# (Laje & Buonomano, 2013) Robust Timing in RNN

Implementation of the paper:

Thanks to the original implementation codes: https://github.com/ReScience-Archives/Vitay-2016

[1]:

import brainpy as bp
import brainpy.math as bm


## Model Descriptions

### Recurrent network

The recurrent network is composed of $$N=800$$ neurons, receiving inputs from a variable number of input neurons $$N_i$$ and sparsely connected with each other. Each neuron’s firing rate $$r_i(t)$$ applies the tanh transfer function on an internal variable $$x_i(t)$$ which follows a first-order linear ordinary differential equation (ODE):

$\tau \cdot \frac{d x_i(t)}{dt} = - x_i(t) + \sum_{j=1}^{N_i} W_{ij}^{in} \cdot y_j(t) + \sum_{j=1}^{N} W_{ij}^{rec} \cdot r_j(t) + I^{noise}_i(t)$
$r_i(t) = \tanh(x_i(t))$

The weights of the input matrix $$W^{in}$$ are taken from the normal distribution, with mean 0 and variance 1, and multiply the rates of the input neurons $$y_j(t)$$. The variance of these weights does not depend on the number of inputs, as only one input neuron is activated at the same time. The recurrent connectivity matrix $$W^{rec}$$ is sparse with a connection probability $$pc = 0.1$$ (i.e. 64000 non-zero elements) and existing weights are taken randomly from a normal distribution with mean 0 and variance $$g/\sqrt{pc \cdot N}$$, where $$g$$ is a scaling factor. It is a well known result for sparse recurrent networks that for high values of $$g$$, the network dynamics become chaotic. $$I^{noise}_i(t)$$ is an additive noise, taken randomly at each time step and for each neuron from a normal distribution with mean 0 and variance $$I_0$$. $$I_0$$ is chosen very small in the experiments reproduced here ($$I_0 = 0.001$$) but is enough to highlight the chaotic behavior of the recurrent neurons (non-reproducibility between two trials).

The read-out neurons simply sum the activity of the recurrent neurons using a matrix $$W^{out}$$:

$z_i(t) = \sum_{j=1}^{N} W_{ij}^{out} \cdot r_j(t)$

The read-out matrix is initialized randomly from the normal distribution with mean 0 and variance $$1/\sqrt{N}$$.

### Learning rule

The particularity of the reservoir network proposed by (Laje & Buonomano, Nature Neuroscience, 2013) is that both the recurrent weights $$W^{rec}$$ and the read-out weights are trained in a supervised manner. More precisely, in this implementation, only 60% of the recurrent neurons have plastic weights, the 40% others keep the same weights throughout the simulation.

Learning is done using the recursive least squares (RLS) algorithm (Haykin, 2002). It is a supervised error-driven learning rule, i.e. the weight changes depend on the error made by each neuron: the difference between the firing rate of a neuron $$r_i(t)$$ and a desired value $$R_i(t)$$.

$e_i(t) = r_i(t) - R_i(t)$

For the recurrent neurons, the desired value is the recorded rate of that neuron during an initial trial (to enforce the reproducibility of the trajectory). For the read-out neurons, it is a function which we want the network to reproduce (e.g. handwriting as in Fig. 2).

Contrary to the delta learning rule which modifies weights proportionally to the error and to the direct input to a synapse ($$\Delta w_{ij} = - \eta \cdot e_i \cdot r_j$$), the RLS learning uses a running estimate of the inverse correlation matrix of the inputs to each neuron:

$\Delta w_{ij} = - e_i \sum_{k \in \mathcal{B}(i)} P^i_{jk} \cdot r_k$

Each neuron $$i$$ therefore stores a square matrix $$P^i$$, whose size depends of the number of weights arriving to the neuron. Read-out neurons receive synapses from all $$N$$ recurrent neurons, so the $$P$$ matrix is $$N*N$$. Recurrent units have a sparse random connectivity ($$pc = 0.1$$), so each recurrent neuron stores only a $$80*80$$ matrix on average. In the previous equation, $$\mathcal{B}(i)$$ represents those existing weights.

