def test_convert_restrictions(self):
# This is a smoke test to make sure that the int/float values in the
# greater or smaller statements are converted to the right type when
# reading them
s = """x1 real [0,1] [0]
x2 real [0,1] [0]
x3 real [0,1] [0]
x4 integer [0,2] [0]
x5 real [0,1] [0]
x6 ordinal {cold, luke-warm, hot} [cold]
x1 | x2 > 0.5
x3 | x4 > 1 && x4 == 2 && x4 in {2}
x5 | x6 > luke-warm"""
pcs_new.read(s.split('\n'))
def test_convert_restrictions(self):
# This is a smoke test to make sure that the int/float values in the
# greater or smaller statements are converted to the right type when
# reading them
s = """x1 real [0,1] [0]
x2 real [0,1] [0]
x3 real [0,1] [0]
x4 integer [0,2] [0]
x5 real [0,1] [0]
x6 ordinal {cold, luke-warm, hot} [cold]
x1 | x2 > 0.5
x3 | x4 > 1 && x4 == 2 && x4 in {2}
x5 | x6 > luke-warm"""
pcs_new.read(s.split('\n'))
def run_test(self):
try:
with open(configuration_space_path) as fh:
cs = pcs_parser.read(fh)
except:
with open(configuration_space_path) as fh:
cs = pcs_new_parser.read(fh)
default = cs.get_default_configuration()
cs._check_configuration_rigorous(default)
for i in range(10):
neighborhood = ConfigSpace.util.get_one_exchange_neighbourhood(
default, seed=i)
for shuffle, n in enumerate(neighborhood):
n.is_valid_configuration()
cs._check_configuration_rigorous(n)
if shuffle == 10:
break
# Sample a little bit
for i in range(10):
cs.seed(i)
configurations = cs.sample_configuration(size=5)
for j, c in enumerate(configurations):
c.is_valid_configuration()
cs._check_configuration_rigorous(c)
neighborhood = ConfigSpace.util.get_one_exchange_neighbourhood(
c, seed=i)
for shuffle, n in enumerate(neighborhood):
n.is_valid_configuration()
cs._check_configuration_rigorous(n)
if shuffle == 20:
break
def run_test(self):
if 'ordinal' in configuration_space_path:
return
try:
with open(configuration_space_path) as fh:
cs = pcs_parser.read(fh)
except:
with open(configuration_space_path) as fh:
cs = pcs_new_parser.read(fh)
# Sample a little bit
for i in range(10):
print(i)
cs.seed(i)
configurations = cs.sample_configuration(size=5)
for j, c in enumerate(configurations):
print(j)
c.is_valid_configuration()
neighborhood = ConfigSpace.util.get_one_exchange_neighbourhood(
c, seed=i)
for shuffle, n in enumerate(neighborhood):
n.is_valid_configuration()
if shuffle == 10:
break
def test_read_new_configuration_space_complex_conditionals(self):
classi = OrdinalHyperparameter("classi", ["random_forest","extra_trees","k_nearest_neighbors","something"])
knn_weights = CategoricalHyperparameter("knn_weights", ["uniform", "distance"])
weather = OrdinalHyperparameter("weather",["sunny", "rainy", "cloudy", "snowing"])
temperature = CategoricalHyperparameter("temperature", ["high", "low"])
rain = CategoricalHyperparameter("rain", ["yes", "no"])
gloves = OrdinalHyperparameter("gloves",["none", "yarn", "leather", "gortex"])
heur1 = CategoricalHyperparameter("heur1", ["off", "on"])
heur2 = CategoricalHyperparameter("heur2", ["off", "on"])
heur_order = CategoricalHyperparameter("heur_order", ["heur1then2", "heur2then1"])
gloves_condition = OrConjunction(EqualsCondition(gloves, rain, "yes"),
EqualsCondition(gloves, temperature, "low"))
heur_condition = AndConjunction(EqualsCondition(heur_order, heur1, "on"),
EqualsCondition(heur_order, heur2, "on"))
and_conjunction = AndConjunction(NotEqualsCondition(knn_weights, classi, "extra_trees"),
