I have a question for those who have some experience with timeseries forecasting.
I have been experiment with this field for few weeks and i was trying to forecast some timeseries with both ARIMA and LSTM models to compare the results.
Basically i did plot this graph Figure 1 that has 4 plots :
Top left : ARIMA training data points and fitted model points.
Top right : ARIMA test and forecast points.
Bottom Left : LSTM training data and fitted data (i could not really find fitted point for LSTM so i just forecasted the training data but you can just ignore that part).
Bottom right : Test and forecast data for the LSTM model.
This graph was acceptable and also i did compute the RMSE and MSE and LSTM gave lower error which agrees with most literature online that states the superiority of LSTM over ARIMA models.
However after i did plot the loss and validation loss of the LSTM model to have more insights, i noticed that the validation_loss is following a wierd flectuating pattern Figure 2.
I can explain this as follow : the time series has a lot of outliers or abnormal behaviour, so splitting it to train/validation/test would mean validation cannot be really a good metric to show how good the model can learn.
But since all research papers never show this graph and explain this problem, i don't have a solid argument to defende this idea.
what do you guys think?
Thank you in advance
import pandas as pd
import matplotlib.pyplot as plt
from statsmodels.tsa.stattools import adfuller
from statsmodels.graphics.tsaplots import plot_acf,plot_pacf
import statsmodels.api as sm
from statsmodels.tsa.arima.model import ARIMA
from sklearn.metrics import r2_score,mean_squared_error,mean_absolute_percentage_error,mean_absolute_percentage_error
from statsmodels.tsa.seasonal import STL
import numpy as np
from pandas import Series, DataFrame
from scipy import stats
from statsmodels.tsa.stattools import adfuller
import statsmodels
from statsmodels.tsa.seasonal import seasonal_decompose
from pandas.plotting import register_matplotlib_converters
import pmdarima as pm
register_matplotlib_converters()
import warnings
import time
from numpy import array
from keras.models import Sequential
from keras.layers import LSTM
from keras.layers import Dense
from numpy import array
import keras_tuner as kt
import tensorflow as tf
print(tf.__version__)
from numpy import array
from tensorflow import keras
import keras_tuner as kt
from sklearn.preprocessing import MinMaxScaler
from keras.layers import Bidirectional
from keras.models import Sequential
from keras.preprocessing.sequence import TimeseriesGenerator
from keras.layers import Bidirectional
from tensorflow.keras import initializers
import random as rn
np.random.seed(123)
rn.seed(123)
tf.random.set_seed(123)
tf.keras.utils.set_random_seed(123)
keras.utils.set_random_seed(123)
warnings.filterwarnings('ignore')
df3 = pd.read_csv('favorita_train.csv')
## 1 - Get TS and do STL
print("TS lenbgth : "+str(len(df3)))
results = seasonal_decompose(df3['unit_sales'],period=30)
results.plot();
train_all = df3.iloc[:int(len(df3)*0.8)]
train = df3.iloc[:int(len(df3)*0.6)]
val = df3.iloc[int(len(df3)*0.6):int(len(df3)*0.8)]
test = df3.iloc[int(len(df3)*0.8):]
scaler = MinMaxScaler()
scaler.fit(train_all)
scaled_all = scaler.transform(df3)
scaled_train = scaler.transform(train)
scaled_train_all = scaler.transform(train_all)
scaled_val = scaler.transform(val)
scaled_test = scaler.transform(test)
# We do the same thing, but now instead for 12 months
n_features = 1
n_input =5
train_generator_all = TimeseriesGenerator(scaled_train_all, scaled_train_all, length=n_input, batch_size=1,shuffle=True)
train_generator = TimeseriesGenerator(scaled_train, scaled_train, length=n_input, batch_size=1,shuffle=True)
val_generator = TimeseriesGenerator(scaled_val, scaled_val, length=n_input, batch_size=1,shuffle=True)
adfPValue = adfuller(scaled_all)
adfPValue=adfPValue[1]
