I am a new in Machine Learning area & I am (trying to) implementing anomaly detection algorithms, one algorithm is Autoencoder implemented with help of keras from tensorflow library and the second one is IsolationForest implemented with help of sklearn library and I want to compare these algorithms with help of roc_auc_score ( function from Python), but I am not sure if I am doing it correct.
In documentation of roc_auc_score function I can see, that for input it should be like:
sklearn.metrics.roc_auc_score(y_true, y_score, average=’macro’, sample_weight=None, max_fpr=None
y_true :
True binary labels or binary label indicators.
y_score :
Target scores, can either be probability estimates of the positive class, confidence values, or non-thresholded measure of decisions (as returned by “decision_function” on some classifiers). For binary y_true, y_score is supposed to be the score of the class with greater label.
For AE I am computing roc_auc_score like this:
model.fit(...) # model from https://www.tensorflow.org/api_docs/python/tf/keras/Sequential
pred = model.predict(x_test) # predict function from https://www.tensorflow.org/api_docs/python/tf/keras/Sequential#predict
metric = np.mean(np.power(x_test - pred, 2), axis=1) #MSE
print(roc_auc_score(y_test, metric) # where y_test is true binary labels 0/1
For IsolationForest I am computing roc_auc_score like this:
model.fit(...) # model from https://scikit-learn.org/stable/modules/generated/sklearn.ensemble.IsolationForest.html
metric = -(model.score_samples(x_test)) # https://scikit-learn.org/stable/modules/generated/sklearn.ensemble.IsolationForest.html#sklearn.ensemble.IsolationForest.score_samples
print(roc_auc_score(y_test, metric) #where y_test is true binary labels 0/1
I am just curious if returned roc_auc_score from both implementations of AE and IsolationForest are comparable (I mean, if I am computing them in the correct way)? Especially in AE model, where I am putting MSE into the roc_auc_score (if not, what should be the input as y_score to this function?)
Comparing AE and IsolationForest in the context of anomaly dection using sklearn.metrics.roc_auc_score based on scores coming from AE MSE loss and IF decision_function() respectively is okay. Varying range of the y_score when switching classifier isn't an issue, since this range is taken into account for each classifier when computing the AUC.
To understand that AUC isn't range dependent, remember that you travel along the decision function values to obtain the ROC points. Rescaling the decision function values will only change the decision function thresholds accordingly, defining similar points of the ROC since the new thresholds will lead each to the same TPR and FPR as they did before the rescaling.
Couldn't find a convincing code line in sklearn.metrics.roc_auc_score's implementation, but you can easily observe this comparison in published code associated with a research paper. For example, in the Deep One-Class Classification paper's code (I'm not an author, I know the paper's code because I'm reproducing their results), AE MSE loss and IF decision_function() are the roc_auc_score inputs (whose outputs the paper is comparing):
AE roc_auc_score computation
Found in this script on github.
from sklearn.metrics import roc_auc_score
(...)
scores = torch.sum((outputs - inputs) ** 2, dim=tuple(range(1, outputs.dim())))
(...)
auc = roc_auc_score(labels, scores)
IsolationForest roc_auc_score computation
Found in this script on github.
from sklearn.metrics import roc_auc_score
(...)
scores = (-1.0) * self.isoForest.decision_function(X.astype(np.float32)) # compute anomaly score
y_pred = (self.isoForest.predict(X.astype(np.float32)) == -1) * 1 # get prediction
(...)
auc = roc_auc_score(y, scores.flatten())
Note: The two scripts come from two different repositories but are actually the source of a single paper's results. The authors only chose to create an extra repository for their PyTorch implementation of an AD method requiring a neural network.
Related
My LightGBM regressor model returns negative values.
For XGBoost there is objective='count:poisson' hyperparameter in order to prevent returning negative predicitons.
Is there any chance to do this ?
