The development of the toolbox continues in a new repository: NNMT

LIF Meanfield Tools

This Python package provides tools for analyzing neuronal networks consisting of leaky integrate-and-fire (LIF) neurons. These tools are based on mean-field theory of neuronal networks. That is why this package is called lif_meanfield_tools (LMT).

The package provides implementations used in the same or a similar version in the following scientific publications: Fourcaud & Brunel (2002), Schuecker et al. (2014), Schuecker et al. (2015), Schuecker et al. (2017), Bos et al. (2016), and Senk et al. (2020).

Using this package, you can calculate quantities like firing rates, power spectra, and many more, which give you a deeper and more intuitive understanding of what your network does. If your network is not behaving the way you want it to, these tools might help you to figure out, or even tell you, what you need to change in order to achieve the desired behaviour. The toolbox allows storing results and reuse them for further analyses.

If you are using this toolbox, please cite us: For a specific release, we recommend to use the reference from Zenodo. Otherwise, you can also provide a link to this repository with the hash of the respective commit. In addition, please also cite the publications that used the methods implemented here first. In How to Use This Package you can find details on which function of this package refers to which publication.

The figure shows power spectra calculated with this toolbox using the minimal example script examples/power_spectra.py.

Structure

lif_meanfield_tools consists of four modules:

• The central module is network.py. It defines a class Network which is a container for network parameters, analysis parameters and calculated results. Network comes with all the methods that can be used to calculate network properties, like firing rates or power spectra. Additionally, there are some 'administrative' methods for changing parameters or saving.

• input_output.py is called by network.py for everything that is related to input or output. Here we defined saving and loading routines, quantity format conversions and hash creation.

• meanfield_calcs.py is the module which is called every time a mean-field related method of Network is called. Here we put all the mathematical details of the mean-field theory.

• aux_calcs.py is a module where auxiliary calculations that are needed in meanfield_calcs.py are defined. These functions are supposed to be generic, non-specific building blocks. However, it is difficult to draw a line between the calculations that belong to meanfield_calcs.py and the ones that belong to aux_calcs.py.

• utils.py is a module which contains utility functions. It contains functions that simplify working with pint quantities and decorators for checking that passed parameters are in valid regimes.

How to Get Started / Installation

If you have a local copy of this repository, you can install LMT by running:

pip install .

An alternative is to install directly from GitHub:

pip install git+https://github.com/INM-6/lif_meanfield_tools.git

If you are using conda, you can create an environment including LMT:

conda env create -f environment.yaml

Current Issues

As the package is still maturing, we currently have some issues that you should be aware of:

• Network model used: Currently, the toolbox is specialized on the microcircuit model (first published by Potjans and Diesmann (2014)) which is why the network parameter label should only be set to microcircuit at the moment. See the function _calculate_dependent_network_parameters() in network.py.

• Accuracy of transfer function at high frequencies: This actually is not a real issue, but you should be aware that the current implementation is only accurate for moderate frequencies. This is expected from the theory implemented. In the future we might add a support for high frequencies (see Schuecker et al. (2015) for further discussion).

• Accuracy of transfer function depends on ratio of synaptic and membrane time constant: This is a part of the theory as well. It is only accurate for small values of which is used as a perturbation parameter in the analysis (see Schuecker et al. (2015) for further discussion).

How to Use This Package

In order to give you a quick and simple start, we wrote some example scripts in the folder examples. You can start with minimal_usage_example.py. First of all, you should have a look at this file. Actually, we hope that the usage might be self-explanatory, once you have seen an example. But, if you need a little more hints, just continue reading.

For using LMT, you need to store all your network parameters and your analysis parameters in .yaml files, as we have done it for the example script. If you don't know how the .yaml file format works, you could either first read something about it, or use our example .yaml files as templates.

So, let us start coding. First of all you need to import the package itself. Additionally, you might want to define a variable to store the pint unit registry (ureg). This is needed for dealing with units and some of the functionality implemented needs the usage of pint units.

Now, you can instantiate a network by calling the central LMT class Network and passing the .yaml file names. A Network object represents your network. When it is instantiated, it first calculates all the parameters that are derived from the passed parameters. Then, it stores all the parameters associated with the network under consideration. Additionally, it checks whether these parameters have been used for an analysis before, and if so loads the corresponding results. Newly calculated results are stored withing the Network object as well.

