def main():
response_columns = []
columns = []
filename = sys.argv[1]
#columns = sys.argv[2].strip('[]').split(',')
response_columns_classification = sys.argv[2].strip('[]').split(', ')
response_columns_predictin = sys.argv[3].strip('[]').split(', ')
#features
columns = [
'MO', 'N', 'INDICE20', 'PHEAU', 'PHSMP', 'KECH', 'CAECH', 'MGECH',
'NAECH', 'HECH', 'CEC', 'PM3', 'MNM3', 'CUM3', 'FEM3', 'ALM3', 'BM3',
'ZNM3', 'PBM3', 'MOM3', 'CDM3', 'COM3', 'CRM3', 'KM3', 'CAM3', 'MGM3',
'NAM3'
]
columns_M3 = columns[1:5] + [columns[9]] + columns[11:]
columns = columns_M3
#single target classification
for response_target in response_columns_classification:
df = read_data(filename, columns, response_target)
data_view(df, columns, response_target)
classification(df, columns, response_target)
#regression
df = read_data(filename, columns, response_columns_predictin)
df.dropna(inplace=True)
prediction(df, columns, response_columns_predictin)
def evaluate_accuracy(task_id, dificulty, errors=False, outputFile='result.txt', silent=False):
if not silent:
print('reading and processing testing data')
X, Y = read_data(training=False, task_id=task_id, difficulty=dificulty)
if not silent:
print("Getting representation")
# representation = _classifier.get_representation(task_id)
# if representation is None:
# representation = _classifier.default_representation(Y)
Y = _classifier.labels_remove_twos(Y)
representation = _classifier.find_representation(Y)
print('Representation for accuracy: ', representation)
if not silent:
print('read')
print('predicting..')
raw_predicted = nn.get_model(tasks_encoded[(task_id, dificulty)]).predict(X)
# _classifier.print_labels(raw_predicted[:5])
predicted = _classifier.get_normal_output(raw_predicted, representation)
# print(predicted.shape)
acc = accuracy(predicted, Y, raw_predicted, errors)
print('Accuracy %.4f' % acc)
return acc
def check():
#raw_labels = np.array([[0.0, 0.142, 0.542, 0.001, 0.0, 0.13, 0.124, 0.0, 0.0, 0.061000001]])
#r#epresentation = [(8,1)]
#Y, _ = tra#nsform_labels_with_representation(labels_remove_twos(Y), 4)
_, Y = read_data(task_id=3, difficulty=2)
Y = labels_remove_twos(Y)
rep = find_representation(Y)
print(rep)
def read_data_sheet(self):
datafile = frame_1.datafile.GetValue()
if not os.path.exists(datafile):
self.popup_box("Can't find "+datafile, "Can't find "+datafile)
return
#print all_genes_and_traits
#data_sheet.update(readdata.read_data(datafile))
data_list, column_labels = readdata.read_data(datafile)
self.data_sheet.extend(data_list)
#column_labels = data_sheet.keys()
self.all_genes_and_traits.extend(column_labels)
#print "all", all_genes_and_traits
#all_genes_and_traits.sort()
frame_1.gene_list.Set(self.all_genes_and_traits)
frame_1.trait_list.Set(self.all_genes_and_traits)
# assume that the selection variable is in first columns
frame_1.selection_variable_list.SetItems(self.all_genes_and_traits[0:20])
def main():
# uncomment this to create new model
prepare_training_set()
# return
# load model back
clf = joblib.load('model.pkl')
# read sample
image = read_data(sys.stdin)
# extract the characters
characters = extract_characters(image)
for character in characters:
prediction = clf.predict(character.ravel().reshape(1, -1))
sys.stdout.write(prediction[0])
sys.stdout.write('\n')
def get_original_output(task_id, difficulty):
X, Y = read_data(training=False, task_id=task_id, difficulty=difficulty)
Y = _classifier.labels_remove_twos(Y)
representation = _classifier.find_representation(Y)
raw_predicted = nn.get_model(tasks_encoded[(task_id, difficulty)]).predict(X)
predicted = _classifier.get_normal_output(raw_predicted, representation)
def transform_single_label(label, how):
i = 0
new = []
for id in range(len(how)):
if how[id]==2:
new.append(0)
else:
new.append(label[i])
i += 1
return how
return list(map(lambda label: transform_single_label(label, Y[0]), predicted))
def model_statistics_on_task(task_id, difficulty, epochs):
# train for 1
X_, Y = read_data(task_id=task_id, difficulty=difficulty)
X_, Y, _ = transform_data(X_, Y, task_id)
nn.construct_model(X_[0].shape)
nn.add_new_task(len(Y[0]))
model = nn.get_model().model
X = nn.get_model().make_input(X_)
tasks_encoded[(task_id, difficulty)] = len(nn.tasks) - 1
acc_history = []
for epoch in range(epochs + 1):
print('Epoch #', epoch)
if epoch > 0:
model.fit(X, Y, nb_epoch=1)
acc_history.append(evaluate_accuracy(task_id, difficulty, silent=True))
return acc_history
def read_data_sheet(self):
datafile = frame_1.datafile.GetValue()
if not os.path.exists(datafile):
self.popup_box("Can't find " + datafile, "Can't find " + datafile)
return
#print all_genes_and_traits
#data_sheet.update(readdata.read_data(datafile))
data_list, column_labels = readdata.read_data(datafile)
self.data_sheet.extend(data_list)
#column_labels = data_sheet.keys()
self.all_genes_and_traits.extend(column_labels)
#print "all", all_genes_and_traits
#all_genes_and_traits.sort()
frame_1.gene_list.Set(self.all_genes_and_traits)
frame_1.trait_list.Set(self.all_genes_and_traits)
# assume that the selection variable is in first columns
frame_1.selection_variable_list.SetItems(
self.all_genes_and_traits[0:20])
def train_network_ui(task_id, difficulty, epochs=3):
# tasks[(task_id, difficulty)] = len(tasks.keys())
X, Y = read_data(task_id=task_id, difficulty=difficulty)
train_network(X, Y, epochs=epochs, train=True, load_model=False, filename=['model.txt', 'weights.hdf5'],
task_id=task_id)
tasks_encoded[(task_id, difficulty)] = len(nn.tasks) - 1
old_accuracy = evaluate_accuracy(task_id, difficulty, silent=True)
print('Old accuracy: ', old_accuracy)
if len(nn.tasks)>1:
buffered = nn.tasks[-1]
nn.tasks.pop()
train_network(X, Y, epochs=epochs, train=True, load_model=False, filename=['model.txt', 'weights.hdf5'],
task_id=task_id, independent=True)
new_accuracy = evaluate_accuracy(task_id, difficulty, silent=True)
print('New accuracy: ', new_accuracy)
if new_accuracy<old_accuracy:
nn.tasks[-1] = buffered
old_accuracy = new_accuracy
if old_accuracy<0.9:
nn.tasks[-1].kill()
def evaluate_accuracy(task_id, difficulty, errors=False, outputFile='result.txt'):
print('reading and processing testing data')
X, Y = read_data(training=False, task_id=task_id, difficulty=difficulty)
print("Getting representation")
print('read')
Y = _classifier.labels_remove_twos(Y)
print('predicting..')
