New to python neural networks and sklearn, i wrote the following neural model. On a train set, it works nicely around 98% accuracy.
Now i have some questions.
from sklearn.ensemble import GradientBoostingClassifier
model = GradientBoostingClassifier(learning_rate=0.99,max_depth=3)
model.fit(X_standardized, y)
predictions = model.predict(X_standardized)
from sklearn.metrics import confusion_matrix, classification_report
print(confusion_matrix(y, predictions))
print ()
print(classification_report(y,predictions))
Can the state of the neural network be saved and loaded.
ea store the weights gradients.
#something like:
Model.save("c:\neural\testnet.xml")
How to perform individual tests on a single data frame ea:
print ("answer =" ,Model.TestSample(test_data_frame)) # single input
>>> answer = 0.78 ...estimated accuracy 97% # or so
Regarding saving the state of the model: you can save the model using pickle package, e.g.:
import pickle
pickle.dump(model, open('model.sav', 'wb'))
Not sure what you mean by 'individual tests on a single data frame', but if you want to test the model on some different (test) data, you can just create something like that:
import sklearn
df_predictions = model.predict( *input X data* )
accuracy = sklearn.metrics.r2_score(*target (y data)*, df_predictions)
Related
I am an electrical engineer and I am looking for a solution to calculate the DC current of a permanent synchronous motor. So I decided to check the ANN solutions with Keras and so on.Long story short, I'll show you a screenshot of some measured signals.
The first 5 signals are the measured signals. The last one is the DC current, which I will estimate. Here the value was recorded with the help of a current clamp. Okay, I started building a model in Python and tried some things that I assume will increase the accuracy of the model. But after all that, I am not getting that good results from the model and my hope is that maybe I am choosing wrong parameters or not an ideal model for this purpose.
Here is my code:
import numpy as np
from keras.layers import Dense, LSTM
from keras.models import Sequential
from keras.callbacks import EarlyStopping
import pandas as pd
from sklearn import preprocessing
from sklearn.model_selection import train_test_split
from sklearn.metrics import r2_score
from matplotlib import pyplot as plt
import seaborn as sns
# Import input (x) and output (y) data, and asign these to df1 and df1
df = pd.read_csv('train_data.csv')
df = df[['rpm','iq','uq','udc','idc']]
X = df[df.columns[:-1]]
Y = df.idc
plt.figure()
sns.heatmap(df.corr(),annot=True)
plt.show()
# Split the data into input (x) training and testing data, and ouput (y) training and testing data,
# with training data being 80% of the data, and testing data being the remaining 20% of the data
X_train, X_test, y_train, y_test = train_test_split(X, Y, test_size=0.2)#, shuffle=True)
# Scale both training and testing input data
X_train = preprocessing.maxabs_scale(X_train)
X_test = preprocessing.maxabs_scale(X_test)
model = Sequential()
model.add(Dense(4, input_shape=(4,)))
model.add(Dense(4, input_shape=(4,)))
model.add(Dense(1, input_shape=(4,)))
model.compile(optimizer="adam", loss="msle", metrics=['mean_squared_logarithmic_error','accuracy'])
# Pass several parameters to 'EarlyStopping' function and assign it to 'earlystopper'
earlystopper = EarlyStopping(monitor='val_loss', min_delta=0, patience=15, verbose=1, mode='auto')
model.summary()
history = model.fit(X_train, y_train, epochs = 2000, validation_split = 0.3, verbose = 2, callbacks = [earlystopper])
# Runs model (the one with the activation function, although this doesn't really matter as they perform the same)
# with its current weights on the training and testing data
y_train_pred = model.predict(X_train)
y_test_pred = model.predict(X_test)
# Calculates and prints r2 score of training and testing data
print("The R2 score on the Train set is:\t{:0.3f}".format(r2_score(y_train, y_train_pred)))
print("The R2 score on the Test set is:\t{:0.3f}".format(r2_score(y_test, y_test_pred)))
df = pd.read_csv('test_two_data.csv')
df = df[['rpm','iq','uq','udc','idc']]
X = df[df.columns[:-1]]
Y = df.idc
X_validate = preprocessing.maxabs_scale(X)
y_pred = model.predict(X_validate)
plt.plot(Y)
plt.plot(y_pred)
plt.show()
(weight_0,bias_0) = model.layers[0].get_weights()
(weight_1,bias_1) = model.layers[1].get_weights()
One limitation is that I can't use LSTM layers or other complex algorithms because I need to implement the trained model in a microcontroller on a motor application later.