adi = len(scaled_all)/((scaled_all != 0).sum())
sd=scaled_all.std()
mean=scaled_all.mean()
cv2 = np.square(sd/mean)
print("CV2 (describe magnitude of demande variability <0.5 is good) :"+str(cv2))
print("SD (-2,2 is good | mean data variance is low) :"+str(sd))
print("ADI (1.3 or smaller means smooth ts) :"+str(adi))
print("Stationarity test (stationary if <0.05) :"+str(adfPValue))
def model_builder(hp):
model = keras.Sequential()
hp_units = hp.Int('units', min_value=1, max_value=50, step=1)
hp_layers = hp.Int('layers', min_value=1, max_value=3, step=1)
if hp_layers==1 :
model.add(Bidirectional(LSTM(hp_units,activation='relu'), input_shape=(n_input, n_features)))
elif hp_layers==2:
model.add(Bidirectional(LSTM(hp_units, activation='relu', return_sequences=True), input_shape=(n_input, n_features)))
model.add(Bidirectional(LSTM(hp_units, activation='relu')))
else:
model.add(Bidirectional(LSTM(hp_units, activation='relu', return_sequences=True), input_shape=(n_input, n_features)))
for i in range(hp_layers-2):
model.add(Bidirectional(LSTM(hp_units, activation='relu', return_sequences=True)))
model.add(Bidirectional(LSTM(hp_units, activation='relu')))
model.add(Dense(1))
hp_learning_rate = hp.Choice('learning_rate', values=[1e-2, 1e-3, 1e-4])
model.compile(optimizer=keras.optimizers.Adam(learning_rate=hp_learning_rate), loss='mse',metrics=['accuracy'])
return model
tuner = kt.Hyperband(model_builder,
objective='val_loss',
max_epochs=300,
factor=3,
directory='499',
project_name='949',
seed=123)
stop_early = tf.keras.callbacks.EarlyStopping(monitor='val_loss', patience=30)
tuner.search(train_generator, epochs=300, validation_data=val_generator, shuffle=True, callbacks=[stop_early], batch_size=len(train_generator))
best_hps=tuner.get_best_hyperparameters(num_trials=1)[0]
print(best_hps.get('units'))
print(best_hps.get('layers'))
print(best_hps.get('window'))
print(best_hps.get('learning_rate'))
best_hps=tuner.get_best_hyperparameters(num_trials=1)[0]
model = tuner.hypermodel.build(best_hps)
history = model.fit(img_train, label_train, epochs=50, validation_split=0.2)
val_acc_per_epoch = history.history['val_accuracy']
best_epoch = val_acc_per_epoch.index(max(val_acc_per_epoch)) + 1
print('Best epoch: %d' % (best_epoch,))
Related
I'm using this code to train hugginface bert. But I saw different batch has different sequence length in training time. But I want to keep the same sequence length for all of the batches. How can I do that? And how does hugging face handles different sequence length in different batches?
from transformers import BertTokenizer
bert_cased_tokenizer = BertTokenizer.from_pretrained("bert-base-uncased", do_lower_case=False)
Define model
from transformers import BertConfig, BertForPreTraining
config = BertConfig()
model = BertForPreTraining(config)
Next sentence prediction
from transformers import TextDatasetForNextSentencePrediction
dataset = TextDatasetForNextSentencePrediction(
tokenizer=bert_cased_tokenizer,
file_path="/path/to/your/dataset",
block_size = 256)
mlm
from transformers import DataCollatorForLanguageModeling
data_collator = DataCollatorForLanguageModeling(
tokenizer=bert_cased_tokenizer,
mlm=True,
mlm_probability= 0.15)
Train
from transformers import Trainer, TrainingArguments
training_args = TrainingArguments(
output_dir= "/path/to/output/dir/for/training/arguments"
overwrite_output_dir=True,
num_train_epochs=2,
per_gpu_train_batch_size= 16,
save_steps=10_000,
save_total_limit=2,
prediction_loss_only=True,)
trainer = Trainer(
model=model,
args=training_args,
data_collator=data_collator,
train_dataset=dataset,)
trainer.train()
trainer.save_model("path/to/your/model")
First of all, thank you for allowing me to use this wonderful library
I am doing Korean NLP now
So I pre-processed Korean and converted it into a Tfidf Vectorizer.
I'm going to put it in setup() and use it, but there are errors
Can't I use the sparse matrix for the pycaret?
