pyod 0.9.6

A Python Toolbox for Scalable Outlier Detection (Anomaly Detection)

Deployment & Documentation & Stats & License

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PyOD is a comprehensive and scalable Python toolkit for detecting outlying objects in multivariate data. This exciting yet challenging field is commonly referred as Outlier Detection or Anomaly Detection.

PyOD includes more than 30 detection algorithms, from classical LOF (SIGMOD 2000) to the latest COPOD (ICDM 2020) and SUOD (MLSys 2021). Since 2017, PyOD has been successfully used in numerous academic researches and commercial products [34] [35]. It is also well acknowledged by the machine learning community with various dedicated posts/tutorials, including Analytics Vidhya, KDnuggets, Towards Data Science, Computer Vision News, and awesome-machine-learning.

PyOD is featured for:

• Unified APIs, detailed documentation, and interactive examples across various algorithms.

• Advanced models, including classical ones from scikit-learn, latest deep learning methods, and emerging algorithms like COPOD.

• Optimized performance with JIT and parallelization when possible, using numba and joblib.

• Fast training & prediction with SUOD [35].

• Compatible with both Python 2 & 3.

Outlier Detection with 5 Lines of Code:

# train the COPOD detector
from pyod.models.copod import COPOD
clf = COPOD()
clf.fit(X_train)

# get outlier scores
y_train_scores = clf.decision_scores_  # raw outlier scores on the train data
y_test_scores = clf.decision_function(X_test)  # predict raw outlier scores on test

Citing PyOD:

PyOD paper is published in Journal of Machine Learning Research (JMLR) (MLOSS track). If you use PyOD in a scientific publication, we would appreciate citations to the following paper:

@article{zhao2019pyod,
  author  = {Zhao, Yue and Nasrullah, Zain and Li, Zheng},
  title   = {PyOD: A Python Toolbox for Scalable Outlier Detection},
  journal = {Journal of Machine Learning Research},
  year    = {2019},
  volume  = {20},
  number  = {96},
  pages   = {1-7},
  url     = {http://jmlr.org/papers/v20/19-011.html}
}

or:

Zhao, Y., Nasrullah, Z. and Li, Z., 2019. PyOD: A Python Toolbox for Scalable Outlier Detection. Journal of machine learning research (JMLR), 20(96), pp.1-7.

Key Links and Resources:

• View the latest codes on Github

• Execute Interactive Jupyter Notebooks

• Anomaly Detection Resources

Table of Contents:

• Installation

• API Cheatsheet & Reference

• Model Save & Load

• Fast Train with SUOD

• Implemented Algorithms

• Algorithm Benchmark

• Quick Start for Outlier Detection

• How to Contribute

• Inclusion Criteria

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Installation

It is recommended to use pip or conda for installation. Please make sure the latest version is installed, as PyOD is updated frequently:

pip install pyod            # normal install
pip install --upgrade pyod  # or update if needed

conda install -c conda-forge pyod

Alternatively, you could clone and run setup.py file:

git clone https://github.com/yzhao062/pyod.git
cd pyod
pip install .

Required Dependencies:

• Python 2.7, 3.5, 3.6, or 3.7

• combo>=0.0.8

• joblib

• numpy>=1.13

• numba>=0.35

• scipy>=0.19.1

• scikit_learn>=0.20.0

• statsmodels

Optional Dependencies (see details below):

• combo (optional, required for models/combination.py and FeatureBagging)

• keras (optional, required for AutoEncoder, and other deep learning models)

• matplotlib (optional, required for running examples)

• pandas (optional, required for running benchmark)

• suod (optional, required for running SUOD model)

• tensorflow (optional, required for AutoEncoder, and other deep learning models)

• xgboost (optional, required for XGBOD)

Warning 1: PyOD has multiple neural network based models, e.g., AutoEncoders, which are implemented in both PyTorch and Tensorflow. However, PyOD does NOT install DL libraries for you. This reduces the risk of interfering with your local copies. If you want to use neural-net based models, please make sure Keras and a backend library, e.g., TensorFlow, are installed. Instructions are provided: neural-net FAQ. Similarly, models depending on xgboost, e.g., XGBOD, would NOT enforce xgboost installation by default.