The inverse correlation matrix $$P$$ is updated at each time step with the following rule:

$\Delta P^i_{jk} = - \frac{\sum_{m \in \mathcal{B}(i)} \sum_{n \in \mathcal{B}(i)} P^i_{jm} \cdot r_m \cdot r_n \cdot P^i_{nk} }{ 1 + \sum_{m \in \mathcal{B}(i)} \sum_{n \in \mathcal{B}(i)} r_m \cdot P^i_{mn} \cdot r_n}$

Each matrix $$P^i$$ is initialized to the diagonal matrix and scaled by a factor $$1/\delta$$, where $$\delta$$ is 1 in the current implementation and can be used to modify implicitly the learning rate (Sussilo & Larry, Neuron, 2009).

Matrix/Vector mode

The above algorithms can be written into the matrix/vector forms. For the recurrent units, each matrix $$P^i$$ has a different size ($$80*80$$ on average), so we will still need to iterate over all post-synaptic neurons. If we note $$\mathbf{W}$$ the vector of weights coming to a neuron (80 on average), $$\mathbf{r}$$ the corresponding vector of firing rates (also 80), $$e$$ the error of that neuron (a scalar) and $$\mathbf{P}$$ the inverse correlation matrix (80*80), the update rules become:

$\Delta \mathbf{W} = - e \cdot \mathbf{P} \cdot \mathbf{r}$
$\Delta \mathbf{P} = - \frac{(\mathbf{P} \cdot \mathbf{r}) \cdot (\mathbf{P} \cdot \mathbf{r})^T}{1 + \mathbf{r}^T \cdot \mathbf{P} \cdot \mathbf{r}}$

In the original Matlab code, one notices that the weight update $$\Delta \mathbf{W}$$ is also normalized by the denominator of the update rule for $$\mathbf{P}$$:

$\Delta \mathbf{W} = - e \cdot \frac{\mathbf{P} \cdot \mathbf{r}}{1 + \mathbf{r}^T \cdot \mathbf{P} \cdot \mathbf{r}}$

Removing this normalization from the learning rule impairs learning completely, so we kept this variant of the RLS rule in our implementation.

### Training procedure

The training procedure is split into different trials, which differ from one experiment to another (Fig. 1, Fig. 2 and Fig. 3). Each trial begins with a relaxation period of t_offset = 200 ms, followed by a brief input impulse of duration 50 ms and variable amplitude. This impulse has the effect of bringing all recurrent neurons into a deterministic state (due to the tanh transfer function, the rates are saturated at either +1 or -1). This impulse is followed by a training window of variable length (in the seconds range) and finally another relaxation period. In Fig. 1 and Fig. 2, an additional impulse (duration 10 ms, smaller amplitude) can be given a certain delay after the initial impulse to test the ability of the network to recover its acquired trajectory after learning.

In all experiments, the first trial is used to acquire an innate trajectory for the recurrent neurons in the absence of noise ($$I_0$$ is set to 0). The firing rate of all recurrent neurons over the training window is simply recorded and stored in an array without applying the learning rules. This innate trajectory for each recurrent neuron is used in the following trials as the target for the RLS learning rule, this time in the presence of noise ($$I_0 = 0.001$$). The RLS learning rule itself is only applied to the recurrent neurons during the training window, not during the impulse or the relaxation periods. Such a learning trial is repeated 20 or 30 times depending on the experiments. Once the recurrent weights have converged and the recurrent neurons are able to reproduce the innate trajectory, the read-out weights are trained using a custom desired function as target (10 trials).

### References

• Laje, Rodrigo, and Dean V. Buonomano. “Robust timing and motor patterns by taming chaos in recurrent neural networks.” Nature neuroscience 16, no. 7 (2013): 925-933.

• Haykin, Simon S. Adaptive filter theory. Pearson Education India, 2008.

• Sussillo, David, and Larry F. Abbott. “Generating coherent patterns of activity from chaotic neural networks.” Neuron 63, no. 4 (2009): 544-557.

