gomi

Introduction

gomi is a software package for the evaluation of morphological intelligence measures on data. gomi includes all currently available morphological intelligence measures. This includes measures with continuous estimators as well as measures that use a discrete estimator.

The following sections will only provide minimal information about the measures. The goal of this post to provide information about the application of the measures, not an introduction of the measures themselves. For this purpose, please visit the other posts on these pages:

Posts:

  1. Morphological Computation: The Good, the Bad, and the Ugly
  2. Evaluating Morphological Computation in Muscle and DC-Motor Driven Models of Hopping Movements
  3. Quantifying morphological computation based on an information decomposition of the sensorimotor loop
  4. Quantifying Morphological Computation

or the following publications:

  • [PDF] K. Ghazi-Zahedi, D. F. B. Haeufle, G. F. Montufar, S. Schmitt, and N. Ay, “Evaluating morphological computation in muscle and dc-motor driven models of hopping movements,” Frontiers in robotics and ai, vol. 3, iss. 42, 2016.
    [Bibtex]
    @article{Ghazi-Zahedi2016aEvaluating,
    Author = {Ghazi-Zahedi, Keyan and Haeufle, Daniel F.B. and Montufar, Guido Francisco and Schmitt, Syn and Ay, Nihat},
    Issn = {2296-9144},
    Journal = {Frontiers in Robotics and AI},
    Number = {42},
    Pdf = {http://www.frontiersin.org/computational_intelligence/10.3389/frobt.2016.00042/abstract},
    Title = {Evaluating Morphological Computation in Muscle and DC-motor Driven Models of Hopping Movements},
    Volume = {3},
    Year = {2016}}
  • [PDF] K. Ghazi-Zahedi and J. Rauh, “Quantifying morphological computation based on an information decomposition of the sensorimotor loop,” in Proceedings of the 13th european conference on artificial life (ecal 2015), 2015, p. 70–-77.
    [Bibtex]
    @inproceedings{Ghazi-Zahedi2015bQuantifying,
    Author = {Ghazi-Zahedi, Keyan and Rauh, Johannes},
    Booktitle = {Proceedings of the 13th European Conference on Artificial Life (ECAL 2015)},
    Date-Modified = {2018-05-26 22:52:07 +0000},
    Month = {July},
    Pages = {70---77},
    Pdf = {http://keyan.ghazi-zahedi.eu/wp-content/uploads/2018/05/Ghazi-Zahedi2015aQuantifying-Morphological-Computation.pdf},
    Read = {1},
    Title = {Quantifying Morphological Computation based on an Information Decomposition of the Sensorimotor Loop},
    Year = {2015}}
  • [PDF] K. Zahedi and N. Ay, “Quantifying morphological computation,” Entropy, vol. 15, iss. 5, p. 1887–1915, 2013.
    [Bibtex]
    @article{Zahedi2013aQuantifying,
    Author = {Zahedi, Keyan and Ay, Nihat},
    Issn = {1099-4300},
    Journal = {Entropy},
    Number = {5},
    Pages = {1887--1915},
    Pdf = {http://www.mdpi.com/1099-4300/15/5/1887},
    Title = {Quantifying Morphological Computation},
    Volume = {15},
    Year = {2013}}
  • [PDF] K. Ghazi-Zahedi, R. Deimel, G. Montúfar, V. Wall, and O. Brock, “Morphological computation: the good, the bad, and the ugly,” in Iros 2017, 2017.
    [Bibtex]
    @inproceedings{Ghazi-Zahedi2017aMorphological,
    Author = {Ghazi-Zahedi, Keyan and Deimel, Raphael and Mont{\'u}far, Guido and Wall, Vincent and Brock, Oliver},
    Booktitle = {IROS 2017},
    PDF = {https://ieeexplore.ieee.org/document/8202194/},
    Title = {Morphological Computation: The Good, the Bad, and the Ugly},
    Year = {2017}}
  • [PDF] [DOI] K. Ghazi-Zahedi, C. Langer, and N. Ay, “Morphological computation: synergy of body and brain,” Entropy, vol. 19, iss. 9, 2017.
    [Bibtex]
    @article{Ghazi-Zahedi2017bMorphological,
    Abstract = {There are numerous examples that show how the exploitation of the body's physical properties can lift the burden of the brain. Examples include grasping, swimming, locomotion, and motion detection. The term Morphological Computation was originally coined to describe processes in the body that would otherwise have to be conducted by the brain. In this paper, we argue for a synergistic perspective, and by that we mean that Morphological Computation is a process which requires a close interaction of body and brain. Based on a model of the sensorimotor loop, we study a new measure of synergistic information and show that it is more reliable in cases in which there is no synergistic information, compared to previous results. Furthermore, we discuss an algorithm that allows the calculation of the measure in non-trivial (non-binary) systems.},
    Article = {456},
    Author = {Ghazi-Zahedi, Keyan and Langer, Carlotta and Ay, Nihat},
    Doi = {10.3390/e19090456},
    Issn = {1099-4300},
    Journal = {Entropy},
    Number = {9},
    Pdf = {http://www.mdpi.com/1099-4300/19/9/456/pdf},
    Title = {Morphological Computation: Synergy of Body and Brain},
    Url = {http://www.mdpi.com/1099-4300/19/9/456},
    Volume = {19},
    Year = {2017},
    Bdsk-Url-1 = {http://www.mdpi.com/1099-4300/19/9/456},
    Bdsk-Url-2 = {https://doi.org/10.3390/e19090456}}

