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executable file
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import tensorflow as tf
import numpy as np
import stimulus
import AdamOpt
import pickle
import matplotlib.pyplot as plt
from parameters_RL import par
from itertools import product
import os, sys, time
# Ignore "use compiled version of TensorFlow" errors
os.environ['TF_CPP_MIN_LOG_LEVEL']='2'
print('TensorFlow version:\t', tf.__version__)
print('Using EI Network:\t', par['EI'])
print('Synaptic configuration:\t', par['synapse_config'], "\n")
"""
Model setup and execution
"""
class Model:
def __init__(self, input_data, target_data, gating, pred_val, actual_action, advantage, mask, drop_mask):
# Load the input activity, the target data, and the training mask for this batch of trials
self.input_data = tf.unstack(input_data, axis=0)
self.target_data = tf.unstack(target_data, axis=0)
self.gating = tf.reshape(gating, [1,-1])
self.pred_val = tf.unstack(pred_val, axis=0)
self.actual_action = tf.unstack(actual_action, axis=0)
self.advantage = tf.unstack(advantage, axis=0)
self.W_ei = tf.constant(par['EI_matrix'])
self.drop_mask = drop_mask
self.time_mask = tf.unstack(mask, axis=0)
# Build the TensorFlow graph
self.rnn_cell_loop()
# Train the model
self.optimize()
def rnn_cell_loop(self):
self.W_ei = tf.constant(par['EI_matrix'])
self.h = [] # RNN activity
self.pol_out = [] # policy output
self.val_out = [] # value output
self.syn_x = [] # STP available neurotransmitter, currently not in use
self.syn_u = [] # STP calcium concentration, currently not in use
# we will add the first element to these lists since we need to input the previous action and reward
# into the RNN
self.action = []
self.reward = []
self.reward.append(tf.constant(np.zeros((par['batch_size'], par['n_val']), dtype = np.float32)))
self.mask = []
self.mask.append(tf.constant(np.ones((par['batch_size'], 1), dtype = np.float32)))
"""
Initialize weights and biases
"""
self.define_vars()
h = self.gating*self.drop_mask*tf.constant(par['h_init'])
c = self.drop_mask*tf.constant(par['h_init'])
if par['LSTM']:
c *= 0.
h *= 0.
syn_x = tf.constant(par['syn_x_init'])
syn_u = tf.constant(par['syn_u_init'])
"""
Loop through the neural inputs to the RNN, indexed in time
"""
for rnn_input, target, time_mask in zip(self.input_data, self.target_data, self.time_mask):
h, c, syn_x, syn_u, action, pol_out, val_out, mask, reward = self.rnn_cell(rnn_input, h, c, syn_x, syn_u, \
self.reward[-1], self.mask[-1], target, time_mask)
self.h.append(h)
self.syn_x.append(syn_x)
self.syn_u.append(syn_u)
self.action.append(action)
self.pol_out.append(pol_out)
self.val_out.append(val_out)
self.mask.append(mask)
self.reward.append(reward)
self.mask = self.mask[1:]
# actions will produce a reward on the next time step
self.reward = self.reward[1:]
def rnn_cell(self, x, h, c, syn_x, syn_u, prev_reward, mask, target, time_mask):
#self.define_vars(reuse = True)
# Modify the recurrent weights if using excitatory/inhibitory neurons
if par['EI']:
self.W_rnn = tf.matmul(self.W_ei, tf.nn.relu(self.W_rnn))
h, c, syn_x, syn_u = self.recurrent_cell(h, c, syn_x, syn_u, x)
# calculate the policy output and choose an action
pol_out = tf.matmul(h, self.W_pol_out) + self.b_pol_out
action_index = tf.multinomial(pol_out, 1)
action = tf.one_hot(tf.squeeze(action_index), par['n_pol'])
pol_out = tf.nn.softmax(pol_out, dim = 1) # needed for loss function
