def init_master_params(self, from_file=False, filepath=None):
"""
Computes initial random gaussian values for master weights and biases
Returns:
(float array): Random gaussian values for neural network weights and biases
"""
if from_file:
master_params = utils.load_array(filepath)
if len(master_params) != self.params_size:
err_msg = "Params from (" + filepath + ") does not match the network shape."
raise ValueError(err_msg)
return utils.load_array(filepath)
master_params = []
weights = np.random.normal(
0, 1, self.config['input_size'] * self.config['n_nodes_per_layer'])
master_params += list(weights)
biases = np.random.normal(0, 1, self.config['n_nodes_per_layer'])
master_params += list(biases)
for i in range(self.config['n_hidden_layers']):
weights = np.random.normal(
0, 1, self.config['n_nodes_per_layer'] *
self.config['n_nodes_per_layer'])
master_params += list(weights)
biases = np.random.normal(0, 1, self.config['n_nodes_per_layer'])
master_params += list(biases)
weights = np.random.normal(
0, 1,
self.config['n_nodes_per_layer'] * self.config['output_size'])
master_params += list(weights)
biases = np.random.normal(0, 1, self.config['output_size'])
master_params += list(biases)
return master_params
def load_data(self,
serialized_data_folder='./',
path_to_vehicle_folder='vehicles/',
path_to_non_vehicle_folder='non-vehicles/'):
path_to_X_dat_file = '{0}/{1}'.format(serialized_data_folder, 'X.dat')
path_to_y_dat_file = '{0}/{1}'.format(serialized_data_folder, 'y.dat')
X_dat_file_exists = os.path.exists(path_to_X_dat_file)
y_dat_file_exists = os.path.exists(path_to_y_dat_file)
if X_dat_file_exists and y_dat_file_exists:
print('Loading from serialized ...')
self.X = load_array(path_to_X_dat_file)
self.y = load_array(path_to_y_dat_file)
print('Done reading serialized arrays')
else:
print('Creating data from image folders')
non_vehicle_class, vehicle_class = 0, 1
non_vehicle_X, non_vehicle_y = self._get_X_y(
path_to_non_vehicle_folder, non_vehicle_class)
vehicle_X, vehicle_y = self._get_X_y(path_to_vehicle_folder,
vehicle_class)
self.X = np.concatenate((non_vehicle_X, vehicle_X))
self.y = np.concatenate((non_vehicle_y, vehicle_y))
print(
'Data created successfully, creating serialized numpy arrays')
save_array(path_to_X_dat_file, self.X)
save_array(path_to_y_dat_file, self.y)
print('Done saving arrays')
def get_data(dataset_version):
feature_names_comps = utils.load_array("%s/feature_names_comps" % dataset_version)
feature_names_ab = utils.load_array("%s/feature_names_ab" % dataset_version)
feature_names_ti = utils.load_array("%s/feature_names_ti" % dataset_version)
X_comps = utils.load_array("%s/X_comps" % dataset_version)
X_ab = utils.load_csr("%s/X_ab" % dataset_version)
X_ti = utils.load_csr("%s/X_ti" % dataset_version)
y = utils.load_array("%s/y" % dataset_version)
return feature_names_comps, feature_names_ab, feature_names_ti, X_comps, X_ab, X_ti, y
def get_data(dataset_version):
feature_names_comps = utils.load_array("%s/feature_names_comps" %
dataset_version)
feature_names_ab = utils.load_array("%s/feature_names_ab" %
dataset_version)
feature_names_ti = utils.load_array("%s/feature_names_ti" %
dataset_version)
X_comps = utils.load_array("%s/X_comps" % dataset_version)
X_ab = utils.load_csr("%s/X_ab" % dataset_version)
X_ti = utils.load_csr("%s/X_ti" % dataset_version)
y = utils.load_array("%s/y" % dataset_version)
return feature_names_comps, feature_names_ab, feature_names_ti, X_comps, X_ab, X_ti, y
def submit(filename):
df_test = pd.read_csv(TEST_LIST_FILE)
preds = load_array(PRED_FILE)
#preds = load_array(PRED_WEATHER)
threshold = load_array(THRESHOLD_FILE_ENS).tolist()
#threshold = 0.18
print(threshold)
for i, pred in enumerate(preds):
tags = get_multi_classes(pred, classes, threshold)
df_test['tags'][i] = tags
df_test.to_csv(RESULT_DIR + '/' + filename, index=False)
print(df_test.head())
def find_best_weather():
thr = load_array(THRESHOLD_FILE_ENS)
labels = load_array(VAL_LABELS)
preds = load_array(PRED_VAL)
print(labels.shape)
weather = preds[:, 0:4]
y = labels[0, :, 0:4]
print(y.shape)
print(weather.shape)
thr = thr[0:4]
def mf(p):
p2 = np.zeros_like(p)
for i in range(4):
p2[:, i] = (p[:, i] > thr[i]).astype(np.int)
score1 = fbeta_score(y, p2, beta=2, average='samples')
return score1
base_score = mf(
weather) #fbeta_score(y, weather, beta=2, average='samples')
print('base score:{}'.format(base_score))
max_score = base_score
d = 0.5
best_d = 0.5
best_w = weather
while d < 1:
w = get_one_weather(weather, thr, d)
score = mf(w) #fbeta_score(y, w, beta=2, average='samples')
print('score{}, d:{}'.format(score, d))
if score > max_score:
max_score = score
best_d = d
best_w = w
d += 0.1
print('best d:{}'.format(best_d))
w1 = force_one_weather(weather, thr)
score1 = mf(w1)
print('force one weather score:{}'.format(score1))
if max_score > base_score + 0.00001:
test_preds = load_array(PRED_FILE)
test_w = test_preds[:, 0:4]
w = get_one_weather(test_w, thr, best_d)
test_preds[:, 0:4] = w
#preds[:, 0:4] = best_w
save_array(PRED_WEATHER, test_preds)
def find_best_threshold():
preds = load_array(PRED_VAL)
labels = load_array(VAL_LABELS)
print(np.array(labels).shape)
for i in range(1, len(labels)):
for j in range(len(labels[i])):
for k in range(len(labels[i][j])):
if labels[i][j][k] != labels[i - 1][j][k]:
print('error, check labels failed')
exit()
x = optimise_f2_thresholds(labels[0], preds)
print('best threshold:')
print(x)
save_array(THRESHOLD_FILE_ENS, x)
def __init__(self, w):
'''
Generates random messages
# Parameter
-------------
w: np.array
Weighted random condition.
# Returns
-------------
sample: integer
Single random message.
'''
self.w = w
self.N = len(w)
# We assign each message version with a unique ID from 0 to N-1
self.setN = np.arange(self.N)
self.M = sum(w)
# w/self.M will generate an array of 0s, use numpy divide
self.norm_w = np.true_divide(w,self.M)
# We randomize M message from N version for only 1 time
if self.M < 6:
self.shuffle = np.random.choice(self.setN, self.M, p=self.norm_w)
else:
# Use bcolz to store array > 1MB to speed up computation
utils.save_array("shuffle.bc", np.random.choice(self.setN, self.M, p=self.norm_w))
self.shuffle = utils.load_array("shuffle.bc")
# Everytime we call the message function that take a random message,
# we increase current_id for the next message
self.current_id = 0
def submit(filename, clip, use_weight=False):
#filenames = [f.split('/')[-1] for f, i in dsets.imgs]
#filenames = get_stage1_test_loader('res50').filenames
filenames = load_array(TEST_FILE_NAMES)
if use_weight:
preds = load_array(PRED_FILE_WEIGHTED)
else:
preds = load_array(PRED_FILE)
if clip > 0.9999:
subm = np.array(preds)
else:
subm = do_clip(preds, clip)
subm_name = RESULT_DIR + '/' + filename
submission = pd.DataFrame(subm, columns=dset_classes)
submission.insert(0, 'image_name', filenames)
print(submission.head())
submission.to_csv(subm_name, index=False)
def submit(filename):
#filenames = [f.split('/')[-1] for f, i in dsets.imgs]
#filenames = get_stage1_test_loader('res50').filenames
preds = load_array(PRED_FILE)
print(preds[:100])
subm_name = RESULT_DIR + '/' + filename
df = pd.read_csv(data_dir + '/sample_submission.csv')
df['invasive'] = preds
print(df.head())
df.to_csv(subm_name, index=False)
def load_precomputed_conv_models(self):
'''
Method loads precomputed conv_model outputs. Initializes:
:return: self.train_precomputed and self.val_precomputed.