representation = _classifier.find_representation(Y)
if (task_id, difficulty) in tasks.keys():
model = nn.get_model(tasks[(task_id, difficulty)])
else:
raise Exception('Task unknown')
return
raw_predicted = model.predict(X, verbose=1)
predicted = _classifier.get_normal_output(raw_predicted, representation)
acc = accuracy(predicted, Y, raw_predicted, errors)
print('Accuracy %.4f' % acc)
return acc
from matplotlib.pyplot import * from numpy import * from Green_function import Green_func from readdata import read_data (rs,r0,R2,kx,kt,Rm2,d,h3,h2,h1,rmax,Q,M,v,muq) = read_data() #kx = [0.0,0.05,0.1,0.15,0.2,0.25,0.3,0.35,0.4,0.45,0.5,0.55,0.6,0.65,0.7,0.75,0.8,0.85,0.9,0.95,1.0] #kx = [0.0,0.5,1.5,2.5,5.0,10.0] kx = 0.0 kt = [1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0,10.0] Scale = 1 Gr_f = zeros(len(kt),complex) for i in range(0,len(kt)): Gr_f[i] = Green_func(rs,r0,R2,kx,kt[i],Rm2,d,h3,h2,h1,rmax,Q,M,v,muq,Scale) print Gr_f[i] print Scale figure(1) plot(kt,Gr_f.imag,label='Scale = %f'%(kx)) ###################################################################################### kx = 5.0 for i in range(0,len(kt)): Gr_f[i] = Green_func(rs,r0,R2,kx,kt[i],Rm2,d,h3,h2,h1,rmax,Q,M,v,muq,Scale) print Gr_f[i] print Scale plot(kt,Gr_f.imag,label='Scale = %f'%(kx)) ###################################################################################### kx = 10.0 for i in range(0,len(kt)): Gr_f[i] = Green_func(rs,r0,R2,kx,kt[i],Rm2,d,h3,h2,h1,rmax,Q,M,v,muq,Scale)
def train_network_ui(task_id, difficulty, epochs=3):
tasks[(task_id, difficulty)] = len(tasks.keys())
X, Y = read_data(task_id=task_id, difficulty=difficulty)
return train_network(X, Y, epochs=epochs, train=True, load_model=False, filename=['model.txt', 'weights.hdf5'])
import numpy as np
import sklearn.linear_model as linear_model
from LogisticRegression import LogisticRegression
from readdata import read_data
from sklearn import cross_validation
from sklearn.pipeline import Pipeline
from sklearn.grid_search import GridSearchCV
X_train,y_train = read_data("./Data/train")
X_train = X_train.toarray()
#convert labels to 0,1
idx = np.where(y_train==-1)
y_train[idx] = 0.
kf = cross_validation.KFold(y_train.shape[0], n_folds=10, indices=False)
X_test,y_test = read_data("./Data/test")
X_test = X_test.toarray()
idx = np.where(y_test==-1)
y_test[idx] = 0.
parameters = dict({
"clf__weight_decay" : [.001,.01,.1,1,10,100,1000],
"clf__init_beta" : [0.,0.00001,.0001,0.001,.01,.1,1.,10],
})
lr = LogisticRegression(learning="LBFGS",X_test=X_test,y_test=y_test)
pipeline = Pipeline([
("clf" ,lr),
])
f = GridSearchCV(pipeline,parameters,n_jobs=-1,verbose=-1,cv=3)
f.fit(X_train,y_train)
best_parameters = f.best_estimator_.get_params()
# Don't need to remember the old paths
path = newpath
n = 0 # if only one element is observed max is sought in the initialization values
if len(obs)!=1:
n = t
(prob, state) = max((V[n][y], y) for y in states)
return (prob, path[state])
if __name__ == '__main__':
try:
datafile = sys.argv[1]
except:
datafile = 'AllDataWithNonHarmonics.csv'
headers = ['module', 'root', 'bar_of_phrase', 'letter', 'bars_per_phrase', 'song_name']
data = read_data(datafile, headers)
transition_probs, emission_probs, initial_probs, states = get_probabilities(data)
# print states
# for one, two in emission_probs:
# print '{}->{}: {:.4f}'.format(one, two, emission_probs[(one, two)])
# for state in initial_probs:
# print state, initial_probs[state]
total_correct = 0
total = 0
for song in data:
obs = [entry['root'] for entry in song]
correct = [entry['module'].split('_')[0] for entry in song]
prob, predictions = viterbi(obs, states, initial_probs, transition_probs, emission_probs)
return chord_counts, transition_counts
def get_transition_probs(chord_counts, transition_counts):
"""
Returns a dictionary of transition probabilities based on counts for chords
and transitions.