I guess you could find some words for me to make my model a little better in accuracy.
At the end here is a figure where I show you the worse prediction performance. Orange is the prediction and blue is the measured current.
The training dataset was this one.
The correlation between the individual values can be found here. Since the values of id and ud have no correlation to idc, I decided to delete them.
The most important thing to keep in mind when trying to improve the accuracy of the model is ALWAYS Normalise the input data which basically means rescaling real-valued numeric attributes into the range 0 and 1. I am not able to understand the way you are providing the training data to the model. Could you please explain that. It would be better in understanding and identifying the scope of higher accuracy.
Now if we talk about parameters, I would suggest you the addition of a Tuning Algorithm for the parameters to get the optimized value of each parameter.
It is always a good parctice to include hidden layers which could provide better feature extract.
Context
I use sklearn machine learning algorithms like SVR for a regression-task.
from sklearn.svm import SVR
model = SVR(kernel='poly', degree=2, epsilon=.5)
model.fit(
features # Numpy array with features
, target # Numpy array with the target
)
Afterwards I return the score of the regression using the .score()-function.
Additionally, I need the prediction-results using .predict() for further processing.
some_data = [...] # Numpy array with some data to predict
correct_targets = [...] # Numpy array with targets according to some data
# Get R²
print("R²:", model.score(
some_data
, correct_targets
))
# Store prediction
pred = model.predict(some_data)
Question
When I run the code in the above version the model is calculated twice - once for .score() and once for .predict().
However, I cannot run the .score() on the saved .predict().
This is a bit nasty since the calculation takes some time.
Is it possible to store the prediction and apply .score() afterwards without recalculating?
If you already have the predicted values:
pred = model.predict(some_data)
and the respective ground truth correct_targets, it is straightforward to get the R^2 score without re-running the model, as scikit-learn has a dedicated function for this:
from sklearn.metrics import r2_score
r2_score(correct_targets, pred)
I was training a model that contains 8 features that allows us to predict the probability of a room been sold.
Region: The region the room belongs to (an integer, taking value between 1 and 10)
Date:The date of stay (an integer between 1‐365, here we consider only one‐day
request)
Weekday: Day of week (an integer between 1‐7)
Apartment: Whether the room is a whole apartment (1) or just a room (0)
#beds:The number of beds in the room (an integer between 1‐4)
Review: Average review of the seller (a continuous variable between 1 and 5)
Pic Quality: Quality of the picture of the room (a continuous variable between 0 and 1)
Price: he historic posted price of the room (a continuous variable)
Accept:Whether this post gets accepted (someone took it, 1) or not (0) in the end
Column Accept is the "y". Hence, this is a binary classification.
We have plot the data and some of the data were skewed so we applied power transform.
We tried a neural network, ExtraTrees, XGBoost, Gradient boost, Random forest. They all gave about 0.77 AUC. However, when we tried them on the test set, the AUC dropped to 0.55 with a precision of 27%.
I am not sure where when wrong but my thinking was that the reason may due to the mixing of discrete and continuous data. Especially some of them are either 0 or 1.
Can anyone help?