## Implementation

[2]:

class RNN(bp.Base):
target_backend = 'numpy'

def __init__(self, num_input=2, num_rec=800, num_output=1, tau=10.0,
g=1.5, pc=0.1, noise=0.001, delta=1.0, plastic_prob=0.6, dt=1.):
super(RNN, self).__init__()

# Copy the parameters
self.num_input = num_input  # number of input neurons
self.num_rec = num_rec  # number of recurrent neurons
self.num_output = num_output  # number of read-out neurons
self.tau = tau  # time constant of the neurons
self.g = g  # synaptic strength scaling
self.pc = pc  # connection probability
self.noise = noise  # noise variance
self.delta = delta  # initial value of the P matrix
self.plastic_prob = plastic_prob  # percentage of neurons receiving plastic synapses
self.dt = dt  # numerical precision

# Initializes the network including the weight matrices.
# ---

# Recurrent population
self.x = bm.Variable(bm.random.uniform(-1.0, 1.0, (self.num_rec,)))
self.r = bm.Variable(bm.tanh(self.x))

self.z = bm.Variable(bm.zeros(self.num_output, dtype=bm.float_))

# Weights between the input and recurrent units
self.W_in = bm.Variable(bm.random.randn(self.num_input, self.num_rec))

# Weights between the recurrent units
self.W_rec = bm.Variable(bm.random.randn(self.num_rec, self.num_rec) * self.g / bm.sqrt(self.pc * self.num_rec))

# The connection pattern is sparse with p=0.1
self.conn_mask = bm.random.random((self.num_rec, self.num_rec)) < self.pc
diag = bm.arange(self.num_rec)

# Store the pre-synaptic neurons to each plastic neuron
train_mask = bm.random.random((self.num_rec, self.num_rec)) < plastic_prob

# Store the pre-synaptic neurons to each plastic neuron
self.W_plastic = bm.Variable([bm.array(bm.nonzero(self.train_mask[i])[0]) for i in range(self.num_rec)])

# Inverse correlation matrix of inputs for learning recurrent weights
self.P_rec = bm.Variable([bm.identity(len(self.W_plastic[i])) / self.delta for i in range(self.num_rec)])

# Output weights
self.W_out = bm.Variable(bm.random.randn(self.num_output, self.num_rec) / bm.sqrt(self.num_rec))

# Inverse correlation matrix of inputs for learning readout weights
P_out = bm.expand_dims(bm.identity(self.num_rec) / self.delta, axis=0)
self.P_out = bm.Variable(bm.repeat(P_out, self.num_output, axis=0))

# loss
self.loss = bm.Variable(bm.array([0.]))

def simulate(self, stimulus, noise=True, target_traj=None,
"""Simulates the recurrent network for the given duration, with or without plasticity.

Parameters
----------

stimulus : bm.ndarray
The external inputs.
noise : bool
if noise should be added to the recurrent units (default: True)
target_traj : bm,ndarray
During learning, defines which output target_traj function should be learned (default: no learning)
learn_start : int, float
Time when learning should start.
learn_stop : int, float
Time when learning should stop.
Defines whether the recurrent (False) or readout (True) weights should be learned.
"""

length, _ = stimulus.shape

# Arrays for recording
record_r = bm.zeros((length, self.num_rec), dtype=bm.float_)
record_z = bm.zeros((length, self.num_output), dtype=bm.float_)

# Reset the recurrent population
self.x[:] = bm.random.uniform(-1.0, 1.0, (self.num_rec,))
self.r[:] = bm.tanh(self.x)

# Reset loss term
self.loss[:] = 0.0

# Simulate for the desired duration
for i in range(length):
# Update the neurons' firing rates
self.update(stimulus[i, :], noise)

# Recording
record_r[i] = self.r
record_z[i] = self.z

# Learning
if target_traj is not None and learn_stop > i * self.dt >= learn_start and i % 2 == 0:
self.train_recurrent(target_traj[i])
else:

return record_r, record_z, self.loss

def update(self, stimulus, noise=True):
"""Updates neural variables for a single simulation step."""
dx = -self.x + bm.dot(stimulus, self.W_in) + bm.dot(self.W_rec, self.r)
if noise:
dx += self.noise * bm.random.randn(self.num_rec)
self.x += dx / self.tau * self.dt
self.r[:] = bm.tanh(self.x)
self.z[:] = bm.dot(self.W_out, self.r)

def train_recurrent(self, target):
"""Apply the RLS learning rule to the recurrent weights."""

