def run_validation_spbn(train_data, folds, patience, result_folder, idx_fold):
hc = GreedyHillClimbing()
pool = OperatorPool([ArcOperatorSet(), ChangeNodeTypeSet()])
for k in folds:
vl = ValidatedLikelihood(train_data, k=k, seed=0)
for p in patience:
fold_folder = result_folder + '/HillClimbing/SPBN_CKDE/Validation_' + str(
k) + '_' + str(p) + '/' + str(idx_fold)
pathlib.Path(fold_folder).mkdir(parents=True, exist_ok=True)
if os.path.exists(fold_folder + '/end.lock'):
continue
cb_save = SaveModel(fold_folder)
node_types = [(name, NodeType.CKDE)
for name in train_data.columns.values]
start_model = SemiparametricBN(list(train_data.columns.values),
node_types)
bn = hc.estimate(pool,
vl,
start_model,
callback=cb_save,
patience=p,
verbose=True)
iters = sorted(glob.glob(fold_folder + '/*.pickle'))
last_file = os.path.basename(iters[-1])
number = int(os.path.splitext(last_file)[0])
bn.save(fold_folder + '/' + str(number + 1).zfill(6) + ".pickle")
with open(fold_folder + '/end.lock', 'w') as f:
pass
def find_node_types(df, dag, model_folder, type_of_dag_string, patience):
vl = ValidatedLikelihood(df, k=10, seed=experiments_helper.SEED)
hc = GreedyHillClimbing()
change_node_type = ChangeNodeTypeSet()
for p in patience:
result_folder = model_folder + '/PC/SPBN_CKDE/' + type_of_dag_string + '/' + str(
p)
pathlib.Path(result_folder).mkdir(parents=True, exist_ok=True)
if os.path.exists(result_folder + '/end.lock'):
continue
cb_save = SaveModel(result_folder)
node_types = [(name, NodeType.CKDE) for name in df.columns.values]
start_model = SemiparametricBN(dag, node_types)
bn = hc.estimate(change_node_type,
vl,
start_model,
callback=cb_save,
patience=p)
iters = sorted(glob.glob(result_folder + '/*.pickle'))
last_file = os.path.basename(iters[-1])
number = int(os.path.splitext(last_file)[0])
bn.save(result_folder + '/' + str(number + 1).zfill(6) + ".pickle")
with open(result_folder + '/end.lock', 'w') as f:
pass
def remove_crossvalidated_nan(dataset, folds):
to_delete = set()
# Outer for: Performance CV
for (idx_fold, (train_indices, test_indices)) in enumerate(
KFold(EVALUATION_FOLDS, shuffle=True,
random_state=SEED).split(dataset)):
train_data = dataset.iloc[train_indices, :]
# Inner for: Validation CV
for k in folds:
vl = ValidatedLikelihood(train_data, k=k, seed=SEED)
for (train_fold, _) in vl.cv_lik.cv:
train_fold_pandas = train_fold.to_pandas()
d = train_fold_pandas.columns[np.isclose(
train_fold_pandas.var(), 0)].tolist()
to_delete.update(d)
return to_delete
def run_pc_lc_spbn(train_data, folds, patience, result_folder, idx_fold):
hc = GreedyHillClimbing()
change_node_type = ChangeNodeTypeSet()
pdag = load(result_folder + '/PC/graph-lc-' + str(idx_fold) + ".pickle")
try:
dag = pdag.to_dag()
except ValueError:
dag = pdag.to_approximate_dag()
for k in folds:
vl = ValidatedLikelihood(train_data, k=k, seed=experiments_helper.SEED)
for p in patience:
fold_folder = result_folder + '/PC/SPBN_CKDE/LinearCorrelation/Validation_' + str(
k) + '_' + str(p) + '/' + str(idx_fold)
pathlib.Path(fold_folder).mkdir(parents=True, exist_ok=True)
if os.path.exists(fold_folder + '/end.lock'):
continue
cb_save = SaveModel(fold_folder)
node_types = [(name, NodeType.CKDE) for name in dag.nodes()]
start_model = SemiparametricBN(dag, node_types)
bn = hc.estimate(change_node_type,
vl,
start_model,
callback=cb_save,
patience=p,
verbose=True)
iters = sorted(glob.glob(fold_folder + '/*.pickle'))