Github issue => https://github.com/microsoft/LightGBM/issues/5629
LightGBM also supports poisson regression. For example, consider the following Python code.
import lightgbm as lgb
import numpy as np
from matplotlib import pyplot
# random Poisson-distributed target and one informative feature
y = np.random.poisson(lam=15.0, size=1_000)
X = y + np.random.normal(loc=10.0, scale=2.0, size=(y.shape[0], ))
X = X.reshape(-1, 1)
# fit a Poisson regression model
reg = lgb.LGBMRegressor(
objective="poisson",
n_estimators=150,
min_data=1
)
reg.fit(X, y)
# get predictions
preds = reg.predict(X)
print("summary of predicted values")
print(f" * min: {round(np.min(preds), 3)}")
print(f" * max: {round(np.max(preds), 3)}")
# compare predicted distribution to the empirical one
bins = np.linspace(0, 30, 50)
pyplot.hist(y, bins, alpha=0.5, label='actual')
pyplot.hist(preds, bins, alpha=0.5, label='predicted')
pyplot.legend(loc='upper right')
pyplot.show()
This example uses Python 3.10 and lightgbm==3.3.3.
However... I don't recommend using Poisson regression just to achieve "no negative predictions". The Poisson loss function is intended to be used for cases where you believe your target is Poisson-distributed, e.g. it looks like counts of events observed over some regular interval like time or space.
Other options you might consider to try to achieve the behavior "never predict a negative number from LightGBM regression":
write a custom objective function in one of the interfaces that support it, like the R or Python package
post-process LightGBM's predictions, recoding negative values to 0
pre-process the target variable such that there are no negative values (e.g. dropping such observations, re-scaling, taking the absolute value)
LightGBM also facilitates an objective parameter which can be set to 'poisson'. Follow this link for more information.
An example for LGBMRegressor (scikit-learn API):
from lightgbm import LGBMRegressor
regressor = LGBMRegressor(objective='poisson')
I have trained LightGBM on a binary-classification problem, and when plotting the tree I get some leafs like this
I struggle to find the loss-function for the classification trees - Does LightGBM minimize the cross-entropy in the binary case, and is that the leaf score?
I struggle to find the loss-function for the classification trees - Does LightGBM minimize the cross-entropy in the binary case
Yes, if you don't specify an objective then LGBMClassifier will use cross-entropy by default. The documentation in https://lightgbm.readthedocs.io/en/latest/pythonapi/lightgbm.LGBMClassifier.html#lightgbm.LGBMClassifier says that the default for objective is "binary", and then https://lightgbm.readthedocs.io/en/latest/Parameters.html#objective notes that binary is cross-entropy loss.
and is that the leaf score?
The values like leaf 33: -2.209 ("leaf scores") represent the value of the target that will be predicted for instances in that leaf node, multiplied by the learning rate.
Negative values are possible because of the way the boosting process works. Each tree is trained on the residuals of the model up to that tree. A prediction from a model is obtained by summing the output of all trees. The XGBoost docs have a very good explanation of this: "Introduction to Boosted Trees".
In the future, please try to provide a small reproducible example explaining how you created a figure that you're asking questions about. I assumed something like the following Python code, using lightgbm 3.1.0. You can change the values of tree_index to see the different trees in the model.
import lightgbm as lgb
from sklearn.datasets import load_breast_cancer
X, y = load_breast_cancer(return_X_y=True)
gbm = lgb.LGBMClassifier(
n_estimators=10,
num_leaves=3,
max_depth=8,
min_data_in_leaf=3,
)
gbm.fit(X, y)
# visualize tree structure as a directed graph
ax = lgb.plot_tree(
gbm,
tree_index=0,
figsize=(15, 8),
show_info=[
'data_percentage',
]
)
# visualize tree structure in a dataframe
gbm.booster_.trees_to_dataframe()
I am trying to do sentiment classification and I used sklearn SVM model. I used the labeled data to train the model and got 89% accuracy. Now I want to use the model to predict the sentiment of unlabeled data. How can I do that? and after classification of unlabeled data, how to see whether it is classified as positive or negative?