EqualsCondition(knn_weights, classi, "random_forest"))
Cl_condition = OrConjunction(EqualsCondition(knn_weights, classi, "k_nearest_neighbors"),
and_conjunction,
EqualsCondition(knn_weights, classi, "something"))
and1 = AndConjunction(EqualsCondition(temperature, weather, "rainy"),
EqualsCondition(temperature, weather, "cloudy"))
and2 = AndConjunction(EqualsCondition(temperature, weather, "sunny"),
NotEqualsCondition(temperature, weather, "snowing"))
another_condition = OrConjunction(and1,and2)
complex_conditional_space = ConfigurationSpace()
complex_conditional_space.add_hyperparameter(classi)
complex_conditional_space.add_hyperparameter(knn_weights)
complex_conditional_space.add_hyperparameter(weather)
complex_conditional_space.add_hyperparameter(temperature)
complex_conditional_space.add_hyperparameter(rain)
complex_conditional_space.add_hyperparameter(gloves)
complex_conditional_space.add_hyperparameter(heur1)
complex_conditional_space.add_hyperparameter(heur2)
complex_conditional_space.add_hyperparameter(heur_order)
complex_conditional_space.add_condition(gloves_condition)
complex_conditional_space.add_condition(heur_condition)
complex_conditional_space.add_condition(Cl_condition)
complex_conditional_space.add_condition(another_condition)
complex_cs = list()
complex_cs.append("classi ordinal {random_forest,extra_trees,k_nearest_neighbors, something} [random_forest]")
complex_cs.append("knn_weights categorical {uniform, distance} [uniform]")
complex_cs.append("weather ordinal {sunny, rainy, cloudy, snowing} [sunny]")
complex_cs.append("temperature categorical {high, low} [high]")
complex_cs.append("rain categorical { yes, no } [yes]")
complex_cs.append("gloves ordinal { none, yarn, leather, gortex } [none]")
complex_cs.append("heur1 categorical { off, on } [off]")
complex_cs.append("heur2 categorical { off, on } [off]")
complex_cs.append("heur_order categorical { heur1then2, heur2then1 } [heur1then2]")
complex_cs.append("gloves | rain == yes || temperature == low")
complex_cs.append("heur_order | heur1 == on && heur2 == on")
complex_cs.append("knn_weights | classi == k_nearest_neighbors || classi != extra_trees && classi == random_forest || classi == something")
complex_cs.append("temperature | weather == rainy && weather == cloudy || weather == sunny && weather != snowing")
cs_new = pcs_new.read(complex_cs)
self.assertEqual(cs_new, complex_conditional_space)
def test_write_restrictions(self):
s = "c integer [0, 2] [0]\n" + \
"d ordinal {cold, luke-warm, hot} [cold]\n" + \
"e real [0.0, 1.0] [0.0]\n" + \
"b real [0.0, 1.0] [0.0]\n" + \
"a real [0.0, 1.0] [0.0]\n" + \
"\n" + \
"b | d in {luke-warm, hot} || c > 1\n" + \
"a | b == 0.5 && e > 0.5"
a = pcs_new.read(s.split('\n'))
out = pcs_new.write(a)
self.assertEqual(out, s)
def test_read_new_configuration_space_easy(self):
expected = StringIO()
expected.write('# This is a \n')
expected.write(' # This is a comment with a leading whitespace ### ffds \n')
expected.write('\n')
expected.write('float_a real [-1.23, 6.45] [2.61] # bla\n')
expected.write('e_float_a real [.5E-2, 4.5e+06] [2250000.0025]\n')
expected.write('int_a integer [-1, 6] [2]\n')
expected.write('log_a real [4e-1, 6.45] [1.6062378404]log\n')
expected.write('int_log_a integer [1, 6] [2]log\n')
expected.write('cat_a categorical {a,"b",c,d} [a]\n')
expected.write('@.:;/\?!$%&_-<>*+1234567890 categorical {"const"} ["const"]\n')
expected.seek(0)
cs = pcs_new.read(expected)