# Compute the error of the recurrent neurons
error = self.r - target  # output_traj : (num_rec, )
self.loss += bm.mean(error ** 2)

# Apply the FORCE learning rule to the recurrent weights
for i in range(self.num_rec):  # for each plastic post neuron
# Get the rates from the plastic synapses only
r_plastic = bm.expand_dims(self.r[self.W_plastic[i]], axis=1)
# Multiply with the inverse correlation matrix P*R
PxR = bm.dot(self.P_rec[i], r_plastic)
# Normalization term 1 + R'*P*R
RxPxR = (1. + bm.dot(r_plastic.T, PxR))
# Update the inverse correlation matrix P <- P - ((P*R)*(P*R)')/(1+R'*P*R)
self.P_rec[i][:] -= bm.dot(PxR, PxR.T) / RxPxR
# Learning rule W <- W - e * (P*R)/(1+R'*P*R)
for j, idx in enumerate(self.W_plastic[i]):
self.W_rec[i, idx] -= error[i] * (PxR[j, 0] / RxPxR[0, 0])

"""Apply the RLS learning rule to the readout weights."""

# Compute the error of the output neurons
error = self.z - target  # output_traj : (O, )
# loss
self.loss += bm.mean(error ** 2)
# Apply the FORCE learning rule to the readout weights
for i in range(self.num_output):  # for each readout neuron
# Multiply the rates with the inverse correlation matrix P*R
r = bm.expand_dims(self.r, axis=1)
PxR = bm.dot(self.P_out[i], r)
# Normalization term 1 + R'*P*R
RxPxR = (1. + bm.dot(r.T, PxR))
# Update the inverse correlation matrix P <- P - ((P*R)*(P*R)')/(1+R'*P*R)
self.P_out[i] -= bm.dot(PxR, PxR.T) / RxPxR
# Learning rule W <- W - e * (P*R)/(1+R'*P*R)
self.W_out[i] -= error[i] * (PxR / RxPxR)[:, 0]

def init(self):
# Recurrent population
self.x[:] = bm.random.uniform(-1.0, 1.0, (self.num_rec,))
self.r[:] = bm.tanh(self.x)

self.z[:] = bm.zeros((self.num_output,))

# Weights between the input and recurrent units
self.W_in[:] = bm.random.randn(self.num_input, self.num_rec)

# Weights between the recurrent units
self.W_rec[:] = bm.random.randn(self.num_rec, self.num_rec) * self.g / bm.sqrt(self.pc * self.num_rec)

# Inverse correlation matrix of inputs for learning recurrent weights
for i in range(self.num_rec):
self.P_rec[i][:] = bm.identity(len(self.W_plastic[i])) / self.delta

# Output weights
self.W_out[:] = bm.random.randn(self.num_output, self.num_rec) / bm.sqrt(self.num_rec)

# Inverse correlation matrix of inputs for learning readout weights
P_out = bm.expand_dims(bm.identity(self.num_rec) / self.delta, axis=0)
self.P_out[:] = bm.repeat(P_out, self.num_output, axis=0)

# loss
self.loss[:] = 0.


## Results

[3]:

from Laje_Buonomano_2013_simulation import *


The simulation.py can be downloaded from here.

### Fig. 1: an initially chaotic network can become deterministic after training

[4]:

net = RNN(
num_input=2,  # Number of inputs
num_rec=800,  # Number of recurrent neurons
num_output=1,  # Number of read-out neurons
tau=10.0,  # Time constant of the neurons
g=1.8,  # Synaptic strength scaling
pc=0.1,  # Connection probability
noise=0.001,  # Noise variance
delta=1.0,  # Initial diagonal value of the P matrix
plastic_prob=0.6,  # Percentage of neurons receiving plastic synapses
dt=1.,
)
net.update = bp.math.jit(net.update)
net.train_recurrent = bp.math.jit(net.train_recurrent)

fig1(net)

