unit {leabRa}

Leabra unit (neuron) class

Description

This class simulates a biologically realistic neuron (also called unit) in the Leabra framework. When you use the layer class, you will see that a layer object has a variable (field) units, which is a list of unit objects.

Usage

unit

Format

R6Class object.

Value

Object of R6Class with methods for calculating neuron activation changes.

Fields

activation

Percentage activation ("firing rate") of the unit, which is sent to other units, think of it as a percentage of how many neurons are active in a microcolumn of 100 neurons.

avg_s

Short-term running average activation, integrates over avg_ss (a private variable, which integrates over activation), represents plus phase learning signal.

avg_m

Medium-term running average activation, integrates over avg_s, represents minus phase learning signal.

avg_l

Long-term running average activation, integrates over avg_m, drives long-term floating average for self-organized learning.

unit_number

Number of unit in layer, if the unit is not created within a layer, this value will be 1.

Methods

new()

Creates an object of this class with default parameters.

cycle(g_e_raw, g_i)

Cycles 1 ms with given excitatory conductance g_e_raw and inhibitory conductance g_i. Excitatory conductance depends on the connection weights to other units and the activity of those other units. Inhibitory conductance depends on feedforward and feedback inhibition. See layer cycle method.

g_e_raw

Raw excitatory conductance. The actual excitatory conductance will incrementally approach this value with every cycle.

g_i

Inhibitory conductance.

clamp_cycle(activation)

Clamps the value of activation to the activation variable of the unit without any time integration. Then updates averages (avg_ss, avg_s, avg_m). This is usually done when presenting external input.

activation

Activation to clamp.

updt_avg_l()

Updates the variable avg_l. This usually happens before the weights are changed in the network (after the plus phase), and not every cycle.

get_vars(show_dynamics = TRUE, show_constants = FALSE)

Returns a data frame with 1 row with the current state of all the variables of the unit. You can choose whether you want dynamic values and / or constant values. This might be useful if you want to analyze what happens in a unit, which would otherwise not be possible, because most of the variables (fields) are private in this class.

show_dynamics

Should dynamic values be shown? Default is TRUE

show_constants

Should constant values be shown? Default is FALSE

References

O'Reilly, R. C., Munakata, Y., Frank, M. J., Hazy, T. E., and Contributors (2016). Computational Cognitive Neuroscience. Wiki Book, 3rd (partial) Edition. URL: http://ccnbook.colorado.edu

Have also a look at https://grey.colorado.edu/emergent/index.php/Leabra (especially the link to the 'MATLAB' code) and https://en.wikipedia.org/wiki/Leabra

Examples

u <- unit$new() # creates a new unit with default leabra values

print(u) # a lot of private values
u$v # private values cannot be accessed
# if you want to see alle variables, you need to use the function
u$get_vars(show_dynamics = TRUE, show_constants = TRUE)

# let us clamp the activation to 0.7
u$activation
u$clamp_cycle(0.7)
c(u$activation, u$avg_s, u$avg_m, u$avg_l)
# activation is indeed 0.7, but avg_l was not updated, this only happens
# before the weights are changed, let us update it now
u$updt_avg_l()
c(u$activation, u$avg_s, u$avg_m, u$avg_l)
# seems to work

# let us run 10 cycles with unclamped activation and output the activation
# produced because of changes in conductance
u <- unit$new()
cycle_number <- 1:10
result <- lapply(cycle_number, function(x)
                 u$cycle(g_e_raw = 0.5, g_i = 0.5)$get_vars())
# make a data frame out of the list
result <- plyr::ldply(result)
# plot activation
plot(result$activation, type = "b", xlab = "cycle", ylab = "activation")
# add conductance g_e to plot, should approach g_e_raw
lines(result$g_e, type = "b", col = "blue")