'''
print("loading precomputed conv. outputs...")
fName1 = "precomputed_trn_features." + self.runID + ".h5"
fName2 = "precomputed_val_features." + self.runID + ".h5"
self.train_precomputed = load_array(fName1)
self.val_precomputed = load_array(fName2)
# since we're loading precomputed outputs from the conv_model,
# set this flag to true.
self.use_precomputed_conv_output = True
print("done...")
return self
def submit(filename, clip):
filenames = [f.split('/')[-1] for f, i in dsets.imgs]
preds = load_array(PRED_FILE)
subm = do_clip(preds, clip)
#classes = dsets['train'].classes
subm_name = RESULT_DIR+'/'+filename
submission = pd.DataFrame(subm, columns=dset_classes)
submission.insert(0, 'image_name', filenames)
print(submission.head())
submission.to_csv(subm_name, index=False)
def load_data(self):
self.file = h5py.File(self.input, "r")
print("[MVA_HELPER] INPUT FILE: %s" % self.input)
print("[MVA_HELPER] INPUT FILE KEYS: ", self.file.keys())
self.data = {}
self.data["feature_names"] = utils.load_array(self.file, "feature_names")
for set in ["train", "test", "data"]:
self.data[set] = {}
for aux in default_branches + self.additional_branches:
self.data[set][aux] = utils.load_array(self.file,
"%s_%s" % (aux, set))
self.data[set]["label"] = utils.load_array(self.file,
"%s_%s" % ("label", set))
self.data[set]["global"] = utils.load_array(self.file,
"%s_%s" % ("global", set))
self.data[set]["objects"] = utils.load_array(
self.file, "%s_%s" % ("objects", set))
self.data[set]["n_events_raw"] = len(self.data[set]["label"])
for check in default_branches + ["global"] + self.additional_branches:
if not len(
self.data[set][check]) == self.data[set]["n_events_raw"]:
print(
"[MVA_HELPER] WARNING -- %s set: entry %s does not have the same number of events as the label (%d vs. %d)"
% (set, check, len(self.data[set][check]),
self.data[set]["n_events_raw"]))
self.data[set]["n_events"] = numpy.sum(self.data[set]["evt_weight_"])
print(
"[MVA_HELPER] LOADING DATA -- %s set: %d raw events with a normalization of %.3f"
%
(set, self.data[set]["n_events_raw"], self.data[set]["n_events"]))
self.data["train"]["train_id"] = numpy.zeros(
len(self.data["train"]["label"]))
self.data["test"]["train_id"] = numpy.ones(len(self.data["test"]["label"]))
self.data["data"]["train_id"] = numpy.ones(len(self.data["data"]["label"]))
def submit(filename, clip):
filenames = [f.split('/')[-1] for f, i in dsets.imgs]
preds = load_array(PRED_FILE)
if clip > 0.9999:
subm = np.array(preds)
else:
subm = do_clip(preds, clip)
#up_clip(subm, clip, 0.8)
#print(subm[:10])
subm_name = RESULT_DIR + '/' + filename
submission = pd.DataFrame(subm, columns=dset_classes)
submission.insert(0, 'image_name', filenames)
print(submission.head())
submission.to_csv(subm_name, index=False)
def submit(filename):
preds_raw = []
pred_files = glob.glob(settings.PREDICT_DIR + os.sep + '*.dat')
for pred_file in pred_files:
print("loading predictions: % s" % pred_file)
preds_raw.append(load_array(pred_file))
preds = np.mean(preds_raw, axis=0)
print(preds[:100])
subm_name = settings.RESULT_DIR + os.sep + filename
df = pd.read_csv(settings.DATA_DIR + os.sep + 'sample_submission.csv')
df['invasive'] = preds
print(df.head())
df.to_csv(subm_name, index=False)
preds2 = (preds > 0.5).astype(np.int)
df2 = pd.read_csv(settings.DATA_DIR + os.sep + 'sample_submission.csv')
df2['invasive'] = preds2
df2.to_csv(subm_name + '01', index=False)
use_ti = True
test_percent = .25
scoring = 'precision'
(feature_names_comps, feature_names_ab, feature_names_ti, X_comps, X_ab, X_ti,
y) = get_data(dataset_version)
# <codecell>
############################################################################
# extract features via chi2
# assemble X_train, X_test, and feature_names
print("assembling features")
t0 = time()
fnab = utils.load_array('data/feature_names_ab')
fnti = utils.load_array('data/feature_names_ti')
fn = np.append(fnab, fnti)
X_train = utils.load_coo('data/X_train').todense()
y_train = utils.load_array('data/y_train')
X_test = utils.load_coo('data/X_test').todense()
y_test = utils.load_array('data/y_test')
print("done assembling features in %fs" % (time() - t0))
# <codecell>
fitted = []
def grid_search(estimator):
# try:
with open(HELIOS, 'r') as f:
config = json.load(f)
logging.basicConfig(filename='../log/forest_gater_par.txt',
level=logging.INFO)
start_time = time.time()
logging.info('##### NEW EXPERIMENT_' + str(start_time) + '_#####')
logging.info(HELIOS)
logging.info(json.dumps(config, indent=4))
TRAIN = PATH + 'train/100/'
TEST = PATH + 'test/100/'
VAL = PATH + 'val/100/'
X_train = load_array(TRAIN + 'X_train.bc/')
y_train = load_array(TRAIN + 'y_train.bc/')
X_test = load_array(TEST + 'X_test.bc/')
y_test = load_array(TEST + 'y_test.bc/')
X_val = load_array(VAL + 'X_val.bc/')
y_val = load_array(VAL + 'y_val.bc/')
y_train[y_train == 0] = -1
y_test[y_test == 0] = -1
y_val[y_val == 0] = -1
logging.info('Training Size ' + str(X_train.shape[0]))
logging.info('Testing Size ' + str(X_test.shape[0]))
logging.info('Val Size ' + str(X_val.shape[0]))
moe = MOE()
def train_bdt(config):
# Trains BDT with given hyperparams and returns max Z_A (as calculated on bkg MC), requiring at least 4 signal events
if config["invert_test_and_train"]:
config["input_file"] = config["input_file_2"]
else:
config["input_file"] = config["input_file_1"]
f = h5py.File(config["input_file"], "r")
feature_names = utils.load_array(f, 'feature_names')
training_feature_names = utils.load_array(f, 'training_feature_names')
print(("Training with the following features: ", training_feature_names))
#if config["invert_test_and_train"]:
#print "Inverting test and train splits"
#if config["sideband"]:
# print "Not yet implemented how to handle inverting the test/train set when training on data sidebands, exiting"
# return -1
#global_features = utils.load_array(f, 'global_validation')
#label = utils.load_array(f, 'label_validation')
#multi_label = utils.load_array(f, 'multi_label_validation')
#weights = utils.load_array(f, 'weights_validation')
#mass = utils.load_array(f, 'mass_validation')
#global_features_validation = utils.load_array(f, 'global')
#label_validation = utils.load_array(f, 'label')
#multi_label_validation = utils.load_array(f, 'multi_label')
#weights_validation = utils.load_array(f, 'weights')
#mass_validation = utils.load_array(f, 'mass')
#else:
global_features = utils.load_array(f, 'global')
label = utils.load_array(f, 'label')
multi_label = utils.load_array(f, 'multi_label')
weights = utils.load_array(f, 'weights')
mass = utils.load_array(f, 'mass')
global_features_validation = utils.load_array(f, 'global_validation')
label_validation = utils.load_array(f, 'label_validation')
multi_label_validation = utils.load_array(f, 'multi_label_validation')
weights_validation = utils.load_array(f, 'weights_validation')