Warning 2: PyOD contains multiple models that also exist in scikit-learn. However, these two libraries’ API is not exactly the same–it is recommended to use only one of them for consistency but not mix the results. Refer Differences between scikit-learn and PyOD for more information.

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API Cheatsheet & Reference

Full API Reference: (https://pyod.readthedocs.io/en/latest/pyod.html). API cheatsheet for all detectors:

• fit(X): Fit detector.

• decision_function(X): Predict raw anomaly score of X using the fitted detector.

• predict(X): Predict if a particular sample is an outlier or not using the fitted detector.

• predict_proba(X): Predict the probability of a sample being outlier using the fitted detector.

• predict_confidence(X): Predict the model’s sample-wise confidence (available in predict and predict_proba) [25].

Key Attributes of a fitted model:

• decision_scores_: The outlier scores of the training data. The higher, the more abnormal. Outliers tend to have higher scores.

• labels_: The binary labels of the training data. 0 stands for inliers and 1 for outliers/anomalies.

Fast training and prediction: it is possible to train and predict with a large number of detection models in PyOD by leveraging SUOD framework [35]. See SUOD Paper and repository.

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Model Save & Load

PyOD takes a similar approach of sklearn regarding model persistence. See model persistence for clarification.

In short, we recommend to use joblib or pickle for saving and loading PyOD models. See “examples/save_load_model_example.py” for an example. In short, it is simple as below:

from joblib import dump, load

# save the model
dump(clf, 'clf.joblib')
# load the model
clf = load('clf.joblib')

It is known that there are challenges in saving neural network models. Check #328 and #88 for temporary workaround.

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Fast Train with SUOD

Fast training and prediction: it is possible to train and predict with a large number of detection models in PyOD by leveraging SUOD framework [35]. See SUOD Paper and SUOD example.

from pyod.models.suod import SUOD

# initialized a group of outlier detectors for acceleration
detector_list = [LOF(n_neighbors=15), LOF(n_neighbors=20),
                 LOF(n_neighbors=25), LOF(n_neighbors=35),
                 COPOD(), IForest(n_estimators=100),
                 IForest(n_estimators=200)]

# decide the number of parallel process, and the combination method
# then clf can be used as any outlier detection model
clf = SUOD(base_estimators=detector_list, n_jobs=2, combination='average',
           verbose=False)

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Implemented Algorithms

PyOD toolkit consists of three major functional groups:

(i) Individual Detection Algorithms :