A Network object has the ability to tell you about it's properties by calling the corresponding method as

	network.<property>()

Here, <property> can be replaced by lots of stuff, like for example firing_rates, transfer_function, or power_spectra. You can find the complete list of Network methods at the end of this section. When such a method is called, the network first checks whether this quantity has been calculated before. If so, it returns the stored value. If not, it does the calculations, stores the results, and returns them. If you want to calculate properties that need another quantity to be calculated first, you will receive an error message telling you which quantities to calculate first. For example the power_spectra need the delay_dist_matrix and the transfer_function, which in turn needs the working_point So a correct call would look like

  network.working_point()
  network.transfer_function()
  network.delay_dist_matrix()
  network.power_spectra()

Functions like transfer_function will use the previously calculated results. This allows you to use different methods for calculating the same quantities (like taylor and shift for the firing rates and the tranfer function) in a building block like fashion.

Sometimes, you might want to know a property for some specific parameter, like for example the power_spectra at a certain frequency. Then, you need to pass the parameter including its unit to the method, e.g.,

	network.power_spectra(10 * ureg.Hz)

If you want to save your results, you can simply call

	network.save()

and the calculated results, together with the corresponding parameters, will be stored inside a .h5 file, whose name contains a hash, which reflects the used network parameters.

Network methods:

• save: Save all calculated results together with network and analysis parameters into an .h5 file.
• show: Return a list of quantities that have already been calculated.
• change_parameters: Create a new instance of Network class with adjusted specified parameters.
• firing_rates: Calculate the firing rates in a self-consistent mean-field manner. The algorithm starts with firing rate zero for all populations, then calculates the resulting mean and variance of the input to a neuron, and uses the results and Eq. (4.33) in Fourcaud & Brunel (2002) to calculate the resulting firing rate again. This procedure is continued until the rates converge.
• mean_input: Calculate mean input to a neuron, given the population firing rates and external inputs.
• std_input: Calculate the standard deviation of the input to a neuron, given the population firing rates and external inputs.
• working_point: Return firing rate, mean and standard deviation of input.
• delay_dist_matrix: Compute a matrix of prefactors in frequency domain dependent on a given delay distribution.
• transfer_function: Calculate the transfer function following Eq. (93) in Schuecker et al. (2014) in first order perturbation theory in , the square root of the synaptic time constant divided by the membrane time constant. You can choose between two implementations: taylor and shift. The difference is the way the colored noise is treated mathematically, which leads to two slightly different approximations, which are however equivalent up to first order (see Schuecker et al. (2015) for further discussion).
• sensitivity_measure: Calculate the sensitivity measure, introduced in Eq. (7) of Bos et al. (2016), which can be used to identify the connections crucial for the peak amplitude and frequency of network oscillations, visible in the power spectrum.
• power_spectra: Calculate the power spectra of all populations following Eq. (18) in Bos et al. (2016).
• eigen_spectra: Calculate the eigenvalue spectrum, or left of right eigenvectors of the effective connectivity matrix (Eq. 4), the propagator Eq. (16) or the inverse propagator in the frequency domain as defined in Bos et al. (2016).

The following additional Network methods have been used in Senk et al. (2020):

• additional_rates_for_fixed_input: Compute external excitatory and inhibitory rates to obtain a fixed working point (see Appendix F).
• fit_transfer_function: Fit the transfer function with a low-pass filter (see Fig. 5(b) and (c)).
• scan_fit_transfer_function_mean_std_input: Iterate different combinations of mean and standard deviation of input using fit_transfer_function() (see Fig. 5).
• effective_coupling_strength: Compute the effective coupling strength according to Eq. (E1).
• linear_interpolation_alpha: Linear interpolation between LIF transfer function and low-pass filter (see Fig. 6),
• eigenvals_branches_rate: Compute eigenvalues for branches of the Lambert W function corresponding to the analytically exact solution of the neural-field model (see Fig. 6 for alpha=0).
• xi_of_k: Effective spatial profile (see Fig. 3(b) and (d)).
• solve_chareq_rate_boxcar: Analytical solution of the characteristic equation for a neural-field model with boxcar-shaped connectivity kernels.

Testing

We have an extensive test suite using the pytest framework. If you want to run all the tests, you can do so by installing and activating the conda environment specified in the provided environment.yaml file, and running

pytest

from the root directory (the one containing tests and lif_meanfield_tools). If you want to be more specific, you can run single tests as well

pytest tests/unit/test_meanfield_calcs.py::Test_firing_rates::test_correct_output

See the pytest documentation for all available options.

Note that some tests currently fail. This points towards pieces of code that still need to be improved (see current issues).