Installation

gomi is written in Go. For the installation of Go, please read the installation documentation provided [here]. Pre-compiled binaries of gomi for Windows, Linux, and macOS are available in the release files [here].

Once Go is installed, gomi can easily be installed using the following commands:

The following two packages are required and might have to be installed manually:

A zip (and tarball) of stable releases can be downloaded [here].

Discrete Measures

MI_W

\fn_phv \mathrm{MI}_\mathrm{W} = I(W';W|A)\\ \hspace*{1.5cm}= \sum_{w',w,a} p(w',w,a) \log_2\frac{pw(w'|w,a)}{p(w'|a)}

To calculate this measure, we need to estimate the joint distribution \fn_phv p(w',w,a) from which the two conditional distributions can be calculated in the following way:

\fn_phv p(w,a) = \sum_{w'}p(w',w,a)\\ \hspace*{0.5cm}p(w',a) = \sum_{w}p(w',w,a)\\ \hspace*{1.15cm}p(a) = \sum_{w',w}p(w',w,a)\\ \hspace*{0.1cm}p(w'|w,a) = \frac{p(w',w,a)}{p(w,a)}\\ \hspace*{0.65cm}p(w'|a) = \frac{p(w',a)}{p(a)}

These calculations (which are required for the discrete estimator), are done automatically by gomi. The user only needs to provide the data and some parameters, which are explained next.

Using the gomi binary
To calculate MI_W with the binary, use the following command line parameters:

The file musfib was used in [1] and can be downloaded [here].

Explanation of the command line options used in the example above:

-mi MI_W Chooses MI_W as the measure
-file musfib.csv Data is provided in the file musfib.csv
-wi 1,2,3 Columns 1,2,3 of the data provided in musfib.csv define the world state (counting starts with 0)
-ai 9 Column 9 of the data provided in musfib.csv defines the action state (counting starts with 0)
-v gomi will print useful information while it is running and it will print the result
-bins 300 Global definition of the binning. This value will be used for each of the four columns
-o MI_W.csv The result and the specified parameters will be written to MI_W.csv

The full list of command line options is given below.

Using gomi as a library
The measures implemented in gomi can also be used as a library. The following code snippet gives an example:

MI_A

\fn_phv \mathrm{MI}_\mathrm{A} = I(W';A|W)\\ \hspace*{1.5cm}= \sum_{w',w,a} p(w',w,a) \log_2\frac{pw(w'|w,a)}{p(w'|w)}

To calculate this measure, we need to estimate the joint distribution \fn_phv p(w',w,a) from which the two conditional distributions can be calculated in the following way:

\fn_phv p(w,a) = \sum_{w'}p(w',w,a)\\ \hspace*{0.5cm}p(w',w) = \sum_{a}p(w',w,a)\\ \hspace*{1.15cm}p(w) = \sum_{w',a}p(w',w,a)\\ \hspace*{0.1cm}p(w'|w,a) = \frac{p(w',w,a)}{p(w,a)}\\ \hspace*{0.65cm}p(w'|w) = \frac{p(w',w)}{p(w)}

These calculations (which are required for the discrete estimator), are done automatically by gomi. The user only needs to provide the data and some parameters, which are explained next.

