auryn::IzhikevichGroup Class Reference

This NeuronGroup implements the Izhikevich neuron model with conductance based AMPA and GABA synapses. More...

#include <IzhikevichGroup.h>

Inheritance diagram for auryn::IzhikevichGroup:

Collaboration diagram for auryn::IzhikevichGroup:

Public Member Functions
	IzhikevichGroup (NeuronID size)
	The default constructor of this NeuronGroup. More...
virtual	~IzhikevichGroup ()
void	set_tau_ampa (AurynFloat tau)
	Sets the exponential time constant for the AMPA channel (default 5ms) More...
AurynFloat	get_tau_ampa ()
	Gets the exponential time constant for the AMPA channel. More...
void	set_tau_gaba (AurynFloat tau)
	Sets the exponential time constant for the GABA channel (default 10ms) More...
AurynFloat	get_tau_gaba ()
	Gets the exponential time constant for the GABA channel. More...
void	clear ()
	Resets all neurons to defined and identical initial state. More...
void	evolve ()
	Integrates the NeuronGroup state. More...
Public Member Functions inherited from auryn::NeuronGroup
	NeuronGroup (NeuronID n, NodeDistributionMode mode=AUTO)
	Default constructor. More...
	NeuronGroup (NeuronID n, double loadmultiplier, NeuronID total)
	Old default constructor. More...
virtual	~NeuronGroup ()
void	set_state (std::string name, AurynState val)
	Conveniently sets all values in a state vector identified by name in this group. More...
void	set_state (std::string name, NeuronID i, AurynState val)
	Conveniently sets a single value of element i in a state vector identified by name in this group. More...
virtual AurynStateVector *	get_default_exc_target ()
	Returns default exc target input. More...
virtual AurynStateVector *	get_default_inh_target ()
	Returns default inh target input. More...
void	random_mem (AurynState mean=-60e-3, AurynState sigma=5e-3)
virtual void	init_state ()
void	safe_tadd (NeuronID id, AurynWeight amount, TransmitterType t=GLUT)
void	tadd (NeuronID id, AurynWeight amount, TransmitterType t=GLUT)
void	tadd (AurynStateVector *state, NeuronID id, AurynWeight amount)
Public Member Functions inherited from auryn::SpikingGroup
void	add_state_vector (std::string key, AurynStateVector *state_vector)
	Adds a state vector passed as an argument to the dictinary. More...
void	remove_state_vector (std::string key)
	Removes a state vector passed as an argument to the dictinary. More...
AurynStateVector *	find_state_vector (std::string key)
	Returns existing state vector by name or NULL if it does not exist. More...
AurynStateVector *	get_state_vector (std::string key)
	Creates a new or returns an existing state vector by name. More...
AurynStateVector *	get_existing_state_vector (std::string key)
	Returns an existing state with the supplied name. More...
AurynStateVector *	create_state_vector (std::string key)
	Creates a new state vector and throws an exception if a vector with the same name exists. More...
AurynState *	get_state_variable (std::string key)
	Creates a new group-wide state variable or returns an existing group-wide variable by name then returns a pointer to it. More...
void	randomize_state_vector_gauss (std::string state_vector_name, AurynState mean, AurynState sigma, int seed=12239)
	Randomizes the content of a state vector with Gaussian random numbers. Seeding is MPI save. More...
	SpikingGroup (NeuronID size, NodeDistributionMode mode=AUTO)
	Default constructor. More...
virtual	~SpikingGroup ()
	Default destructor. More...
virtual void	evolve_traces ()
	Evolves traces. More...
void	set_name (std::string s)
	Set connection name. More...
std::string	get_name ()
	Retrieves the groups name. More...
std::string	get_file_name ()
	Extracts the class name of the connection from the file name. More...
std::string	get_log_name ()
	Returns a string which is the combination of file and connection name for logging. More...
void	inc_num_spike_attributes (int x)
	Instructs SpikingGroup to increase the number of spike attributes by x. More...
int	get_num_spike_attributes ()
void	conditional_evolve ()
	Conditional evolve functino which is called by System. More...
unsigned int	get_locked_rank ()
	Returns locked rank for SpikingGroups which are not distributed across all ranks. More...
unsigned int	get_locked_range ()
	Returns locked range of ranks for SpikingGroups which are not distributed across all ranks. More...
SpikeContainer *	get_spikes ()
	Returns pointer to a spike container that contains spikes which arrive in this timestep from all neurons in this group. More...
SpikeContainer *	get_spikes_immediate ()
	Returns pointer to SpikeContainer of spikes generated during the last evolve() step. More...
AttributeContainer *	get_attributes ()
	Returns pointer to Attributecontainer for usage in propagating Connection objects. Same as get_spikes_immediate(), however might be overwritten to contain Spikes that have been delayed. More...
AttributeContainer *	get_attributes_immediate ()
	Returns pointer to Attributecontainer of spikes generated during the last evolve() step. More...
NeuronID	get_size ()
	Returns the size of the group. More...
NeuronID	get_pre_size ()
	Returns the size of the group. More...
NeuronID	calculate_rank_size (int rank=-1)
	Determines rank size and stores it in local variable. More...
NeuronID	get_rank_size ()
	Returns the size on this rank. More...
NeuronID	get_post_size ()
	Returns the size on this rank. More...
void	set_clock_ptr (AurynTime *clock)
bool	evolve_locally ()
	Returns true if the calling instance has units which are integrated on the current rank. More...
NeuronID	get_uid ()
	Get the unique ID of the class. More...
Trace *	get_pre_trace (AurynFloat x)
	Returns a pre trace with time constant x. More...
void	add_pre_trace (Trace *tr)
	Adds trace to pretrace stack of a connection. More...
Trace *	get_post_trace (AurynFloat x)
	Returns a post trace with time constant x. More...
void	add_post_trace (Trace *tr)
	Adds trace to posttrace stack of a connection. More...
void	push_spike (NeuronID spike)
	Pushes a local NeuronID as spike into the axonal SpikeDelay buffer. More...
void	push_attribute (AurynFloat attrib)
	Pushes a spike attribute into the axonal SpikeDelay buffer. More...
void	clear_spikes ()
	Clears all spikes stored in the delays which is useful to reset a network during runtime. More...
Trace *	get_post_state_trace (std::string state_name="mem", AurynFloat tau=10e-3, AurynFloat b=0.0)
	Returns a post trace of a neuronal state variable e.g. the membrane potential with time constant tau. More...
Trace *	get_post_state_trace (AurynStateVector *state, AurynFloat tau=10e-3, AurynFloat b=0.0)
	Returns a post trace of a neuronal state variable specified by pointer. More...
void	set_delay (int d)
	Sets axonal delay for this SpikingGroup. More...
virtual bool	write_to_file (const char *filename)
	Writes current states of SpikingGroup to human-readible textfile if implemented in derived class. More...
virtual bool	load_from_file (const char *filename)
	Reads current states of SpikingGroup to human-readible textfile if implemented in derived class. More...
NeuronID	ranksize ()
	Returns size (num of neurons) on the current rank. More...
NeuronID	global2rank (NeuronID i)
	Converts global NeuronID within the SpikingGroup to the local NeuronID on this rank. More...
NeuronID	rank2global (NeuronID i)
	Converts local NeuronID from the local rank to a global NeuronID. More...
bool	localrank (NeuronID i)
	Checks if the global NeuronID i is integrated on this MPI rank. More...
NeuronID	get_vector_size ()
	Rank size but rounded up to multiples of 4 (or potentially some other and larger number in future versions) for SSE compatibility. More...

