channel-capacity-estimator 1.1

Package for estimation of information channel capacity.

Channel Capacity Estimator (cce) is a Python module to estimate information capacity of a communication channel. Mutual information, computed as proposed by Kraskov et al. [Physical Review E 69:066138, 2004, equation 8], is maximized over input probabilities by means of a constrained gradient-based stochastic optimization. The only parameter of the Kraskov algorithm is the number of neighbors, k, used in the nearest neighbor search. In cce, channel input is expected to be of categorical type (meaning that it should be described by labels), whereas channel output is assumed to be in the form of points in real space of any dimensionality.

The code performs local gradient-based optimization which, owing to the fact that mutual information is a concave function of input probabilities, is able to locate global maximum of mutual information. Maximization is performed according to ADAM algorithm as implemented in TensorFlow. To use cce, you should have TensorFlow (with Python bindings) installed on your system. See file requirements.txt for a complete list of dependencies.

Module cce features the research article “Limits to the rate of information transmission through the MAPK pathway” by Grabowski et al. [Journal of the Royal Society Interface 16:20180792, 2019]. Version 1.0 of cce has been included as the article supplementary code.

For any updates and fixes to cce, please visit project homepage: http://pmbm.ippt.pan.pl/software/cce (this is a permalink that currently directs to a GitHub repository: https://github.com/pawel-czyz/channel-capacity-estimator).

Usage

There are three major use cases of cce:

1. Calculation of mutual information (for equiprobable input distributions).

In the example below, mutual information is calculated between three sets of points drawn at random from two-dimensional Gaussian distributions, located at (0,0), (0,1), and at (3,3); covariance matrices of all three distributions are identity matrices (this is default in SciPy). Auxiliary function label_all_with() helps to prepare the list of all points, in which each point is labeled according to its distribution of origin.

>>> from scipy.stats import multivariate_normal as mvn
>>> from cce import WeightedKraskovEstimator as wke
>>>
>>> def label_all_with(label, values): return [(label, v) for v in values]
>>>
>>> data = label_all_with('A', mvn(mean=(0,0)).rvs(10000)) \
         + label_all_with('B', mvn(mean=(0,1)).rvs(10000)) \
         + label_all_with('C', mvn(mean=(3,3)).rvs(10000))
>>>
>>> wke(data).calculate_mi(k=10)
0.9552107248613955

In this example, probabilities of input distributions, henceforth referred to as weights, are assumed to be equal for all input distributions. Format of data is akin to [(‘A’, array([-0.4, 2.8])), (‘A’, array([-0.9, -0.1])), …, (‘B’, array([1.7, 0.9])), …, (‘C’, array([3.2, 3.3])), …). Entries of data are not required to be grouped according to the label. Distribution labels can be given as strings, not just single characters. Instead of NumPy arrays, ordinary lists with coordinates will be also accepted. (This example involves random numbers, so your result may vary slightly.)

2. Calculation of mutual information for input distributions with non-equal probabilities.

This example is structured as above, with an addition of weights of each input distributions:

>>> from scipy.stats import multivariate_normal as mvn
>>> from cce import WeightedKraskovEstimator as wke
>>>
>>> def label_all_with(label, values): return [(label, v) for v in values]
>>>
>>> data = label_all_with('A', mvn(mean=(0,0)).rvs(10000)) \
         + label_all_with('B', mvn(mean=(0,1)).rvs(10000)) \
         + label_all_with('C', mvn(mean=(3,3)).rvs(10000))
>>>
>>> weights = {'A': 2/6, 'B': 1/6, 'C': 3/6}
>>> wke(data).calculate_weighted_mi(weights=weights, k=10)
1.0065891280377155

(This example involves random numbers, so your result may vary slightly.)

3. Estimation of channel capacity by maximizing MI with respect to input weights.

>>> from scipy.stats import multivariate_normal as mvn
>>> from cce import WeightedKraskovEstimator as wke
>>>
>>> def label_all_with(label, values): return [(label, v) for v in values]
>>>
>>> data = label_all_with('A', mvn(mean=(0,0)).rvs(10000)) \
         + label_all_with('B', mvn(mean=(0,1)).rvs(10000)) \
         + label_all_with('C', mvn(mean=(3,3)).rvs(10000))
>>>
>>> wke(data).calculate_maximized_mi(k=10)
(1.0154510500713743, {'A': 0.33343804, 'B': 0.19158363, 'C': 0.4749783})

The output tuple contains the maximized mutual information (channel capacity) and probabilities of input distributions that maximize mutual information (argmax). Optimization is performed within TensorFlow with multiple threads and takes less than one minute on a computer with quad-core processor. (This example involves random numbers, so your result may vary slightly.)

Installation

Before installing the package, we recommend creating a new Python environment using venv or Micromamba.

Python Package Index

Once the environment has been created, the most convenient manner is to install the package from PyPI using:

$ pip install channel-capacity-estimator

Then, you can directly start using the package:

$ python
>>> from cce import WeightedKraskovEstimator
>>> ...

Local installation

Alternatively, you can build the package locally.

$ git clone https://github.com/pawel-czyz/channel-capacity-estimator.git
$ cd channel-capacity-estimator

To install cce locally via pip, run:

$ make install

Then, you can directly start using the package:

$ python
>>> from cce import WeightedKraskovEstimator
>>> ...

Testing

To launch a suite of unit tests, run:

$ make test

Documentation

Developer’s code documentation may be generated with:

$ cd docs
$ make html

Authors

The code was developed by Frederic Grabowski and Paweł Czyż, with some guidance from Marek Kochańczyk and under supervision of Tomasz Lipniacki from the Laboratory of Modeling in Biology and Medicine, Institute of Fundamental Technological Reasearch, Polish Academy of Sciences (IPPT PAN) in Warsaw.

License

This software is distributed under GNU GPL 3.0 license.