self.assertEqual(cs, easy_space)
def test_read_new_configuration_space_easy(self):
expected = StringIO()
expected.write('# This is a \n')
expected.write(
' # This is a comment with a leading whitespace ### ffds \n')
expected.write('\n')
expected.write('float_a real [-1.23, 6.45] [2.61] # bla\n')
expected.write('e_float_a real [.5E-2, 4.5e+06] [2250000.0025]\n')
expected.write('int_a integer [-1, 6] [2]\n')
expected.write('log_a real [4e-1, 6.45] [1.6062378404]log\n')
expected.write('int_log_a integer [1, 6] [2]log\n')
expected.write('cat_a categorical {a,"b",c,d} [a]\n')
expected.write(
'@.:;/\?!$%&_-<>*+1234567890 categorical {"const"} ["const"]\n')
expected.seek(0)
cs = pcs_new.read(expected)
self.assertEqual(cs, easy_space)
def test_read_new_configuration_space_conditional(self):
# More complex search space as string array
complex_cs = list()
complex_cs.append("preprocessing categorical {None, pca} [None]")
complex_cs.append("classifier categorical {svm, nn} [svm]")
complex_cs.append("kernel categorical {rbf, poly, sigmoid} [rbf]")
complex_cs.append("C real [0.03125, 32768] [32]log")
complex_cs.append("neurons integer [16, 1024] [520] # Should be Q16")
complex_cs.append("lr real [0.0001, 1.0] [0.50005]")
complex_cs.append("degree integer [1, 5] [3]")
complex_cs.append("gamma real [0.000030518, 8] [0.0156251079996]log")
complex_cs.append("C | classifier in {svm}")
complex_cs.append("kernel | classifier in {svm}")
complex_cs.append("lr | classifier in {nn}")
complex_cs.append("neurons | classifier in {nn}")
complex_cs.append("degree | kernel in {poly, sigmoid}")
complex_cs.append("gamma | kernel in {rbf}")
cs_new = pcs_new.read(complex_cs)
self.assertEqual(cs_new, conditional_space)
# same in older version
complex_cs_old = list()
complex_cs_old.append("preprocessing {None, pca} [None]")
complex_cs_old.append("classifier {svm, nn} [svm]")
complex_cs_old.append("kernel {rbf, poly, sigmoid} [rbf]")
complex_cs_old.append("C [0.03125, 32768] [32]l")
complex_cs_old.append("neurons [16, 1024] [520]i # Should be Q16")
complex_cs_old.append("lr [0.0001, 1.0] [0.50005]")
complex_cs_old.append("degree [1, 5] [3]i")
complex_cs_old.append("gamma [0.000030518, 8] [0.0156251079996]l")
complex_cs_old.append("C | classifier in {svm}")
complex_cs_old.append("kernel | classifier in {svm}")
complex_cs_old.append("lr | classifier in {nn}")
complex_cs_old.append("neurons | classifier in {nn}")
complex_cs_old.append("degree | kernel in {poly, sigmoid}")
complex_cs_old.append("gamma | kernel in {rbf}")
cs_old = pcs.read(complex_cs_old)
self.assertEqual(cs_old, cs_new)
def test_read_new_configuration_space_conditional(self):
# More complex search space as string array
complex_cs = list()
complex_cs.append("preprocessing categorical {None, pca} [None]")
complex_cs.append("classifier categorical {svm, nn} [svm]")
complex_cs.append("kernel categorical {rbf, poly, sigmoid} [rbf]")
complex_cs.append("C real [0.03125, 32768] [32]log")
complex_cs.append("neurons integer [16, 1024] [520] # Should be Q16")
complex_cs.append("lr real [0.0001, 1.0] [0.50005]")
complex_cs.append("degree integer [1, 5] [3]")
complex_cs.append("gamma real [0.000030518, 8] [0.0156251079996]log")
complex_cs.append("C | classifier in {svm}")
complex_cs.append("kernel | classifier in {svm}")
complex_cs.append("lr | classifier in {nn}")
complex_cs.append("neurons | classifier in {nn}")
complex_cs.append("degree | kernel in {poly, sigmoid}")
