auryn::STPConnection Class Reference

This class implements short term plasticity according to the Tsodyks-Markram synapse. More...

#include <STPConnection.h>

Inheritance diagram for auryn::STPConnection:

Collaboration diagram for auryn::STPConnection:

Public Member Functions
	STPConnection (const char *filename)
	STPConnection (NeuronID rows, NeuronID cols)
	STPConnection (SpikingGroup *source, NeuronGroup *destination, TransmitterType transmitter=GLUT)
	STPConnection (SpikingGroup *source, NeuronGroup *destination, const char *filename, TransmitterType transmitter=GLUT)
	STPConnection (SpikingGroup *source, NeuronGroup *destination, AurynWeight weight, AurynFloat sparseness=0.05, TransmitterType transmitter=GLUT, string name="STPConnection")
void	set_tau_d (AurynFloat taud)
void	set_tau_f (AurynFloat tauf)
void	set_ujump (AurynFloat r)
void	clear ()
	Clear. More...
void	clone_parameters (STPConnection *con)
	Clone parameters. More...
virtual	~STPConnection ()
virtual void	propagate ()
void	push_attributes ()
void	evolve ()
Public Member Functions inherited from auryn::SparseConnection
	SparseConnection ()
	Empty constructor which should not be used – TODO should be deprecated at some point. More...
	SparseConnection (const char *filename)
	Load from wmat file constructor which should not be used – TODO should be deprecated at some point. More...
	SparseConnection (NeuronID rows, NeuronID cols)
	Deprecated constructor for manual filling. More...
	SparseConnection (SpikingGroup *source, NeuronGroup *destination, const char *filename, TransmitterType transmitter=GLUT)
	Deprecated constructor for loading from file. More...
	SparseConnection (SpikingGroup *source, NeuronGroup *destination, TransmitterType transmitter=GLUT, string name="SparseConnection")
	Constructor for manual filling. More...
	SparseConnection (SpikingGroup *source, NeuronGroup *destination, AurynWeight weight, AurynDouble sparseness=0.05, TransmitterType transmitter=GLUT, string name="SparseConnection")
	Default constructor which sets up a random sparse matrix with fixed weight between the source and destination group. More...
	SparseConnection (SpikingGroup *source, NeuronGroup *destination, SparseConnection *con, string name="SparseConnection")
	This constructor tries to clone a connection by guessing all parameters except source and destination from another connection instance. More...
	SparseConnection (SpikingGroup *source, NeuronGroup *destination, AurynWeight weight, AurynDouble sparseness, NeuronID lo_row, NeuronID hi_row, NeuronID lo_col, NeuronID hi_col, TransmitterType transmitter=GLUT)
	Sparse block constructor. More...
virtual	~SparseConnection ()
	The default destructor. More...
void	allocate_manually (AurynLong expected_size)
	Is used whenever memory has to be allocated manually. Automatically adjusts for number of ranks and for security margin. More...
AurynLong	estimate_required_nonzero_entires (AurynLong nonzero, double sigma=5.)
	This function estimates the required size of the nonzero entry buffer. More...
void	seed (NeuronID randomseed)
	This function seeds the pseudo random number generator for all random fill operatios. More...
virtual AurynWeight	get (NeuronID i, NeuronID j)
	Returns weight value of a given element if it exists. More...
virtual AurynWeight *	get_ptr (NeuronID i, NeuronID j)
	Returns pointer to given weight element if it exists. Returns NULL if element does not exist. More...
virtual AurynWeight	get_data (NeuronID i)
	Returns weight value of a given element referenced by index in the data array. More...
virtual void	set_data (NeuronID i, AurynWeight value)
	Sets weight value of a given element referenced by its index in the data array. More...
virtual void	set (NeuronID i, NeuronID j, AurynWeight value)
	Sets a single connection to value if it exists. More...
virtual void	set (std::vector< neuron_pair > element_list, AurynWeight value)
	Sets a list of connection to value if they exists. More...
void	random_data (AurynWeight mean, AurynWeight sigma)
	Synonym for random_data. More...
void	random_data_normal (AurynWeight mean, AurynWeight sigma)
	Set weights of all existing connections randomly using a normal distrubtion. More...
