13,
0.40,
0.94,
0.19,
0.60,
0.68,
0.36,
0.67,
0.12,
0.38,
0.42,
0.81,
0.00,
0.20,
0.85,
0.01,
0.55,
0.30,
0.30,
0.11,
0.83,
0.96,
0.41,
0.65,
0.29,
0.40,
0.54,
0.23,
0.74,
0.65,
0.38,
0.41,
0.82,
0.08,
0.39,
0.97,
0.95,
0.01,
0.62,
0.32,
0.56,
0.68,
0.32,
0.27,
0.77,
0.74,
0.79,
0.11,
0.29,
0.69,
0.99,
0.79,
0.21,
0.20,
0.43,
0.81,
0.90,
0.00,
0.91,
0.01,
]
)
printV(["samples: ", self.samples], 1)
self.cpt = {"cloudy": [0.5], "sprinkler": [0.1, 0.5], "rain": [0.8, 0.2], "wet": [0.99, 0.90, 0.90, 0.00]}
self.valid_array = []
self.sample_cnt = 0
def calcConditional(self,key,E_list):
E_list=self.get_arg_list(E_list);
printV("in calcConditional",1);
printV(["key: ",key," evidence: ",E_list],1);
#compute marginal for key and all E nodes
self.calcMarginal(key);
self.marg_E(E_list);
#check if the evidence is causal
if (self.isCausal(key,E_list) == 1):
printV("the evidence is purely causal",1);
# set priors according to evidence
self.prior_given_E(E_list);
return_val = self.calcProb_given_E(key)
printV(["probability of", key,"given",E_list,"is:",return_val],2);
return return_val;
#check if the evidence is diagnostic
if (self.isDiagnostic(key,E_list) == 1):
printV("the evidence is purely diagnostic",1);
# use bayes to calculate by finding causal conditionals and marginals
# only works for 1 evidence
for E in E_list:
if '~' is not E[0]:
cond_flip = self.calcConditional(E[0],key);
return_val= ((cond_flip * self.marginal[key])/self.marginal[E[0]]);
printV(["probability of", key,"given",E_list,"is:",return_val],2);
return return_val;
else:
cond_flip = (1 - self.calcConditional(E[1],key));
return_val ((cond_flip * self.marginal[key])/self.marginal[E[1]]);
printV(["probability of", key,"given",E_list,"is:",return_val],2);
return return_val;
def main():
BN = BN_dict();
# set parents and children
#printV(BN.pollution_dict['prob_dist'],1);
#printV(BN.smoker_dict['prob_dist'],1);
#printV(BN.cancer_dict['prob_dist'],1);
#printV(BN.x_dict['prob_dist'],1);
#printV(BN.d_dict['prob_dist'],1);
## next organize possible inputs
try:
opts, args = getopt.getopt(sys.argv[1:], "m:g:j:p:")
except getopt.GetoptError as err:
# print help information and exit:
print str(err) # will print something like "option -a not recognized"
sys.exit(2)
for o, a in opts:
if o in ("-p"):
printV(["flag", o],1);
printV(["args", a],1);
printV(a[0],1);
printV(float(a[1:]),1);
printV("command to set prior",1);
#setting the prior here works if the Bayes net is already built
prior_out=BN.setPrior(a[0], float(a[1:]));
printV(["prior for ",prior_out[0],"is now",prior_out[1]],2);
elif o in ("-m"):
printV(["flag", o],1);
printV(["args", a],1);
printV(type(a),1);
printV("command to compute marginal prob",1);
# FIXME: matt
# calculate marginal for a
a_list=BN.get_arg_list(a);
printV(["marginal list",a_list],2);
for a_index in a_list:
if ('~' is not a_index[0]):
printV(['Marginal of',a, "is: ",BN.calcMarginal(a[0])],2);
else:
printV(['Marginal of',a, "is: ",(1-BN.calcMarginal(a[1]))],2);
elif o in ("-g"):
printV(["flag", o],1);
printV(["args", a],1);
printV(type(a),1);
printV("command to compute conditional prob",1);
'''you may want to parse a here and pass the left of |
and right of | as arguments to calcConditional
'''
p = a.find("|")
printV(a[:p],1);
printV(a[p+1:],1);
BN.calcConditional(a[:p], a[p+1:]);
elif o in ("-j"):
printV(["flag", o],1);
printV(["args", a],1);
printV("command to compute joint prob",1)
printV(["J= ",BN.calcJoint(a)],2);
else:
assert False, "unhandled option"