Using the gomi binary
To calculate MI_A with the binary, use the following command line parameters:

The file musfib was used in [1] and can be downloaded [here].

Explanation of the command line options used in the example above:

-mi MI_A Chooses MI_A as the measure
-file musfib.csv Data is provided in the file musfib.csv
-wi 1,2,3 Columns 1,2,3 of the data provided in musfib.csv define the world state (counting starts with 0)
-ai 9 Column 9 of the data provided in musfib.csv defines the action state (counting starts with 0)
-v gomi will print useful information while it is running and it will print the result
-bins 300 Global definition of the binning. This value will be used for each of the four columns
-o MI_A.csv The result and the specified parameters will be written to MI_A.csv

The full list of command line options is given below.

Using gomi as a library
The measures implemented in gomi can also be used as a library. The following code snippet gives an example:

MI_A_Prime

\fn_phv \mathrm{MI'}_\mathrm{A} = 1 - \frac{1}{\log_2|W|}\sum_{w',w,a} p(w',w,a) \log_2\frac{pw(w'|w,a)}{p(w'|w)}

This is a version of the previous measure that increases with increasing effect of W on W’. It is normalised to one.

Using the gomi binary
To calculate MI_A_Prime with the binary, use the following command line parameters:

The file musfib was used in [1] and can be downloaded [here].

Explanation of the command line options used in the example above:

-mi MI_A_Prime Chooses MI_A_Prime as the measure
-file musfib.csv Data is provided in the file musfib.csv
-wi 1,2,3 Columns 1,2,3 of the data provided in musfib.csv define the world state (counting starts with 0)
-ai 9 Column 9 of the data provided in musfib.csv defines the action state (counting starts with 0)
-v gomi will print useful information while it is running and it will print the result
-bins 300 Global definition of the binning. This value will be used for each of the four columns
-o MI_A_Prime.csv The result and the specified parameters will be written to MI_A_Prime.csv

The full list of command line options is given below.

Using gomi as a library
The measures implemented in gomi can also be used as a library. The following code snippet gives an example:

MI_MI

\fn_phv \mathrm{MI}_\mathrm{MI} = I(W';W)-I(A;S)

Using the gomi binary
To calculate MI_MI with the binary, use the following command line parameters:

The file musfib was used in [1] and can be downloaded [here].

Explanation of the command line options used in the example above:

-mi MI_MI Chooses MI_MI as the measure
-file musfib.csv Data is provided in the file musfib.csv
-wi 1,2,3 Columns 1,2,3 of the data provided in musfib.csv define the world state (counting starts with 0)
-ai 9 Column 9 of the data provided in musfib.csv defines the action state (counting starts with 0)
-si 4 Column 4 of the data provided in musfib.csv defines the sensor state (counting starts with 0)
-v gomi will print useful information while it is running and it will print the result
-bins 300 Global definition of the binning. This value will be used for each of the four columns
-o MI_MI.csv The result and the specified parameters will be written to MI_MI.csv

The full list of command line options is given below.

Using gomi as a library
The measures implemented in gomi can also be used as a library. The following code snippet gives an example:

MI_CA

\fn_phv \mathrm{MI}_\mathrm{CA} = I(W';W)-I(W';A)

Using the gomi binary
To calculate MI_CA with the binary, use the following command line parameters:

The file musfib was used in [1] and can be downloaded [here].