complex_cs.append("gamma | kernel in {rbf}")
cs_new = pcs_new.read(complex_cs)
self.assertEqual(cs_new, conditional_space)
# same in older version
complex_cs_old = list()
complex_cs_old.append("preprocessing {None, pca} [None]")
complex_cs_old.append("classifier {svm, nn} [svm]")
complex_cs_old.append("kernel {rbf, poly, sigmoid} [rbf]")
complex_cs_old.append("C [0.03125, 32768] [32]l")
complex_cs_old.append("neurons [16, 1024] [520]i # Should be Q16")
complex_cs_old.append("lr [0.0001, 1.0] [0.50005]")
complex_cs_old.append("degree [1, 5] [3]i")
complex_cs_old.append("gamma [0.000030518, 8] [0.0156251079996]l")
complex_cs_old.append("C | classifier in {svm}")
complex_cs_old.append("kernel | classifier in {svm}")
complex_cs_old.append("lr | classifier in {nn}")
complex_cs_old.append("neurons | classifier in {nn}")
complex_cs_old.append("degree | kernel in {poly, sigmoid}")
complex_cs_old.append("gamma | kernel in {rbf}")
cs_old = pcs.read(complex_cs_old)
self.assertEqual(cs_old, cs_new)
def run_test(self):
try:
with open(configuration_space_path) as fh:
cs = pcs_parser.read(fh)
except:
with open(configuration_space_path) as fh:
cs = pcs_new_parser.read(fh)
# Sample a little bit
for i in range(10):
cs.seed(i)
configurations = cs.sample_configuration(size=5)
for j, c in enumerate(configurations):
c.is_valid_configuration()
cs._check_configuration_rigorous(c)
neighborhood = ConfigSpace.util.get_one_exchange_neighbourhood(
c, seed=i)
for shuffle, n in enumerate(neighborhood):
n.is_valid_configuration()
cs._check_configuration_rigorous(n)
if shuffle == 10:
break
def test_read_new_configuration_space_complex_conditionals(self):
classi = OrdinalHyperparameter("classi", [
"random_forest", "extra_trees", "k_nearest_neighbors", "something"
])
knn_weights = CategoricalHyperparameter("knn_weights",
["uniform", "distance"])
weather = OrdinalHyperparameter(
"weather", ["sunny", "rainy", "cloudy", "snowing"])
temperature = CategoricalHyperparameter("temperature", ["high", "low"])
rain = CategoricalHyperparameter("rain", ["yes", "no"])
gloves = OrdinalHyperparameter("gloves",
["none", "yarn", "leather", "gortex"])
heur1 = CategoricalHyperparameter("heur1", ["off", "on"])
heur2 = CategoricalHyperparameter("heur2", ["off", "on"])
heur_order = CategoricalHyperparameter("heur_order",
["heur1then2", "heur2then1"])
gloves_condition = OrConjunction(
EqualsCondition(gloves, rain, "yes"),
EqualsCondition(gloves, temperature, "low"))
heur_condition = AndConjunction(
EqualsCondition(heur_order, heur1, "on"),
EqualsCondition(heur_order, heur2, "on"))
and_conjunction = AndConjunction(
NotEqualsCondition(knn_weights, classi, "extra_trees"),
EqualsCondition(knn_weights, classi, "random_forest"))
Cl_condition = OrConjunction(
EqualsCondition(knn_weights, classi, "k_nearest_neighbors"),
and_conjunction, EqualsCondition(knn_weights, classi, "something"))
and1 = AndConjunction(EqualsCondition(temperature, weather, "rainy"),
EqualsCondition(temperature, weather, "cloudy"))
and2 = AndConjunction(
EqualsCondition(temperature, weather, "sunny"),
NotEqualsCondition(temperature, weather, "snowing"))
another_condition = OrConjunction(and1, and2)
complex_conditional_space = ConfigurationSpace()
complex_conditional_space.add_hyperparameter(classi)
complex_conditional_space.add_hyperparameter(knn_weights)
complex_conditional_space.add_hyperparameter(weather)
complex_conditional_space.add_hyperparameter(temperature)