If so, is there any way to do Korean NLP?
X_train = train_data.Text.tolist()
Y_train =train_data['Label'].values
X_test = test_data.Text.tolist()
Y_test =test_data['Label'].values
from soynlp.word import WordExtractor
word_extractor = WordExtractor(min_frequency=100,
min_cohesion_forward=0.05,
min_right_branching_entropy=0.0
)
word_extractor.train(X_train) # list of str or like
words = word_extractor.extract()
scores = word_extractor.word_scores()
import math
score_dict = {key: scores[key].cohesion_forward *
math.exp(scores[key].right_branching_entropy)
for key in scores}
from soynlp.tokenizer import LTokenizer
cohesion_score = {word:score.cohesion_forward for word, score in words.items()}
tokenizer = LTokenizer(scores=score_dict)
import os
from scipy.sparse import save_npz, load_npz
from sklearn.feature_extraction.text import TfidfVectorizer
# if not os.path.isfile('soy_train.npz'):
tfidf = TfidfVectorizer(ngram_range=(1, 2),
min_df=3,
tokenizer=tokenizer.tokenize,
token_pattern=None)
tfidf.fit(X_train)
X_train_soy = tfidf.transform(X_train)
X_test_soy = tfidf.transform(X_test)
save_npz('soy_train.npz', X_train_soy)
save_npz('soy_test.npz', X_test_soy)
type(X_train_soy[0])
import numpy as np
train = pd.DataFrame(X_train_soy)
y_train = np.array(Y_train,dtype=float)
train['Label'] = y_train
from pycaret.classification import *
import numpy as np
exp1 = setup(train,train_size=0.8, target = 'Label',use_gpu = True)
TypeError: Cannot compare types 'ndarray(dtype=object)' and 'float'
I used transfer learning to train the model. The fundamental model was efficientNet.
You can read more about it here
from tensorflow import keras
from keras.models import Sequential,Model
from keras.layers import Dense,Dropout,Conv2D,MaxPooling2D,
Flatten,BatchNormalization, Activation
from keras.optimizers import RMSprop , Adam ,SGD
from keras.backend import sigmoid
Activation function
class SwishActivation(Activation):
def __init__(self, activation, **kwargs):
super(SwishActivation, self).__init__(activation, **kwargs)
self.__name__ = 'swish_act'
def swish_act(x, beta = 1):
return (x * sigmoid(beta * x))
from keras.utils.generic_utils import get_custom_objects
from keras.layers import Activation
get_custom_objects().update({'swish_act': SwishActivation(swish_act)})
Model Definition
model = enet.EfficientNetB0(include_top=False, input_shape=(150,50,3), pooling='avg', weights='imagenet')
Adding 2 fully-connected layers to B0.
x = model.output
x = BatchNormalization()(x)
x = Dropout(0.7)(x)
x = Dense(512)(x)
x = BatchNormalization()(x)
x = Activation(swish_act)(x)
x = Dropout(0.5)(x)
x = Dense(128)(x)
x = BatchNormalization()(x)
x = Activation(swish_act)(x)
x = Dense(64)(x)
x = Dense(32)(x)
x = Dense(16)(x)
# Output layer
predictions = Dense(1, activation="sigmoid")(x)
model_final = Model(inputs = model.input, outputs = predictions)
model_final.summary()
I saved it using:
model.save('model.h5')
I get the following error trying to load it:
model=tf.keras.models.load_model('model.h5')
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-12-e3bef1680e4f> in <module>()
1 # Recreate the exact same model, including its weights and the optimizer
----> 2 model = tf.keras.models.load_model('PhoneDetection-CNN_29_July.h5')
3
4 # Show the model architecture
5 model.summary()
10 frames
/usr/local/lib/python3.6/dist-packages/tensorflow/python/keras/utils/generic_utils.py in class_and_config_for_serialized_keras_object(config, module_objects, custom_objects, printable_module_name)
319 cls = get_registered_object(class_name, custom_objects, module_objects)
320 if cls is None:
--> 321 raise ValueError('Unknown ' + printable_module_name + ': ' + class_name)
322
323 cls_config = config['config']
ValueError: Unknown layer: FixedDropout
```python
I was getting the same error while trying to do the inference by loading my saved model.