Explanation of the command line options used in the example above:

-mi MI_CA Chooses MI_CA as the measure
-file musfib.csv Data is provided in the file musfib.csv
-wi 1,2,3 Columns 1,2,3 of the data provided in musfib.csv define the world state (counting starts with 0)
-ai 9 Column 9 of the data provided in musfib.csv defines the action state (counting starts with 0)
-v gomi will print useful information while it is running and it will print the result
-bins 300 Global definition of the binning. This value will be used for each of the four columns
-o MI_CA.csv The result and the specified parameters will be written to MI_CA.csv

The full list of command line options is given below.

Using gomi as a library
The measures implemented in gomi can also be used as a library. The following code snippet gives an example:

MI_WA

\fn_phv \mathrm{MI}_\mathrm{WA} = I(W';W,A)-I(W';A)

Using the gomi binary
To calculate MI_WA with the binary, use the following command line parameters:

The file musfib was used in [1] and can be downloaded [here].

Explanation of the command line options used in the example above:

-mi MI_WA Chooses MI_WA as the measure
-file musfib.csv Data is provided in the file musfib.csv
-wi 1,2,3 Columns 1,2,3 of the data provided in musfib.csv define the world state (counting starts with 0)
-ai 9 Column 9 of the data provided in musfib.csv defines the action state (counting starts with 0)
-v gomi will print useful information while it is running and it will print the result
-bins 300 Global definition of the binning. This value will be used for each of the four columns
-o MI_WA.csv The result and the specified parameters will be written to MI_WA.csv

The full list of command line options is given below.

Using gomi as a library
The measures implemented in gomi can also be used as a library. The following code snippet gives an example:

MI_WS

\fn_phv \mathrm{MI}_\mathrm{WS} = I(W';W,S)-I(W';S)

Using the gomi binary
To calculate MI_WS with the binary, use the following command line parameters:

The file musfib was used in [1] and can be downloaded [here].

Explanation of the command line options used in the example above:

-mi MI_WS Chooses MI_WS as the measure
-file musfib.csv Data is provided in the file musfib.csv
-wi 1,2,3 Columns 1,2,3 of the data provided in musfib.csv define the world state (counting starts with 0)
-si 4 Column 4 of the data provided in musfib.csv defines the sensor state (counting starts with 0)
-v gomi will print useful information while it is running and it will print the result
-bins 300 Global definition of the binning. This value will be used for each of the four columns
-o MI_WS.csv The result and the specified parameters will be written to MI_WS.csv

The full list of command line options is given below.

Using gomi as a library
The measures implemented in gomi can also be used as a library. The following code snippet gives an example:

MI_IN

\fn_phv \mathrm{MI}_\mathrm{IN} = \log_2|A|-I(A;S)

Using the gomi binary

To calculate MI_MI with the binary, use the following command line parameters:

The file musfib was used in [1] and can be downloaded [here].

Explanation of the command line options used in the example above:

-mi MI_IN Chooses MI_IN as the measure
-file musfib.csv Data is provided in the file musfib.csv
-si 4 Columns 4 of the data provided in musfib.csv define the sensor state (counting starts with 0)
-ai 9 Column 9 of the data provided in musfib.csv defines the action state (counting starts with 0)
-v gomi will print useful information while it is running and it will print the result
-bins 300 Global definition of the binning. This value will be used for each of the four columns
-o MI_IN.csv The result and the specified parameters will be written to MI_IN.csv

The full list of command line options is given below.

Using gomi as a library
The measures implemented in gomi can also be used as a library. The following code snippet gives an example:

CA

\fn_phv \mathrm{C}_\mathrm{A} = CIF(S \rightarrow S') - CIF(A\rightarrow S')

Using the gomi binary
To calculate CA with the binary, use the following command line parameters:

The file musfib was used in [1] and can be downloaded [here].

Explanation of the command line options used in the example above:

-mi CA Chooses CA as the measure
-file musfib.csv Data is provided in the file musfib.csv
-si 4 Columns 4 of the data provided in musfib.csv define the sensor state (counting starts with 0)
-ai 9 Column 9 of the data provided in musfib.csv defines the action state (counting starts with 0)
-v gomi will print useful information while it is running and it will print the result
-bins 300 Global definition of the binning. This value will be used for each of the four columns
-o CA.csv The result and the specified parameters will be written to CA.csv

The full list of command line options is given below.