val_out = tf.matmul(h, self.W_val_out) + self.b_val_out
# if previous reward was non-zero, then end the trial, unless the new trial signal cue is on
continue_trial = tf.cast(tf.equal(prev_reward, 0.), tf.float32)
mask *= continue_trial
reward = tf.reduce_sum(action*target, axis = 1, keep_dims = True)*mask*time_mask
return h, c, syn_x, syn_u, action, pol_out, val_out, mask, reward
def optimize(self):
epsilon = 1e-7
self.variables = [var for var in tf.trainable_variables()]
adam_optimizer = AdamOpt.AdamOpt(self.variables, learning_rate = par['learning_rate'])
self.previous_weights_mu_minus_1 = {}
reset_prev_vars_ops = []
self.big_omega_var = {}
aux_losses = []
for var in self.variables:
self.big_omega_var[var.op.name] = tf.Variable(tf.zeros(var.get_shape()), trainable=False)
self.previous_weights_mu_minus_1[var.op.name] = tf.Variable(tf.zeros(var.get_shape()), trainable=False)
if not 'val' in var.op.name:
# don't stabilizae the value weights or biases
aux_losses.append(par['omega_c']*tf.reduce_sum(tf.multiply(self.big_omega_var[var.op.name], \
tf.square(self.previous_weights_mu_minus_1[var.op.name] - var) )))
reset_prev_vars_ops.append( tf.assign(self.previous_weights_mu_minus_1[var.op.name], var ) )
self.aux_loss = tf.add_n(aux_losses)
self.spike_loss = par['spike_cost']*tf.reduce_mean(tf.stack([mask*time_mask*tf.reduce_mean(h) \
for (h, mask, time_mask) in zip(self.h, self.mask, self.time_mask)]))
self.pol_loss = -tf.reduce_mean(tf.stack([advantage*time_mask*mask*act*tf.log(epsilon + pol_out) \
for (pol_out, advantage, act, mask, time_mask) in zip(self.pol_out, self.advantage, \
self.actual_action, self.mask, self.time_mask)]))
self.entropy_loss = -par['entropy_cost']*tf.reduce_mean(tf.stack([tf.reduce_sum(time_mask*mask*pol_out*tf.log(epsilon+pol_out), axis = 1) \
for (pol_out, mask, time_mask) in zip(self.pol_out, self.mask, self.time_mask)]))
self.val_loss = 0.5*tf.reduce_mean(tf.stack([time_mask*mask*tf.square(val_out - pred_val) \
for (val_out, mask, time_mask, pred_val) in zip(self.val_out[:-1], self.mask, self.time_mask, self.pred_val[:-1])]))
# Gradient of the loss+aux function, in order to both perform training and to compute delta_weights
with tf.control_dependencies([self.pol_loss, self.aux_loss, self.spike_loss, self.val_loss]):
self.train_op = adam_optimizer.compute_gradients(self.pol_loss + self.val_loss + \
self.aux_loss + self.spike_loss - self.entropy_loss)
# Stabilizing weights
if par['stabilization'] == 'pathint':
# Zenke method
self.pathint_stabilization(adam_optimizer)
elif par['stabilization'] == 'EWC':
# Kirkpatrick method
self.EWC()
self.reset_prev_vars = tf.group(*reset_prev_vars_ops)
self.reset_adam_op = adam_optimizer.reset_params()
self.make_recurrent_weights_positive()
def make_recurrent_weights_positive(self):
reset_weights = []
for var in self.variables:
if 'W_rnn' in var.op.name:
# make all negative weights slightly positive
reset_weights.append(tf.assign(var,tf.maximum(1e-9, var)))
self.reset_rnn_weights = tf.group(*reset_weights)
def EWC(self):
# Kirkpatrick method
var_list = [var for var in tf.trainable_variables() if not 'val' in var.op.name]
epsilon = 1e-6
fisher_ops = []
opt = tf.train.GradientDescentOptimizer(learning_rate = 1.0)
log_p_theta = tf.stack([mask*time_mask*action*tf.log(epsilon + pol_out) for (pol_out, action, mask, time_mask) in \
zip(self.pol_out,self.action, self.mask, self.time_mask)], axis = 0)
grads_and_vars = opt.compute_gradients(log_p_theta, var_list = var_list)