void	random_data_lognormal (AurynWeight m, AurynWeight s)
	Set weights of all existing connections randomly using a lognormal distribution. More...
void	init_random_binary (AurynFloat prob=0.5, AurynWeight wlo=0.0, AurynWeight whi=1.0)
	Initialize with random binary at wlo and whi. More...
void	random_col_data (AurynWeight mean, AurynWeight sigma)
	Sets weights in cols to the same value drewn from a Gaussian distribution. More...
void	set_block (NeuronID lo_row, NeuronID hi_row, NeuronID lo_col, NeuronID hi_col, AurynWeight weight)
	Sets all weights of existing connections in a block spanned by the first 4 parameters to the value given. More...
void	scale_block (NeuronID lo_row, NeuronID hi_row, NeuronID lo_col, NeuronID hi_col, AurynWeight alpha)
	Scale all weights of existing connections in a block spanned by the first 4 parameters to the value given. More...
virtual void	set_all (AurynWeight weight)
	Sets all weights of existing connections to the given value. More...
virtual void	scale_all (AurynFloat value)
	Scales all weights in the weight matrix with the given value. More...
virtual void	clip (AurynWeight lo, AurynWeight hi)
	Clip weights. More...
void	set_upper_triangular (AurynWeight weight)
	Sets weights in a upper triangular matrix. More...
virtual void	sparse_set_data (AurynDouble sparseness, AurynWeight value)
	Sets a sparse random subset of connection elements wight the given value. More...
void	connect_random (AurynWeight weight=1.0, AurynDouble sparseness=0.05, bool skip_diag=false)
	Connect src and dst SpikingGroup and NeuronGroup randomly with given sparseness. More...
void	connect_block_random (AurynWeight weight, AurynDouble sparseness, NeuronID lo_row, NeuronID hi_row, NeuronID lo_col, NeuronID hi_col, bool skip_diag=false)
	Underlying sparse fill method. More...
virtual void	finalize ()
	Finalizes connection after random or manual initialization of the weights. More...
bool	push_back (NeuronID i, NeuronID j, AurynWeight weight)
	Pushes a single element to the ComplexMatrix. More...
AurynLong	get_nonzero ()
	Returns number of nonzero elements in this SparseConnection. More...
void	put_pattern (type_pattern *pattern, AurynWeight strength, bool overwrite)
	Puts cell assembly to existing sparse weights. More...
void	put_pattern (type_pattern *pattern1, type_pattern *pattern2, AurynWeight strength, bool overwrite)
	Puts cell assembly or synfire pattern to existing sparse weights. More...
void	load_patterns (string filename, AurynWeight strength, int nb_max_patterns=10000, bool overwrite=false, bool chainmode=false)
	Reads first n patterns from a .pat file and adds them as Hebbian assemblies onto an existing weight matrix. More...
void	load_pre_post_patterns (std::string pre_file, std::string post_file, AurynWeight strength, int nb_max_patterns=10000, bool overwrite=false)
	Reads patterns from two files and connects them. More...
void	sanity_check ()
	Quick an dirty function that checks if all units on the local rank are connected. More...
virtual AurynDouble	sum ()
	Computes sum of all weight elements in the Connection. More...
virtual void	stats (AurynDouble &mean, AurynDouble &std)
	Computes mean and variance of weights in default weight matrix. More...
virtual void	stats (AurynDouble &mean, AurynDouble &std, NeuronID zid)
	Computes mean and variance of weights for matrix state zid. More...
bool	write_to_file (ForwardMatrix *m, string filename)
	Writes rank specific weight matrix on the same rank to a file. More...
virtual bool	write_to_file (string filename)
	Writes rank specific default weight matrix on the same rank to a file. More...
virtual bool	load_from_complete_file (string filename)
	Loads weight matrix from a single file. More...
virtual bool	load_from_file (string filename)
	Loads weight matrix from Matrix Market (wmat) file. More...
bool	load_from_file (ForwardMatrix *m, string filename, AurynLong data_size=0)
	Loads weight matrix from Matrix Market (wmat) file to specified weight matrix. More...
virtual void	set_min_weight (AurynWeight minimum_weight)
	Sets minimum weight (for plastic connections). More...
AurynWeight	get_min_weight ()
	Gets minimum weight (for plastic connections). More...