"""
probs = dict(transition_counts) # make a copy so we don't destroy the counts dictionary
for (first, second), count in transition_counts.items():
probability = transition_counts[(first, second)] / chord_counts[first]
probs[(first, second)] = probability
return probs
if __name__ == '__main__':
try:
datafile = sys.argv[1]
except:
datafile = 'AlldataWithNonHarmonics.csv'
data = read_data(datafile)
chord_counts, transition_counts = get_overall_counts(data)
transition_probs = get_transition_probs(chord_counts, transition_counts)
# map roman numerals to integers for sorting, and covert back to display
transitions = [(RN.index(c1), RN.index(c2)) for c1, c2 in transition_probs]
print '\n' +'Phrase Length = ' + z[j]
for c1, c2 in sorted(transitions):
print '({} -> {}): {:.4f}'.format(RN[c1], RN[c2], transition_probs[(RN[c1], RN[c2])])
#init_state = np.tile(1e-5 * np.random.uniform(low=0.0,high=1.0,size=(n,n)),[batch_size,a_num,1,1])
loss_p = 0
batch_num_idx = range(batch_num)
k_fold = KFold(n_splits=10)
final_acc_fold = np.zeros((10, 1))
#CL = Chol_de(current_X,n)
#CC = Chol_com(CL,n,eps)
data = []
label = []
for idx in range(batch_num):
print(idx)
data_batch_in, label_batch_in = read_data(
idx, '../../TTRNN/UCF11_updated_mpg/processed_data/', matrix_length,
sample_rate)
data.append(data_batch_in)
label.append(label_batch_in)
with tf.Session() as sess:
final_acc = 0.
co = 0
for tr_indices, ts_indices in k_fold.split(batch_num_idx):
sess.run(tf.global_variables_initializer())
print(
np.sum([
np.prod(v.get_shape().as_list())
for v in tf.trainable_variables()
]))
#start_time = time.time()
def read_data(filename):
with open(filename, 'r') as csvf:
return [row for row in csv.reader(csvf)]
def write_csv(data, filename):
with open(filename, 'w') as csvfile:
writer = csv.writer(csvfile, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
for line in data:
writer.writerow(line)
if __name__ == '__main__':
try:
datafile = sys.argv[1]
except:
datafile = 'new_cluster_chord_by_chord.csv'
inputdata = read_data(datafile)
outputdata = []
uniquesongs = []
header = ['song', 'artist', 'year', 'meter', 'cluster15','cluster6'] #add kmeans6 when ready
outputdata.append(header)
for line in inputdata:
if line[0] not in uniquesongs:
uniquesongs.append(line[0])
songmeta = [line[0], line[1], line[2], line[3], line[8], line[9]] # add line[9] when kmeans6 is ready
outputdata.append(songmeta)
write_csv(outputdata, 'metadata_with_clusters.csv')
def evaluateDataset():
"""
Returns
-------
clf : Classifier Model
Evaluate and choose a classifier with the best suited options.
Evaluation includes accuracy, F1 score, precision and recall.
The output lists the importance of the selected features.
"""
### Add a couple features to this list.
# from newDataPoint import createNewPoints
# createNewPoints(data_dict)
alldata = read_data('flightdelays-2010-2020.csv')
key_features_list = [
'arr_del15', 'carrier_ct', ' weather_ct', 'nas_ct', 'security_ct',
'late_aircraft_ct'
]
features_list = [
'arr_del15', ' weather_ct', 'nas_ct', 'security_ct', 'late_aircraft_ct'
]
data = pd.DataFrame(alldata, columns=key_features_list)
target = []
data = data.dropna()
### Create a prediction target for late flights because of carrier delays.
for e in data['carrier_ct']:
if (e > 0):
target.append(1)
else:
target.append(0)
### Remove carrier_ct from the list as we used that to create the
### target data for the predictions.
### carrier_ct = weather_ct + nas_ct + security_ct + late_aircraft_ct
newdata = pd.DataFrame(data, columns=features_list)
data = newdata
### Decision Tree
from time import time
from sklearn import tree
clf = tree.DecisionTreeClassifier()
t0 = time()
clf.fit(data, target)
print("training time for all data:", round(time() - t0, 3), "s")
### print accuracy
print("Decision Tree Accuracy on All the data: ",
round(clf.score(data, target), 3))
from classifyDT import classifyDT
from sklearn.model_selection import train_test_split
features_train, features_test, labels_train, labels_test = \
train_test_split(data, target, test_size=0.5, random_state=42)
### features_train and features_test are the features for the training
### and testing datasets, respectively
### labels_train and labels_test are the corresponding item labels
# features_train, features_test, labels_train, labels_test = preprocess()
clf = classifyDT(features_train, labels_train, features_test, labels_test)
### Determine the importance of the features that we chose.
lat = [i for i in clf.feature_importances_]