Note that pytest distinguishes between failures and errors:

• A failure occurs if a test did not run successfully.
• An error occurs if an exception happened outside of the test function, for example inside a fixture.

Test Directory Structure

tests/
  conftest.
  checks.py
  fixtures/
    Snakefile
    unit/
      config/
      data/
      create_fixtures.py
    integration/
      config/
      data/
      create_fixtures.py
  integration/
    test_functionality.py
    test_reproduce_Bos2016.py
    test_reproduce_Schuecker2015.py
    test_usage_examples.py
  meta/
    test_checks.py
  unit/
    test_input_output.py
    test_network.py
    test_aux_calcs.py
    test_meafield_calcs.py

conftest.py is a special pytest file, in which custom fixtures and special pytest functions are defined. We, in particular, make use of the pytest_generate_tests function, which considerably simplifies complex parametrizations of tests.

checks.py is a collection of custom assert functions.

fixtures/ contains all the data that is used for tests comparing real and expected output of functions, as well as the files that creates the data create_fixtures.py using the parameters defined in config/. The Snakefile defines a workflow to create all fixtures at once.

integration/ contains all integration tests.

meta/ contains tests for custom assert functions.

unit/ contains all unit tests.

Test Design

Many test classes define the tested function as staticmethod, because the function itself is not tightly related to class, but we still want to attach it to the class for later reference. This allows us to call the function as an 'unbound function', without passing the instance to the function: self.func() = func() != func(self).

There are two special fixtures that are definded in conftest.py:

If a test requires the pos_keys fixture, it will be parametrized such that it tests all positive arguments the tested function (defined as a staticmethod of the test class) takes. The list of all possible positive arguments is defined within conftest.py.

If a test requires output_test_fixtures, pytest will pass the output fixtures corresponding to the output_key defined as a test class variable. Those output key results are checked into the repository for convenience, but can be created from the sources (see Fixture Creation Workflow). This allows us to parametrize the tests such that the function is tested in different parameter regimes (e.g. mean-driven regime vs. fluctuation-driven regime).

Fixture Creation Workflow

Fixture creation is a sensible part of the testing framework as it supplies a kind of ground truth to test against. Please make sure that your code is trustworthy before running the fixture creation. Otherwise, tests might incorrectly fail or pass.

The fixture creation workflow is defined using Snakemake, a workflow management system using a Python based syntax. It is recommended to install it in a separate conda environment (see Installation).

To invoke the workflow and create the fixtures using the same conda environment you are using the toolbox with, you first need to export the conda environment. Therefore set tests/fixtures/envs as current working directory, activate the corresponding conda environment and type

conda env export -f environment.yaml

Then open the created environment.yaml file, remove the last line starting with prefix and add the line - -e ../../../../ to the list at the end. Change your current working directory to tests/fixtures, activate the conda environment you have installed sakemake in and type

snakemake --use-conda --cores 1

The workflow then takes care of installing the necessary conda environments and creating all fixtures that are specified within tests/fixtures/config.yaml. By default, the workflow looks whether the requested fixtures exists and only creates them if they don't.

It might be useful to first see what the workflow is planning to do by triggering a 'dry-run' with: snakemake -n. Furthermore the execution of single rules can be enforced with the -R flag, e.g.: snakemake --use-conda --cores 1 -R make_Bos2016_data. This is useful if one specific fixture should be re-created.

Have a look at the Snakemake Documentation for more information.

History of this Project

Mean-field theory is a tool that can help you understand the behaviour of your network. Using this theory allows you to predict some features of a network without running a single (often very time consuming) simulation.

At our institute, the INM-6 at the Research Center Juelich, we, among other things, investigate and develop such mean-field tools. Over the years, more and more of the tools, developed by ourselves and other researchers, have been implemented. In particular, the primary work for this package has been done by Hannah Bos, Jannis Schuecker and Moritz Helias. Here we extend the work published in the repository [https://github.com/INM-6/neural_network_meanfield] and make it available to a wider audience.

We restructured and rewrote the code with the aim to make it usable without having to understand all details of the underlying theory. We simplified the code. We introduced units and decided to store the parameters in separate .yaml files. We wanted the users to only have to interact with one module. So, we collected all the functionality in the network.py module. We ported the code to Python 3. We made the whole thing a package. We expanded the documentation a lot. We simplified saving results together with the parameters. And so on.

What we ended up with is the package that you are currently interested in. It contains several tools for analyzing neuronal networks and makes them available in a reusable format.