virtual void	set_max_weight (AurynWeight maximum_weight)
	Sets maximum weight (for plastic connections). More...
AurynWeight	get_max_weight ()
	Gets maximum weight (for plastic connections). More...
std::vector< neuron_pair >	get_block (NeuronID lo_row, NeuronID hi_row, NeuronID lo_col, NeuronID hi_col)
	Returns a vector of ConnectionsID of a block specified by the arguments. More...
std::vector< neuron_pair >	get_post_partners (NeuronID i)
	Returns a vector of ConnectionsID of postsynaptic parterns of neuron i. More...
std::vector< neuron_pair >	get_pre_partners (NeuronID j)
	Returns a vector of ConnectionsID of presynaptic parterns of neuron i. More...
Public Member Functions inherited from auryn::Connection
	Connection ()
	Connection (NeuronID rows, NeuronID cols)
	Connection (SpikingGroup *source, NeuronGroup *destination, TransmitterType transmitter=GLUT, std::string name="Connection")
virtual	~Connection ()
void	set_size (NeuronID i, NeuronID j)
void	set_name (std::string name)
	Set name of connection. More...
std::string	get_name ()
	Returns name of connection. 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...
AurynStateVector *	get_target_vector ()
	Returns target state vector if one is defined. More...
NeuronID	get_m_rows ()
	Get number of rows (presynaptic) in connection. More...
NeuronID	get_n_cols ()
	Get number of columns (postsynaptic) in connection. More...
TransmitterType	get_transmitter ()
	Returns transmitter type. More...
void	set_target (AurynWeight *ptr)
	Sets target state of this connection directly via a pointer. More...
void	set_target (AurynStateVector *ptr)
	Sets target state of this connection directly via a StateVector. More...
void	set_receptor (AurynStateVector *ptr)
	Same as set_target. More...
void	set_transmitter (AurynStateVector *ptr)
	Same as set_target. More...
void	set_transmitter (TransmitterType transmitter)
	Sets target state of this connection for a given receptor as one of Auryn's default transmitter types. More...
void	set_receptor (string state_name)
	Sets target state of this connection directly the name of a state vector. More...
void	set_target (string state_name)
	Same as set_receptor. More...
void	set_transmitter (string state_name)
	Same as set_receptor, but DEPRECATED. More...
void	set_source (SpikingGroup *source)
	Sets source SpikingGroup of this connection. More...
SpikingGroup *	get_source ()
	Returns pointer to the presynaptic group. More...
void	set_destination (NeuronGroup *source)
	Sets destination SpikingGroup of this connection. More...
NeuronGroup *	get_destination ()
	Returns pointer to the postsynaptic group. More...
void	conditional_propagate ()
	DEPRECATED. (Such connections should not be registered in the first place) Calls propagate only if the postsynaptic NeuronGroup exists on the local rank. More...
Trace *	get_pre_trace (const AurynDouble tau)
	Returns a pointer to a presynaptic trace object. More...
Trace *	get_post_trace (const AurynDouble tau)
	Returns a pointer to a postsynaptic trace object. More...
Trace *	get_post_state_trace (const string state_name, const AurynDouble tau, const AurynDouble jump_size=0.0)
	Returns a pointer to a postsynaptic state trace object. More...
void	transmit (const NeuronID id, const AurynWeight amount)
	Default way to transmit a spike to a postsynaptic partner. More...
void	targeted_transmit (SpikingGroup *target_group, AurynStateVector *target_state, const NeuronID id, const AurynWeight amount)
	Transmits a spike to a given target group and state. More...
void	safe_transmit (NeuronID id, AurynWeight amount)
	Same as transmit but first checks if the target neuron exists and avoids segfaults that way (but it's also slower). More...
SpikeContainer *	get_pre_spikes ()
	Supplies pointer to SpikeContainer of all presynaptic spikes. More...
SpikeContainer *	get_post_spikes ()
	Returns pointer to SpikeContainer for postsynaptic spikes on this node. More...
void	add_number_of_spike_attributes (int x)
	Set up spike delay to accomodate x additional spike attributes. More...
AurynFloat	get_spike_attribute (const NeuronID i, const int attribute_id=0)
	Returns spike attribute belonging to the spike at position i in the get_spikes() SpikeContainer. More...