Using gomi as a library
The measures implemented in gomi can also be used as a library. The following code snippet gives an example:

MI_SY

\fn_phv \mathrm{MI}_\mathrm{SY} = D(p_\mathrm{full}(w'|w,a)||p_\mathrm{split}(w'|w,a))

Using the gomi binary
To calculate MI_SY with the binary, use the following command line parameters:

The file musfib was used in [1] and can be downloaded [here].

Explanation of the command line options used in the example above:

-mi MI_SY Chooses MI_SY as the measure
-file musfib.csv Data is provided in the file musfib.csv
-wi 1,2,3 Columns 1,2,3 of the data provided in musfib.csv define the world state (counting starts with 0)
-ai 9 Column 9 of the data provided in musfib.csv defines the action state (counting starts with 0)
-v gomi will print useful information while it is running and it will print the result
-bins 300 Global definition of the binning. This value will be used for each of the four columns
-o MI_SY.csv The result and the specified parameters will be written to MI_SY.csv

The full list of command line options is given below.

Using gomi as a library
The measures implemented in gomi can also be used as a library. The following code snippet gives an example:

MI_SY_NID

\fn_phv \mathrm{MI}_\mathrm{SY}^\mathrm{NID} = D(p_\mathrm{full}(w'|w,a)||p_\mathrm{split}(w'|w,a))

without including the input distribution p(w,a).

Using the gomi binary
To calculate MI_SY_NID with the binary, use the following command line parameters:

The file musfib was used in [1] and can be downloaded [here].

Explanation of the command line options used in the example above:

-mi MI_SY_NID Chooses MI_SY_NID as the measure
-file musfib.csv Data is provided in the file musfib.csv
-wi 1,2,3 Columns 1,2,3 of the data provided in musfib.csv define the world state (counting starts with 0)
-ai 9 Column 9 of the data provided in musfib.csv defines the action state (counting starts with 0)
-v gomi will print useful information while it is running and it will print the result
-bins 300 Global definition of the binning. This value will be used for each of the four columns
-o MI_SY_NID.csv The result and the specified parameters will be written to MI_SY_NID.csv

The full list of command line options is given below.

Using gomi as a library
The measures implemented in gomi can also be used as a library. The following code snippet gives an example:

Continuous Measures

MI_W

\fn_phv \mathrm{MI}_\mathrm{W} = I(W';W|A)

where I(W’;W|A) uses the Frenzel-Pompe estimator on continuous data.

Using the gomi binary
To calculate MI_W with the binary, use the following command line parameters:

The file musfib was used in [1] and can be downloaded [here].

Explanation of the command line options used in the example above:

-mi MI_W Chooses MI_W as the measure
-file musfib.csv Data is provided in the file musfib.csv
-wi 1,2,3 Columns 1,2,3 of the data provided in musfib.csv define the world state (counting starts with 0)
-ai 9 Column 9 of the data provided in musfib.csv defines the action state (counting starts with 0)
-v gomi will print useful information while it is running and it will print the result
-c gomi will Frenzel-Pompe estimator for conditional mutual information
-o MI_W.csv The result and the specified parameters will be written to MI_W.csv

The full list of command line options is given below.

Using gomi as a library
The measures implemented in gomi can also be used as a library. The following code snippet gives an example:

MI_A

\fn_phv \mathrm{MI}_\mathrm{A} = I(W';A|W)

where I(W’;A|W) uses the Frenzel-Pompe estimator on continuous data.

Using the gomi binary
To calculate MI_A with the binary, use the following command line parameters:

The file musfib was used in [1] and can be downloaded [here].

Explanation of the command line options used in the example above:

-mi MI_A Chooses MI_A as the measure
-file musfib.csv Data is provided in the file musfib.csv
-wi 1,2,3 Columns 1,2,3 of the data provided in musfib.csv define the world state (counting starts with 0)
-ai 9 Column 9 of the data provided in musfib.csv defines the action state (counting starts with 0)
-v gomi will print useful information while it is running and it will print the result
-c gomi will Frenzel-Pompe estimator for conditional mutual information
-o MI_A.csv The result and the specified parameters will be written to MI_A.csv

The full list of command line options is given below.

