evalAIRR 0.0.3

Comparison of real and simulated AIRR datasets

evalAIRR

A tool that allows comparison of real and simulated datasets by providing different statistical indicators and dataset visualizations in one report.

Installation

Clone the repository and install the required dependencies using this command:

pip install -r <INSTALL_DIRECTORY>/requirements.txt

The versions of python that evalAIRR was tested with are 3.8 and 3.10

It is recommended to use a virtual python environment to run evalAIRR if another python environment is used. Here is a quick guide on how you can set up a virtual environment:

https://docs.python.org/3/tutorial/venv.html#creating-virtual-environments

Quickstart

evalAIRR uses a YAML file for configuration. If you are unfamiliar with how YAML files are structured, read this guide to the syntax:

https://docs.fileformat.com/programming/yaml/#syntax

This is the stucture of a sample report configuration file you can use to start off with (it is included in the repository location ./yaml_files/quickstart.yaml):

datasets:

  real:

    path: ./data/encoded_real_1000_200.csv

  sim:

    path: ./data/encoded_sim_1000_200.csv

reports:

  ks:

    - TGT

    - ANV

  distr_densityplot:

    - TGT

    - ANV

output:

  path: './output/report.html'

This report will process the two provided datasets (real and simulated), and create two reports - Kolmogorov–Smirnov test (indicated by ks) and a feature distribution density plot (indicated by distr_densityplot) for the features TGT and ANV. It will then export the report to the path ./output/report.html. More details on what reports can be created can be found in the YAML Configuration Guidelines secion.

You can run the program by running this command within the installation directory:

python main.py ./yaml_files/quickstart.yaml

The report will be generated in the specified output path in the configuration file or, if a specific path is not provided, in <INSTALL_DIRECTORY>/output/report.html. The report is exported in the HTML format.

YAML Configuration Guidelines

The configuration YAML file consists of 3 main sections: datasets, reports and output.

Datasets

In the datasets section, you have to provide paths to a real and a simulated datasets that you are comparing. This can be done by specifying the file path of each file in the path variable under the sections real and sim respectively. Here is an example of how a configured datasets section looks like:

datasets:

  real:

    path: ./data/encoded_real_1000_200.csv

  sim:

    path: ./data/encoded_sim_1000_200.csv

Reports

In the reports section, you can provide the list of report types you want to create and their parameters. Here is the list of reports you can create that compare the features of the real dataset with the simulated dataset:

• ks - Kolmogorov–Smirnov statistic. Parameters: list of features you are creating the report for.

• distr_histogram - feature distribution histogram. Parameters: list of features you are creating the report for.

• observation_distr_histogram - observation distribution histogram. Parameters: list of observations you are creating the report for.

• distr_boxplot - feature distribution boxplot. Parameters: list of features you are creating the report for.

• observation_distr_boxplot - observation distribution boxplot. Parameters: list of observations you are creating the report for.

• distr_violinplot - feature distribution violin plot. Parameters: list of features you are creating the report for.

• observation_distr_violinplot - observation distribution violin plot. Parameters: list of observations you are creating the report for.

• distr_densityplot - feature distribution density plot. Parameters: list of features you are creating the report for.

• observation_distr_densityplot - observation distribution density plot. Parameters: list of observations you are creating the report for.

• distance - Euclidean distance between the real and simulated feature. Parameters: list of features you are creating the report for.

• observation_distance - Euclidean distance between the real and simulated observation. Parameters: list of observations you are creating the report for.

• statistics - statistical indicators (average, median, standard deviation and variance) of a feature in both real and simulated datasets. Parameters: list of features you are creating the report for.

• observation_statistics - statistical indicators (average, median, standard deviation and variance) of an observation in both real and simulated datasets. Parameters: list of observations you are creating the report for.

• copula_2d - a 2D scatter plot that displays two features in a Gausian Multivariate copula space. Parameters: a report section of any name, under which the compared features are specified.

• copula_3d - a 3D scatter plot that displays three features in a Gausian Multivariate copula space. Parameters: a report section of any name, under which the compared features are specified.

• feature_average_vs_variance - a scatter plot that displays the average value of every feature on one axis and the variance of every feature on the other axis.

• observation_average_vs_variance - a scatter plot that displays the average value of every observation on one axis and the variance of every observation on the other axis.

• corr - correlation matrix heatmaps of the real and simulated datasets. Parameters: percent_features - an optional parameter for dimensionality reduction using PCA. A float value corresponding with the ratio of feature reduction (e.g. percent_features equal to 0.5 would reduce the feature count by half).

• pca_2d - two scatter plots with both datasets reduced to two dimensions using PCA.

Here is a sample reports section of a configuration file with all of the reports:

reports:

  ks:

    - TGT

  distr_histogram:

    - TGT

  observation_distr_histogram:

    - 0

    - 199

  distr_boxplot:

    - TGT

  observation_distr_boxplot:

    - 0

    - 199

  distr_violinplot:

    - TGT

  observation_distr_violinplot:

    - 0

    - 199

  distr_densityplot:

    - TGT

  observation_distr_densityplot:

    - 0

    - 199

  distance:

    - TGT

  observation_distance:

    - 0

    - 199

  statistics:

    - TGT

  observation_statistics:

    - 0

    - 199

  copula_2d:

    report1:

      - TGT

      - ANV

  copula_3d:

    report1:

      - TGT

      - ANV

      - CAS

  feature_average_vs_variance:

  observation_average_vs_variance:

  corr:

    percent_features: 0.6

  pca_2d:

Output

An optional section where you can specify the file path of the generated report. The default path of the generated report is <INSTALL_DIRECTORY>/output/report.html. The report is exported in the HTML format.

An example output section:

output:

  path: './output/report.html'