C:\Users\adadu\miniconda3\envs\brainmodels\lib\site-packages\numpy\core\_asarray.py:102: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
return array(a, dtype, copy=False, order=order)
C:\Users\adadu\miniconda3\envs\brainmodels\lib\site-packages\numpy\core\_asarray.py:102: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
return array(a, dtype, copy=False, order=order)

Initial trial to determine a target_traj (without noise)
Pre-training test trial
5 perturbation trials
Learning trial recurrent 1 loss: 0.141811, time: 14.100062131881714 s
Learning trial recurrent 2 loss: 0.193710, time: 12.426777839660645 s
Learning trial recurrent 3 loss: 0.195481, time: 12.623185634613037 s
Learning trial recurrent 4 loss: 0.191801, time: 12.061197519302368 s
Learning trial recurrent 5 loss: 0.146302, time: 12.319267749786377 s
Learning trial recurrent 6 loss: 0.116965, time: 12.173625469207764 s
Learning trial recurrent 7 loss: 0.172879, time: 12.333614826202393 s
Learning trial recurrent 8 loss: 0.133463, time: 12.423139333724976 s
Learning trial recurrent 9 loss: 0.130180, time: 12.330845355987549 s
Learning trial recurrent 10 loss: 0.111944, time: 12.26445198059082 s
Learning trial recurrent 11 loss: 0.164418, time: 12.31094241142273 s
Learning trial recurrent 12 loss: 0.098953, time: 12.424531698226929 s
Learning trial recurrent 13 loss: 0.069846, time: 12.460671424865723 s
Learning trial recurrent 14 loss: 0.061045, time: 12.602559566497803 s
Learning trial recurrent 15 loss: 0.056891, time: 12.420866250991821 s
Learning trial recurrent 16 loss: 0.050837, time: 12.11101245880127 s
Learning trial recurrent 17 loss: 0.051228, time: 12.30343222618103 s
Learning trial recurrent 18 loss: 0.050307, time: 12.85206151008606 s
Learning trial recurrent 19 loss: 0.047070, time: 12.546154975891113 s
Learning trial recurrent 20 loss: 0.044937, time: 12.491156816482544 s
Learning trial recurrent 21 loss: 0.040711, time: 14.512023448944092 s
Learning trial recurrent 22 loss: 0.039551, time: 12.259568452835083 s
Learning trial recurrent 23 loss: 0.042985, time: 11.74307894706726 s
Learning trial recurrent 24 loss: 0.039123, time: 12.342232942581177 s
Learning trial recurrent 25 loss: 0.036156, time: 12.340661525726318 s
Learning trial recurrent 26 loss: 0.036647, time: 12.48307180404663 s
Learning trial recurrent 27 loss: 0.036481, time: 11.80998182296753 s
Learning trial recurrent 28 loss: 0.035189, time: 12.13218069076538 s
Learning trial recurrent 29 loss: 0.034166, time: 11.727820634841919 s
Learning trial recurrent 30 loss: 0.033342, time: 12.333296775817871 s
Learning trial readout 1 loss: 0.000336, time: 5.794511795043945 s
Learning trial readout 2 loss: 0.000058, time: 5.765017747879028 s
Learning trial readout 3 loss: 0.000055, time: 5.879965543746948 s
Learning trial readout 4 loss: 0.000097, time: 5.7293548583984375 s
Learning trial readout 5 loss: 0.000025, time: 5.748337268829346 s
Learning trial readout 6 loss: 0.000014, time: 5.749148607254028 s
Learning trial readout 7 loss: 0.000025, time: 5.773593187332153 s
Learning trial readout 8 loss: 0.000008, time: 5.691660165786743 s
Learning trial readout 9 loss: 0.000007, time: 5.672274589538574 s
Learning trial readout 10 loss: 0.000007, time: 5.791287183761597 s
2 test trials
5 perturbation trials
Simulation done in 435.14744448661804 seconds.


