- Generated on Mon Jul 10 2023 12:42:34 for CARLsim by
1.8.13
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CARLsim
6.1.0
CARLsim: a GPU-accelerated SNN simulator
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SpikeMonitors can be used to record output spikes for different neuronal groups.
CARLsim supports two different recording mechanisms: Recording to a spike file (binary) and recording to a SpikeMonitor object. The former is useful for off-line analysis of activity (e.g., using Chapter 9: MATLAB Offline Analysis Toolbox (OAT)). The latter is useful to calculate different spike metrics and statistics on-line, such as mean firing rate and standard deviation, or the number of neurons whose firing rate lies in a certain interval.
The easiest way to start recording the spikes of a group g0 to file is to call the following function in CARLsim state CONFIG_STATE or SETUP_STATE:
This will dump all spikes of the group (in AER format) to a binary, over the timecourse of the entire simulation. The default file name is "results/spk_{grpName}.dat", where {grpName} is the name that was assigned to the group g0 in createGroup or createSpikeGeneratorGroup.
The Offline Analysis Toolbox will automatically look for names created according to this template, so that group or network activity can be plotted right away. If a custom name is used, setSpikeFileAttributes must be called in the Matlab utilities GroupMonitor.m or NetworkMonitor.m
A custom name is passed to the function like this:
However, make sure that the directory myDirectory exists.
If no binary shall be created, use:
A second way to record group activity is to use the SpikeMonitor object that is returned by setSpikeMonitor, and query it for spike data, metrics, and statistics.
Spike data will not be recorded until the SpikeMonitor member function SpikeMonitor::startRecording is called. Before any metrics can be computed, the user must call SpikeMonitor::stopRecording. In general, a new recording period (the time period between startRecording and stopRecording calls) can be started at any point in time, and can last any number of milliseconds. The SpikeMonitor has a PersistentMode, which is off by default. When PersistentMode is off, only the last recording period will be considered. When PersistentMode is on, all the recording periods will be considered. By default, PersistentMode can be switched on/off by calling SpikeMonitor::setPersistentData(bool). The total time over which the metric is calculated can be retrieved by calling SpikeMonitor::getRecordingTotalTime().
The following code starts recording spikes for the first second of the simulation then stops recording the spikes. The next second of simulation time is not recorded:
There are two different modes that define what information is collected exactly, AER and COUNT mode.
AER mode: AER mode will collect the exact spike times of all neurons in the group and store them in a 2D spike spike vector. The first dimension of the vector is neuron id, the second dimension is spike times. Each element spkVector[i] is thus a vector of all spike times for the i-th neuron in the group. This mode is activated by default.
COUNT mode: SpikeCount mode will only collect spike count information, such as the number of spikes per neuron. This mode cannot retrieve exact spike times. Thus it is not possible to calculate some of the more elaborate metrics, such as spike-time correlations.
SpikeMonitor objects come with a number of useful metrics that allows the user to query CARLsim simulations programmatically. Users can get the total of number of spikes for the entire group using SpikeMonitor::getPopNumSpikes or the number of spikes per neuron in the group using SpikeMonitor::getNeuronNumSpikes. To get the maximum or minimum average firing rate of the group, SpikeMonitor::getMaxFiringRate or SpikeMonitor::getMinFiringRate can be used. An entire vector of firing rates is available using the function call SpikeMonitor::getAllFiringRates. Additionally, SpikeMonitor::getAllFiringRatesSorted returns the vector of firing rates for every neuron sorted. Another useful function is SpikeMonitor::getNumNeuronsWithFiringRate which allows users to find out how many neurons had an average firing rate within a specific user-specified range. These metrics become particularly useful when we begin to tune SNNs as we will see in ch10_ecj and ch12s3_online_weight_tuning.
Users may want to get the AER 2D spike vector described in AER mode to do their own metrics or statistics, to do this, they can call SpikeMonitor::getSpikeVector2D. Users can manually clear the spike data stored in SpikeMonitor objects by calling SpikeMonitor::clear(). If PersistentMode is off this function is automatically called at the beginning of the SpikeMonitor::startRecording function call. Users can also print all the spiking informationin the group in legible format to the console with the SpikeMonitor::print call with an option for including the list of spike times for each neuron.
Below is an example of a user printing data generated during a simulation. After that, the average firing rates for every neuron are output to a vector.
The average firing rate of the group as whole can be found using SpikeMonitor::getPopMeanFiringRate and the standard deviation can be calculated using SpikeMonitor::getPopStdFiringRate. A useful metric in characterizing neural activity can be found with SpikeMonitor::getPercentNeuronsWithFiringRate which returns the percentage of neurons found within a user-defined range. Code for this function is shown below.