I used python 3.7. Below is the code.
import random
import pandas as pd
data = pd.read_csv("label data for testing .csv", header=0)
sentiment_data = list(zip(data['Articles'], data['Sentiment']))
random.shuffle(sentiment_data)
train_x, train_y = zip(*sentiment_data[:350])
test_x, test_y = zip(*sentiment_data[350:])
from nltk import word_tokenize
from sklearn.feature_extraction.text import CountVectorizer
from sklearn.pipeline import Pipeline
from sklearn.svm import LinearSVC
from sklearn import metrics
clf = Pipeline([
('vectorizer', CountVectorizer(analyzer="word",
tokenizer=word_tokenize,
preprocessor=lambda text: text.replace("<br />", " "),
max_features=None)),
('classifier', LinearSVC())
])
clf.fit(train_x, train_y)
pred_y = clf.predict(test_x)
print("Accuracy : ", metrics.accuracy_score(test_y, pred_y))
print("Precision : ", metrics.precision_score(test_y, pred_y))
print("Recall : ", metrics.recall_score(test_y, pred_y))
When I run this code, I get the output:
ConvergenceWarning: Liblinear failed to converge, increase the number of iterations. "the number of iterations.", ConvergenceWarning)
Accuracy : 0.8977272727272727
Precision : 0.8604651162790697
Recall : 0.925
What is the meaning of ConvergenceWarning?
Thanks in Advance!
What is the meaning of ConvergenceWarning?
As Pavel already mention, ConvergenceWArning means that the max_iteris hitted, you can supress the warning here: How to disable ConvergenceWarning using sklearn?
Now I want to use the model to predict the sentiment of unlabeled
data. How can I do that?
You will do it with the command: pred_y = clf.predict(test_x), the only thing you will adjust is :pred_y (this is your free choice), and test_x, this should be your new unseen data, it has to have the same number of features as your data test_x and train_x.
In your case as you are doing:
sentiment_data = list(zip(data['Articles'], data['Sentiment']))
You are forming a tuple: Check this out
then you are shuffling it and unzip the first 350 rows:
train_x, train_y = zip(*sentiment_data[:350])
Here you train_x is the column: data['Articles'], so all you have to do if you have new data:
new_ data = pd.read_csv("new_data.csv", header=0)
new_y = clf.predict(new_data['Articles'])
how to see whether it is classified as positive or negative?
You can run then: pred_yand there will be either a 1 or a 0 in your outcome. Normally 0 should be negativ, but it depends on your dataset-up
Check out this site about model's persistence. Then you just load it and call predict method. Model will return predicted label. If you used any encoder (LabelEncoder, OneHotEncoder), you need to dump and load it separately.
If I were you, I'd rather do full data-driven approach and use some pretrained embedder. It'll also work for dozens of languages out-of-the-box with is quite neat.
There's LASER from facebook. There's also pypi package, though unofficial. It works just fine.
Nowadays there's a lot of pretrained models, so it shouldn't be that hard to reach near-seminal scores.
Now I want to use the model to predict the sentiment of unlabeled data. How can I do that? and after classification of unlabeled data, how to see whether it is classified as positive or negative?
Basically, you aggregate unlabeled data in same way as train_x or test_x is generated. Probably, it's 2D matrix of shape n_samples x 1, which you would then use in clf.predict to obtain predictions. clf.predict outputs most probable class. In your case 0 is negative and 1 is positive, but it's hard to tell without the dataset.
What is the meaning of ConvergenceWarning?
LinearSVC model is optimized using iterative algorithm. There is an argument max_iter (1000 by default) that controls maximum amount of iterations. If stopping criteria wasn't met during this process, you will get ConvergenceWarning. It shouldn't bother you much, as long as you have acceptable performance in terms of accuracy, or other metrics.
So far I have resourced another post and sklearn documentation
So in general I want to produce the following example:
X = np.matrix([[1,2],[2,3],[3,4],[4,5]])
y = np.array(['A', 'B', 'B', 'C', 'D'])
Xt = np.matrix([[11,22],[22,33],[33,44],[44,55]])
model = model.fit(X, y)
pred = model.predict(Xt)
However for output, I would like to see 3 columns per observation as output from pred:
A | B | C
.5 | .2 | .3
.25 | .25 | .5
...
and a different probability for each class showing up in my prediction.