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
from sklearn.model_selection import train_test_split
from sklearn.metrics import roc_auc_score
from sklearn.neural_network import MLPClassifier
from sklearn.preprocessing import MinMaxScaler
from sklearn.preprocessing import OneHotEncoder
import warnings
warnings.filterwarnings('ignore')
df_train = pd.read_csv('case2_training.csv')
X, y = df_train.iloc[:, 1:-1], df_train.iloc[:, -1]
y = y.astype(np.float32)
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2, random_state=123)
from sklearn.preprocessing import PowerTransformer
pt = PowerTransformer()
transform_list = ['Pic Quality', 'Review', 'Price']
X_train[transform_list] = pt.fit_transform(X_train[transform_list])
X_test[transform_list] = pt.transform(X_test[transform_list])
for i in transform_list:
df = X_train[i]
ax = df.plot.hist()
ax.set_title(i)
plt.show()
# Normalization
sc = MinMaxScaler()
X_train = sc.fit_transform(X_train)
X_test = sc.transform(X_test)
X_train = X_train.astype(np.float32)
X_test = X_test.astype(np.float32)
from sklearn.ensemble import RandomForestClassifier
clf = RandomForestClassifier(random_state=123, n_estimators=50)
clf.fit(X_train,y_train)
yhat = clf.predict_proba(X_test)
# AUC metric
train_accuracy = roc_auc_score(y_test, yhat[:,-1])
print("AUC",train_accuracy)
from sklearn.ensemble import GradientBoostingClassifier
clf = GradientBoostingClassifier(random_state=123, n_estimators=50)
clf.fit(X_train,y_train)
yhat = clf.predict_proba(X_test)
# AUC metric
train_accuracy = roc_auc_score(y_test, yhat[:,-1])
print("AUC",train_accuracy)
from torch import nn
from skorch import NeuralNetBinaryClassifier
import torch
model = nn.Sequential(
nn.Linear(8,64),
nn.BatchNorm1d(64),
nn.GELU(),
nn.Linear(64,32),
nn.BatchNorm1d(32),
nn.GELU(),
nn.Linear(32,16),
nn.BatchNorm1d(16),
nn.GELU(),
nn.Linear(16,1),
# nn.Sigmoid()
)
net = NeuralNetBinaryClassifier(
model,
max_epochs=100,
lr=0.1,
# Shuffle training data on each epoch
optimizer=torch.optim.Adam,
iterator_train__shuffle=True,
)
net.fit(X_train, y_train)
from xgboost.sklearn import XGBClassifier
clf = XGBClassifier(silent=0,
learning_rate=0.01,
min_child_weight=1,
max_depth=6,
objective='binary:logistic',
n_estimators=500,
seed=1000)
clf.fit(X_train,y_train)
yhat = clf.predict_proba(X_test)
# AUC metric
train_accuracy = roc_auc_score(y_test, yhat[:,-1])
print("AUC",train_accuracy)
Here is an attachment of a screenshot of the data.
Sample data
This is the fundamental first step of Data Analytics. You need to do two things here:
Data understanding - do the data fields in their current format make sense (data types, value range etc.)
Data preparation - what should I do to update these data fields before passing them to our model? Also which inputs do you think will be useful for your model and which will provide little benefit? Are there outliers I need to consider/handle?
A good book if you're starting in the field of data analytics is Fundamentals of Machine Learning for Predictive Data Analytics (I have no affiliation with this book).
Looking at your dataset there's a couple of things you could try to see how it influences your prediction results:
Unless region order is actually ranked in importance/value I would change this to a one hot encoded feature, you can do this in sklearn. Otherwise you run the risk of your model thinking that regions with a higher number (say 10) are more important than regions with a lower value (say 1).
You could attempt to normalise certain categories if they are much larger than some of your other data fields Why Data Normalization is necessary for Machine Learning models
Consider looking at the Kaggle competition House Prices: Advanced Regression Techniques. It's doing a similar thing to what you're attempting to do, and it might have some pointers for how you should approach the problem in the Notebooks and Discussion tabs.