Then i just imported the effiecientNet library in my inference notebook as well and the error was gone.
My import command looked like:
import efficientnet.keras as efn
(Note that if you havent installed effiecientNet already(which is unlikely), you can do so by using !pip install efficientnet command.)
I had this same issue with a recent model. Researching the source code you can find the FixedDropout Class. I added this to my inference code with import of backend and layers. The rate should also match the rate from your efficientnet model, so for the EfficientNetB0 the rate is .2 (others are different).
from tensorflow.keras import backend, layers
class FixedDropout(layers.Dropout):
def _get_noise_shape(self, inputs):
if self.noise_shape is None:
return self.noise_shape
symbolic_shape = backend.shape(inputs)
noise_shape = [symbolic_shape[axis] if shape is None else shape
for axis, shape in enumerate(self.noise_shape)]
return tuple(noise_shape)
model = keras.models.load_model('model.h5',
custom_objects={'FixedDropout':FixedDropout(rate=0.2)})
I was getting the same error. Then I import the below code. then it id working properly
import cv2
import matplotlib.pyplot as plt
import tensorflow as tf
from sklearn.metrics import confusion_matrix
import itertools
import os, glob
from tqdm import tqdm
from efficientnet.tfkeras import EfficientNetB4
if you don't have to install this. !pip install efficientnet. If you have any problem put here.
In my case, I had two files train.py and test.py.
I was saving my .h5 model inside train.py and was attempting to load it inside test.py and got the same error. To fix it, you need to add the import statements for your efficientnet models inside the file that is attempting to load it as well (in my case, test.py).
from efficientnet.tfkeras import EfficientNetB0
I would like to fit the following function:
def invlaplace_stehfest2(time,EL,tau):
upsilon=0.25
pmax=6.9
E0=0.0154
M=8
results=[]
for t in time:
func=0
for k in range(1,2*M+1):
SUM=0
for j in range(int(math.floor((k+1)/2)),min(k,M)+1):
dummy=j**(M+1)*scipy.special.binom(M,j)*scipy.special.binom(2*j,j)*scipy.special.binom(j,k-j)/scipy.math.factorial(M)
SUM+=dummy
s=k*math.log(2)/t[enter image description here][1]
func+=(-1)**(M+k)*SUM*pmax*EL/(mp.exp(tau*s)*mp.expint(1,tau*s)*E0+EL)/s
func=func*math.log(2)/t
results.append(func)
return [float(i) for i in results]
To do so I use the following data:
data_time=np.array([69.0,99.0,139.0,179.0,219.0,259.0,295.5,299.03])
data_relax=np.array([6.2536,6.1652,6.0844,6.0253,5.9782,5.9404,5.9104,5.9066])
With the folowing guess:
guess=np.array([0.1,0.05])
And scipy.optimize.curve_fit() as folow:
Parameter,Covariance=scipy.optimize.curve_fit(invlaplace_stehfest2,data_time,data_relax,guess)
For A reason that I don't understand I am not able to fit the data correctly. I get the following graph.
Bad fitting
My function is undoubtedly correct since when I use the correct guess:
guess=np.array([0.33226685047281592707364253044085038793404361200072,8.6682623502960394383501102909774397295654841654769])
I am able to fit correctly my data.
Expected fitting
Any hint on why I am not able to fit correctly? Should I use another method?