Type	Abbr	Algorithm	Year	Ref
Linear Model	PCA	Principal Component Analysis (the sum of weighted projected distances to the eigenvector hyperplanes)	2003	[30]
Linear Model	MCD	Minimum Covariance Determinant (use the mahalanobis distances as the outlier scores)	1999	[11] [27]
Linear Model	OCSVM	One-Class Support Vector Machines	2001	[29]
Linear Model	LMDD	Deviation-based Outlier Detection (LMDD)	1996	[6]
Proximity-Based	LOF	Local Outlier Factor	2000	[7]
Proximity-Based	COF	Connectivity-Based Outlier Factor	2002	[31]
Proximity-Based	(Incremental) COF	Memory Efficient Connectivity-Based Outlier Factor (slower but reduce storage complexity)	2002	[31]
Proximity-Based	CBLOF	Clustering-Based Local Outlier Factor	2003	[12]
Proximity-Based	LOCI	LOCI: Fast outlier detection using the local correlation integral	2003	[23]
Proximity-Based	HBOS	Histogram-based Outlier Score	2012	[9]
Proximity-Based	kNN	k Nearest Neighbors (use the distance to the kth nearest neighbor as the outlier score)	2000	[26]
Proximity-Based	AvgKNN	Average kNN (use the average distance to k nearest neighbors as the outlier score)	2002	[5]
Proximity-Based	MedKNN	Median kNN (use the median distance to k nearest neighbors as the outlier score)	2002	[5]
Proximity-Based	SOD	Subspace Outlier Detection	2009	[17]
Proximity-Based	ROD	Rotation-based Outlier Detection	2020	[4]
Probabilistic	ABOD	Angle-Based Outlier Detection	2008	[16]
Probabilistic	COPOD	COPOD: Copula-Based Outlier Detection	2020	[20]
Probabilistic	FastABOD	Fast Angle-Based Outlier Detection using approximation	2008	[16]
Probabilistic	MAD	Median Absolute Deviation (MAD)	1993	[13]
Probabilistic	SOS	Stochastic Outlier Selection	2012	[14]
Outlier Ensembles	IForest	Isolation Forest	2008	[21]
Outlier Ensembles	FB	Feature Bagging	2005	[18]
Outlier Ensembles	LSCP	LSCP: Locally Selective Combination of Parallel Outlier Ensembles	2019	[34]
Outlier Ensembles	XGBOD	Extreme Boosting Based Outlier Detection (Supervised)	2018	[33]
Outlier Ensembles	LODA	Lightweight On-line Detector of Anomalies	2016	[24]
Outlier Ensembles	SUOD	SUOD: Accelerating Large-scale Unsupervised Heterogeneous Outlier Detection (Acceleration)	2021	[35]
Neural Networks	AutoEncoder	Fully connected AutoEncoder (use reconstruction error as the outlier score)		[1] [Ch.3]
Neural Networks	VAE	Variational AutoEncoder (use reconstruction error as the outlier score)	2013	[15]
Neural Networks	Beta-VAE	Variational AutoEncoder (all customized loss term by varying gamma and capacity)	2018	[8]
Neural Networks	SO_GAAL	Single-Objective Generative Adversarial Active Learning	2019	[22]
Neural Networks	MO_GAAL	Multiple-Objective Generative Adversarial Active Learning	2019	[22]
Neural Networks	DeepSVDD	Deep One-Class Classification	2018	[28]

(ii) Outlier Ensembles & Outlier Detector Combination Frameworks:

Type	Abbr	Algorithm	Year	Ref
Outlier Ensembles		Feature Bagging	2005	[18]
Outlier Ensembles	LSCP	LSCP: Locally Selective Combination of Parallel Outlier Ensembles	2019	[34]
Outlier Ensembles	XGBOD	Extreme Boosting Based Outlier Detection (Supervised)	2018	[33]
Outlier Ensembles	LODA	Lightweight On-line Detector of Anomalies	2016	[24]
Outlier Ensembles	SUOD	SUOD: Accelerating Large-scale Unsupervised Heterogeneous Outlier Detection (Acceleration)	2021	[35]
Combination	Average	Simple combination by averaging the scores	2015	[2]
Combination	Weighted Average	Simple combination by averaging the scores with detector weights	2015	[2]
Combination	Maximization	Simple combination by taking the maximum scores	2015	[2]
Combination	AOM	Average of Maximum	2015	[2]
Combination	MOA	Maximization of Average	2015	[2]
Combination	Median	Simple combination by taking the median of the scores	2015	[2]
Combination	majority Vote	Simple combination by taking the majority vote of the labels (weights can be used)	2015	[2]

(iii) Utility Functions:

Type	Name	Function	Documentation
Data	generate_data	Synthesized data generation; normal data is generated by a multivariate Gaussian and outliers are generated by a uniform distribution	generate_data
Data	generate_data_clusters	Synthesized data generation in clusters; more complex data patterns can be created with multiple clusters	generate_data_clusters
Stat	wpearsonr	Calculate the weighted Pearson correlation of two samples	wpearsonr
Utility	get_label_n	Turn raw outlier scores into binary labels by assign 1 to top n outlier scores	get_label_n
Utility	precision_n_scores	calculate precision @ rank n	precision_n_scores

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Algorithm Benchmark

The comparison among of implemented models is made available below (Figure, compare_all_models.py, Interactive Jupyter Notebooks). For Jupyter Notebooks, please navigate to “/notebooks/Compare All Models.ipynb”.