Public Attributes
AurynFloat	avar
AurynFloat	bvar
AurynFloat	cvar
AurynFloat	dvar
Public Attributes inherited from auryn::NeuronGroup
AurynStateVector *	mem
AurynStateVector *	g_ampa
AurynStateVector *	g_gaba
AurynStateVector *	g_nmda
AurynStateVector *	thr
Public Attributes inherited from auryn::SpikingGroup
SpikeDelay *	delay
bool	active
	Toggles group active. More...
std::map< std::string, AurynStateVector * >	state_vectors
std::map< std::string, AurynState >	state_variables

Additional Inherited Members
Protected Member Functions inherited from auryn::NeuronGroup
void	init ()
void	free ()
Protected Member Functions inherited from auryn::SpikingGroup
void	free ()
	Frees potentially allocated memory. More...
Protected Attributes inherited from auryn::NeuronGroup
AurynStateVector *	default_exc_target_state
AurynStateVector *	default_inh_target_state
Protected Attributes inherited from auryn::SpikingGroup
std::vector< Trace * >	pretraces
	Pretraces. More...
std::vector< Trace * >	posttraces
	Posttraces. More...
std::vector< Trace * >	post_state_traces
	Post state traces. More...
std::vector< AurynFloat >	post_state_traces_spike_biases
std::vector< AurynStateVector * >	post_state_traces_states
std::string	group_name
	Identifying name for object. More...
NeuronID	size
	Stores the size of the group. More...
NeuronID	rank_size
	Stores the size of the group on this rank. More...
SpikeContainer *	spikes
	SpikeContainers to store spikes produced during one step of evolve. More...
AttributeContainer *	attribs
Static Protected Attributes inherited from auryn::SpikingGroup
static AurynTime *	clock_ptr = NULL

Detailed Description

This NeuronGroup implements the Izhikevich neuron model with conductance based AMPA and GABA synapses.

