An implementation of the COREQ (CORrelation EQuivalence) algorithm to compute low redundancy estimates for large correlation matrices. The algorithm is described and analysed in detail in the paper:
Erik Scharwächter, Fabian Geier, Lukas Faber, Emmanuel Müller. Low Redundancy Estimation of Correlation Matrices for Time Series using Triangular Bounds. In: Proceedings of the 22nd Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD), 2018.
- Corresponding author: Erik Scharwächter
- Please cite our paper if you use or modify our code for your own work.
Please check our our project website at https://hpi.de/mueller/coreq.html for more information on the method, supplementary material and visualizations.
Automatically build and install the BlockCorr module for Python2 and Python3 with
$ make
$ make install
or use the setup.py script (check --help for details).
Example: A dataset of 1000 time series (length 50) that consists of two perfectly separated clusters of size 700 and 300.
>>> import numpy as np
>>> import BlockCorr
>>> np.random.seed(0)
>>> X = np.random.permutation(np.concatenate((np.repeat(np.random.randn(1, 50), 700, axis=0),
np.repeat(np.random.randn(1, 50), 300, axis=0))))
>>> X.shape
(1000, 50)
>>> alpha = 0.8
>>> labels, pivots, pivot_corr_triu, computations = BlockCorr.COREQ(X, BlockCorr.ESTIMATE_AVERAGE, alpha)
clustering finished with 1300 correlation computations --- 2 clusters detected
>>> pivot_corr_triu
array([ 1. , -0.05918059, 1. ])
>>> # full pivot correlation matrix:
>>> pivot_corr = np.zeros((len(pivots), len(pivots)))
>>> pivot_corr[np.triu_indices(len(pivots))] = pivot_corr_triu
>>> pivot_corr[np.tril_indices(len(pivots))] = pivot_corr_triu
>>> # full time series correlation matrix:
>>> cluster_matrix = np.zeros((X.shape[0], len(pivots)))
>>> cluster_matrix[range(0,len(labels)), labels] = 1
>>> R = cluster_matrix.dot(pivot_corr).dot(cluster_matrix.transpose())
>>> np.abs(R - np.corrcoef(X)).sum()
0.0
The code is released under the MIT license.
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