Using gomi as a library
The measures implemented in gomi can also be used as a library. The following code snippet gives an example:

MI_MI

\fn_phv \mathrm{MI}_\mathrm{MI} = I(W';W)-I(A;S)

where I(W’;A) and I(A;S) use the KSG estimator for mutual information on continuous data.

Using the gomi binary
To calculate MI_MI with the binary, use the following command line parameters:

The file musfib was used in [1] and can be downloaded [here].

Explanation of the command line options used in the example above:

-mi MI_MI Chooses MI_MI as the measure
-file musfib.csv Data is provided in the file musfib.csv
-wi 1,2,3 Columns 1,2,3 of the data provided in musfib.csv define the world state (counting starts with 0)
-ai 9 Column 9 of the data provided in musfib.csv defines the action state (counting starts with 0)
-si 4 Column 4 of the data provided in musfib.csv defines the sensor state (counting starts with 0)
-v gomi will print useful information while it is running and it will print the result
-c gomi will use the KSG Estimator for mutual information.
-cm 2 gomi will use the KSG Estimator 2 for mutual information. KSG 1 estimator can be chosen with -cm 1
-o MI_MI.csv The result and the specified parameters will be written to MI_MI.csv

The full list of command line options is given below.

Using gomi as a library
The measures implemented in gomi can also be used as a library. The following code snippet gives an example:

MI_CA

\fn_phv \mathrm{MI}_\mathrm{CA} = I(W';W)-I(W';A)

where I(W’;W) and I(W’;A) use the KSG estimator for mutual information on continuous data.

Using the gomi binary
To calculate MI_CA with the binary, use the following command line parameters:

The file musfib was used in [1] and can be downloaded [here].

Explanation of the command line options used in the example above:

-mi MI_CA Chooses MI_CA as the measure
-file musfib.csv Data is provided in the file musfib.csv
-wi 1,2,3 Columns 1,2,3 of the data provided in musfib.csv define the world state (counting starts with 0)
-ai 9 Column 9 of the data provided in musfib.csv defines the action state (counting starts with 0)
-v gomi will print useful information while it is running and it will print the result
-c gomi will use the KSG Estimator for mutual information.
-cm 2 gomi will use the KSG Estimator 2 for mutual information. KSG 1 estimator can be chosen with -cm 1
-o MI_CA.csv The result and the specified parameters will be written to MI_CA.csv

The full list of command line options is given below.

Using gomi as a library
The measures implemented in gomi can also be used as a library. The following code snippet gives an example:

MI_WA

\fn_phv \mathrm{MI}_\mathrm{WA} = I(W';W,A)-I(W';A)

where I(W’;W,A) and I(W’;A) use the KSG estimator for mutual information on continuous data.

Using the gomi binary
To calculate MI_WA with the binary, use the following command line parameters:

The file musfib was used in [1] and can be downloaded [here].

Explanation of the command line options used in the example above:

-mi MI_CA Chooses MI_CA as the measure
-file musfib.csv Data is provided in the file musfib.csv
-wi 1,2,3 Columns 1,2,3 of the data provided in musfib.csv define the world state (counting starts with 0)
-ai 9 Column 9 of the data provided in musfib.csv defines the action state (counting starts with 0)
-v gomi will print useful information while it is running and it will print the result
-c gomi will use the KSG Estimator for mutual information.
-cm 2 gomi will use the KSG Estimator 2 for mutual information. KSG 1 estimator can be chosen with -cm 1
-o MI_CA.csv The result and the specified parameters will be written to MI_CA.csv

The full list of command line options is given below.

Using gomi as a library
The measures implemented in gomi can also be used as a library. The following code snippet gives an example:

MI_WS

\fn_phv \mathrm{MI}_\mathrm{WS} = I(W';W,S)-I(W';S)

where I(W’;W,S) and I(W’;S) use the KSG estimator for mutual information on continuous data.

Using the gomi binary
To calculate MI_WS with the binary, use the following command line parameters:

The file musfib was used in [1] and can be downloaded [here].