last_file = os.path.basename(iters[-1])
number = int(os.path.splitext(last_file)[0])
bn.save(fold_folder + '/' + str(number + 1).zfill(6) + ".pickle")
with open(fold_folder + '/end.lock', 'w') as f:
pass
def run_validation_kdebn(train_data, folds, patience, result_folder, idx_fold):
hc = GreedyHillClimbing()
arc_set = ArcOperatorSet()
for k in folds:
vl = ValidatedLikelihood(train_data, k=k, seed=0)
for p in patience:
fold_folder = result_folder + '/HillClimbing/KDEBN/Validation_' + str(k) + '_' + str(p) + '/' + str(idx_fold)
pathlib.Path(fold_folder).mkdir(parents=True, exist_ok=True)
if os.path.exists(fold_folder + '/end.lock'):
continue
cb_save = SaveModel(fold_folder)
start_model = KDENetwork(list(train_data.columns.values))
bn = hc.estimate(arc_set, vl, start_model, callback=cb_save, patience=p, verbose=True)
iters = sorted(glob.glob(fold_folder + '/*.pickle'))
last_file = os.path.basename(iters[-1])
number = int(os.path.splitext(last_file)[0])
bn.save(fold_folder + '/' + str(number+1).zfill(6) + ".pickle")
with open(fold_folder + '/end.lock', 'w') as f:
pass
import time
patience = experiments_helper.PATIENCE
small_results = pd.DataFrame()
medium_results = pd.DataFrame()
large_results = pd.DataFrame()
for n in experiments_helper.INSTANCES:
df = pd.read_csv('data/small_' + str(n) + ".csv")
executions = np.empty((800, ))
for i in range(800):
if i % 10 == 0:
print(str(i) + " executions")
vl = ValidatedLikelihood(df, k=10, seed=i)
start_model = SemiparametricBN(list(df.columns.values))
hc = GreedyHillClimbing()
pool = OperatorPool([ArcOperatorSet(), ChangeNodeTypeSet()])
start = time.time()
bn = hc.estimate(pool, vl, start_model, patience=0)
end = time.time()
executions[i] = end - start
small_results['SPBN_' + str(n)] = pd.Series(executions,
name="SPBN_" + str(n))
print("Small " + str(n) + " -- Time: " + str(executions.mean()) +
", std: " + str(np.std(executions, ddof=1)))
from pybnesian.learning.algorithms import GreedyHillClimbing
from pybnesian.learning.algorithms.callbacks import SaveModel
from pybnesian.learning.operators import OperatorPool, ArcOperatorSet, ChangeNodeTypeSet
from pybnesian.learning.scores import ValidatedLikelihood
import pathlib
import os
import experiments_helper
hc = GreedyHillClimbing()
pool = OperatorPool([ArcOperatorSet(), ChangeNodeTypeSet()])
for d in experiments_helper.DATASETS:
for i in experiments_helper.INSTANCES:
df = pd.read_csv(d + "_" + str(i) + '.csv')
vl = ValidatedLikelihood(df, k=10, seed=experiments_helper.SEED)
for p in experiments_helper.PATIENCE:
result_folder = 'models/' + d + '/' + str(i) + '/HillClimbing/SPBN/' + str(p)
pathlib.Path(result_folder).mkdir(parents=True, exist_ok=True)
if not os.path.exists(result_folder + '/end.lock'):
cb_save = SaveModel(result_folder)
start_model = SemiparametricBN(list(df.columns.values))
bn = hc.estimate(pool, vl, start_model, callback=cb_save, patience=p)
iters = sorted(glob.glob(result_folder + '/*.pickle'))
last_file = os.path.basename(iters[-1])
number = int(os.path.splitext(last_file)[0])
bn.save(result_folder + '/' + str(number+1).zfill(6) + ".pickle")
import pandas as pd
from pybnesian import load
from pybnesian.factors import NodeType
from pybnesian.learning.scores import ValidatedLikelihood
from pybnesian.models import SemiparametricBN
import glob
df_10000 = pd.read_csv('synthetic_10000.csv')
df_test = pd.read_csv('synthetic_test.csv')