Public Attributes
double	tau_d
double	tau_f
double	Ujump
Public Attributes inherited from auryn::SparseConnection
bool	patterns_ignore_gamma
	Switch that toggles for the load_patterns function whether or not to use the intensity (gamma) value. Default is false. More...
NeuronID	patterns_every_pre
	The every_pre parameter allows to skip presynaptically over pattern IDs when loading patterns. Default is 1. This can be useful to when loading patterns into the exc->inh connections and there significantly less inhibitory cells than exc ones. More...
NeuronID	patterns_every_post
	The every_post parameter allows to skip postsynaptically over pattern IDs when loading patterns. Default is 1. This can be useful to when loading patterns into the exc->inh connections and there significantly less inhibitory cells than exc ones. More...
bool	wrap_patterns
	Switch that toggles the behavior when loading a pattern to wrap neuron IDs back onto existing cells via the modulo function. More...
ForwardMatrix *	w
	A pointer that points per default to the ComplexMatrix that stores the connectinos. More...
Public Attributes inherited from auryn::Connection
SpikingGroup *	src
	Pointer to the source group of this connection. More...
NeuronGroup *	dst
	Pointer to the destination group of this connection. More...

Additional Inherited Members
Protected Member Functions inherited from auryn::SparseConnection
void	virtual_serialize (boost::archive::binary_oarchive &ar, const unsigned int version)
void	virtual_serialize (boost::archive::binary_iarchive &ar, const unsigned int version)
void	free ()
void	allocate (AurynLong bufsize)
std::vector< type_pattern >	load_pattern_file (string filename, int nb_max_patterns)
	Reads patterns from a .pat file and returns a vector with the patterns. More...
Protected Member Functions inherited from auryn::Connection
void	init (TransmitterType transmitter=GLUT)
Protected Attributes inherited from auryn::SparseConnection
AurynWeight	wmin
AurynWeight	wmax
bool	skip_diagonal
Protected Attributes inherited from auryn::Connection
TransmitterType	trans
AurynStateVector *	target_state_vector
AurynFloat *	target
	A more direct reference on the first element of the target_state_vector. More...
NeuronID	number_of_spike_attributes
	Number of spike attributes to expect with each spike transmitted through this connection. More...
NeuronID	spike_attribute_offset
	Stores spike attribute offset in attribute array. More...
Static Protected Attributes inherited from auryn::SparseConnection
static boost::mt19937	sparse_connection_gen = boost::mt19937()

Detailed Description

This class implements short term plasticity according to the Tsodyks-Markram synapse.

This class implements the short-term plasticity model following Markram, H., Wang, Y., Tsodyks, M., 1998. Differential signaling via the same axon of neocortical pyramidal neurons. Proc Natl Acad Sci U S A 95, 5323–5328.

also see Mongillo, G., Barak, O., Tsodyks, M., 2008. Synaptic Theory of Working Memory. Science 319, 1543–1546. doi:10.1126/science.1150769

Constructor & Destructor Documentation

STPConnection() [1/5]

STPConnection::STPConnection

(

const char *

filename

)

Minimal constructor for from file init – deprecated

Parameters

filename

Filename to load

: SparseConnection(filename)
{
        init();
}

STPConnection() [2/5]

STPConnection::STPConnection	(	NeuronID	rows,
		NeuronID	cols
	)

Minimal constructor to which leaves the connection uninitialized

Parameters

source	The presynaptic SpikingGroup
destination	the postsynaptic NeuronGroup

: SparseConnection(rows,cols)
{
        init();
}

STPConnection() [3/5]

STPConnection::STPConnection	(	SpikingGroup *	source,
		NeuronGroup *	destination,
		TransmitterType	transmitter = GLUT
	)

Default constructor to which leaves the connection uninitialized

Parameters

source	The presynaptic SpikingGroup
destination	the postsynaptic NeuronGroup
transmitter	The transmitter type

: SparseConnection(source, destination, transmitter)
{
}

STPConnection() [4/5]

STPConnection::STPConnection	(	SpikingGroup *	source,
		NeuronGroup *	destination,
		const char *	filename,
		TransmitterType	transmitter = GLUT
	)

Default constructor to initialize connection from file

Parameters

source	The presynaptic SpikingGroup
destination	the postsynaptic NeuronGroup
filename	The file to load the connectivity from upon initialization
transmitter	The transmitter type
name	The connection name as it appears in debugging output

: SparseConnection(source, destination, filename, transmitter)
{
        init();
}

STPConnection() [5/5]

STPConnection::STPConnection	(	SpikingGroup *	source,
		NeuronGroup *	destination,
		AurynWeight	weight,
		AurynFloat	sparseness = 0.05,
		TransmitterType	transmitter = GLUT,
		std::string	name = "STPConnection"
	)

Default constructor to initialize connection with random sparse connectivity

Parameters

source	The presynaptic SpikingGroup
destination	the postsynaptic NeuronGroup
weight	The default weight for connections
sparseness	The probability of a connection for the sparse connectivity
transmitter	The transmitter type
name	The connection name as it appears in debugging output

: SparseConnection(source,destination,weight,sparseness,transmitter, name)
{
        init();
}

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~STPConnection()

STPConnection::~STPConnection ( )

virtual

Default destructor.