Explanation of the command line options used in the example above:

-mi MI_WS Chooses MI_WS as the measure
-file musfib.csv Data is provided in the file musfib.csv
-wi 1,2,3 Columns 1,2,3 of the data provided in musfib.csv define the world state (counting starts with 0)
-ai 9 Column 9 of the data provided in musfib.csv defines the action state (counting starts with 0)
-v gomi will print useful information while it is running and it will print the result
-c gomi will use the KSG Estimator for mutual information.
-cm 2 gomi will use the KSG Estimator 2 for mutual information. KSG 1 estimator can be chosen with -cm 1
-o MI_WS.csv The result and the specified parameters will be written to MI_WS.csv

The full list of command line options is given below.

Using gomi as a library
The measures implemented in gomi can also be used as a library. The following code snippet gives an example:

Command line parameters

OptionExplanation
-helpWill show command line parameters with explantions.
-vVerbose. If not provided, gomi will be executed silently.
-miString identifier for the morphological intelligence quantification. One example is MI_W. For a full list, please use the help command line option.
-cThe discrete (frequency based) estimators are used by default. If this options is provided, the estimators on continuous data (KSG Estimator and Frenzel-Pompe) are used instead.
-cmContinuous mode. There are two different KSG Estimators for mutual information. For those continuous morphological intelligence quantification which operate with mutual information, the KSG Estimator can be chosen with this command line options. Possible values are 1 and 2.
-sState-dependent results. By default, the averaged results are provided. If this option is given, the results are calculated for each state, i.e., the result is a vector with a value for each row in the original dataset.
-binsThis option is used only for the discrete estimators. It determines the number of bins for each column of the W, S, and A datasets.
-iIteration. This command line option is only used for MI_SY, MI_Wp, and MI_SY_NID. It determines the number of iterations for the iterative scaling algorithm.
-oOutput file. The default value is "out.csv". gomi writes all results to the output file, including a header section that includes the full parameterisation of the calculation.
-wbinsOnly used for discrete measures. In case the world state is given by more than one column in the dataset, this option allows to set the binning for each column.
-abinsOnly used for discrete measures. In case the action state is given by more than one column in the dataset, this option allows to set the binning for each column.
-sbinsOnly used for discrete measures. In case the sensor state is given by more than one column in the dataset, this option allows to set the binning for each column.
-fileThis option should be used if W, S, A are provided in a single file. The columns for W, S, and A are the specified with the -wi, -si, and -ai options (see below).
-wiThe values here specify the column of the file provided with -file that relate to the world state.
-aiThe values here specify the column of the file provided with -file that relate to the action state.
-siThe values here specify the column of the file provided with -file that relate to the sensor state.
-wfileWorld state file. All columns of this file will be considered in the calculations.
-afileAction state file. All columns of this file will be considered in the calculations.
-sfileSensor state file. All columns of this file will be considered in the calculations.
-dfileDomain file. This option will only be used for discrete measures. During discretisation, each column is normalised. For comparability between different files, a domain file can be specified, which provides the minimum and maximum values for the world state, action state, and sensor state data.
kThis parameter is only used for continuous estimators. It is the parameter used for the k-nearest neighbour estimation of entropies.

Bibliography

[1] [pdf] K. Ghazi-Zahedi, D. F. B. Haeufle, G. F. Montufar, S. Schmitt, and N. Ay, “Evaluating morphological computation in muscle and dc-motor driven models of hopping movements,” Frontiers in robotics and ai, vol. 3, iss. 42, 2016.
[Bibtex]
@article{Ghazi-Zahedi2016aEvaluating,
Author = {Ghazi-Zahedi, Keyan and Haeufle, Daniel F.B. and Montufar, Guido Francisco and Schmitt, Syn and Ay, Nihat},
Issn = {2296-9144},
Journal = {Frontiers in Robotics and AI},
Number = {42},
Pdf = {http://www.frontiersin.org/computational_intelligence/10.3389/frobt.2016.00042/abstract},
Title = {Evaluating Morphological Computation in Muscle and DC-motor Driven Models of Hopping Movements},
Volume = {3},
Year = {2016}}

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