models = sorted(glob.glob('models/10000/HillClimbing/SPBN_CKDE/0/*.pickle'))
vl = ValidatedLikelihood(df_10000, k=10, seed=0)
node_types = [(name, NodeType.CKDE) for name in df_10000.columns.values]
start_model = SemiparametricBN(list(df_10000.columns.values), node_types)
print("Start model")
print("\tTraining score: " + str(vl.score(start_model)))
print("\tValidation score: " + str(vl.vscore(start_model)))
start_model.fit(df_10000)
print("\tTest score: " + str(start_model.slogl(df_test)))
for m in models:
bn = load(m)
print("Model " + m)
print("\tTraining score: " + str(vl.score(bn)))
print("\tValidation score: " + str(vl.vscore(bn)))
bn.fit(df_10000)
axis_width="20.5cm",
axis_height="5cm")
plt.figure()
good = pd.concat(
[atrium11.iloc[labels0_11, :], atrium12.iloc[labels0_12, :]])
mid = pd.concat(
[atrium11.iloc[labels1_11, :], atrium12.iloc[labels1_12, :]])
poor = pd.concat(
[atrium11.iloc[labels2_11, :], atrium12.iloc[labels2_12, :]])
hc = GreedyHillClimbing()
pool = OperatorPool([ArcOperatorSet(), ChangeNodeTypeSet()])
start_model = SemiparametricBN(list(good.columns.values))
vl = ValidatedLikelihood(good, k=10)
good_model = hc.estimate(pool, vl, start_model)
good_model.fit(good)
hc = GreedyHillClimbing()
pool = OperatorPool([ArcOperatorSet(), ChangeNodeTypeSet()])
start_model = SemiparametricBN(list(mid.columns.values))
vl = ValidatedLikelihood(mid, k=10)
mid_model = hc.estimate(pool, vl, start_model)
mid_model.fit(mid)
hc = GreedyHillClimbing()
pool = OperatorPool([ArcOperatorSet(), ChangeNodeTypeSet()])
start_model = SemiparametricBN(list(poor.columns.values))
vl = ValidatedLikelihood(poor, k=10)
poor_model = hc.estimate(pool, vl, start_model)
def test_pc_time(df, n_exec):
local_results = pd.DataFrame()
pc = PC()
lc = LinearCorrelation(df)
executions = np.empty((n_exec,))
for i in range(n_exec):
start = time.time()
graph_lc = pc.estimate(lc)
end = time.time()
executions[i] = end - start
local_results['PC-LC-Graph'] = pd.Series(executions, name="PC-LC-Graph")
print("LC Graph Time: " + str(executions.mean()))
try:
dag = graph_lc.to_dag()
except ValueError:
dag = graph_lc.to_approximate_dag()
executions = np.empty((n_exec,))
for i in range(n_exec):
hc = GreedyHillClimbing()
change_node_type = ChangeNodeTypeSet()
vl = ValidatedLikelihood(df, k=10, seed=experiments_helper.SEED)
start_model = SemiparametricBN(dag)
start = time.time()
bn = hc.estimate(change_node_type, vl, start_model, patience=0)
end = time.time()
executions[i] = end - start
local_results['PC-LC-NodeType'] = pd.Series(executions, name="PC-LC-NodeType")
print("LC HC NodeType Time: " + str(executions.mean()))
rcot = RCoT(df)
for i in range(n_exec):
start = time.time()
graph_rcot = pc.estimate(rcot)
end = time.time()
executions[i] = end - start
local_results['PC-RCoT-Graph'] = pd.Series(executions, name="PC-RCoT-Graph")
print("RCoT Graph Time: " + str(executions.mean()))
for i in range(n_exec):
hc = GreedyHillClimbing()
change_node_type = ChangeNodeTypeSet()
vl = ValidatedLikelihood(df, k=10, seed=experiments_helper.SEED)
try:
dag = graph_rcot.to_dag()
except ValueError:
dag = graph_rcot.to_approximate_dag()
start_model = SemiparametricBN(dag)
start = time.time()
bn = hc.estimate(change_node_type, vl, start_model, patience=0)
end = time.time()
executions[i] = end - start
local_results['PC-RCoT-NodeType'] = pd.Series(executions, name="PC-RCoT-NodeType")
print("RCoT HC NodeType Time: " + str(executions.mean()))
return local_results