mass_validation = utils.load_array(f, 'mass_validation')
if config["sideband"]:
global_features = utils.load_array(f, 'global_data_sideband')
label = utils.load_array(f, 'label_data_sideband')
multi_label = utils.load_array(f, 'multi_label_data_sideband')
weights = utils.load_array(f, 'weights_data_sideband')
mass = utils.load_array(f, 'mass_data_sideband')
global_features_data = utils.load_array(f, 'global_data')
label_data = utils.load_array(f, 'label_data')
multi_label_data = utils.load_array(f, 'multi_label_data')
weights_data = utils.load_array(f, 'weights_data')
mass_data = utils.load_array(f, 'mass_data')
print((global_features.shape))
print((label.shape))
print((weights.shape))
print((global_features_validation.shape))
print((label_validation.shape))
print((weights_validation.shape))
print((global_features_data.shape))
print((label_data.shape))
print((weights_data.shape))
x_train, y_train, y_train_multi, weights_train = global_features, label, multi_label, weights
x_test, y_test, y_test_multi, weights_test = global_features_validation, label_validation, multi_label_validation, weights_validation
X_train = pandas.DataFrame(data=x_train, columns=training_feature_names)
X_test = pandas.DataFrame(data=x_test, columns=training_feature_names)
X_data = pandas.DataFrame(data=global_features_data,
columns=training_feature_names)
if config["multiclassifier"]:
Y_train = y_train_multi
Y_test = y_test_multi
else:
Y_train = y_train
Y_test = y_test
sum_neg_weights = utils.sum_of_weights_v2(weights_train, label, 0)
sum_pos_weights = utils.sum_of_weights_v2(weights_train, label, 1)
print((sum_pos_weights, sum_neg_weights))
d_train = xgboost.DMatrix(X_train, label=Y_train, weight=weights_train)
d_test = xgboost.DMatrix(X_test, label=Y_test)
d_data = xgboost.DMatrix(X_data)
param = {
'max_depth': config["max_depth"],
'eta': config["eta"],
'subsample': config["subsample"],
'colsample_bytree': config["colsample_bytree"],
'min_child_weight': config["min_child_weight"],
'gamma': config["gamma"],
'reg_alpha': config["reg_alpha"],
'reg_lambda': config["reg_lambda"],
'scale_pos_weight': sum_neg_weights / sum_pos_weights,
'objective': 'binary:logistic',
'nthread': 16,
}
if config["multiclassifier"]:
param["num_class"] = config["n_class"]
param["objective"] = "multi:softprob"
param["scale_pos_weight"] = 1
evallist = [(d_train, 'train'), (d_test, 'test')]
progress = {}
n_round = config["n_round"]
print((param, n_round))
# train
bdt = xgboost.train(param,
d_train,
n_round,
evallist,
evals_result=progress)
bdt.save_model(config["tag"] + "_bdt.xgb")
model = bdt.get_dump()
input_variables = []
for name in feature_names:
input_variables.append((name, 'F'))
#tmva_utils.convert_model(model, input_variables = input_variables, output_xml = config["tag"] + '_bdt.xml')
# predict
pred_train = bdt.predict(d_train, output_margin=config["multiclassifier"])
pred_test = bdt.predict(d_test, output_margin=config["multiclassifier"])
pred_data = bdt.predict(d_data, output_margin=config["multiclassifier"])
fpr_train, tpr_train, thresh_train = metrics.roc_curve(
y_train, pred_train, pos_label=1, sample_weight=weights_train)
fpr_test, tpr_test, thresh_test = metrics.roc_curve(
y_test, pred_test, pos_label=1, sample_weight=weights_test)
auc_train, auc_train_unc = utils.auc_and_unc(y_train, pred_train,
weights_train, 100)
auc_test, auc_test_unc = utils.auc_and_unc(y_test, pred_test, weights_test,
100)
#auc_train = metrics.auc(fpr_train, tpr_train, reorder = True)
#auc_test = metrics.auc(fpr_test , tpr_test , reorder = True)
print(("Training AUC: %.3f" % auc_train))
print(("Testing AUC: %.3f" % auc_test))
# estimate z_a w/at least 4 signal events
n_quantiles = 25
signal_mva_scores = {
"bdt_score": ks_test.logical_vector(pred_test, y_test, 1)
}
bkg_mva_scores = {
"bdt_score": ks_test.logical_vector(pred_test, y_test, 0)
}
data_mva_scores = {"bdt_score": pred_data}
signal_mass = ks_test.logical_vector(mass_validation, y_test, 1)
bkg_mass = ks_test.logical_vector(mass_validation, y_test, 0)
signal_weights = ks_test.logical_vector(weights_validation, y_test, 1)
bkg_weights = ks_test.logical_vector(weights_validation, y_test, 0)
optimization_vars = config["optimization_vars"].split(
",") if config["optimization_vars"] else []
for var in optimization_vars:
signal_mva_scores[var] = ks_test.logical_vector(
utils.load_array(f, var + '_validation'), y_test, 1)
bkg_mva_scores[var] = ks_test.logical_vector(
utils.load_array(f, var + '_validation'), y_test, 0)
data_mva_scores[var] = utils.load_array(f, var + '_data')
signal_events = {
"mass": signal_mass,
"weights": signal_weights,
"mva_score": signal_mva_scores
}
bkg_events = {
"mass": bkg_mass,
"weights": bkg_weights,
"mva_score": bkg_mva_scores
}
data_events = {
"mass": mass_data,
"weights": weights_data,
"mva_score": data_mva_scores
}
za, za_unc, s, b, sigma_eff = significance_utils.za_scores(
n_quantiles, signal_events, bkg_events, False)
za_data, za_unc_data, s_data, b_data, sigma_eff_data = significance_utils.za_scores(
n_quantiles, signal_events, data_events, True)
za = numpy.asarray(za)
za_data = numpy.asarray(za_data)
if numpy.all(za == 0) or numpy.all(za_data == 0):
return 0.0, 0.0, 0.0, 0.0
max_za_mc = numpy.max(za[numpy.where(numpy.asarray(s) >= 4.)])
max_za_data = numpy.max(za_data[numpy.where(numpy.asarray(s_data) >= 4.)])
max_za_mc, max_za_mc_idx = utils.find_nearest(za, max_za_mc)
max_za_data, max_za_data_idx = utils.find_nearest(za_data, max_za_data)
max_za_mc_unc = za_unc[max_za_mc_idx]
max_za_data_unc = za_unc_data[max_za_data_idx]
print(("Max Z_A on MC: %.4f +/- %.4f" % (max_za_mc, max_za_mc_unc)))
print(("Max Z_A on data: %.4f +/- %.4f" % (max_za_data, max_za_data_unc)))
return max_za_mc, max_za_mc_unc, max_za_data, max_za_data_unc, auc_train, auc_train_unc, auc_test, auc_test_unc
for i in range(0, len(labels)):
if labels[i]:
used.add(i)
used_in_new.add(counter)
data_new[counter] = data[i]
counter += 1
#reorder the array with labels
for i in range(0, counter):
labels_new[i] = True
#reorder the array with images
filler_new = 0
for i in range(counter, len(data)):
if i not in used_in_new:
data_new[i] = data[filler_new]
filler_new += 1
#np.save("data/PV/balanced/PV_split.npy")
#np.save("data/PV/balanced/labels.npy", labels_new)
data = utils.load_array("data/PV/X_cells_only.bc")
labels = np.load("data/PV/labels.npy")
create_dataset(labels, data)
# In[157]:
utils.save_array(data_path + 'train/train.bc', train.as_matrix())
# In[158]:
utils.save_array(data_path + 'train/meta_train.bc', meta.as_matrix())
# ## Further Feature Engineering
# After converting 'csv_to_hdf5.py' functionality to pandas, I saved that array and then simply constructed the rest of the features as specified in the paper using pandas. I didn't bother seeing how the author did it as it was extremely obtuse and involved the fuel module.
