bulkdgd find probability_density

For a set of given representations and the Gaussian mixture model (GMM) modelling the representation space in the bulkDGD model, this command outputs the probability density of each representation for each GMM component.

This is useful, for instance, to identify a representative sample for each GMM component, namely the one having the highest probability for that component for all samples under consideration.

bulkdgd find probability_density takes as input a CSV file containing the representations for a set of samples formatted as the one produced by bulkdgd find representations. This CSV file stores a data frame in which each row represents a sample’s representation, and each column represents a dimension of the latent space where the representations live.

Parallelization

If the command is parallelized over several input files or configuration files, each is assumed to be identically named and placed in a different directory. The paths to such directories must be specified using the -ds, --dirs option (see the full description in the Parallelization options section below) and must be relative to the specified working directory (-d, --work-dir option).

You can also run the command with the same input file using different configuration files and vice versa.

In these cases, the files that vary among the runs must be placed in different directories and referenced by their corresponding options by name (not path).

In contrast, the input/configuration files that stay the same among runs may be placed anywhere and referenced by their corresponding options using their absolute path or path relative to the specified working directory.

The output and log files for each run will be written in the directory where the corresponding input/configuration files were placed. If the command is not parallelized, these files will be written in the working directory.

Command line

bulkdgd find probability_density [-h] -ir INPUT_REP [-or OUTPUT_PROB_REP] [-oc OUTPUT_PROB_COMP] -cm CONFIG_FILE_MODEL [-d WORK_DIR] [-lf LOG_FILE] [-lc] [-v] [-vv] [-p] [-n N_PROC] [-ds DIRS [DIRS ...]]

Options

Help options

Option	Description
-h, --help	Show the help message and exit.

Input files

Option	Description
-ir, --input-rep	The input CSV file containing the data frame with the representations.

Output files

Option	Description
-or, --output-prob-rep	The name of the output CSV file containing, for each representation, its probability density for each of the Gaussian mixture model’s components, the maximum probability density found, and the component the maximum probability density comes from. The default file name is probability_density_representations.csv.
-oc, --output-prob-comp	The name of the output CSV file containing, for each component of the Gaussian mixture model, the representation(s) having the maximum probability density with respect to it. The default file name is probability_density_components.csv.

Configuration files

Option	Description
-cm, --config-file-model	The YAML configuration file specifying the bulkDGD model’s parameters and files containing the trained model. If it is a name without an extension, it is assumed to be the name of a configuration file in $INSTALLDIR/bulkDGD/configs/model.

Working directory options

Option	Description
-d, --work-dir	The working directory. The default is the current working directory.

Logging options

Option	Description
-lf, --log-file	The name of the log file. The default file name is bulkdgd_find_probability_density.log.
-lc, --log-console	Show log messages also on the console.
-v, --logging-verbose	Enable verbose logging (INFO level).
-vv, --logging-debug	Enable maximally verbose logging for debugging purposes (DEBUG level).

Parallelization options

Option	Description
-p, --parallelize	Whether to run the command in parallel.
-n, --n-proc	The number of processes to start. The default number of processes started is 1.
-ds, --dirs	The directories containing the input/configuration files. It can be either a list of names or paths, a pattern that the names or paths match, or a plain text file containing the names of or the paths to the directories. If names are given, the directories are assumed to be inside the working directory. If paths are given, they are assumed to be relative to the working directory.