### use the cut off 0.2 to determine the features of importance.
#def condition(x): return x > 0.2
def condition(x):
return x
output = [idx for idx, element in enumerate(lat) if condition(element)]
print("output:", output)
for i in output:
print("importance: of ", features_list[i], " is ", round(lat[i], 3))
return clf
from matplotlib.pyplot import * from numpy import * from Green_function import Green_func from readdata import read_data (rs,r0,L,kx,kt,ms,d,h3,h2,h1,rmax,Q,M,muq) = read_data() #kx = [0.0,0.05,0.1,0.15,0.2,0.25,0.3,0.35,0.4,0.45,0.5,0.55,0.6,0.65,0.7,0.75,0.8,0.85,0.9,0.95,1.0] #kx = [0.0,0.5,1.5,2.5,5.0,10.0] kx = 3.0 kt = linspace(-2.0,2.0,81) Scale = 1 Gr_f = zeros(len(kt),complex) for i in range(0,len(kt)): Gr_f[i] = Green_func(rs,r0,L,kx,kt[i],ms,d,h3,h2,h1,rmax,Q,M,muq,Scale) print Gr_f[i] print Scale figure(1) plot(kt,Gr_f.imag,label='Scale = %f'%Scale) ####################################################################################### #Scale = 10 #Gr_f = zeros(len(kt),complex) #for i in range(0,len(kt)): # Gr_f[i] = Green_func(rs,r0,L,kx,kt[i],ms,d,h3,h2,h1,rmax,Q,M,v,muq,Scale) # print Gr_f[i] #print Scale #figure(1) #plot(kt,Gr_f.imag,label='Scale = %f'%Scale) ''' ######################################################################################
def train(use_data,semi_sv,output,data_aug,epoch=1000):
def get_subset(dataset,idx):
data = {}
for key,value in dataset.items():
data[key] = value[idx]
return data
def concat_data(data1,data2):
result = {}
for k in data1.keys():
result[k] = np.concatenate([data1[k],data2[k]])
return result
from readdata import read_data
tr,te, embedding_matrix, labels = read_data(use_data,data_aug=data_aug)
print(use_data)
print('Shape of label tensor:', labels.shape)
y = labels
from config import model_path
from sklearn.cross_validation import StratifiedKFold, KFold
from config import n_folds
y_pred = pd.read_csv("./data/y_pred.csv")['y_pre'].values
y_pos_ = y_pred == 1
y_neg_ = y_pred == 0
add_idx = np.any([y_pos_, y_neg_], axis=0)
add_y = y_pred[add_idx]
y_pos = y_pred > 0.75
y_neg = y_pred < 0.25
y_idx = np.any([y_pos, y_neg], axis=0)
y_pred = y_pred[y_idx]
print(y_idx.shape)
folds = StratifiedKFold(y, n_folds=n_folds, shuffle=True)
result = np.zeros((len(te['q1']), 1))
oof_y = np.zeros((len(y), 1))
for n_fold, (tr_idx, val_idx) in enumerate(folds):
tr_x = get_subset(tr,tr_idx)
if semi_sv:
te_x = get_subset(te, y_idx)
tr_data = concat_data(tr_x,te_x)
tr_y = np.concatenate([y[tr_idx],y_pred])
else:
add_data = get_subset(te,add_idx)
tr_data = concat_data(tr_x,add_data)
tr_y = np.concatenate([y[tr_idx], add_y])
# tr_data = tr_x
# tr_y = y[tr_idx]
val_x = get_subset(tr, val_idx)
val_y = y[val_idx]
use_word = True
if use_data!='words':
use_word = False
model = get_model(word_embedding_matrix=embedding_matrix,use_word=use_word)
if n_fold == 0:
print(model.summary())
hist = epochHistory()
print(n_fold)
model.fit(tr_data,
tr_y,
epochs=epoch,
validation_data=[val_x,val_y],
verbose=1,
batch_size=256,
callbacks=[
EarlyStopping(patience=2, monitor='val_binary_crossentropy'),
# LearningRateScheduler(lr_de,verbose=1)
hist,
ModelCheckpoint('./weight/weights.{epoch:d}.hdf5',monitor='val_binary_crossentropy',save_weights_only=True)
])
result += iter_ense(hist.epochs,model,te)
# result += model.predict(te, batch_size=1024)
oof_y[val_idx] = model.predict(val_x, batch_size=2048)
K.clear_session()
tf.reset_default_graph()
# 提交结果
result /= n_folds
submit = pd.DataFrame()
submit['y_pre'] = list(result[:, 0])
submit.to_csv(output, index=False)
## 保存预测的训练标签
# oof_y = oof_y[:,0]
# oof_y_ = oof_y.round().astype(int)
#
# error_idx = oof_y_!=y
# print(np.sum(error_idx))
# oof_y[error_idx] = 1-oof_y[error_idx]
submit = pd.DataFrame()
submit['y_pre'] = oof_y[:,0]
submit.to_csv('./data/oofy.csv',index=False)
#! /usr/bin/python
from numpy import *
from pylab import *
from matplotlib.pyplot import *
from matplotlib import rc
from cmath import exp, cos, sin
from curvfit import *
from readdata import read_data
from RK_solver import RK4_solver, Adaptive_RK4_solver
#Constants
(rs,r0,L,kx,kt,ms,d,h3,h2,h1,rmax,Q,M,v,muq) = read_data('input.xml')
#k = 1.0
Scale = 1
mm = int((rmax-r0)*Scale/5)
Delta = d/2 + sqrt(d**2/4 + ms)
pow_r = [-Delta,Delta-d]
[r,fpr,fnr] = RK4_solver(rs,r0,L,kx,kt,ms,d,h3,h2,h1,rmax,Q,M,v,muq)
fp_real = zeros(len(fpr))
for i in range(0, len(fpr)):
fp_real[i] = fpr[i].real
fp_imag = zeros(len(fpr))
for i in range(0, len(fpr)):