# In[424]:
train = pd.DataFrame(utils.load_array(data_path + 'train/train.bc'),
columns=[
'TRIP_ID', 'CALL_TYPE', 'ORIGIN_CALL', 'ORIGIN_STAND',
'TAXI_ID', 'TIMESTAMP', 'DAY_TYPE', 'MISSING_DATA',
'POLYLINE', 'LATITUDE', 'LONGITUDE'
])
# In[425]:
train.head()
# The paper discusses how many categorical variables there are per category. The following all check out
# In[426]:
train['ORIGIN_CALL'].max()
num2 = int(two[0].split('/')[-1].split('.')[0])
return num1 - num2
dsets = datasets.ImageFolder(test_dir, data_transforms['test'])
#dsets.imgs = sorted(dsets.imgs, key=cmp_to_key(mycmp))
dsets.imgs = sorted(dsets.imgs)
dsetsv3 = datasets.ImageFolder(test_dir, data_transforms['testv3'])
#dsetsv3.imgs = sorted(dsetsv3.imgs, key=cmp_to_key(mycmp))
dsetsv3.imgs = sorted(dsetsv3.imgs)
print(dsets.imgs[:5])
print(dsetsv3.imgs[:5])
dset_classes = load_array(CLASSES_FILE)
print(dset_classes)
test_loader = torch.utils.data.DataLoader(dsets,
batch_size=batch_size,
shuffle=False,
num_workers=4)
test_v3_loader = torch.utils.data.DataLoader(dsetsv3,
batch_size=batch_size,
shuffle=False,
num_workers=4)
use_gpu = torch.cuda.is_available()
#!/usr/bin/env python
import numpy as np
from utils import load_array
data_arry = [
'part-time-job', 'full-time-job', 'hourly-wage', 'salary',
'associate-needed', 'bs-degree-needed', 'ms-or-phd-needed',
"licence-needed", '1-year-experience-needed',
'2-4-years-experience-needed', '5-plus-years-experience-needed',
'supervising-job'
]
if __name__ == '__main__':
sub_data = load_array('../save_data/save_array.bc')
labels = [['tags']]
for k1, v1 in enumerate(sub_data):
each_row = []
for k2, v2 in enumerate(v1):
if v2 == 1:
each_row.append(data_arry[k2])
labels.append(each_row)
res_file = open("../submissions/submit.tsv", 'w')
for r in labels:
res_file.write(' '.join(r) + "\n")
res_file.close()
def getPretrainDataPerFolder(self, data):
x = utils.load_array(self.baseFolder + data.pretrain[0])
y = utils.load_array(self.baseFolder + data.pretrain[1])
f = utils.load_array(self.baseFolder + data.pretrain[2])
return [x, y, f]
def load_pred_data():
preds = load_array(RESULTS_DIR + '/test_preds')
filenames = load_array(RESULTS_DIR + '/filenames')
return filenames, preds
test_percent=.25
scoring='precision'
(feature_names_comps, feature_names_ab,
feature_names_ti, X_comps, X_ab, X_ti, y) = get_data(dataset_version)
# <codecell>
############################################################################
# extract features via chi2
# assemble X_train, X_test, and feature_names
print("assembling features")
t0 = time()
fnab = utils.load_array('data/feature_names_ab')
fnti = utils.load_array('data/feature_names_ti')
fn = np.append(fnab, fnti)
X_train = utils.load_coo('data/X_train').todense()
y_train = utils.load_array('data/y_train')
X_test = utils.load_coo('data/X_test').todense()
y_test = utils.load_array('data/y_test')
print("done assembling features in %fs" % (time() - t0))
# <codecell>
fitted=[]
def grid_search(estimator):
# try:
from vgg16 import Vgg16 vgg = Vgg16() model = vgg.model # Use batch size of 1 since we're just doing preprocessing on the CPU val_batches = get_batches(path+'valid', shuffle=False, batch_size=1) batches = get_batches(path+'train', shuffle=False, batch_size=1) val_data = get_data(path+'valid') trn_data = get_data(path+'train') save_array(model_path+'train_data.bc', trn_data) save_array(model_path+'valid_data.bc', val_data) trn_data = load_array(model_path+'train_data.bc') val_data = load_array(model_path+'valid_data.bc') val_classes = val_batches.classes trn_classes = batches.classes val_labels = onehot(val_classes) trn_labels = onehot(trn_classes) # trn_features = model.predict(trn_data, batch_size=batch_size) # val_features = model.predict(val_data, batch_size=batch_size) # # save_array(model_path+'train_lastlayer_features.bc', trn_features) # save_array(model_path+'valid_lastlayer_features.bc', val_features) # # trn_features = load_array(model_path+'train_lastlayer_features.bc') # val_features = load_array(model_path+'valid_lastlayer_features.bc')
def train_bdt(config, invert=False):
results = {}
args = config["args"]
### Read features ###
if not invert:
f = h5py.File(args.input.replace(".hdf5", "") + ".hdf5", "r")
else:
f = h5py.File(args.input_invert.replace(".hdf5", "") + ".hdf5", "r")
feature_names = utils.load_array(f, 'feature_names')
training_feature_names = utils.load_array(f, 'training_feature_names')
print(training_feature_names)
global_features = utils.load_array(f, 'global')
global_dnn_features = utils.load_array(f, 'global_dnn')
label = utils.load_array(f, 'label')
multi_label = utils.load_array(f, 'multi_label')
weights = utils.load_array(f, 'weights')
mass = utils.load_array(f, 'mass')
njets = utils.load_array(f, 'njets')
lead_sigmaEtoE = utils.load_array(f, 'lead_sigmaEtoE')
sublead_sigmaEtoE = utils.load_array(f, 'sublead_sigmaEtoE')
signal_mass_label = utils.load_array(f, 'signal_mass_label')
signal_mass_category = utils.load_array(f, 'signal_mass_category')
tth_2017_reference_mva = utils.load_array(f, 'tth_2017_reference_mva')
evt = utils.load_array(f, 'evt')
run = utils.load_array(f, 'run')
lumi = utils.load_array(f, 'lumi')
process_id = utils.load_array(f, 'process_id')
year = utils.load_array(f, 'year')
#objects = utils.load_array(f, 'objects')
tth_runII_mva = utils.load_array(f, 'tth_runII_mva')
if args.sideband:
global_features = utils.load_array(f, 'global_data_sideband')
label = utils.load_array(f, 'label_data_sideband')
multi_label = utils.load_array(f, 'multi_label_data_sideband')
weights = utils.load_array(f, 'weights_data_sideband')
mass = utils.load_array(f, 'mass_data_sideband')
#lead_sigmaEtoE = utils.load_array(f, 'lead_sigmaEtoE_data_sideband')
#sublead_sigmaEtoE = utils.load_array(f, 'sublead_sigmaEtoE_data_sideband')
global_features_validation = utils.load_array(f, 'global_validation')
global_dnn_features_validation = utils.load_array(f,
'global_dnn_validation')
label_validation = utils.load_array(f, 'label_validation')
multi_label_validation = utils.load_array(f, 'multi_label_validation')
weights_validation = utils.load_array(f, 'weights_validation')
mass_validation = utils.load_array(f, 'mass_validation')
njets_validation = utils.load_array(f, 'njets_validation')
signal_mass_label_validation = utils.load_array(
f, 'signal_mass_label_validation')
signal_mass_category_validation = utils.load_array(
