Temporal Silhouette for Stream Clustering Validation

Instructions for experiment replication

author: Félix Iglesias

contact: [email protected]

The TS index and the experiments here implemented are from the paper:

Iglesias Vázquez, F., Zseby, T. Temporal silhouette: validation of stream clustering robust to concept drift. Mach Learn (2023). https://doi.org/10.1007/s10994-023-06462-2

If you use Temporal Silhouette and/or the experiments described here, please cite the paper.

0. Requirements

Experiments require the following general-purpose Python packages:

• numpy
• pandas
• scipy
• sklearn
• glob
• re
• sys

Stream clustering algoriths used are:

• Birch from sklearn
• DenStream from https://github.com/issamemari/DenStream
• CluStream and Streamkm from https://github.com/giuliano-oliveira/clusopt_core

Incremental cvis are obtained from the package:

• cvi

1. Temporal Silhouette Index (TS)

Use TS in your codes by importing the "tempsil" function:

    from TSindex import tempsil

    tempsil(t,x,l,s,kn,c)
    # INPUTS
    # t: 1D-array with timestamps
    # x: 2D-array with data vectors
    # l: 1D-array with labels
    # s: window-size of the simple-moving-average (SMA), default s=200 
    # kn: number-of-neighbors of other clusters for calculating beta, default kn=200
    # c: sigma parameter to weight the penalization over contextual outliers [0...1], default=1
    #
    # OUTPUTS
    # k: 1D-array with cluster-labels
    # ts2: 1D-array with quadratic cluster temporal silhouettes
    # TS: global Temporal Silhuette

For a simple example, open a terminal and run:

    $ python3 toy_tests.py c

where "c" is a real number for the TS sigma parameter. In the paper, Section 4.6 uses this script for the examples, with c=1 and c=0.

2. Datasets

Synthetic datasets are located within the [dataS] folder. They are also publicly available in Mendeley:

“Data for Evaluation of Stream Data Analysis Algorithms”. Mendeley Data, V1, doi: 10.17632/c43kr4t7h8.1, https://data.mendeley.com/datasets/c43kr4t7h8/1

The clean (without outliers) versions and the versions with out-of-phase outliers are created online during the runing of the experiments

Real datasets are located within the [dataR] folder (they are preprocessed versions in arff format). Original data has been obtained from:

• kaggle - Retail and Retailers Sales Time Series Collection: https://www.kaggle.com/datasets/census/retail-and-retailers-sales-time-series-collection

• Gapminder data repository - Fertility vs Income: https://www.gapminder.org/data/

Stationary datasets are located within the [dataT] folder (they are preprocessed versions in arff format). Original data has been obtained from:

• Clustering Basic Benchmark of the University of Eastern Finland (Fränti and Sieranoja, 2018): https://cs.joensuu.fi/sipu/datasets/

  • s1 (Fränti and Virmajoki, 2006)
  • unbalance2b (based on the umbalance2 dataset (Rezaei and Fränti, 2020)
  • d64 (Fränti et al, 2006).

• The noise dataset has been created with the MDCgen tool (Iglesias et al, 2019): https://github.com/CN-TU/mdcgen-matlab

• Fränti P, Sieranoja S (2018) K-means properties on six clustering benchmark datasets. Applied Intelligence 48(12):4743–4759

• Fränti P, Virmajoki O (2006) Iterative shrinking method for clustering problems. Pattern Recognition 39(5):761–765

• Rezaei M, Fränti P (2020) Can the number of clusters be determined by external indices? IEEE Access 8:89,239–89,257

• Fränti P, Virmajoki O, Hautamäki V (2006) Fast agglomerative clustering using a k-nearest neighbor graph. IEEE Trans on Pattern Analysis and Machine Intelligence 28(11):1875–1881

• Iglesias F, Zseby T, Ferreira D, Zimek A (2019) Mdcgen: Multidimensional dataset generator for clustering. Jour of Classification 36(3):599–618

3. Replicating experiments

For the synthetic data, open a terminal in the current folder. Run:

    $ python3 run_analysis_synthetic.py

A results_synthetic.csv file will be created in the [results/] folder.

For the real data, open a terminal in the current folder. Run:

    $ python3 run_analysis_real.py

Three files (fert_vs_gdp_labels.csv, results_real.csv and retail_labels.csv) will be created in the [results/] folder.

Warning! The [results/] folder already contain files with the results published in the paper. Remove, rename or copy these files in a different folder before running the scripts; otherwise, results will be appended in the synthetic case and overwriten in the real case.

4. Comparing performances of CVIs/iCVIs of stream clustering performances over datasets with concept drift

For a comparison with the Ground Truth (GT) as benchmark:

    $ python3 utils/compare_results.py results/results_synthetic.csv gt

For a comparison with the best clustering according to external validation (AMI) as benchmark:

    $ python3 utils/compare_results.py results/results_synthetic.csv ami

5. Plotting peformances of stream clustering for real data cases

To visualize the performances of the stream clustering algorithms used in real data cases, run:

    $ python3 utils/plots_retail.py dataR/retail.arff results/retail_labels.csv 

    $ python3 utils/plots_gapminder.py dataR/fert_vs_gdp.arff results/fert_vs_gdp_labels.csv

6. Comparing performances of CVIs/iCVIs in stationary datasets

Open a terminal in the current folder. Run:

    $ python3 run_stationary.py

A results_stationary.csv file will be created in the [results/] folder. You can plot these results as heatmaps by running:

    $ python3 utils/plots_stationary.py results/results_stationary.csv

It will create the following figures in the [results/] folder: noise.pdf, unbalanced2b.pdf, s1.pdf, d64.pdf.

7. Sensitivity analysis on TS w and k parameters

Open a terminal in the current folder. Run:

    $ python3 run_TS_stability.py

A results_TSstability.csv file will be created in the [results/] folder. You can plot these results as boxplots by running:

    $ python3 utils/plots_TSstab.py results/results_TSstability.csv

It will create the TS_stab.pdf figure in the [results/] folder.