### Fig. 2: read-out neurons robustly learn trajectories in the 2D space

[4]:

net = RNN(
num_input=4,  # Number of inputs
num_rec=800,  # Number of recurrent neurons
num_output=2,  # Number of read-out neurons
tau=10.0,  # Time constant of the neurons
g=1.5,  # Synaptic strength scaling
pc=0.1,  # Connection probability
noise=0.001,  # Noise variance
delta=1.0,  # Initial value of the P matrix
plastic_prob=0.6,  # Percentage of neurons receiving plastic synapses
dt=1.
)
net.update = bp.math.jit(net.update)
net.train_recurrent = bp.math.jit(net.train_recurrent)

fig2(net)

C:\Users\adadu\miniconda3\envs\brainmodels\lib\site-packages\numpy\core\_asarray.py:102: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
return array(a, dtype, copy=False, order=order)
C:\Users\adadu\miniconda3\envs\brainmodels\lib\site-packages\numpy\core\_asarray.py:102: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
return array(a, dtype, copy=False, order=order)

Initial chaos trial
Initial neuron trial
Learning recurrent 1 "chaos" loss: 0.03024 used 9.585194 s, "neuron" loss: 0.068696 used 7.557857 s
Learning recurrent 2 "chaos" loss: 0.04035 used 7.712137 s, "neuron" loss: 0.049718 used 7.040077 s
Learning recurrent 3 "chaos" loss: 0.03334 used 7.632152 s, "neuron" loss: 0.038121 used 6.890412 s
Learning recurrent 4 "chaos" loss: 0.03709 used 7.543250 s, "neuron" loss: 0.027921 used 6.712800 s
Learning recurrent 5 "chaos" loss: 0.03522 used 7.641539 s, "neuron" loss: 0.030041 used 7.152696 s
Learning recurrent 6 "chaos" loss: 0.02818 used 7.359621 s, "neuron" loss: 0.024535 used 6.964830 s
Learning recurrent 7 "chaos" loss: 0.02867 used 7.660184 s, "neuron" loss: 0.025658 used 7.088823 s
Learning recurrent 8 "chaos" loss: 0.02053 used 7.319214 s, "neuron" loss: 0.025591 used 7.207662 s
Learning recurrent 9 "chaos" loss: 0.02193 used 7.674067 s, "neuron" loss: 0.018955 used 7.258080 s
Learning recurrent 10 "chaos" loss: 0.01775 used 7.495978 s, "neuron" loss: 0.017003 used 7.470245 s
Learning recurrent 11 "chaos" loss: 0.01273 used 7.409800 s, "neuron" loss: 0.016854 used 6.984492 s
Learning recurrent 12 "chaos" loss: 0.01035 used 7.529435 s, "neuron" loss: 0.017449 used 6.963933 s
Learning recurrent 13 "chaos" loss: 0.00941 used 7.492759 s, "neuron" loss: 0.016982 used 6.740342 s
Learning recurrent 14 "chaos" loss: 0.00920 used 7.536858 s, "neuron" loss: 0.014747 used 7.242281 s
Learning recurrent 15 "chaos" loss: 0.00865 used 7.752437 s, "neuron" loss: 0.012919 used 7.066189 s
Learning recurrent 16 "chaos" loss: 0.00842 used 7.489711 s, "neuron" loss: 0.011628 used 7.036339 s
Learning recurrent 17 "chaos" loss: 0.00891 used 7.312427 s, "neuron" loss: 0.011047 used 7.160348 s
Learning recurrent 18 "chaos" loss: 0.00743 used 7.558361 s, "neuron" loss: 0.010265 used 6.903052 s
Learning recurrent 19 "chaos" loss: 0.00797 used 7.515602 s, "neuron" loss: 0.010391 used 7.047833 s
Learning recurrent 20 "chaos" loss: 0.00801 used 7.349970 s, "neuron" loss: 0.009953 used 7.003936 s
Learning recurrent 21 "chaos" loss: 0.00791 used 7.403649 s, "neuron" loss: 0.009723 used 7.131582 s
Learning recurrent 22 "chaos" loss: 0.00769 used 7.639846 s, "neuron" loss: 0.010519 used 6.903835 s
Learning recurrent 23 "chaos" loss: 0.00800 used 7.516979 s, "neuron" loss: 0.011919 used 6.986399 s
