File: modelfitting.txt

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.. currentmodule:: brian.library.modelfitting

.. _model-fitting-library:

Model fitting
=============
The modelfitting library is used for fitting a neuron model to data. 

The library provides a single function :func:`modelfitting`, which accepts the model
and the data as arguments and returns the model parameters that fit best the data.
The model is a spiking neuron model, whereas the data consists of both an input
(time-varying signal, for example an injected current) and a set of spike trains.
Only spikes are considered for the fitness. Several target spike trains can be
specified in order to fit independently several data sets. In this case,
the :func:`modelfitting` function returns as many parameters sets as there are target spike trains.

The model is defined as any spiking neuron model in Brian, by giving the equations
as mathematical equations, and the reset and threshold values. The free parameters
of the model that shall be fitted by the library are also specified. The data is
specified by the input (a vector containing the time-varying injected current),
the timestep of the input, and the data as a list of spike times.

How it works
------------

Fitting a spiking neuron model to electrophysiological data is performed by maximizing
a fitness function measuring the adequacy of the model to the data.
This function is defined as the gamma factor, which is based on
the number of coincidences between the model spikes and the experimentally-recorded spikes, defined
as the number of spikes in the experimental train such that there is at least one spike
in the model train within plus or minus ``delta``, where ``delta`` is the size of the temporal window
(typically a few milliseconds). For more details on the gamma factor, see
`Jolivet et al. 2008, "A benchmark test for a quantitative assessment of simple neuron models", J. Neurosci. Methods <http://www.ncbi.nlm.nih.gov/pubmed/18160135>`__ (available in PDF
`here <http://icwww.epfl.ch/~gerstner/PUBLICATIONS/Jolivet08.pdf>`__).

The optimization procedure is performed by an optimization algorithm. The optimization toolbox
used by modelfitting is implemented in the external Python package `Playdoh
<https://code.google.com/p/playdoh/>`__. It also
supports distributed and parallel optimization across CPUs and machines.
Different optimization algorithms are supported, the default one is :class:`CMAES`.
All those algorithms require the evaluation of the fitness function for a large number of parameter
sets. Each iteration of the algorithm
involves the simulation of a large number of neurons (one neuron corresponding to one parameter set) 
as well as the computation of the gamma factor for each neuron. 
The quality of the result depends
on the number of neurons used, which is specified in the :func:`modelfitting` function. 

Playdoh supports the use of graphical processing
units (GPUs) in order to accelerate the speed of convergence of the algorithm.
If multiple cores are detected, the library will use all of them by default.
Also, if a CUDA-enabled GPU is present on the system, and if PyCUDA is installed,
the library will automatically use the GPU by default. In addition, several computers
can be networked over IP, see :ref:`modelfitting-clusters`.

Usage example
-------------

To import the library, use ::

  from brian.library.modelfitting import *

To fit the parameters of a neuron model with respect to some data, use the
:func:`modelfitting` function ::
                        
    results = modelfitting(model = equations, reset = 0, threshold = 1,
                         data = spikes, 
                         input = input, dt = .1*ms,
                         popsize = 1000, maxiter = 10, 
                         R = [1.0e9, 1.0e10], tau = [1*ms, 50*ms])

    print_table(results)

.. warning::

	Windows users should read the section :ref:`note-for-windows-users`. 

The model is defined by ``equations`` (an :class:`~brian.Equations` object), 
``reset`` (a scalar value or a set of equations as a string) and 
``threshold`` (a scalar value or a set of equations as a string).

The target spike trains are defined by ``data`` (a list of pairs ``(neuron index, spike time)``
or a list of spike times if there is only one target spike train).

The input is specified with ``input`` (a vector containing the time-varying signal)
and ``dt`` (the time step of the signal).
The input variable should be ``I`` in the equations, although the input variable name
can be specified with ``input_var``.

The number of particles per target train used in the optimization algorithm is
specified with ``popsize``. The total number of neurons is  ``popsize`` multiplied
by the number of target spike trains.
The number of iterations in the algorithm is specified with ``maxiter``.