f, 'signal_mass_category_validation')
tth_2017_reference_mva_validation = utils.load_array(
f, 'tth_2017_reference_mva_validation')
evt_validation = utils.load_array(f, 'evt_validation')
run_validation = utils.load_array(f, 'run_validation')
lumi_validation = utils.load_array(f, 'lumi_validation')
process_id_validation = utils.load_array(f, 'process_id_validation')
year_validation = utils.load_array(f, 'year_validation')
#objects_validation = utils.load_array(f, 'objects_validation')
tth_runII_mva_validation = utils.load_array(f, 'tth_runII_mva_validation')
global_features_data = utils.load_array(f, 'global_data')
global_dnn_features_data = utils.load_array(f, 'global_dnn_data')
label_data = utils.load_array(f, 'label_data')
multi_label_data = utils.load_array(f, 'multi_label_data')
weights_data = utils.load_array(f, 'weights_data')
mass_data = utils.load_array(f, 'mass_data')
njets_data = utils.load_array(f, 'njets_data')
signal_mass_label_data = utils.load_array(f, 'signal_mass_label_data')
signal_mass_category_data = utils.load_array(f,
'signal_mass_category_data')
tth_2017_reference_mva_data = utils.load_array(
f, 'tth_2017_reference_mva_data')
evt_data = utils.load_array(f, 'evt_data')
run_data = utils.load_array(f, 'run_data')
lumi_data = utils.load_array(f, 'lumi_data')
process_id_data = utils.load_array(f, 'process_id_data')
year_data = utils.load_array(f, 'year_data')
#objects_data = utils.load_array(f, 'objects_data')
tth_runII_mva_data = utils.load_array(f, 'tth_runII_mva_data')
global_features_final_fit = utils.load_array(f, 'global_final_fit')
global_dnn_features_final_fit = utils.load_array(f, 'global_dnn_final_fit')
label_final_fit = utils.load_array(f, 'label_final_fit')
multi_label_final_fit = utils.load_array(f, 'multi_label_final_fit')
weights_final_fit = utils.load_array(f, 'weights_final_fit')
mass_final_fit = utils.load_array(f, 'mass_final_fit')
njets_final_fit = utils.load_array(f, 'njets_final_fit')
signal_mass_label_final_fit = utils.load_array(
f, 'signal_mass_label_final_fit')
signal_mass_category_final_fit = utils.load_array(
f, 'signal_mass_category_final_fit')
tth_2017_reference_mva_final_fit = utils.load_array(
f, 'tth_2017_reference_mva_final_fit')
evt_final_fit = utils.load_array(f, 'evt_final_fit')
run_final_fit = utils.load_array(f, 'run_final_fit')
lumi_final_fit = utils.load_array(f, 'lumi_final_fit')
process_id_final_fit = utils.load_array(f, 'process_id_final_fit')
year_final_fit = utils.load_array(f, 'year_final_fit')
#objects_final_fit = utils.load_array(f, 'objects_final_fit')
tth_runII_mva_final_fit = utils.load_array(f, 'tth_runII_mva_final_fit')
print global_dnn_features.shape, global_dnn_features_validation.shape, global_dnn_features_data.shape, global_dnn_features_final_fit.shape
num_multi_class = 3 #len(numpy.unique(multi_label, return_index = True))
train_frac = 1.0 # use this fraction of data for training, use 1-train_frac for testing
nTrain = int(len(label) * train_frac)
print((global_features.shape))
print((label.shape))
print((weights.shape))
print((global_features_validation.shape))
print((label_validation.shape))
print((weights_validation.shape))
print((global_features_data.shape))
print((label_data.shape))
print((weights_data.shape))
x_train, y_train, y_train_multi, weights_train = global_features, label, multi_label, weights
x_test, y_test, y_test_multi, weights_test = global_features_validation, label_validation, multi_label_validation, weights_validation
X_train = pandas.DataFrame(data=x_train, columns=training_feature_names)
X_test = pandas.DataFrame(data=x_test, columns=training_feature_names)
X_data = pandas.DataFrame(data=global_features_data,
columns=training_feature_names)
X_final_fit = pandas.DataFrame(data=global_features_final_fit,
columns=training_feature_names)
if args.multi:
Y_train = y_train_multi
Y_test = y_test_multi
else:
Y_train = y_train
Y_test = y_test
#unique, count = numpy.unique(multi_label,return_counts=True)
#weights_train = numpy.multiply(weights_train, numpy.where(multi_label == 0, 1/(count[0]/float(sum(count))), 1) )
#weights_train = numpy.multiply(weights_train, numpy.where(multi_label == 1, 1/(count[1]/float(sum(count))), 1) )
#weights_train = numpy.multiply(weights_train, numpy.where(multi_label == 2, 1/(count[2]/float(sum(count))), 1) )
#weights_train = numpy.multiply(weights_train, numpy.where(multi_label == 3, 1/(count[3]/float(sum(count))), 1) )
#weights_train = numpy.multiply(weights_train, numpy.where(multi_label == 4, 1/(count[4]/float(sum(count))), 1) )
sum_neg_weights = utils.sum_of_weights(weights_train, label, 0)
sum_pos_weights = utils.sum_of_weights(weights_train, label, 1)
print((sum_pos_weights, sum_neg_weights))
scale_tth = False
if scale_tth:
for i in range(len(weights_train)):
if multi_label[i] == 1:
weights_train[i] *= 6.
weights_train_modified = weights_train
equal_weights = args.equal_weights
if args.multi:
if not equal_weights:
for j in range(len(weights_train_modified)):
if multi_label[j] == 0:
weights_train_modified[
j] *= sum_neg_weights / sum_pos_weights
else:
for i in range(num_multi_class):
sum_class_weights = utils.sum_of_weights(
weights_train_modified, multi_label, i)
print(("Normalizing class %d by %.6f" %
(i, sum_class_weights)))
for j in range(len(weights_train_modified)):
if multi_label[j] == i:
weights_train_modified[j] *= 1. / sum_class_weights
if args.res:
for i in range(len(weights_train_modified)):
if label[i] == 1:
print((
weights_train_modified[i], 1 /
math.sqrt(lead_sigmaEtoE[i]**2 + sublead_sigmaEtoE[i]**2)))
weights_train_modified[i] *= 1 / math.sqrt(
lead_sigmaEtoE[i]**2 + sublead_sigmaEtoE[i]**2)
print((weights_train_modified[i]))
sum_neg_weights = utils.sum_of_weights(weights_train_modified, label, 0)
sum_pos_weights = utils.sum_of_weights(weights_train_modified, label, 1)
print((sum_pos_weights, sum_neg_weights))
d_train = xgboost.DMatrix(X_train,
label=Y_train,
weight=weights_train_modified)
d_test = xgboost.DMatrix(X_test, label=Y_test)
d_data = xgboost.DMatrix(X_data)
d_final_fit = xgboost.DMatrix(X_final_fit)
# Define BDT parameters
if "kparam" not in list(config.keys()):
param = {
'max_depth': 4,
'eta': 0.2,
'objective': 'binary:logistic',
'scale_pos_weight': sum_neg_weights / sum_pos_weights,
'subsample': 1.0,
'colsample_bytree': 1.0,
'nthread': 12,
'min_child_weight': min(
1, (sum_neg_weights) / 100000.