fp_imag[i] = fpr[i].imag
for i in range(0, len(r)):
r[i] = r[i]-r0
#! /usr/bin/python
from numpy import *
from pylab import *
from matplotlib.pyplot import *
from matplotlib import rc
from cmath import exp, cos, sin
from curvfit import *
from readdata import read_data
from RK_solver import RK4_solver, Adaptive_RK4_solver
#Constants
(rs, r0, R2, kx, kt, Rm2, d, h3, h2, h1, rmax, Q, M, v,
muq) = read_data('input.xml')
#k = 1.0
Scale = 1
mm = int((rmax - r0) * Scale / 5)
Delta = d / 2 + sqrt(d**2 / 4 + Rm2)
pow_r = [-Delta, Delta - d]
err = 1e-9
[r, fr, tot_err] = Adaptive_RK4_solver(rs, r0, R2, kx, kt, Rm2, d, rmax, Q, M,
v, muq, err)
print "Total Error is ", tot_err
f_real = zeros(len(fr))
for i in range(0, len(fr)):
f_real[i] = fr[i].real
f_imag = zeros(len(fr))
for i in range(0, len(fr)):
def main():
# Set up the database of objects
X = readdata.read_data(infl)
# Choose initial means with K-means
means = ChooseInitialMeans(X)
# Set up initial clusters
distmat = SetDistMat(X, means)
clusters = InitialAssignment(distmat)
## debug code
#keys = sorted(clusters.keys())
#for key in keys:
# print("cluster %i:"%key)
# print(clusters[key])
## end of debug
# Iteration step
for iter in range(max_iter):
active = 0 # indicate the number of transfers in the current iteration
tranlst = (-1) * np.ones(
k, dtype='int') # set up transfer list for each cluster
# Compute the cluster means
oldmeans = means.copy()
means = CalcMeans(X, oldmeans, clusters)
# Get statistics about the clustering
#ClusterStat(X, means, clusters)
## debug code
#print("old means:")
#print(oldmeans)
#print("new means:")
#print(means)
## end of debug
# For each object, compute the distances to the cluster means
distmat = SetDistMat(X, means)
# Sort objects based on the delta of the current assignment and the best
# possible alternate assignment
objlst = SortObj(X, clusters, means, distmat)
##debug code
#print(objlst)
##return
#end of debug
# For each element by prioty:
while (len(objlst)):
(i, key, temp) = objlst.pop()
obj2key = GetDist(X[i], means[key])
transferred = False #record if any transfering has occured to i
if (key == distmat[i, 0][0]):
##debug
#print("%i is already the opt cluster for obj %i. no transfer"%(clu, i))
##end of debug
continue
# For each other clusters by element gain:
else:
for j in range(k):
clu = distmat[i, j][0] # the key of another cluster
objgain = obj2key - distmat[i, j][
1] # gain by transfering i from cluster key to clu
if (clu == key): # already in the cluster
continue
if (len(clusters[clu]) < cluster_size):
active += 1
transferred = True
clusters = Transfer(i, key, clu, clusters)
##debug
#print("cluster %i not full. transfer obj %i from cluster %i to it."%(clu, i, key))
##end of debug
break
elif (tranlst[clu] != -1
): # if the tranlst of another cluster is not empty
# distance between the obj in the tranlst and the current cluster
tran2key = GetDist(X[tranlst[clu]], means[key])
tran2clu = GetDist(X[tranlst[clu]], means[clu])
# gain by transfering the obj in tranlst from cluster clu to key
trangain = tran2clu - tran2key
if (
objgain + trangain > 0
): # transfer if the sum of gains are positive, ie net gain
active += 2
transferred = True
clusters = Transfer(i, key, clu, clusters)
clusters = Transfer(tranlst[clu], clu, key,
clusters)
##debug
#print("obj %i is transfered from cluster %i to %i"%(i, key, clu))
#print("obj %i is transfered from cluster %i to %i"%(tranlst[clu], clu, key))
#print("objgain: %f, trangain: %f"%(objgain, trangain))
##end of debug
tranlst[clu] = -1 # reset the tranlst to empty
break
if (not transferred):
tranlst[key] = i
##debug
#print("add obj %i in cluster %i to the transfer list"%(i, key))
##end of debug
# nothing is transferred during this iteration, return the clustering result
if (not active):
break
#debug code
print("number of transfers in iter %i: %i\n" % (iter + 1, active))
#end of debug
print("K-means clustering converged in %d iterations!\n" % (iter + 1))
# Output the clustering results
WriteResult(outfl, X, means, clusters)
ClusterStat(X, means, clusters)
return (0)
# -*- coding: utf-8 -*-
"""
Created by Maya May 9, 2021
"""
import pandas as pd
from readdata import read_data
alldata = read_data('flightdelays-2010-2020.csv')
def evaluateDataset():
"""
Returns
-------
clf : Classifier Model
Evaluate and choose a classifier with the best suited options.
Evaluation includes accuracy, F1 score, precision and recall.
The output lists the importance of the selected features.