Each free parameter of the model that shall be fitted is defined by two values ::
  
    param_name = [min, max]

``param_name`` should correspond to the parameter name in the model equations.
``min`` and ``max`` specify the initial interval from which the parameter values
will be uniformly sampled at the beginning of the optimization algorithm.
A boundary interval can also be specified by giving four values ::

    param_name = [bound_min, min, max, bound_max]

The parameter values will be forced to stay inside the interval [bound_min, bound_max]
during the optimization.

The complete list of arguments can be found in the reference
section of the :func:`modelfitting` function.

The best parameters and the corresponding best fitness values found by the optimization 
procedure are returned in the :class:`OptimizationResult`
object ``result``.

.. _note-for-windows-users:

Important note for Windows users
--------------------------------

The model fitting library uses the Python `multiprocessing <http://docs.python.org/library/multiprocessing.html>`__
package to distribute fitting across processors in a single computer or across
multiple computers. However, there is a limitation of the Windows version of
multiprocessing which you can read about `here <http://docs.python.org/library/multiprocessing.html#windows>`__.
The end result is that a script like this::

	from brian.library.modelfitting import *
	...
	results = modelfitting(...)
	
will crash, going into an endless loop and creating hundreds of Python processes
that have to be shut down by hand. Instead, you have to do this::

	from brian.library.modelfitting import *
	...
	if __name__=='__main__':
		results = modelfitting(...)

.. _modelfitting-clusters:

Clusters
--------

The model fitting package can be used with a cluster of computers connected over
IP. Every computer must have Brian and Playdoh installed, and they must run
the Playdoh server: see 
`the Playdoh documentation <http://playdoh.googlecode.com/svn/docs/playdoh.html#launching-the-playdoh-server>`__.
Then, you can launch the ```modelfitting`` function with the ``machines`` keyword,
which is the list of the IP addresses of the machines to use in parallel 
for the fitting procedure. You must also specify the ``unit_type`` keyword, which is ``CPU`` or ``GPU``,
to indicate whether you want to use CPUs or GPUs on these computers. You can't mix CPUs and GPUs
for the same optimization.

IP
~~

To connect several machines via IP, pass a list of host names or IP addresses
as strings to the ``machines`` keyword of the :func:`modelfitting` function.
To specify a specific port, use a tuple ``(IP, port)`` instead
of a string. You can also specify a default port in the Playdoh user preferences, see 
`the Playdoh documentation <http://playdoh.googlecode.com/svn/docs/playdoh.html#userpref>`__.

Authentication
~~~~~~~~~~~~~~

You can specify an authentication string on all the computers running the Playdoh server
to secure communications.
See 
`the Playdoh documentation <http://playdoh.googlecode.com/svn/docs/playdoh.html#userpref>`__.

Example
~~~~~~~

The following script launches a fitting procedure in parallel on two machines::

	from brian import loadtxt, ms, Equations
	from brian.library.modelfitting import *
	
	if __name__ == '__main__':
	    # List of machines IP addresses
	    machines = ['bobs-machine.university.com',
	                'jims-machine.university.com']
	    
	    equations = Equations('''
	        dV/dt=(R*I-V)/tau : 1
	        I : 1
	        R : 1
	        tau : second
	    ''')
	    input = loadtxt('current.txt')
	    spikes = loadtxt('spikes.txt')
	    results = modelfitting( model = equations,
	                            reset = 0,
	                            threshold = 1,
	                            data = spikes,
	                            input = input,
	                            dt = .1*ms,
	                            popsize = 1000,
	                            maxiter = 3,
	                            delta = 4*ms,
	                            unit_type = 'CPU',
	                            machines = machines,
	                            R = [1.0e9, 9.0e9],
	                            tau = [10*ms, 40*ms],
	                            refractory = [0*ms, 10*ms])
	    print_table(results)


The two remote machines would run the `Playdoh server <http://playdoh.googlecode.com/svn/docs/playdoh.html#launching-the-playdoh-server>`__.