Here is the hole program:
##############################################
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.mlab as mlab
import matplotlib.pylab as mplab
import math
from math import *
import numpy as np
import scipy
from scipy.optimize import curve_fit
import mpmath as mp
############################################################################################
def invlaplace_stehfest2(time,EL,tau):
upsilon=0.25
pmax=6.9
E0=0.0154
M=8
results=[]
for t in time:
func=0
for k in range(1,2*M+1):
SUM=0
for j in range(int(math.floor((k+1)/2)),min(k,M)+1):
dummy=j**(M+1)*scipy.special.binom(M,j)*scipy.special.binom(2*j,j)*scipy.special.binom(j,k-j)/scipy.math.factorial(M)
SUM+=dummy
s=k*math.log(2)/t
func+=(-1)**(M+k)*SUM*pmax*EL/(mp.exp(tau*s)*mp.expint(1,tau*s)*E0+EL)/s
func=func*math.log(2)/t
results.append(func)
return [float(i) for i in results]
############################################################################################
###Constant###
####Value####
data_time=np.array([69.0,99.0,139.0,179.0,219.0,259.0,295.5,299.03])
data_relax=np.array([6.2536,6.1652,6.0844,6.0253,5.9782,5.9404,5.9104,5.9066])
###Fitting###
guess=np.array([0.33226685047281592707364253044085038793404361200072,8.6682623502960394383501102909774397295654841654769])
#guess=np.array([0.1,0.05])
Parameter,Covariance=scipy.optimize.curve_fit(invlaplace_stehfest2,data_time,data_relax,guess)
print Parameter
residu=sum(data_relax-invlaplace_stehfest2(data_time,Parameter[0],Parameter[1]))
Graph_Curves=plt.figure()
ax = Graph_Curves.add_subplot(111)
ax.plot(data_time,invlaplace_stehfest2(data_time,Parameter[0],Parameter[1]),"-")
ax.plot(data_time,data_relax,"o")
plt.show()
Non-linear fitters such as the default Levenberg-Marquardt solver used in scipy.optimize.curve_fit(), like most iterative solvers, can stop in a local minimum in error space. If error space is "bumpy" then initial parameter estimates become very important, as in this case.
Scipy has added the Differential Evolution genetic algorithm to the optimize module, which can be used to determine initial parameter estimates for curve_fit(). Scipy's implementation uses the Latin Hypercube algorithm to ensure a thorough search of parameter space, requiring parameter upper and lower bounds within which to search. As you can see below, I have used this scipy module to replace the hard-coded values for the value named "guess" in your code. This does not run quickly, but a somewhat slower correct result is much better than a fast wrong result. Try this code:
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.mlab as mlab
import matplotlib.pylab as mplab
import math
from math import *
import numpy as np
import scipy
from scipy.optimize import curve_fit
from scipy.optimize import differential_evolution
import mpmath as mp
############################################################################################
def invlaplace_stehfest2(time,EL,tau):
upsilon=0.25
pmax=6.9
E0=0.0154
M=8
results=[]
for t in time:
func=0
for k in range(1,2*M+1):
SUM=0
for j in range(int(math.floor((k+1)/2)),min(k,M)+1):
dummy=j**(M+1)*scipy.special.binom(M,j)*scipy.special.binom(2*j,j)*scipy.special.binom(j,k-j)/scipy.math.factorial(M)
SUM+=dummy
s=k*math.log(2)/t
func+=(-1)**(M+k)*SUM*pmax*EL/(mp.exp(tau*s)*mp.expint(1,tau*s)*E0+EL)/s
func=func*math.log(2)/t
results.append(func)
return [float(i) for i in results]
############################################################################################
###Constant###
####Value####
data_time=np.array([69.0,99.0,139.0,179.0,219.0,259.0,295.5,299.03])
data_relax=np.array([6.2536,6.1652,6.0844,6.0253,5.9782,5.9404,5.9104,5.9066])
# function for genetic algorithm to minimize (sum of squared error)
def sumOfSquaredError(parameterTuple):
return np.sum((data_relax - invlaplace_stehfest2(data_time, *parameterTuple)) ** 2)
###Fitting###
#guess=np.array([0.33226685047281592707364253044085038793404361200072,8.6682623502960394383501102909774397295654841654769])
#guess=np.array([0.1,0.05])
parameterBounds = [[0.0, 1.0], [0.0, 10.0]]
# "seed" the numpy random number generator for repeatable results
# note the ".x" here to return only the parameter estimates in this example
guess = differential_evolution(sumOfSquaredError, parameterBounds, seed=3).x
Parameter,Covariance=scipy.optimize.curve_fit(invlaplace_stehfest2,data_time,data_relax,guess)
print Parameter
residu=sum(data_relax-invlaplace_stehfest2(data_time,Parameter[0],Parameter[1]))
Graph_Curves=plt.figure()
ax = Graph_Curves.add_subplot(111)
ax.plot(data_time,invlaplace_stehfest2(data_time,Parameter[0],Parameter[1]),"-")
ax.plot(data_time,data_relax,"o")
plt.show()
I'm new to scikit learn and I'm banging my head against the wall. I've used both real world and test data and the scikit algorithms are not performing above chance level in predicting anything. I've tried knn, decision trees, svc and naive bayes.