"""
### Add a couple features to this list.
# from newDataPoint import createNewPoints
# createNewPoints(data_dict)
alldata = read_data('flightdelays-2010-2020.csv')
key_features_list = [
'arr_del15', 'carrier_ct', ' weather_ct', 'nas_ct', 'security_ct',
'late_aircraft_ct'
]
features_list = [
'arr_del15', ' weather_ct', 'nas_ct', 'security_ct', 'late_aircraft_ct'
def main():
# Set up the database of objects
X = readdata.read_data(infl)
# Choose initial means with K-means
means = ChooseInitialMeans(X)
# Set up initial clusters
distmat = SetDistMat(X, means)
clusters = InitialAssignment(distmat)
## debug code
#keys = sorted(clusters.keys())
#for key in keys:
# print("cluster %i:"%key)
# print(clusters[key])
## end of debug
# Iteration step
for iter in range(max_iter):
active = 0 # indicate the number of transfers in the current iteration
tranlst = (-1)*np.ones(k, dtype='int') # set up transfer list for each cluster
# Compute the cluster means
oldmeans = means.copy()
means = CalcMeans(X, oldmeans, clusters)
# Get statistics about the clustering
#ClusterStat(X, means, clusters)
## debug code
#print("old means:")
#print(oldmeans)
#print("new means:")
#print(means)
## end of debug
# For each object, compute the distances to the cluster means
distmat = SetDistMat(X, means)
# Sort objects based on the delta of the current assignment and the best
# possible alternate assignment
objlst = SortObj(X, clusters, means, distmat)
##debug code
#print(objlst)
##return
#end of debug
# For each element by prioty:
while (len(objlst)):
(i, key, temp) = objlst.pop()
obj2key = GetDist(X[i], means[key])
transferred = False #record if any transfering has occured to i
if (key == distmat[i,0][0]):
##debug
#print("%i is already the opt cluster for obj %i. no transfer"%(clu, i))
##end of debug
continue
# For each other clusters by element gain:
else:
for j in range(k):
clu = distmat[i,j][0] # the key of another cluster
objgain = obj2key - distmat[i,j][1] # gain by transfering i from cluster key to clu
if (clu==key): # already in the cluster
continue
if (len(clusters[clu]) < cluster_size):
active += 1
transferred = True
clusters = Transfer(i, key, clu, clusters)
##debug
#print("cluster %i not full. transfer obj %i from cluster %i to it."%(clu, i, key))
##end of debug
break
elif (tranlst[clu] != -1): # if the tranlst of another cluster is not empty
# distance between the obj in the tranlst and the current cluster
tran2key = GetDist(X[tranlst[clu]], means[key])
tran2clu = GetDist(X[tranlst[clu]], means[clu])
# gain by transfering the obj in tranlst from cluster clu to key
trangain = tran2clu - tran2key
if (objgain + trangain > 0): # transfer if the sum of gains are positive, ie net gain
active += 2
transferred = True
clusters = Transfer(i, key, clu, clusters)
clusters = Transfer(tranlst[clu], clu, key, clusters)
##debug
#print("obj %i is transfered from cluster %i to %i"%(i, key, clu))
#print("obj %i is transfered from cluster %i to %i"%(tranlst[clu], clu, key))
#print("objgain: %f, trangain: %f"%(objgain, trangain))
##end of debug
tranlst[clu] = -1 # reset the tranlst to empty
break
if (not transferred):
tranlst[key] = i
##debug
#print("add obj %i in cluster %i to the transfer list"%(i, key))
##end of debug
# nothing is transferred during this iteration, return the clustering result
if (not active):
break
#debug code
print("number of transfers in iter %i: %i\n"%(iter+1, active))
#end of debug
print("K-means clustering converged in %d iterations!\n"%(iter+1))
# Output the clustering results
WriteResult(outfl, X, means, clusters)
ClusterStat(X, means, clusters)
return(0)
#! /usr/bin/python
from numpy import *
from pylab import *
from matplotlib.pyplot import *
from matplotlib import rc
from cmath import exp, cos, sin
from curvfit import *
from readdata import read_data
from RK_solver import RK4_solver, Adaptive_RK4_solver
#Constants
(rs,r0,R2,kx,kt,Rm2,d,h3,h2,h1,rmax,Q,M,v,muq) = read_data('input.xml')
#k = 1.0
Scale = 1
mm = int((rmax-r0)*Scale/5)
Delta = d/2 + sqrt(d**2/4 + Rm2)
pow_r = [-Delta,Delta-d]
err = 1e-9
[r,fr,tot_err]= Adaptive_RK4_solver(rs,r0,R2,kx,kt,Rm2,d,rmax,Q,M,v,muq,err)
print "Total Error is " , tot_err
f_real = zeros(len(fr))
for i in range(0, len(fr)):
f_real[i] = fr[i].real
f_imag = zeros(len(fr))
for i in range(0, len(fr)):
f_imag[i] = fr[i].imag
pre_train_epoch = 5000
epoch_num = 500 #50
depth = len(out_channels)