{
        free();
}

Member Function Documentation

clear()

void STPConnection::clear

(

)

Clear.

{
        for (NeuronID i = 0; i < src->get_rank_size() ; i++)
        {
                   auryn_vector_float_set (state_x, i, 1 ); // TODO
                   auryn_vector_float_set (state_u, i, Ujump );
        }
}

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clone_parameters()

void STPConnection::clone_parameters

(

STPConnection *

con

)

Clone parameters.

{
        tau_d = con->tau_d;
        tau_f = con->tau_f;
        Ujump = con->Ujump;
        clear();
}

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evolve()

void STPConnection::evolve ( )

virtual

Implements the connections evolve function (auryn internal use).

Reimplemented from auryn::Connection.

{
        if ( src->evolve_locally() ) {
                // dynamics of x
                auryn_vector_float_set_all( state_temp, 1);
                auryn_vector_float_saxpy(-1,state_x,state_temp);
                auryn_vector_float_saxpy(auryn_timestep/tau_d,state_temp,state_x);

                // dynamics of u
                auryn_vector_float_set_all( state_temp, Ujump);
                auryn_vector_float_saxpy(-1,state_u,state_temp);
                auryn_vector_float_saxpy(auryn_timestep/tau_f,state_temp,state_u);
        }
}

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propagate()

void STPConnection::propagate ( )

virtual

Implements the connections propagate function (auryn internal use).

Reimplemented from auryn::SparseConnection.

{
        if ( src->evolve_locally()) {
                push_attributes(); // stuffs all attributes into the SpikeDelays for sync
        }

        if ( dst->evolve_locally() ) { // necessary 
                NeuronID * ind = w->get_row_begin(0); // first element of index array
                AurynWeight * data = w->get_data_begin(); // first element of data array

                // loop over spikes
                for (NeuronID i = 0 ; i < src->get_spikes()->size() ; ++i ) {
                        // get spike at pos i in SpikeContainer
                        NeuronID spike = src->get_spikes()->at(i);

                        // extract spike attribute from attribute stack;
                        AurynFloat attribute = get_spike_attribute(i);

                        // loop over postsynaptic targets
                        for (NeuronID * c = w->get_row_begin(spike) ; 
                                        c != w->get_row_end(spike) ; 
                                        ++c ) {
                                AurynWeight value = data[c-ind] * attribute; 
                                transmit( *c , value );
                        }
                }
        }
}

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push_attributes()

void STPConnection::push_attributes

(

)

Internal function to push spike attributes.

{
        // need to push one attribute for each spike
        SpikeContainer * spikes = src->get_spikes_immediate();
        for (SpikeContainer::const_iterator spike = spikes->begin() ;
                        spike != spikes->end() ; ++spike ) {
                // dynamics 
                NeuronID spk = src->global2rank(*spike);
                double x = auryn_vector_float_get( state_x, spk );
                double u = auryn_vector_float_get( state_u, spk );
                auryn_vector_float_set( state_x, spk, x-u*x );
                auryn_vector_float_set( state_u, spk, u+Ujump*(1-u) );

                // TODO spike translation or introduce local_spikes 
                // function in SpikingGroup and implement this there ... (better option)
                src->push_attribute( x*u ); 

        }

        // If we had two spike attributes in this connection we push 
        // the second attribute for each spike here:
        //
        // SpikeContainer * spikes = src->get_spikes_immediate();
        // for (SpikeContainer::const_iterator spike = spikes->begin() ;
        //              spike != spikes->end() ; ++spike ) {
        //      AurynFloat other_attribute = foo+bar;
        //      src->push_attribute( other_attribute ); 
        // }
}

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set_tau_d()

void STPConnection::set_tau_d

(

AurynFloat

taud

)

Setter for tau_d, the timescale of synaptic depression.

                                             {
        tau_d = taud;
}

set_tau_f()

void STPConnection::set_tau_f

(

AurynFloat

tauf

)

Setter for tau_f, the timescale of synaptic facilitation.

                                             {
        tau_f = tauf;
}

set_ujump()

void STPConnection::set_ujump

(

AurynFloat

r

)

Setter for U_jump, which specifies the spike triggered change in the U equation in the model. Typically the same as urest.

                                          {
        Ujump = r;
}

Member Data Documentation

tau_d

double auryn::STPConnection::tau_d

tau_f

double auryn::STPConnection::tau_f

Ujump

double auryn::STPConnection::Ujump

---

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

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