for grad, var in grads_and_vars:
fisher_ops.append(tf.assign_add(self.big_omega_var[var.op.name], \
grad*grad/par['EWC_fisher_num_batches']))
self.update_big_omega = tf.group(*fisher_ops)
def pathint_stabilization(self, adam_optimizer):
# Zenke method
optimizer_task = tf.train.GradientDescentOptimizer(learning_rate = 1.0)
self.small_omega_var = {}
small_omega_var_div = {}
reset_small_omega_ops = []
update_small_omega_ops = []
update_big_omega_ops = []
initialize_prev_weights_ops = []
self.previous_reward = tf.Variable(-tf.ones([]), trainable=False)
self.current_reward = tf.Variable(-tf.ones([]), trainable=False)
reward_stacked = tf.stack(self.reward, axis = 0)
current_reward = tf.reduce_mean(tf.reduce_sum(reward_stacked, axis = 0))
self.update_current_reward = tf.assign(self.current_reward, current_reward)
self.update_previous_reward = tf.assign(self.previous_reward, self.current_reward)
for var in self.variables:
self.small_omega_var[var.op.name] = tf.Variable(tf.zeros(var.get_shape()), trainable=False)
small_omega_var_div[var.op.name] = tf.Variable(tf.zeros(var.get_shape()), trainable=False)
reset_small_omega_ops.append( tf.assign(self.small_omega_var[var.op.name], self.small_omega_var[var.op.name]*0.0 ) )
update_big_omega_ops.append( tf.assign_add( self.big_omega_var[var.op.name], tf.div(tf.abs(self.small_omega_var[var.op.name]), \
(par['omega_xi'] + small_omega_var_div[var.op.name]))))
# After each task is complete, call update_big_omega and reset_small_omega
self.update_big_omega = tf.group(*update_big_omega_ops)
# Reset_small_omega also makes a backup of the final weights, used as hook in the auxiliary loss
self.reset_small_omega = tf.group(*reset_small_omega_ops)
# This is called every batch
self.delta_grads = adam_optimizer.return_delta_grads()
delta_reward = self.current_reward - self.previous_reward
for grad,var in zip(self.delta_grads, self.variables):
update_small_omega_ops.append(tf.assign_add(self.small_omega_var[var.op.name], self.delta_grads[var.op.name]*delta_reward))
update_small_omega_ops.append(tf.assign_add(small_omega_var_div[var.op.name], tf.abs(self.delta_grads[var.op.name]*delta_reward)))
self.update_small_omega = tf.group(*update_small_omega_ops) # 1) update small_omega after each train!
def recurrent_cell(self, h, c, syn_x, syn_u, x):
if par['LSTM']:
# forgetting gate
f = tf.sigmoid(tf.matmul(x, self.Wf) + tf.matmul(h, self.Uf) + self.bf)
# input gate
i = tf.sigmoid(tf.matmul(x, self.Wi) + tf.matmul(h, self.Ui) + self.bi)
# updated cell state
cn = tf.tanh(tf.matmul(x, self.Wc) + tf.matmul(h, self.Uc) + self.bc)
c = tf.multiply(f, c) + tf.multiply(i, cn)
# output gate
o = tf.sigmoid(tf.matmul(x, self.Wo) + tf.matmul(h, self.Uo) + self.bo)
h = self.drop_mask*self.gating*tf.multiply(o, tf.tanh(c))
syn_x = tf.constant(-1.)
syn_u = tf.constant(-1.)
else:
if par['synapse_config'] == 'std_stf':
syn_x += par['alpha_std']*(1-syn_x) - par['dt_sec']*syn_u*syn_x*h
syn_u += par['alpha_stf']*(par['U']-syn_u) + par['dt_sec']*par['U']*(1-syn_u)*h
syn_x = tf.minimum(np.float32(1), tf.nn.relu(syn_x))
syn_u = tf.minimum(np.float32(1), tf.nn.relu(syn_u))
h_post = syn_u*syn_x*h
else:
h_post = h
h = self.drop_mask*self.gating*tf.nn.relu((1-par['alpha_neuron'])*h +par['alpha_neuron']*(tf.matmul(x, tf.nn.relu(self.W_in)) + \
tf.matmul(h_post, self.W_rnn) + self.b_rnn) + tf.random_normal(h.shape, 0, par['noise_rnn'], dtype=tf.float32))
c = tf.constant(-1.)