Basically, I made a test data set consisting of a column of 0s and 1s, with all the 0s having a feature between 0 and .5 and all the 1s having a feature value between .5 and 1. This should be extremely easy and give near 100% accuracy. However, none of the algorithms are performing above chance level. Accurasies range from 45 to 55 %. I've already tried tweaking a whole bunch of parameters for every algorithm but noting helps. I think something is fundamentally wrong with my implementation.
Please help me out. Here's my code:
from sklearn.cross_validation import train_test_split
from sklearn import preprocessing
from sklearn.preprocessing import OneHotEncoder
from sklearn.metrics import accuracy_score
import sklearn
import pandas
import numpy as np
df=pandas.read_excel('Test.xlsx')
# Make data into np arrays
y = np.array(df[1])
y=y.astype(float)
y=y.reshape(399)
x = np.array(df[2])
x=x.astype(float)
x=x.reshape(399, 1)
# Creating training and test data
labels_train, labels_test = train_test_split(y)
features_train, features_test = train_test_split(x)
#####################################################################
# PERCEPTRON
#####################################################################
from sklearn import linear_model
perceptron=linear_model.Perceptron()
perceptron.fit(features_train, labels_train)
perc_pred=perceptron.predict(features_test)
print sklearn.metrics.accuracy_score(labels_test, perc_pred, normalize=True, sample_weight=None)
print 'perceptron'
#####################################################################
# KNN classifier
#####################################################################
from sklearn.neighbors import KNeighborsClassifier
knn = KNeighborsClassifier()
knn.fit(features_train, labels_train)
knn_pred = knn.predict(features_test)
# Accuraatheid
print sklearn.metrics.accuracy_score(labels_test, knn_pred, normalize=True, sample_weight=None)
print 'knn'
#####################################################################
## SVC
#####################################################################
from sklearn.svm import SVC
from sklearn import svm
svm2 = SVC(kernel="linear")
svm2 = svm.SVC()
svm2.fit(features_train, labels_train)
SVC(C=1.0, cache_size=200, class_weight=None, coef0=0.0, degree=3,
gamma=1.0, kernel='linear', max_iter=-1, probability=False,
random_state=None,
shrinking=True, tol=0.001, verbose=False)
svc_pred = svm2.predict(features_test)
print sklearn.metrics.accuracy_score(labels_test, svc_pred, normalize=True,
sample_weight=None)
#####################################################################
# Decision tree
#####################################################################
from sklearn import tree
clf = tree.DecisionTreeClassifier()
clf = clf.fit(features_train, labels_train)
tree_pred=clf.predict(features_test)
# Accuraatheid
print sklearn.metrics.accuracy_score(labels_test, tree_pred, normalize=True,
sample_weight=None)
print 'tree'
#####################################################################
# Naive bayes
#####################################################################
import sklearn
from sklearn.naive_bayes import GaussianNB
clf = GaussianNB()
clf.fit(features_train, labels_train)
print "training time:", round(time()-t0, 3), "s"
GaussianNB()
bayes_pred = clf.predict(features_test)
print sklearn.metrics.accuracy_score(labels_test, bayes_pred,
normalize=True, sample_weight=None)
You seem to use train_test_split the wrong way.
labels_train, labels_test = train_test_split(y) #WRONG
features_train, features_test = train_test_split(x) #WRONG
the splitting of your labels and data isn't necessary the same. One easy way to split your data manually:
randomvec=np.random.rand(len(data))
randomvec=randomvec>0.5
train_data=data[randomvec]
train_label=labels[randomvec]
test_data=data[np.logical_not(randomvec)]
test_label=labels[np.logical_not(randomvec)]
or to use the scikit method properly:
x_train, x_test, y_train, y_test = train_test_split(x, y, test_size=0.5, random_state=42)