This NeuronGroup implements the nonlinear integrate and fire neuron model by Eugene M. Izhikevich as described in Izhikevich, E.M. (2003). Simple model of spiking neurons. IEEE Transactions on Neural Networks 14, 1569–1572.

In this implementation the state variables have been rescaled to V and seconds for consistency. The model is controlled via the public members: avar, bvar, cvar, dvar which correspond to the a,b,c and d parameters in the paper.

Note that since this model has been rescaled to volts and seconds the reset and jump size parameters (cvar and dvar) also need to be given in volts (i.e. scaled by 1e-3).

Also keep in mind that the default interpretation of synaptic synaptic strength given in multiples of the leak conductance is not longer true for this group and you will need to "gauge" synaptic strength according to the size of membrane potential deflection it causes.

Constructor & Destructor Documentation

IzhikevichGroup()

IzhikevichGroup::IzhikevichGroup

(

NeuronID

size

)

The default constructor of this NeuronGroup.

                                              : NeuronGroup(size)
{
        auryn::sys->register_spiking_group(this);
        if ( evolve_locally() ) init();
}

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~IzhikevichGroup()

IzhikevichGroup::~IzhikevichGroup ( )

virtual

{
        if ( !evolve_locally() ) return;
}

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Member Function Documentation

clear()

void IzhikevichGroup::clear ( )

virtual

Resets all neurons to defined and identical initial state.

Implements auryn::NeuronGroup.

{
        clear_spikes();
   mem->set_all(cvar);
   g_ampa->set_all(0.);
   g_gaba->set_all(0.);
}

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evolve()

void IzhikevichGroup::evolve ( )

virtual

Integrates the NeuronGroup state.

The evolve method internally used by System.

Implements auryn::SpikingGroup.

{
        // compute synaptic conductance based currents
    // excitatory
        cur_exc->copy(g_ampa);
        cur_exc->scale(-1);
        cur_exc->mul(mem);
    
    // inhibitory
        cur_inh->diff(mem,e_rev_gaba);
        cur_inh->mul(g_gaba);

        // compute izhikevich neuronal dynamics
        temp_vector->copy(mem);
        temp_vector->sqr();
        temp_vector->scale(40);

        temp_vector->saxpy(5,mem);
        temp_vector->add(0.140);
        temp_vector->sub(adaptation_vector);

        // add synaptic currents
        temp_vector->add(cur_exc);
        temp_vector->sub(cur_inh);

        // update membrane voltage
        mem->saxpy(auryn_timestep/1e-3,temp_vector); // division by 1e-3 due to rescaling of time from ms -> s

        // update adaptation variable
        temp_vector->copy(mem);
        temp_vector->scale(bvar);
        temp_vector->sub(adaptation_vector);

        adaptation_vector->saxpy(avar*auryn_timestep/1e-3,temp_vector);

        check_thresholds();

        // decay synaptic conductances
        g_ampa->scale(scale_ampa);
        g_gaba->scale(scale_gaba);
}

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get_tau_ampa()

AurynFloat IzhikevichGroup::get_tau_ampa

(

)

Gets the exponential time constant for the AMPA channel.

{
        return tau_ampa;
}

get_tau_gaba()

AurynFloat IzhikevichGroup::get_tau_gaba

(

)

Gets the exponential time constant for the GABA channel.

{
        return tau_gaba;
}

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set_tau_ampa()

void IzhikevichGroup::set_tau_ampa

(

AurynFloat

tau

)

Sets the exponential time constant for the AMPA channel (default 5ms)

{
        tau_ampa = taum;
        calculate_scale_constants();
}

set_tau_gaba()

void IzhikevichGroup::set_tau_gaba

(

AurynFloat

tau

)

Sets the exponential time constant for the GABA channel (default 10ms)

{
        tau_gaba = taum;
        calculate_scale_constants();
}

Member Data Documentation

avar

AurynFloat auryn::IzhikevichGroup::avar

The "a" parameter in the Izhikevich model which controls the time course of the adaptation variable u

bvar

AurynFloat auryn::IzhikevichGroup::bvar

The "b" parameter in the Izhikevich model which controls the fixed point of the adaptation variable u

cvar

AurynFloat auryn::IzhikevichGroup::cvar

The "c" parameter in the Izhikevich model which is the reset voltage

dvar

AurynFloat auryn::IzhikevichGroup::dvar

The "d" parameter in the Integrates model which is the spike triggered jump size of the adaptation variable u (note that it needs to be rescaled to units of V (i.e. multiplied by 1e-3) when paramters from Izhikevich's original publication are used because the model has been renormalized to volts for consistency reasons.

---

The documentation for this class was generated from the following files:

• /home/zenke/auryn/src/auryn/IzhikevichGroup.h
• /home/zenke/auryn/src/auryn/IzhikevichGroup.cpp