I believe that the best approach would be Multilabel classification from the second link I provided above. Additionally, I think it might be a good idea to hop into one of the multi-label or multi-output models listed below:
Support multilabel:
sklearn.tree.DecisionTreeClassifier
sklearn.tree.ExtraTreeClassifier
sklearn.ensemble.ExtraTreesClassifier
sklearn.neighbors.KNeighborsClassifier
sklearn.neural_network.MLPClassifier
sklearn.neighbors.RadiusNeighborsClassifier
sklearn.ensemble.RandomForestClassifier
sklearn.linear_model.RidgeClassifierCV
Support multiclass-multioutput:
sklearn.tree.DecisionTreeClassifier
sklearn.tree.ExtraTreeClassifier
sklearn.ensemble.ExtraTreesClassifier
sklearn.neighbors.KNeighborsClassifier
sklearn.neighbors.RadiusNeighborsClassifier
sklearn.ensemble.RandomForestClassifier
However, I am looking for someone who is has more confidence and experience at doing this the right way. All feedback is appreciated.
-bmc
From what I understand you want to obtain probabilities for each of the potential classes for multi-class classifier.
In Scikit-Learn it can be done by generic function predict_proba. It is implemented for most of the classifiers in scikit-learn. You basically call:
clf.predict_proba(X)
Where clf is the trained classifier.
As output you will get a decimal array of probabilities for each class for each input value.
One word of caution - not all classifiers naturally evaluate class probabilities. For instance, SVM doesn't do that. You still can obtain the class probabilities though, but to do that upon constructing such classifiers you need to instruct it to perform probability estimation. For SVM it would look like:
SVC(Probability=True)
After you fit it you will be able to use predict_proba as before.
I need to warn you that if classifier doesn't naturally evaluate probabilities that means that the probabilities will be evaluated using rather expansive computational methods which may significantly increase training time. So I advice you to use classifiers which naturally evaluate class probabilities (neural networks with softmax output, logistic regression, gradient boosting etc)
Try to use calibrated model:
# define model
model = SVC()
# define and fit calibration model
calibrated = CalibratedClassifierCV(model, method='sigmoid', cv=5)
calibrated.fit(trainX, trainy)
# predict probabilities
print(calibrated.predict_proba(testX)[:, 1])
i wanted to code the linear kernel regression in sklearn so i made this code :
model = LinearRegression()
weights = rbf_kernel(X_train,X_test)
for i in range(weights.shape[1]):
model.fit(X_train,y_train,weights[:,i])
model.predict(X_test[i])
then i found that there is KernelRidge in sklearn :
model = KernelRidge(kernel='rbf')
model.fit(X_train,y_train)
pred = model.predict(X_train)
my question is:
1-what is the difference between these 2 codes?
2-in model.fit() that come after KernelRidge(), i found in the documentation that i can add a third argument "weight" to fit() function, i would i do that if i already applied a kernel function to the model?
What is the difference between these two code snippets?
Basically, they have nothing in common. Your first code snippet implements linear regression, with arbitrary set weights of samples. (How did you even come up with calling rbf_kernel this way?) This is still just a linear model, nothing more. You simply assigned (a bit randomly) which samples are important and then looped over features (?). This makes no sense at all. In general: what you have done with rbf_kernel is simply wrong; this is completely not how it is supposed to be used (and why it gave you errors when you tried to pass it to the fit method and you ended up doing a loop and passing each column separately).
Example of fitting such a model to data which is a cosine (thus 0 in mean):
I found in the documentation for the model.fit() function that comes after KernelRidge() that I can add a third argument, weight. Would I do that if I had already applied a kernel function to the model?
This is actual kernel method, kernel is not samples weighting. (One might use kernel function to assign weights, but this is not the meaning of kernel in "linear kernel regression" or in general "kernel methods".) Kernel is a method of introducing nonlinearity to the classifier, which comes from the fact that many methods (including linear regression) can be expressed as dot products between vectors, which can be substituted by kernel function leading to solving the problem in different space (Reproducing Hilbert Kernel Space), which might have very high complexity (like the infinite dimensional space of continuous functions induced by the RBF kernel).
Example of fitting to the same data as above:
from sklearn.linear_model import LinearRegression
from sklearn.kernel_ridge import KernelRidge
import numpy as np
from matplotlib import pyplot as plt
X = np.linspace(-10, 10, 100).reshape(100, 1)
y = np.cos(X)
for model in [LinearRegression(), KernelRidge(kernel='rbf')]:
model.fit(X, y)
p = model.predict(X)
plt.figure()
plt.title(model.__class__.__name__)
plt.scatter(X[:, 0], y)
plt.plot(X, p)
plt.show()