return h, c, syn_x, syn_u
def define_vars(self):
# W_in0, and W_in1 are feedforward weights whose input is the convolved image, and projects onto the RNN
# W_reward_pos, W_reward_neg project the postive and negative part of the reward from the previous time point onto the RNN
# W_action projects the action from the previous time point onto the RNN
# Wnn projects the activity of the RNN from the previous time point back onto the RNN (i.e. the recurrent weights)
# W_pol_out projects from the RNN onto the policy output neurons
# W_val_out projects from the RNN onto the value output neuron
with tf.variable_scope('recurrent_pol'):
if par['LSTM']:
# following conventions on https://en.wikipedia.org/wiki/Long_short-term_memory
self.Wf = tf.get_variable('Wf', initializer = par['Wf_init'])
self.Wi = tf.get_variable('Wi', initializer = par['Wi_init'])
self.Wo = tf.get_variable('Wo', initializer = par['Wo_init'])
self.Wc = tf.get_variable('Wc', initializer = par['Wc_init'])
self.Uf = tf.get_variable('Uf', initializer = par['Ui_init'])
self.Ui = tf.get_variable('Ui', initializer = par['Ui_init'])
self.Uo = tf.get_variable('Uo', initializer = par['Uo_init'])
self.Uc = tf.get_variable('Uc', initializer = par['Uc_init'])
self.bf = tf.get_variable('bf', initializer = par['bf_init'])
self.bi = tf.get_variable('bi', initializer = par['bi_init'])
self.bo = tf.get_variable('bo', initializer = par['bo_init'])
self.bc = tf.get_variable('bc', initializer = par['bc_init'])
else:
self.W_in = tf.get_variable('W_in', initializer = par['W_in_init'])
self.b_rnn = tf.get_variable('b_rnn', initializer = par['b_rnn_init'])
self.W_rnn = tf.get_variable('W_rnn', initializer = par['W_rnn_init'])
self.W_pol_out = tf.get_variable('W_pol_out', initializer = par['W_pol_out_init'])
self.b_pol_out = tf.get_variable('b_pol_out', initializer = par['b_pol_out_init'])
self.W_val_out = tf.get_variable('W_val_out', initializer = par['W_val_out_init'])
self.b_val_out = tf.get_variable('b_val_out', initializer = par['b_val_out_init'])
def main(gpu_id = None, save_fn = 'test.pkl'):
if gpu_id is not None:
os.environ["CUDA_VISIBLE_DEVICES"] = gpu_id
"""
Reset TensorFlow before running anything
"""
tf.reset_default_graph()
"""
Create the stimulus class to generate trial paramaters and input activity
"""
stim = stimulus.MultiStimulus()
"""
Define all placeholder
"""
x, target, mask, pred_val, actual_action, advantage, mask, gating, drop_mask = generate_placeholders()
config = tf.ConfigProto()
#config.gpu_options.allow_growth=True
print_key_params()
with tf.Session(config = config) as sess:
device = '/cpu:0' if gpu_id is None else '/gpu:0'
with tf.device(device):
model = Model(x, target, gating, pred_val, actual_action, advantage, mask, drop_mask)
sess.run(tf.global_variables_initializer())
# keep track of the model performance across training
model_performance = {'reward': [], 'entropy_loss': [], 'val_loss': [], 'pol_loss': [], 'spike_loss': [], 'trial': [], 'task': []}
reward_matrix = np.zeros((par['n_tasks'], par['n_tasks']))
accuracy_full = []
sess.run(model.reset_prev_vars)
for task in range(17, par['n_tasks']):
accuracy_iter = []
task_start_time = time.time()
for i in range(par['n_train_batches']):
dm = get_drop_mask(task)
# make batch of training data
name, input_data, _, mk, reward_data = stim.generate_trial(task)
mk = mk[..., np.newaxis]
"""
Run the model
"""
pol_out_list, val_out_list, h_list, action_list, mask_list, reward_list = sess.run([model.pol_out, model.val_out, model.h, model.action, \
model.mask, model.reward], {x: input_data, target: reward_data, mask: mk, gating:par['gating'][task], drop_mask: dm})
"""
Unpack all lists, calculate predicted value and advantage functions