Without deeply exploring all the data you are using it is hard to say for certain what is causing the drop in accuracy (or AUC) when moving from your training set to the testing set. It is unlikely to be caused by the mixed discrete/continuous data.
The drop just suggests that your models are over-fitting to your training data (and therefore not transferring well). This could be caused by too many learned parameters (given the amount of data you have)--more often a problem with neural networks than with some of the other methods you mentioned. Or, the problem could be with the way the data was split into training/testing. If the distribution of the data has a significant difference (that's maybe not obvious) then you wouldn't expect the testing performance to be as good. If it were me, I'd look carefully at how the data was split into training/testing (assuming you have a reasonably large set of data). You may try repeating your experiments with a number of random training/testing splits (search k-fold cross validation if you're not familiar with it).
your model is overfit. try to make a simple model first and use a lower parameter value. for tree-based classification, scaling does not have any impact on the model.
This question already has an answer here:
Testing text classification ML model with new data fails
(1 answer)
Closed 2 years ago.
Below is my code I am trying for text classification model;
from sklearn.feature_extraction.text import TfidfVectorizer
ifidf_vectorizer = TfidfVectorizer()
X_train_tfidf = ifidf_vectorizer.fit_transform(X_train)
X_train_tfidf.shape
(3, 16)
from sklearn.svm import LinearSVC
clf = LinearSVC()
clf.fit(X_train_tfidf,y_train)
Till now only training set has been vectorized into a full vocabulary. In order to perform analysis on test set I need to submit it to the same procedures.
So I did
X_test_tfidf = ifidf_vectorizer.fit_transform(X_test)
X_test_tfidf.shape
(2, 12)
And finally when trying to predict its showing error;
predictions = clf.predict(X_test_tfidf)
ValueError: X has 12 features per sample; expecting 16
But when I use pipeline from sklearn.pipeline import Pipeline then it worked fine;
Can’t I code the way I was trying?
The error is with fit_transform of test data. You fit_transform training data and only transform test data:
# change this
X_test_tfidf = ifidf_vectorizer.fit_transform(X_test)
X_test_tfidf.shape
(2, 12)
# to
X_test_tfidf = ifidf_vectorizer.transform(X_test)
X_test_tfidf.shape
Reasons:
When you do fit_transform, you teach your model the vectors with fit. The model learns the vectors to which they are used to transform data. You use the train data to learn the vectors, then you apply them to both train and test with transform
If you do a fit_transform on test data, you replaced the vectors learned in training data and replaced them with test data. Given that your test data is smaller than your train data, it is likely you would get two different vectorisation.
A Better Way
The best way to do what you do is using Pipelines which will make your flow easy to understand
from sklearn.feature_extraction.text import TfidfVectorizer
from sklearn.svm import LinearSVC
from sklearn.pipeline import Pipeline
clf = Pipeline(steps=[
('vectorizer', TfidfVectorizer()),
('model', LinearSVC()),
])
# train
clf.fit(X_train,y_train)
# predict
clf.predict(X_test)
This is easier as the transformation are taking care for you. You don’t have to worry about fit_transform when fitting the model or transform when predicting or scoring.
You can access the features independently if you with with
clf.named_steps('vectorizer') # or 'model'
Under the hood, when you do clf.fit, your data will pass throw your vectorizer using fit_transform and then to the model. When you predict or score, your data will pass throw your vectorizer with transform before reaching your model.
Your code fails as you are refitting the vectorizer with .fit_transform() on the test set X_test again. However, you should only transform the data with the vectorizer:
X_test_tfidf = ifidf_vectorizer.transform(X_test)
Now it should work as expected. You only fit the ifidf_vectorizer according to X_train and transform all data according to this. It ensures that the same vocabulary is used and that you get outputs of the same shape.
As an R user, I wanted to also get up to speed on scikit.
Creating a linear regression model(s) is fine, but can't seem to find a reasonable way to get a standard summary of regression output.