), # min_child_weight depends on the absolute value of the weights
}
else:
param = config["kparam"]
if args.multi:
param["num_class"] = num_multi_class
param["objective"] = "multi:softprob"
param["scale_pos_weight"] = 1
param["min_child_weight"] = 0.000001
print(param)
if "n_round" not in list(config.keys()):
n_round = 300 if args.channel == "Hadronic" else 150
#n_round = 10
if "FCNC" in args.input:
n_round = 150
if args.multi:
n_round = 150
if "SMHiggs" in args.input and args.channel == "Hadronic":
n_round = 500
else:
n_round = config["n_round"]
evallist = [(d_train, 'train'), (d_test, 'test')]
progress = {}
print((param, n_round))
# train
bdt = xgboost.train(param,
d_train,
n_round,
evallist,
evals_result=progress)
bdt.save_model(args.channel + "_" + args.tag + "_" + args.ext + "_bdt.xgb")
model = bdt.get_dump()
input_variables = []
for name in feature_names:
input_variables.append((name, 'F'))
tmva_utils.convert_model(model,
input_variables=input_variables,
output_xml=args.channel + "_" + args.tag + "_" +
args.ext + '_bdt.xml')
# predict
pred_train = bdt.predict(d_train)
pred_test = bdt.predict(d_test)
pred_data = bdt.predict(d_data)
pred_final_fit = bdt.predict(d_final_fit)
if args.reference_mva != "none":
if ".xgb" in args.reference_mva:
ref_mva = xgboost.Booster()
ref_mva.load_model(args.reference_mva)
pred_ref_train = ref_mva.predict(d_train, output_margin=args.multi)
pred_ref_test = ref_mva.predict(d_test, output_margin=args.multi)
pred_ref_data = ref_mva.predict(d_data, output_margin=args.multi)
pred_ref_final_fit = ref_mva.predict(d_final_fit,
output_margin=args.multi)
elif ".json" in args.reference_mva:
import dnn_helper
dnn_features_train = dnn_helper.DNN_Features(
name='train',
global_features=global_dnn_features,
objects=objects)
dnn_features_validation = dnn_helper.DNN_Features(
name='validation',
global_features=global_dnn_features_validation,
objects=objects_validation)
dnn_features_data = dnn_helper.DNN_Features(
name='data',
global_features=global_dnn_features_data,
objects=objects_data)
dnn_features_final_fit = dnn_helper.DNN_Features(
name='final_fit',
global_features=global_dnn_features_final_fit,
objects=objects_final_fit)
with open(args.reference_mva, "r") as f_in:
metadata = json.load(f_in)
dnn = dnn_helper.DNN_Helper(
features_validation=dnn_features_validation,
features_train=dnn_features_train,
features_data=dnn_features_data,
features_final_fit=dnn_features_final_fit,
metadata=metadata,
weights_file="dnn_weights/" + metadata["weights"],
train_mode=False)
dnn.predict(debug=True)
pred_ref_train = dnn.predictions["train"]
pred_ref_test = dnn.predictions["validation"]
pred_ref_data = dnn.predictions["data"]
pred_ref_final_fit = dnn.predictions["final_fit"]
print((pred_test.shape))
#if args.multi:
# pred_train = pred_train[:,0]
# pred_test = pred_test[:,0]
# pred_data = pred_data[:,0]
# pred_final_fit = pred_final_fit[:,0]
print((pred_test.shape))
# analysis
# ks test
if args.multi:
prediction_train = pred_train[:, 0]
prediction_test = pred_test[:, 0]
else:
prediction_train = pred_train
prediction_test = pred_test
d_sig, p_value_sig, d_bkg, p_value_bkg = ks_test.ks_test(
prediction_train, prediction_test, y_train, y_test)
print(
("Results of ks-test (d-score) for signal: %.10f and background: %.10f"
% (d_sig, d_bkg)))
print(
("Results of ks-test (p-value) for signal: %.10f and background: %.10f"
% (p_value_sig, p_value_bkg)))
# roc curves
fpr_train, tpr_train, thresh_train = metrics.roc_curve(
y_train, prediction_train, pos_label=1, sample_weight=weights_train)
fpr_test, tpr_test, thresh_test = metrics.roc_curve(
y_test, prediction_test, pos_label=1, sample_weight=weights_test)
y_train_2016 = ks_test.logical_vector(y_train, year, 2016)
y_test_2016 = ks_test.logical_vector(y_test, year_validation, 2016)
prediction_train_2016 = ks_test.logical_vector(prediction_train, year,
2016)
prediction_test_2016 = ks_test.logical_vector(prediction_test,
year_validation, 2016)
weights_train_2016 = ks_test.logical_vector(weights_train, year, 2016)
weights_test_2016 = ks_test.logical_vector(weights_test, year_validation,
2016)
y_train_2017 = ks_test.logical_vector(y_train, year, 2017)
y_test_2017 = ks_test.logical_vector(y_test, year_validation, 2017)
prediction_train_2017 = ks_test.logical_vector(prediction_train, year,
2017)
prediction_test_2017 = ks_test.logical_vector(prediction_test,
year_validation, 2017)
weights_train_2017 = ks_test.logical_vector(weights_train, year, 2017)
weights_test_2017 = ks_test.logical_vector(weights_test, year_validation,
2017)
y_train_2018 = ks_test.logical_vector(y_train, year, 2018)
y_test_2018 = ks_test.logical_vector(y_test, year_validation, 2018)
prediction_train_2018 = ks_test.logical_vector(prediction_train, year,
2018)
prediction_test_2018 = ks_test.logical_vector(prediction_test,
year_validation, 2018)
weights_train_2018 = ks_test.logical_vector(weights_train, year, 2018)
weights_test_2018 = ks_test.logical_vector(weights_test, year_validation,
2018)
if len(y_train_2016) > 0:
fpr_train_2016, tpr_train_2016, thresh_train_2016 = metrics.roc_curve(
y_train_2016,
prediction_train_2016,
pos_label=1,
sample_weight=weights_train_2016)
fpr_test_2016, tpr_test_2016, thresh_test_2016 = metrics.roc_curve(
y_test_2016,
prediction_test_2016,
pos_label=1,
sample_weight=weights_test_2016)
auc_2016, unc_2016, blah, blah, blah = utils.auc_and_unc(
y_test_2016, prediction_test_2016, weights_test_2016, 25)
print(("Testing AUC (2016): %.3f +/- %.4f" % (auc_2016, unc_2016)))
numpy.savez("bdt_roc_2016_%s.npz" % (args.channel + "_" + args.tag),
y_train=y_train_2016,
y_test=y_test_2016,
prediction_train=prediction_train_2016,
prediction_test=prediction_test_2016,
fpr_train=fpr_train_2016,
fpr_test=fpr_test_2016,
tpr_train=tpr_train_2016,
tpr_test=tpr_test_2016)
if len(y_train_2017) > 0:
fpr_train_2017, tpr_train_2017, thresh_train_2017 = metrics.roc_curve(
y_train_2017,
prediction_train_2017,
pos_label=1,
sample_weight=weights_train_2017)
fpr_test_2017, tpr_test_2017, thresh_test_2017 = metrics.roc_curve(
y_test_2017,
prediction_test_2017,
pos_label=1,
sample_weight=weights_test_2017)
auc_2017, unc_2017, blah, blah, blah = utils.auc_and_unc(
y_test_2017, prediction_test_2017, weights_test_2017, 25)