There are currently plans to include functions that calculate more in-depth statistics related to spike correlations and information theoretic measures in future CARLsim versions.
Using SpikeMonitor::setSpikeFile it is possible to redirect the file streams over the timecourse of a simulation, without having to recompile the network. Say, a simulation consists of three phases: 1) an initial phase, 2) a training phase, and 3) a testing phase. In such a scenario it might be desirable to store the spikes in different files, or, maybe in some phases, not record spikes at all. This can be achieved with ease using the following code snippet:
ConnectionMonitors can be used to record synaptic weights from a specific connection. Instantaneous recordings of a 2D weight matrix ("snapshots") can be taken either programmatically or automatically every second.
CARLsim supports two different recording mechanisms: Recording to a weight file (binary) and recording to a ConnectionMonitor object. The former is useful for off-line analysis of synaptic weights (e.g., using Chapter 9: MATLAB Offline Analysis Toolbox (OAT)). The latter is useful to calculate different weight metrics and statistics on-line, such as the percentage of weight values that fall in a certain weight range, or the number of weights that have been changed since the last snapshot.
The easiest way to start recording weights of a connection between pre-synaptic group grpIdPre and grpIdPost is to call the following function in CARLsim state CONFIG_STATE or SETUP_STATE:
This will take a snapshot of the 2D weight matrix every 1000 ms and dump the data to file. The default file name will be "results/conn_{name of pre-group}_{name of post-group}.dat". The first snapshot will be taken at t=0ms, the next one at t=1000ms, etc., until the end of the simulation is reached.
It is also possible to specify a custom file name instead of using the "DEFAULT" name. Alternatively, the user may suppress creation of the binary file by using file string "NULL" instead.
Periodic storing can be disabled by calling ConnectionMonitor::setUpdateTimeIntervalSec with argument intervalSec=-1.
An additional way to record weights is by quering the ConnectionMonitor object that is returned by CARLsim::setConnectionMonitor for connection data:
where grpIdPre and grpIdPost are the IDs of the pre-synaptic and post-synaptic group, respectively.
Weight snapshots can also be taken programmatically, by quering the ConnectionMonitor object:
This will take an instantaneous snapshot of the weights (at the current simulation time) and return it in a 2D weight matrix. The first dimension of the matrix will be of size ConnectionMonitor::getNumNeuronsPre(), and the second dimension of the matrix will be of size ConnectionMonitor::getNumNeuronsPost(). Synaptic connections in the matrix that do not exist will have value NAN and can be queried with isnan(wt[i][j]).
Note that every snapshot taken with this method will also be dumped to file. If the user wants the binary file to contain only distinct snapshots as opposed to a periodic ones taken every second, the recording interval can be adjusted as follows:
Weights can be printed in two ways: Either as a 2D weight matrix (pre x post) using ConnectionMonitor::print or as a sparse list of only existing synapses using ConnectionMonitor::printSparse:
ConnectionMonitor::printSparse also accepts up to three optional parameters that allow for formatting options. For more information see its code documentation.
For more sophisticated visualization options please refer to Chapter 9: MATLAB Offline Analysis Toolbox (OAT).
The ConnectionMonitor class provides a number of methods useful to compute a variety of weight metrics and statistics.
Metrics can be calculated either for the current snapshot (e.g., fan-in, fan-out) or by considering differences between the last two snapshots (e.g., number or percentage of weights that changed).
Fan-in is the number of incoming synapses for a specific post-synaptic neuron, and can be calculated with ConnectionMonitor::getFanIn. Alternatively, ConnectionMonitor::getFanOut returns the number of outgoing synapses for a specific pre-synaptic neuron.
Weight changes since the last snapshot can be calculated in a number of different ways. The number of weights whose absolute value has changed at least minAbsChanged (inclusive) since the last snapshot was taken can be calculated with ConnectionMonitor::getNumWeightsChanged. The same metric can be obtained as a percentage using ConnectionMonitor::getPercentWeightsChanged.
The absolute sum of weight changes since the last snapshot can be calculated with ConnectionMonitor::getTotalAbsWeightChange. This function might be useful (for example) to run a network with plastic synapses until learning has saturated:
NeuronMonitors allow CARLsim users to record neuron state information, which includes the membrane potential (v), the current (I), and the refactory variable (u). Currently, NeuronMonitors only support storing the neuron state information for the first 128 neuron in each neuron group.
The following function can be called to start recording the neuron state information of a group g0:
This will save the neuron state information to a binary file, with a default file name "results/n_{grpName}.dat".
Alternatively, neuron state information can be recorded by using a NeuronMonitor object.
Neuron state information can be accessed with the following functions:
Voltage information can be printed with the following function:
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