"""
val_out, reward, adv, act, predicted_val, stacked_mask = stack_vars(pol_out_list, val_out_list, reward_list, action_list, mask_list, mk)
"""
Calculate and apply gradients
"""
if par['stabilization'] == 'pathint':
_, _, pol_loss, val_loss, aux_loss, spike_loss, ent_loss = sess.run([model.train_op, \
model.update_current_reward, model.pol_loss, model.val_loss, model.aux_loss, model.spike_loss, \
model.entropy_loss], feed_dict = {x:input_data, target:reward_data, gating:par['gating'][task], mask:mk, \
pred_val: predicted_val, actual_action: act, advantage:adv, drop_mask: dm})
if i>0:
sess.run([model.update_small_omega])
sess.run([model.update_previous_reward])
elif par['stabilization'] == 'EWC':
_, pol_loss,val_loss, aux_loss, spike_loss, ent_loss = sess.run([model.train_op, model.pol_loss, \
model.val_loss, model.aux_loss, model.spike_loss, model.entropy_loss], feed_dict = \
{x:input_data, target:reward_data, gating:par['gating'][task], mask:mk, pred_val: predicted_val, \
actual_action: act, advantage:adv, drop_mask: dm})
acc = np.mean(np.sum(reward>0,axis=0))
accuracy_iter.append(accuracy_iter)
if i > 2000:
if np.mean(accuracy_iter[-2000:]) > 0.98 or (i>25000 and np.mean(accuracy_iter[-2000:]) > 0.98):
print('Accuracy reached threshold')
break
if par['EI']:
sess.run([model.reset_rnn_weights])
if i%500 == 0:
#print('Iter ', i, 'Task name ', name, ' accuracy', acc, ' aux loss', aux_loss, 'spike_loss', spike_loss, ' h > 0 ', above_zero, 'mean h', np.mean(h_stacked))
print('Iter ', i, 'Task name ', name, ' accuracy', acc, ' aux loss', aux_loss, 'mean h', np.mean(np.stack(h_list)), 'time ', np.around(time.time() - task_start_time))
# Update big omegaes, and reset other values before starting new task
if par['stabilization'] == 'pathint':
big_omegas = sess.run([model.update_big_omega, model.big_omega_var])
elif par['stabilization'] == 'EWC':
for n in range(par['EWC_fisher_num_batches']):
name, input_data, _, mk, reward_data = stim.generate_trial(task)
mk = mk[..., np.newaxis]
big_omegas = sess.run([model.update_big_omega,model.big_omega_var], feed_dict = \
{x:input_data, target: reward_data, gating:par['gating'][task], mask:mk})
# Test all tasks at the end of each learning session
num_reps = 10
for (task_prime, r) in product(range(par['n_tasks']), range(num_reps)):
# make batch of training data
name, input_data, _, mk, reward_data = stim.generate_trial(task_prime)
mk = mk[..., np.newaxis]
dm = get_drop_mask(task_prime)
reward_list = sess.run([model.reward], feed_dict = {x:input_data, target: reward_data, \
gating:par['gating'][task_prime], mask:mk, drop_mask: dm})
# TODO: figure out what's with the extra dimension at index 0 in reward
reward = np.squeeze(np.stack(reward_list))
reward_matrix[task,task_prime] += np.mean(np.sum(reward>0,axis=0))/num_reps
print('Accuracy grid after task {}:'.format(task))
print(reward_matrix[task,:])
results = {'reward_matrix': reward_matrix, 'par': par}
pickle.dump(results, open(par['save_dir'] + save_fn, 'wb') )
print('Analysis results saved in ', save_fn)
print('')
# Reset the Adam Optimizer, and set the previous parater values to their current values
sess.run(model.reset_adam_op)
sess.run(model.reset_prev_vars)
if par['stabilization'] == 'pathint':
sess.run(model.reset_small_omega)
def stack_vars(pol_out_list, val_out_list, reward_list, action_list, mask_list, trial_mask):
pol_out = np.stack(pol_out_list)
val_out = np.stack(val_out_list)
stacked_mask = np.stack(mask_list)*trial_mask
reward = np.stack(reward_list)
#val_out_stacked = np.vstack((np.zeros((1,par['batch_size'],par['n_val'])), val_out)) # option 1