print(("Testing AUC (2017): %.3f +/- %.4f" % (auc_2017, unc_2017)))
numpy.savez("bdt_roc_2017_%s.npz" % (args.channel + "_" + args.tag),
y_train=y_train_2017,
y_test=y_test_2017,
prediction_train=prediction_train_2017,
prediction_test=prediction_test_2017,
fpr_train=fpr_train_2017,
fpr_test=fpr_test_2017,
tpr_train=tpr_train_2017,
tpr_test=tpr_test_2017)
if len(y_train_2018) > 0:
fpr_train_2018, tpr_train_2018, thresh_train_2018 = metrics.roc_curve(
y_train_2018,
prediction_train_2018,
pos_label=1,
sample_weight=weights_train_2018)
fpr_test_2018, tpr_test_2018, thresh_test_2018 = metrics.roc_curve(
y_test_2018,
prediction_test_2018,
pos_label=1,
sample_weight=weights_test_2018)
auc_2018, unc_2018, blah, blah, blah = utils.auc_and_unc(
y_test_2018, prediction_test_2018, weights_test_2018, 25)
print(("Testing AUC (2018): %.3f +/- %.4f" % (auc_2018, unc_2018)))
numpy.savez("bdt_roc_2018_%s.npz" % (args.channel + "_" + args.tag),
y_train=y_train_2018,
y_test=y_test_2018,
prediction_train=prediction_train_2018,
prediction_test=prediction_test_2018,
fpr_train=fpr_train_2018,
fpr_test=fpr_test_2018,
tpr_train=tpr_train_2018,
tpr_test=tpr_test_2018)
auc_train = metrics.auc(fpr_train, tpr_train, reorder=True)
auc_test = metrics.auc(fpr_test, tpr_test, reorder=True)
auc, unc, blah, blah, blah = utils.auc_and_unc(y_test, prediction_test,
weights_test, 25)
results["auc_train"] = auc_train
results["auc_test"] = auc_test
results["auc_test_unc"] = unc
if "skip_tree" in list(config.keys()):
return results
print(("Training AUC: %.3f" % auc_train))
print(("Testing AUC: %.3f" % auc_test))
print(("Testing AUC: %.3f +/- %.4f" % (auc, unc)))
numpy.savez("bdt_roc_%s.npz" % (args.channel + "_" + args.tag),
y_train=y_train,
y_test=y_test,
prediction_train=prediction_train,
prediction_test=prediction_test,
fpr_train=fpr_train,
fpr_test=fpr_test,
tpr_train=tpr_train,
tpr_test=tpr_test)
# Write output to TTree
tree_train_id = numpy.concatenate(
(numpy.zeros(len(pred_train)), numpy.ones(len(pred_test)),
numpy.ones(len(pred_data)), numpy.ones(len(pred_final_fit))))
tree_sample_id = numpy.concatenate(
(label, label_validation, label_data, numpy.ones(len(pred_final_fit))))
tree_mass = numpy.concatenate(
(mass, mass_validation, mass_data, mass_final_fit))
tree_weight = numpy.concatenate(
(weights, weights_validation, weights_data, weights_final_fit))
tree_signal_mass_label = numpy.concatenate(
(signal_mass_label, signal_mass_label_validation,
signal_mass_label_data, numpy.zeros(len(pred_final_fit))))
tree_signal_mass_category = numpy.concatenate(
(signal_mass_category, signal_mass_category_validation,
signal_mass_category_data, numpy.zeros(len(pred_final_fit))))
tree_tth_2017_reference_mva = numpy.concatenate(
(tth_2017_reference_mva, tth_2017_reference_mva_validation,
tth_2017_reference_mva_data, tth_2017_reference_mva_final_fit))
tree_evt = numpy.concatenate(
(evt, evt_validation, evt_data, evt_final_fit))
tree_tth_runII_mva = numpy.concatenate(
(tth_runII_mva, tth_runII_mva_validation, tth_runII_mva_data,
tth_runII_mva_final_fit))
tree_run = numpy.concatenate(
(run, run_validation, run_data, run_final_fit))
tree_lumi = numpy.concatenate(
(lumi, lumi_validation, lumi_data, lumi_final_fit))
tree_process_id = numpy.concatenate(
(process_id, process_id_validation, process_id_data,
process_id_final_fit))
tree_year = numpy.concatenate(
(year, year_validation, year_data, year_final_fit))
tree_global_features = numpy.concatenate(
(global_features, global_features_validation, global_features_data,
global_features_final_fit))
if ".json" in args.reference_mva:
tree_dnn_features = numpy.concatenate(
(global_dnn_features, global_dnn_features_validation,
global_dnn_features_data, global_dnn_features_final_fit))
training_feature_names = [
training_feature_names for i in range(len(label))
]
training_feature_names_validation = [
training_feature_names for i in range(len(label_validation))
]
training_feature_names_data = [
training_feature_names for i in range(len(label_data))
]
training_feature_names_final_fit = [
training_feature_names for i in range(len(label_final_fit))
]
#tree_training_feature_names = numpy.concatenate((training_feature_names, training_feature_names_validation, training_feature_names_data, training_feature_names_final_fit))
tree_train_id = tree_train_id.astype(numpy.int64)
tree_sample_id = tree_sample_id.astype(numpy.int64)
tree_mass = tree_mass.astype(numpy.float64)
tree_weight = tree_weight.astype(numpy.float64)
tree_signal_mass_label = tree_signal_mass_label.astype(numpy.int64)
tree_signal_mass_category = tree_signal_mass_category.astype(numpy.int64)
tree_tth_2017_reference_mva = tree_tth_2017_reference_mva.astype(
numpy.float64)
tree_evt = tree_evt.astype(numpy.uint64)
tree_tth_runII_mva = tree_tth_runII_mva.astype(numpy.float64)
tree_run = tree_run.astype(numpy.uint64)
tree_lumi = tree_lumi.astype(numpy.uint64)
tree_process_id = tree_process_id.astype(numpy.int64)
tree_year = tree_year.astype(numpy.int64)
tree_global_features = tree_global_features.astype(numpy.float64)
if ".json" in args.reference_mva:
tree_dnn_features = tree_dnn_features.astype(numpy.float64)
#tree_training_feature_names = tree_training_feature_names.astype(numpy.string_)
dict = {
"train_id": tree_train_id,
"sample_id": tree_sample_id,
"mass": tree_mass,
"weight": tree_weight,
"signal_mass_label": tree_signal_mass_label,
"signal_mass_category": tree_signal_mass_category,
"tth_2017_reference_mva": tree_tth_2017_reference_mva,
"process_id": tree_process_id,
"year": tree_year,
"event": tree_evt,
"lumi": tree_lumi,
"run": tree_run,
"global_features": tree_global_features,
"tth_runII_mva": tree_tth_runII_mva
} #, "training_feature_names" : tree_training_feature_names}
if ".json" in args.reference_mva:
dict["dnn_global_features"] = tree_dnn_features
if args.multi:
tree_bdt_score = []
for i in range(num_multi_class):
tree_bdt_score.append(
numpy.concatenate(
(pred_train[:, i], pred_test[:, i], pred_data[:, i],
numpy.ones(len(pred_final_fit)))))
tree_bdt_score[i] = tree_bdt_score[i].astype(numpy.float64)
dict["mva_score_%d" % i] = tree_bdt_score[i]
else:
tree_bdt_score = numpy.concatenate(
(pred_train, pred_test, pred_data, pred_final_fit))