complex_conditional_space.add_hyperparameter(rain)
complex_conditional_space.add_hyperparameter(gloves)
complex_conditional_space.add_hyperparameter(heur1)
complex_conditional_space.add_hyperparameter(heur2)
complex_conditional_space.add_hyperparameter(heur_order)
complex_conditional_space.add_condition(gloves_condition)
complex_conditional_space.add_condition(heur_condition)
complex_conditional_space.add_condition(Cl_condition)
complex_conditional_space.add_condition(another_condition)
complex_cs = list()
complex_cs.append(
"classi ordinal {random_forest,extra_trees,k_nearest_neighbors, something} [random_forest]"
)
complex_cs.append(
"knn_weights categorical {uniform, distance} [uniform]")
complex_cs.append(
"weather ordinal {sunny, rainy, cloudy, snowing} [sunny]")
complex_cs.append("temperature categorical {high, low} [high]")
complex_cs.append("rain categorical { yes, no } [yes]")
complex_cs.append(
"gloves ordinal { none, yarn, leather, gortex } [none]")
complex_cs.append("heur1 categorical { off, on } [off]")
complex_cs.append("heur2 categorical { off, on } [off]")
complex_cs.append(
"heur_order categorical { heur1then2, heur2then1 } [heur1then2]")
complex_cs.append("gloves | rain == yes || temperature == low")
complex_cs.append("heur_order | heur1 == on && heur2 == on")
complex_cs.append(
"knn_weights | classi == k_nearest_neighbors || classi != extra_trees && classi == random_forest || classi == something"
)
complex_cs.append(
"temperature | weather == rainy && weather == cloudy || weather == sunny && weather != snowing"
)
cs_new = pcs_new.read(complex_cs)
self.assertEqual(cs_new, complex_conditional_space)
# TODO: make the default!
ignore_parameters = fixed_parameters_to_ignore_parameters(
args.fixed_parameters)
runhistory_path, configspace_path = openmlpimp.utils.cache_runhistory_configspace(
task_cache_folder,
args.flow_id,
task_id,
model_type=args.model_type,
required_setups=args.required_setups,
reverse=False,
fixed_parameters=args.fixed_parameters,
ignore_parameters=ignore_parameters)
if total_ranks is None:
with open(configspace_path) as configspace_file:
configspace = read(configspace_file)
total_ranks = {
param.name: 0
for param in configspace.get_hyperparameters()
}
if args.modus == 'fanova':
print('Running FANOVA backend on task %d' % task_id)
results_file = FanovaBackend.execute(
task_save_folder,
runhistory_path,
configspace_path,
use_percentiles=args.use_quantiles,
interaction_effect=args.interaction_effect,
run_limit=args.limit,
draw_plots=args.draw_plots)
def execute(save_folder,
runhistory_location,
configspace_location,
manual_logtransform=True,
use_percentiles=True,
interaction_effect=True,
run_limit=None,
draw_plots=True):
with open(runhistory_location) as runhistory_file:
runhistory = json.load(runhistory_file)
with open(configspace_location) as configspace_file:
configspace = read(configspace_file)
try:
os.makedirs(save_folder)
except FileExistsError:
pass
X = []
y = []
for item in runhistory['data']:
if run_limit is not None and len(X) > run_limit:
break
valid = True
current = []
setup_id = str(item[0][0])
configuration = runhistory['configs'][setup_id]
for param in configspace.get_hyperparameters():
value = configuration[param.name]
if isinstance(param,
UniformFloatHyperparameter) and not isinstance(
value, float):
valid = False
elif isinstance(
param,
UniformIntegerHyperparameter) and not isinstance(