Code example:
# Linear Regression
import numpy as np
from sklearn import datasets
from sklearn.linear_model import LinearRegression
# Load the diabetes datasets
dataset = datasets.load_diabetes()
# Fit a linear regression model to the data
model = LinearRegression()
model.fit(dataset.data, dataset.target)
print(model)
# Make predictions
expected = dataset.target
predicted = model.predict(dataset.data)
# Summarize the fit of the model
mse = np.mean((predicted-expected)**2)
print model.intercept_, model.coef_, mse,
print(model.score(dataset.data, dataset.target))
Issues:
seems like the intercept and coef are built into the model, and I just type print (second to last line) to see them.
What about all the other standard regression output like R^2, adjusted R^2, p values, etc. If I read the examples correctly, seems like you have to write a function/equation for each of these and then print it.
So, is there no standard summary output for lin. reg. models?
Also, in my printed array of outputs of coefficients, there are no variable names associated with each of these? I just get the numeric array. Is there a way to print these where I get an output of the coefficients and the variable they go with?
My printed output:
LinearRegression(copy_X=True, fit_intercept=True, normalize=False)
152.133484163 [ -10.01219782 -239.81908937 519.83978679 324.39042769 -792.18416163
476.74583782 101.04457032 177.06417623 751.27932109 67.62538639] 2859.69039877
0.517749425413
Notes: Started off with Linear, Ridge and Lasso. I have gone through the examples. Below is for the basic OLS.
There exists no R type regression summary report in sklearn. The main reason is that sklearn is used for predictive modelling / machine learning and the evaluation criteria are based on performance on previously unseen data (such as predictive r^2 for regression).
There does exist a summary function for classification called sklearn.metrics.classification_report which calculates several types of (predictive) scores on a classification model.
For a more classic statistical approach, take a look at statsmodels.
I use:
import sklearn.metrics as metrics
def regression_results(y_true, y_pred):
# Regression metrics
explained_variance=metrics.explained_variance_score(y_true, y_pred)
mean_absolute_error=metrics.mean_absolute_error(y_true, y_pred)
mse=metrics.mean_squared_error(y_true, y_pred)
mean_squared_log_error=metrics.mean_squared_log_error(y_true, y_pred)
median_absolute_error=metrics.median_absolute_error(y_true, y_pred)
r2=metrics.r2_score(y_true, y_pred)
print('explained_variance: ', round(explained_variance,4))
print('mean_squared_log_error: ', round(mean_squared_log_error,4))
print('r2: ', round(r2,4))
print('MAE: ', round(mean_absolute_error,4))
print('MSE: ', round(mse,4))
print('RMSE: ', round(np.sqrt(mse),4))
statsmodels package gives a quiet decent summary
from statsmodels.api import OLS
OLS(dataset.target,dataset.data).fit().summary()
You can do using statsmodels
import statsmodels.api as sm
X = sm.add_constant(X.ravel())
results = sm.OLS(y,x).fit()
results.summary()
results.summary() will organize the results into three tabels
You can use the following option to have a summary table:
import statsmodels.api as sm
#log_clf = LogisticRegression()
log_clf =sm.Logit(y_train,X_train)
classifier = log_clf.fit()
y_pred = classifier.predict(X_test)
print(classifier.summary2())
Use model.summary() after predict
# Linear Regression
import numpy as np
from sklearn import datasets
from sklearn.linear_model import LinearRegression
# load the diabetes datasets
dataset = datasets.load_diabetes()
# fit a linear regression model to the data
model = LinearRegression()
model.fit(dataset.data, dataset.target)
print(model)
# make predictions
expected = dataset.target
predicted = model.predict(dataset.data)
# >>>>>>>Print out the statistics<<<<<<<<<<<<<
model.summary()
# summarize the fit of the model
mse = np.mean((predicted-expected)**2)
print model.intercept_, model.coef_, mse,
print(model.score(dataset.data, dataset.target))