tree_bdt_score = tree_bdt_score.astype(numpy.float64)
dict["mva_score"] = tree_bdt_score
if args.reference_mva != "none":
tree_ref_mva_score = numpy.concatenate(
(pred_ref_train, pred_ref_test, pred_ref_data, pred_ref_final_fit))
tree_ref_mva_score = tree_ref_mva_score.astype(numpy.float64)
dict[args.reference_mva_name] = tree_ref_mva_score
tree_utils.numpy_to_tree(
dict, "ttH%s_%s_FinalFitTree.root" % (args.channel, args.tag))
### Make diagnostic plots ###
import matplotlib.pyplot as plt
# variable importance #
fig = plt.figure()
xgboost.plot_importance(bdt)
plt.tight_layout()
plt.savefig('feature_importance_' + args.channel + '.pdf')
# make ROC curve #
fig = plt.figure()
ax = fig.add_subplot(111)
ax.yaxis.set_ticks_position('both')
ax.grid(True)
plt.grid(color='black', linestyle='--', linewidth=0.1, which='both')
plt.plot(fpr_train, tpr_train, color='red', label='Training Set', lw=3)
plt.plot(fpr_test, tpr_test, color='green', label='Testing Set', lw=3)
plt.xscale('log')
plt.xlim([0.005, 1.0])
plt.ylim([0.3, 1.05])
plt.xlabel('False Positive Rate (background efficiency)')
plt.ylabel('True Positive Rate (signal efficiency)')
plt.legend(loc='lower right')
plt.savefig('roc' + args.channel + '.pdf', bbox_inches='tight')
estimate_za = True
use_tth_runII_mva = False
use_tth_2017_mva = False
if estimate_za:
n_quantiles = 30
if args.multi:
signal_mva_scores = {}
bkg_mva_scores = {}
data_mva_scores = {}
for i in range(
0, num_multi_class - 1
): # optimize with each of the bkg probabilities (the signal probability is redundant, i.e. sum of probabilities = 1)
reverse = 1 if i == 0 else -1
signal_mva_scores[
"bdt_score_%d" % i] = reverse * ks_test.logical_vector(
pred_test[:, i], y_test, 1
) # factor of -1 so that we cut *below* certain values, as these are background probabilities, not signal
bkg_mva_scores["bdt_score_%d" %
i] = reverse * ks_test.logical_vector(
pred_test[:, i], y_test, 0)
data_mva_scores["bdt_score_%d" % i] = reverse * pred_data[:, i]
elif use_tth_runII_mva:
print "Using RunII MVA from flashgg"
signal_mva_scores = {
"bdt_score":
ks_test.logical_vector(tth_runII_mva_validation, y_test, 1)
}
bkg_mva_scores = {
"bdt_score":
ks_test.logical_vector(tth_runII_mva_validation, y_test, 0)
}
data_mva_scores = {"bdt_score": tth_runII_mva_data}
elif use_tth_2017_mva:
print "Using 2017 ttH PAS MVA"
signal_mva_scores = {
"bdt_score":
ks_test.logical_vector(tth_2017_reference_mva_validation,
y_test, 1)
}
bkg_mva_scores = {
"bdt_score":
ks_test.logical_vector(tth_2017_reference_mva_validation,
y_test, 0)
}
data_mva_scores = {"bdt_score": tth_2017_reference_mva_data}
else:
print "Using the MVA we just trained"
signal_mva_scores = {
"bdt_score": ks_test.logical_vector(pred_test, y_test, 1)
}
bkg_mva_scores = {
"bdt_score": ks_test.logical_vector(pred_test, y_test, 0)
}
data_mva_scores = {"bdt_score": pred_data}
signal_mass = ks_test.logical_vector(mass_validation, y_test, 1)
bkg_mass = ks_test.logical_vector(mass_validation, y_test, 0)
signal_njets = ks_test.logical_vector(njets_validation, y_test, 1)
bkg_njets = ks_test.logical_vector(njets_validation, y_test, 0)
signal_weights = ks_test.logical_vector(weights_validation, y_test, 1)
#if args.channel == "Leptonic" and "FCNC" in args.input:
# signal_weights *= 1./1.53 # to account for bug in MC sample where W->lv decays don't include taus
bkg_weights = ks_test.logical_vector(weights_validation, y_test, 0)
bkg_process_id = ks_test.logical_vector(process_id_validation, y_test,
0)
optimization_vars = args.optimization_vars.split(
",") if args.optimization_vars else []
for var in optimization_vars:
signal_mva_scores[var] = ks_test.logical_vector(
utils.load_array(f, var + '_validation'), y_test, 1)
bkg_mva_scores[var] = ks_test.logical_vector(
utils.load_array(f, var + '_validation'), y_test, 0)
data_mva_scores[var] = utils.load_array(f, var + '_data')
signal_events = {
"mass": signal_mass,
"weights": signal_weights,
"mva_score": signal_mva_scores
}
bkg_events = {
"mass": bkg_mass,
"weights": bkg_weights,
"mva_score": bkg_mva_scores,
"process_id": bkg_process_id
}
data_events = {
"mass": mass_data,
"weights": weights_data,
"mva_score": data_mva_scores,
"process_id": numpy.ones_like(mass_data)
}
# Trim these dictionaries down
#for evts_dict in [signal_events, bkg_events, data_events]:
# good_indices = [index for index, value in enumerate(evts_dict["mass"]) if value < 180.]
# print float(len(good_indices))/float(len(evts_dict["mass"]))
# for key in evts_dict.iterkeys():
# full_array = evts_dict[key]
# trimmed_array = [full_array[i] for i in good_indices]
# evts_dict[key] = trimmed_array
mass_shift = not (
"FCNC" in args.input
) # if we're using FCNC as signal, all Higgs mass points should be 125
# but, if we're using ttH as signal, we use M127 sample for testing, so need to shift for proper comparison with other M125 samples
za, za_unc, s, b, sigma_eff = significance_utils.za_scores(
n_quantiles, signal_events, bkg_events, False, {}, mass_shift)
za_data, za_unc_data, s_data, b_data, sigma_eff_data = significance_utils.za_scores(
n_quantiles, signal_events, data_events, True, bkg_events,
mass_shift)
za = numpy.asarray(za)
max_za = numpy.max(za)
max_za_unc = za_unc[numpy.argmax(za)]
print((max_za, max_za_unc))
numpy.savez("za_%s.npz" %
(args.channel + "_" + args.ext + "_" + args.tag),
za=za,
za_unc=za_unc,
signal=s,
bkg=b,
sigma_eff=sigma_eff,
za_data=za_data,
za_unc_data=za_unc_data,
signal_data=s_data,
bkg_data=b_data,
sigma_eff_data=sigma_eff_data)
numpy.savez("sigma_eff.npz", sigma_eff=sigma_eff, n_sig=s)
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
fig = plt.figure()
ax1 = fig.add_subplot(111)
ax1.plot(s, za, label='MC', color='red')
ax1.fill_between(s,
numpy.asarray(za) - numpy.asarray(za_unc),
numpy.asarray(za) + numpy.asarray(za_unc),
color='red',
alpha=0.25)
ax1.plot(s_data, za_data, label='Data', color='black')
ax1.fill_between(s_data,
numpy.asarray(za_data) - numpy.asarray(za_unc_data),
numpy.asarray(za_data) + numpy.asarray(za_unc_data),
color='black',
alpha=0.25)
plt.xlabel('# Signal Events')
ax1.set_ylabel('Significance (Z_A)')
plt.ylim([0.0, 3.0])
l, r = plt.xlim()
plt.xlim([1.0, r])
ax1.legend(loc='upper right')
plt.savefig('za_curve.pdf')
return results