assert len(in_channels) == len(middle_channels) and len(
middle_channels) == len(out_channels)
k = 3
d0 = 1
############# pre-process data part
label_CSV = "data/ad_data/APOE.csv"
label_name = "APOE"
class_num = 2 ########
group_test_times = 5000
################
_, _, Label = read_data(label_CSV, label_name, recalculate=False)
NagPos = np.where(Label)
PosPos = np.where(1 - Label)
Length, Nampyte = load_length("./data/ad_data/processed_data/" +
label_name + "/Track_info.txt")
Trackids = [int(sys.argv[1])] ###### all fibers
Track_num = len(Trackids)
matrix_length_all = np.zeros(Track_num, dtype=np.int32)
for i in range(Track_num):
matrix_length_all[i] = Length[Trackids[i]][1]
matrix_length = np.sum(matrix_length_all)
from matplotlib.pyplot import *
from numpy import *
from Green_function import Green_func
from readdata import read_data
(rs, r0, L, kx, kt, ms, d, h3, h2, h1, rmax, Q, M, muq) = read_data()
#kx = [0.0,0.05,0.1,0.15,0.2,0.25,0.3,0.35,0.4,0.45,0.5,0.55,0.6,0.65,0.7,0.75,0.8,0.85,0.9,0.95,1.0]
#kx = [0.0,0.5,1.5,2.5,5.0,10.0]
kx = 3.0
kt = linspace(-2.0, 2.0, 81)
Scale = 1
Gr_f = zeros(len(kt), complex)
for i in range(0, len(kt)):
Gr_f[i] = Green_func(rs, r0, L, kx, kt[i], ms, d, h3, h2, h1, rmax, Q, M,
muq, Scale)
print Gr_f[i]
print Scale
figure(1)
plot(kt, Gr_f.imag, label='Scale = %f' % Scale)
#######################################################################################
#Scale = 10
#Gr_f = zeros(len(kt),complex)
#for i in range(0,len(kt)):
# Gr_f[i] = Green_func(rs,r0,L,kx,kt[i],ms,d,h3,h2,h1,rmax,Q,M,v,muq,Scale)
# print Gr_f[i]
#print Scale
#figure(1)
#plot(kt,Gr_f.imag,label='Scale = %f'%Scale)
'''
######################################################################################
def train_wc(semi_sv,output,epoch=1000):
from readdata import read_data
tr_q1, tr_q2, te_q1, te_q2, word_embedding_matrix, labels = read_data('words')
trc_q1, trc_q2, tec_q1, tec_q2, char_embedding_matrix, labels = read_data('chars')
X = {
'q1': tr_q1,
'q2': tr_q2,
'qc1': trc_q1,
'qc2': trc_q2
}
y = labels
from config import model_path
from sklearn.cross_validation import StratifiedKFold, KFold
from config import n_folds
from nn import aggmodel
y_pred = pd.read_csv("./data/y_pred.csv")['y_pre'].values
y_pos = y_pred > 0.75
y_neg = y_pred < 0.25
y_idx = np.any([y_pos, y_neg], axis=0)
y_pred = y_pred[y_idx]
print(y_idx.shape)
# oof_y = np.zeros((len(X['q1']),1))
oof_y = pd.read_csv("./data/oofy.csv")['y_pre'].values
alpha = 1
oof_y = (1 - alpha) * y + alpha * oof_y
folds = StratifiedKFold(y, n_folds=n_folds, shuffle=True,)
result = np.zeros((len(te_q1), 1))
for n_fold, (tr_idx, val_idx) in enumerate(folds):
if semi_sv:
Q1_tr = np.concatenate([X['q1'][tr_idx], te_q1[y_idx]])
Q2_tr = np.concatenate([X['q2'][tr_idx], te_q2[y_idx]])
Qc1_tr = np.concatenate([X['qc1'][tr_idx],tec_q1[y_idx]])
Qc2_tr = np.concatenate([X['qc2'][tr_idx],tec_q2[y_idx]])
y_tr = np.concatenate([y[tr_idx], y_pred])
# y_tr = np.concatenate([oof_y[tr_idx], y_pred])
idx = list(range(len(y_tr)))
np.random.shuffle(idx)
Q1_tr = Q1_tr[idx]
Q2_tr = Q2_tr[idx]
Qc1_tr = Qc1_tr[idx]
Qc2_tr = Qc2_tr[idx]
y_tr = y_tr[idx]
else:
Q1_tr = X['q1'][tr_idx]
Q2_tr = X['q2'][tr_idx]
Qc1_tr = X['qc1'][tr_idx]
Qc2_tr = X['qc2'][tr_idx]
y_tr = y[tr_idx]
# y_tr = oof_y[tr_idx]
Q1_te = X['q1'][val_idx]
Q2_te = X['q2'][val_idx]
Qc1_te = X['qc1'][val_idx]
Qc2_te = X['qc2'][val_idx]
y_te = y[val_idx]
model = aggmodel(word_embedding_matrix,char_embedding_matrix)
if n_fold == 0:
print(model.summary())
print(n_fold)
model.fit([Q1_tr, Q2_tr,Qc1_tr,Qc2_tr],
y_tr,
epochs=epoch,
validation_data=[[Q1_te, Q2_te,Qc1_te, Qc2_te], y_te],
verbose=1,
batch_size=256,
callbacks=[
EarlyStopping(patience=3, monitor='val_binary_crossentropy'),
# LearningRateScheduler(lr_de,verbose=1)
], )
# model.load_weights(model_path)
result += model.predict([te_q1,te_q2,tec_q1,tec_q2], batch_size=1024)
# 释放显存
K.clear_session()
tf.reset_default_graph()
# 提交结果
result /= n_folds
submit = pd.DataFrame()
submit['y_pre'] = list(result[:, 0])
submit.to_csv(output, index=False)
K.clear_session()
tf.reset_default_graph()
submit = 0
total_w = 0
for y_pred,ense_w in results:
submit += ense_w*y_pred
total_w += ense_w
return submit/total_w
if __name__ == '__main__':
from readdata import read_data
_, te_word, embedding_matrix_word,__ = read_data('words', data_aug=False)
_, te_char, embedding_matrix_char,__ = read_data('chars', data_aug=False)