A benchmark is supplied for select algorithms to provide an overview of the implemented models. In total, 17 benchmark datasets are used for comparison, which can be downloaded at ODDS.

For each dataset, it is first split into 60% for training and 40% for testing. All experiments are repeated 10 times independently with random splits. The mean of 10 trials is regarded as the final result. Three evaluation metrics are provided:

• The area under receiver operating characteristic (ROC) curve

• Precision @ rank n (P@N)

• Execution time

Check the latest benchmark. You could replicate this process by running benchmark.py.

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Quick Start for Outlier Detection

PyOD has been well acknowledged by the machine learning community with a few featured posts and tutorials.

Analytics Vidhya: An Awesome Tutorial to Learn Outlier Detection in Python using PyOD Library

KDnuggets: Intuitive Visualization of Outlier Detection Methods, An Overview of Outlier Detection Methods from PyOD

Towards Data Science: Anomaly Detection for Dummies

Computer Vision News (March 2019): Python Open Source Toolbox for Outlier Detection

“examples/knn_example.py” demonstrates the basic API of using kNN detector. It is noted that the API across all other algorithms are consistent/similar.

More detailed instructions for running examples can be found in examples directory.

1. Initialize a kNN detector, fit the model, and make the prediction.

   from pyod.models.knn import KNN   # kNN detector
   
   # train kNN detector
   clf_name = 'KNN'
   clf = KNN()
   clf.fit(X_train)
   
   # get the prediction label and outlier scores of the training data
   y_train_pred = clf.labels_  # binary labels (0: inliers, 1: outliers)
   y_train_scores = clf.decision_scores_  # raw outlier scores
   
   # get the prediction on the test data
   y_test_pred = clf.predict(X_test)  # outlier labels (0 or 1)
   y_test_scores = clf.decision_function(X_test)  # outlier scores
   
   # it is possible to get the prediction confidence as well
   y_test_pred, y_test_pred_confidence = clf.predict(X_test, return_confidence=True)  # outlier labels (0 or 1) and confidence in the range of [0,1]

2. Evaluate the prediction by ROC and Precision @ Rank n (p@n).

   from pyod.utils.data import evaluate_print
   
   # evaluate and print the results
   print("\nOn Training Data:")
   evaluate_print(clf_name, y_train, y_train_scores)
   print("\nOn Test Data:")
   evaluate_print(clf_name, y_test, y_test_scores)

3. See a sample output & visualization.

   On Training Data:
   KNN ROC:1.0, precision @ rank n:1.0
   
   On Test Data:
   KNN ROC:0.9989, precision @ rank n:0.9

   visualize(clf_name, X_train, y_train, X_test, y_test, y_train_pred,
       y_test_pred, show_figure=True, save_figure=False)

Visualization (knn_figure):

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How to Contribute

You are welcome to contribute to this exciting project:

• Please first check Issue lists for “help wanted” tag and comment the one you are interested. We will assign the issue to you.

• Fork the master branch and add your improvement/modification/fix.

• Create a pull request to development branch and follow the pull request template PR template

• Automatic tests will be triggered. Make sure all tests are passed. Please make sure all added modules are accompanied with proper test functions.

To make sure the code has the same style and standard, please refer to abod.py, hbos.py, or feature_bagging.py for example.

You are also welcome to share your ideas by opening an issue or dropping me an email at [e-mail] :)

Inclusion Criteria

Similarly to scikit-learn, We mainly consider well-established algorithms for inclusion. A rule of thumb is at least two years since publication, 50+ citations, and usefulness.

However, we encourage the author(s) of newly proposed models to share and add your implementation into PyOD for boosting ML accessibility and reproducibility. This exception only applies if you could commit to the maintenance of your model for at least two year period.

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Reference

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Aggarwal, C.C. and Sathe, S., 2015. Theoretical foundations and algorithms for outlier ensembles.ACM SIGKDD Explorations Newsletter, 17(1), pp.24-47.

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Aggarwal, C.C. and Sathe, S., 2017. Outlier ensembles: An introduction. Springer.

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