val_out_stacked = np.vstack((val_out,np.zeros((1,par['batch_size'],par['n_val'])))) # option 2
terminal_state = np.float32(reward != 0) # this assumes that the trial ends when a reward other than zero is received
pred_val = reward + par['discount_rate']*val_out_stacked[1:,:,:]*(1-terminal_state)
adv = pred_val - val_out_stacked[:-1,:,:]
#adv = reward - val_out
act = np.stack(action_list)
return val_out, reward, adv, act, pred_val, stacked_mask
def append_model_performance(model_performance, reward, entropy_loss, pol_loss, val_loss, trial_num):
reward = np.mean(np.sum(reward,axis = 0))/par['trials_per_sequence']
model_performance['reward'].append(reward)
model_performance['entropy_loss'].append(entropy_loss)
model_performance['pol_loss'].append(pol_loss)
model_performance['val_loss'].append(val_loss)
model_performance['trial'].append(trial_num)
return model_performance
def generate_placeholders():
mask = tf.placeholder(tf.float32, shape=[par['num_time_steps'], par['batch_size'], 1])
x = tf.placeholder(tf.float32, shape=[par['num_time_steps'], par['batch_size'], par['n_input']]) # input data
target = tf.placeholder(tf.float32, shape=[par['num_time_steps'], par['batch_size'], par['n_pol']]) # input data
pred_val = tf.placeholder(tf.float32, shape=[par['num_time_steps'], par['batch_size'], par['n_val'], ])
actual_action = tf.placeholder(tf.float32, shape=[par['num_time_steps'], par['batch_size'], par['n_pol']])
advantage = tf.placeholder(tf.float32, shape=[par['num_time_steps'], par['batch_size'], par['n_val']])
gating = tf.placeholder(tf.float32, [par['n_hidden']], 'gating')
drop_mask = tf.placeholder(tf.float32,[par['batch_size'], par['n_hidden']], 'drop_mask')
return x, target, mask, pred_val, actual_action, advantage, mask, gating, drop_mask
def eval_weights():
# TODO: NEEDS FIXING!
with tf.variable_scope('rnn_cell', reuse=True):
W_in = tf.get_variable('W_in')
W_rnn = tf.get_variable('W_rnn')
b_rnn = tf.get_variable('b_rnn')
with tf.variable_scope('output', reuse=True):
W_out = tf.get_variable('W_out')
b_out = tf.get_variable('b_out')
weights = {
'w_in' : W_in.eval(),
'w_rnn' : W_rnn.eval(),
'w_out' : W_out.eval(),
'b_rnn' : b_rnn.eval(),
'b_out' : b_out.eval()
}
return weights
def print_results(iter_num, model_performance):
reward = np.mean(np.stack(model_performance['reward'])[-par['iters_between_outputs']:])
pol_loss = np.mean(np.stack(model_performance['pol_loss'])[-par['iters_between_outputs']:])
val_loss = np.mean(np.stack(model_performance['val_loss'])[-par['iters_between_outputs']:])
entropy_loss = np.mean(np.stack(model_performance['entropy_loss'])[-par['iters_between_outputs']:])
print('Iter. {:4d}'.format(iter_num) + ' | Reward {:0.4f}'.format(reward) +
' | Pol loss {:0.4f}'.format(pol_loss) + ' | Val loss {:0.4f}'.format(val_loss) +
' | Entropy loss {:0.4f}'.format(entropy_loss))
def print_key_params():
key_info = ['synapse_config','spike_cost','weight_cost','entropy_cost','omega_c','omega_xi',\
'constrain_input_weights','num_sublayers','n_hidden','noise_rnn_sd','learning_rate',\
'discount_rate', 'mask_duration', 'stabilization','gating_type', 'gate_pct','drop_rate',\
'fix_break_penalty','wrong_choice_penalty','correct_choice_reward','include_rule_signal']
print('Paramater info...')
for k in key_info:
print(k, ': ', par[k])
def get_drop_mask(task):
if par['gate_pct'] > 0:
M1 = round(par['n_hidden']*(1-par['gate_pct'])*(1-par['drop_rate']))
gate_ind = np.where(par['gating'][task]>0)[0]
dm = np.zeros((par['batch_size'], par['n_hidden']), dtype = np.float32)
for m in range(par['batch_size']):
ind = np.random.permutation(gate_ind)[:M1]
dm[m, ind] = 1
else:
dm = np.ones((par['batch_size'], par['n_hidden']), dtype = np.float32)
return dm