submit_atten = ensemble('esim',te_word,te_char,embedding_matrix_word,embedding_matrix_char)
submit = pd.DataFrame()
submit['y_pre'] = list(submit_atten[:, 0])
submit.to_csv('atten.csv', index=False)
def train(use_data, semi_sv, output, data_aug, use_model):
def get_subset(dataset, idx):
data = {}
for key, value in dataset.items():
data[key] = value[idx]
return data
def concat_data(data1, data2):
result = {}
for k in data1.keys():
result[k] = np.concatenate([data1[k], data2[k]])
return result
def get_aug_data(tr_x, tr_y):
tr_q1 = tr_x['q1']
tr_q2 = tr_x['q2']
tr_gf = tr_x['gf']
tr_q1node = tr_x['q1node']
tr_q2node = tr_x['q2node']
res_q1 = []
res_q2 = []
res_gf = []
res_q1node = []
res_q2node = []
res_y = []
for q1, q2, gf, q1node, q2node, y in zip(tr_q1, tr_q2, tr_gf,
tr_q1node, tr_q2node, tr_y):
r1 = q1[np.in1d(q1, q2, invert=True)]
len1 = len(r1)
if len1 < 4 or len1 == len(q1[q1 != 0]):
continue
r2 = q2[np.in1d(q2, q1, invert=True)]
len2 = len(r2)
if len2 < 4 or len2 == len(q2[q2 != 0]):
continue
out1 = np.zeros(15, dtype=np.int32)
out2 = np.zeros(15, dtype=np.int32)
out1[-len1:] = r1
out2[-len2:] = r2
res_q1.append(out1)
res_q2.append(out2)
res_gf.append(gf)
res_q1node.append(q1node)
res_q2node.append(q2node)
res_y.append(y)
res_x = {
'q1': np.asarray(res_q1),
'q2': np.asarray(res_q2),
'gf': np.asarray(res_gf),
'q1node': np.asarray(res_q1node),
'q2node': np.asarray(res_q2node)
}
res_y = np.asarray(res_y)
return res_x, res_y
from nn import rnnword, aggmodel, esim, attention, rnn_res
if use_model == 'rnnword':
get_model = rnnword
elif use_model == 'aggmodel':
pass
elif use_model == 'esim':
get_model = esim
elif use_model == 'attention':
get_model = attention
elif use_model == 'res':
get_model = rnn_res
else:
raise RuntimeError("don't have this model")
from readdata import read_data
model_name = datetime.datetime.now().strftime(
'%Y-%m-%d_%H:%M:%S') + '_' + use_data + '_' + str(semi_sv) + '_' + str(
data_aug) + '_'
tr, te, embedding_matrix, labels = read_data(use_data, data_aug=data_aug)
print(use_data)
print('Shape of label tensor:', labels.shape)
y = labels
from config import model_path
from sklearn.cross_validation import StratifiedKFold, KFold
from config import n_folds
y_pred = pd.read_csv("./data/y_pred.csv")['y_pre'].values
y_pos_ = y_pred == 1
y_neg_ = y_pred == 0
add_idx = np.any([y_pos_, y_neg_], axis=0)
add_y = y_pred[add_idx]
y_pos = y_pred > 0.75
y_neg = y_pred < 0.25
y_idx = np.any([y_pos, y_neg], axis=0)
y_pred = y_pred[y_idx]
print(y_idx.shape)
folds = StratifiedKFold(y, n_folds=n_folds, shuffle=True)
result = np.zeros((len(te['q1']), 1))
oof_y = np.zeros((len(y), 1))
for n_fold, (tr_idx, val_idx) in enumerate(folds):
tr_x = get_subset(tr, tr_idx)
tr_y = y[tr_idx]
# if data_aug:
# res_x,res_y = get_aug_data(tr_x,tr_y)
# tr_x = concat_data(tr_x,res_x)
# tr_y = np.concatenate([tr_y,res_y])
if semi_sv:
te_x = get_subset(te, y_idx)
tr_data = concat_data(tr_x, te_x)
tr_y = np.concatenate([tr_y, y_pred])
patience = 3
else:
add_data = get_subset(te, add_idx)
tr_data = concat_data(tr_x, add_data)
tr_y = np.concatenate([tr_y, add_y])
patience = 2
# tr_data = tr_x
# tr_y = y[tr_idx]
val_x = get_subset(tr, val_idx)
val_y = y[val_idx]
use_word = True
if use_data != 'words':
use_word = False
model = get_model(word_embedding_matrix=embedding_matrix,
use_word=use_word)
if n_fold == 0:
print(model.summary())
# hist = epochHistory()
print(n_fold)
model.fit(
tr_data,
tr_y,
epochs=1000,
validation_data=[val_x, val_y],
verbose=1,
batch_size=256,
callbacks=[
EarlyStopping(patience=patience,
monitor='val_binary_crossentropy'),
# LearningRateScheduler(lr_de,verbose=1)
# hist,
# ModelCheckpoint('./weight/weights.{epoch:d}.hdf5',monitor='val_binary_crossentropy',save_weights_only=True)
])
# result += iter_ense(hist.epochs,model,te)
result += model.predict(te, batch_size=1024)
model.save_weights('./weight/' + model_name + str(n_fold) + '.h5')
# oof_y[val_idx] = model.predict(val_x, batch_size=2048)
K.clear_session()
tf.reset_default_graph()
# 提交结果
result /= n_folds
submit = pd.DataFrame()
submit['y_pre'] = list(result[:, 0])
submit.to_csv(output, index=False)
## 保存预测的训练标签
# oof_y = oof_y[:,0]
# oof_y_ = oof_y.round().astype(int)
#
# error_idx = oof_y_!=y
# print(np.sum(error_idx))
# oof_y[error_idx] = 1-oof_y[error_idx]
submit = pd.DataFrame()
submit['y_pre'] = oof_y[:, 0]
submit.to_csv('./data/oofy.csv', index=False)