value, int):
valid = False
if isinstance(param, CategoricalHyperparameter):
value = param.choices.index(value)
elif param.log and manual_logtransform:
value = np.log(value)
current.append(value)
if valid:
X.append(current)
y.append(item[1][0])
else:
print('Illegal configuration', current)
X = np.array(X)
y = np.array(y)
if manual_logtransform:
configspace = openmlpimp.utils.scale_configspace_to_log(
configspace)
cutoffs = (-np.inf, np.inf)
if use_percentiles:
p75 = np.percentile(y, 75.0)
p100 = np.percentile(y, 100.0)
cutoffs = (p75, p100)
# start the evaluator
evaluator = fanova_pyrfr(X=X,
Y=y,
config_space=configspace,
config_on_hypercube=False,
cutoffs=cutoffs)
# obtain the results
params = configspace.get_hyperparameters()
result = {}
for idx, param in enumerate(params):
importance = evaluator.quantify_importance(
[idx])[(idx, )]['total importance']
result[param.name] = importance
# store main results to disk
filename = 'pimp_values_fanova.json'
with open(os.path.join(save_folder, filename), 'w') as out_file:
json.dump(result,
out_file,
sort_keys=True,
indent=4,
separators=(',', ': '))
# call plotting fn
yrange = (0, 1)
if use_percentiles:
yrange = (p75, p100)
if draw_plots:
FanovaBackend._plot_result(evaluator, configspace,
save_folder + '/fanova', yrange)
if interaction_effect:
result_interaction = {}
for idx, param in enumerate(params):
for idx2, param2 in enumerate(params):
if param.name >= param2.name: # string comparison cause stable
continue
print('interaction effects between', param.name,
param2.name)
interaction = evaluator.quantify_importance(
[idx, idx2])[(idx, idx2)]['total importance']
interaction -= result[param.name]
interaction -= result[param2.name]
combined_name = param.name + '__' + param2.name
if interaction < 0.0:
raise ValueError(
'interaction score too low. Params: %s score %d' %
(combined_name, interaction))
result_interaction[combined_name] = interaction
for idx, param in enumerate(params):
for idx2, param2 in enumerate(params):
if param.name >= param2.name: # string comparison cause stable
continue
for idx3, param3 in enumerate(params):
if param2.name >= param3.name: # string comparison cause stable
continue
print('interaction effects between', param.name,
param2.name, param3.name)
interaction = evaluator.quantify_importance(
[idx, idx2,
idx3])[(idx, idx2, idx3)]['total importance']
interaction -= result[param.name]
interaction -= result[param2.name]
interaction -= result[param3.name]
combined_name = param.name + '__' + param2.name + '__' + param3.name
interaction -= result_interaction[param.name + '__' +
param2.name]
interaction -= result_interaction[param2.name + '__' +
param3.name]
interaction -= result_interaction[param.name + '__' +
param3.name]
if interaction < 0.0:
raise ValueError(
'interaction score too low. Params: %s score %d'
% (combined_name, interaction))
result_interaction[combined_name] = interaction
# store interaction effects to disk
if sum(result_interaction.values()) + sum(result.values()) > 1:
raise ValueError('Sum of results too high')
with open(
os.path.join(save_folder,
'pimp_values_fanova_interaction.json'),
'w') as out_file:
json.dump(result_interaction,
out_file,
sort_keys=True,
indent=4,
separators=(',', ': '))
if draw_plots:
vis = Visualizer(evaluator, configspace)
vis.create_most_important_pairwise_marginal_plots(
save_folder + '/fanova', zlabel='Predictive Accuracy')
return save_folder + "/" + filename