Learning recurrent 24 "chaos" loss: 0.00925 used 7.506063 s, "neuron" loss: 0.008298 used 7.107485 s
Learning recurrent 25 "chaos" loss: 0.00776 used 7.608427 s, "neuron" loss: 0.008515 used 7.002964 s
Learning recurrent 26 "chaos" loss: 0.00677 used 7.667391 s, "neuron" loss: 0.007936 used 7.174983 s
Learning recurrent 27 "chaos" loss: 0.00637 used 7.421215 s, "neuron" loss: 0.008999 used 7.015823 s
Learning recurrent 28 "chaos" loss: 0.00639 used 7.454128 s, "neuron" loss: 0.007222 used 6.506436 s
Learning recurrent 29 "chaos" loss: 0.00649 used 7.540340 s, "neuron" loss: 0.008663 used 7.035977 s
Learning recurrent 30 "chaos" loss: 0.00792 used 7.490908 s, "neuron" loss: 0.006528 used 6.961112 s
Learning readout 1 "chaos" loss: 0.00052 used 10.545170 s, "neuron" loss: 0.003734 used 8.998858 s
Learning readout 2 "chaos" loss: 0.00018 used 9.379586 s, "neuron" loss: 0.000148 used 8.866671 s
Learning readout 3 "chaos" loss: 0.00004 used 9.498058 s, "neuron" loss: 0.000108 used 8.791036 s
Learning readout 4 "chaos" loss: 0.00003 used 9.426720 s, "neuron" loss: 0.000144 used 8.919076 s
Learning readout 5 "chaos" loss: 0.00009 used 9.380355 s, "neuron" loss: 0.000089 used 8.956023 s
Learning readout 6 "chaos" loss: 0.00010 used 9.426417 s, "neuron" loss: 0.000063 used 8.832359 s
Learning readout 7 "chaos" loss: 0.00024 used 9.514052 s, "neuron" loss: 0.000044 used 8.823996 s
Learning readout 8 "chaos" loss: 0.00008 used 9.352005 s, "neuron" loss: 0.000062 used 8.788356 s
Learning readout 9 "chaos" loss: 0.00001 used 9.601972 s, "neuron" loss: 0.000038 used 8.866985 s
Learning readout 10 "chaos" loss: 0.00003 used 9.553325 s, "neuron" loss: 0.000027 used 8.837973 s
Test chaos trial
Test neuron trial
Test chaos trial
Test neuron trial
Test chaos trial
Test neuron trial
Test chaos trial
Test neuron trial
Test chaos trial
Test neuron trial
Perturbation chaos trial
Perturbation neuron trial
Perturbation chaos trial
Perturbation neuron trial
Perturbation chaos trial
Perturbation neuron trial
Perturbation chaos trial
Perturbation neuron trial
Perturbation chaos trial
Perturbation neuron trial
Simulation done in 627.2733964920044 seconds.


### Fig. 3: the timing capacity of the recurrent network

[4]:

nets = []
for _ in range(10):
net = RNN(
num_input=2,  # Number of inputs
num_rec=800,  # Number of recurrent neurons
num_output=1,  # Number of read-out neurons
tau=10.0,  # Time constant of the neurons
g=1.5,  # Synaptic strength scaling
pc=0.1,  # Connection probability
noise=0.001,  # Noise variance
delta=1.0,  # Initial diagonal value of the P matrix
plastic_prob=0.6,  # Percentage of neurons receiving plastic synapses
dt=1.
)
net.update = bp.math.jit(net.update)
net.train_recurrent = bp.math.jit(net.train_recurrent)
nets.append(net)

fig3(nets, verbose=False)

C:\Users\adadu\miniconda3\envs\brainmodels\lib\site-packages\numpy\core\_asarray.py:102: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
return array(a, dtype, copy=False, order=order)
C:\Users\adadu\miniconda3\envs\brainmodels\lib\site-packages\numpy\core\_asarray.py:102: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
return array(a, dtype, copy=False, order=order)
C:\Users\adadu\miniconda3\envs\brainmodels\lib\site-packages\numpy\core\_asarray.py:102: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
return array(a, dtype, copy=False, order=order)