def main():
import time
start_time = time.time()
for seed in range(10):
random.seed(seed)
stabiter = 10000
runiter = 1000
grn = GRN(delta=1)
#grn.read_genome("moo.dat")
grn.build_genes()
grn.add_extra("EXTRA_sineval", 0.0, [0] * 32)
grn.precalc_matrix()
grn.regulate_matrix(stabiter)
onff = 0
for i in range(0, 50):
if i % 10 == 0:
if onff == 1:
onff = 0
else:
onff = 1
inputval = onff
extra_vals = {'sineval': inputval}
grn.set_extras(extra_vals)
grn.regulate_matrix(runiter)
for conc in grn.conc_list:
print conc[-1]
filename = "conc" + str(seed)
graph.plot_2d(grn.conc_list, filename)
print "took", str(time.time() - start_time)
def multicore():
delta = 20
#set up the evo strategy
best_list, mut_list = [], []
evo = popstrat.Evostrategy(5000, 50)
children = evo.iterate(evo.pop)
nodes = ("*",)
job_server = pp.Server(8, ppservers=nodes)
print "Starting pp with", job_server.get_ncpus(), "workers"
start_time = time.time()
for i in range(50):
run_time = time.time()
jobs = [(child, job_server.submit(run_grn,
(child['genome'],
delta),
(),
("grn","numpy","math")))
for child in children]
for child, result in jobs:
results, conclist = result()
bestidx = results.index(max(results))
child['fitness'] = results[bestidx]
#plotting the best with colors
children = evo.iterate(children)
bestgenome = evo.pop[-1]['genome']
bestresult, conclist = run_grn(bestgenome, delta)
bestidx = bestresult.index(max(bestresult))
filename = "best_gen_"+str("%03d" % i)
print filename
colors = []
simplist = []
for idx, result in enumerate(bestresult):
if idx == len(bestresult)-1:
simplist.append(conclist[idx])
colors.append('k')
elif idx == bestidx:
colors.append('g')
simplist.append(conclist[idx])
# elif result == 0:
# colors.append('b')
# else:
# colors.append('r')
graph.plot_2d(simplist, filename, colors)
print "gen:", evo.gen_count, "fitness:", evo.pop[-1]['fitness']
if evo.adaptive:
evo.adapt_mutation()
best_list.append(evo.pop[-1]['fitness'])
mut_list.append(evo.mut_rate)
mutfile = open('mutrate.txt','a')
mutfile.write(str(mut_list)+'\n')
mutfile.close()
def main():
"""Read data, train on data, test on data, BAM"""
esn = ESN(input_size=1, hidden_size=100, output_size=1)
test_damping(esn, 200)
#create inputs and training data
#data = datagen.mackeyglass(900, trunc=300) * 0.5
data = loadtxt('varsine.dat')
inputs = empty(300)
inputs.fill(0.0)
tmp = empty(300)
tmp.fill(0.5)
inputs = hstack((inputs, tmp))
tmp.fill(1.0)
inputs = hstack((inputs, tmp))
graph.plot_2d([inputs, data],"data")
#train and test the esn
train_out = esn.train(data, inputs)
test_out = esn.test(data, inputs)
graph.plot_2d([train_out, data[100:900]], "train_out")
graph.plot_2d([test_out, data], "test_out")
#plot residuals
train_res = residual(train_out, data[100:])
test_res = residual(test_out, data)
graph.plot_2d([train_res],"train_residual")
graph.plot_2d([test_res],"test_residual")
#calculate mean square error
print "Train MSE", mse(train_out, data[100:])
print "Test MSE", mse(test_out, data)
def main():
"""Read data, train on data, test on data, BAM"""
esn = ESN(input_size=1, hidden_size=100, output_size=1)
test_damping(esn, 200)
#create inputs and training data
#data = datagen.mackeyglass(900, trunc=300) * 0.5
data = loadtxt('varsine.dat')
inputs = empty(300)
inputs.fill(0.0)
tmp = empty(300)
tmp.fill(0.5)
inputs = hstack((inputs, tmp))
tmp.fill(1.0)
inputs = hstack((inputs, tmp))
graph.plot_2d([inputs,data],"data")
#train and test the esn
train_out = esn.train(data, inputs)
test_out = esn.test(data, inputs)
graph.plot_2d([train_out, data[100:900]], "train_out")
graph.plot_2d([test_out, data], "test_out")
#plot residuals
train_res = residual(train_out, data[100:])
test_res = residual(test_out, data)
graph.plot_2d([train_res],"train_residual")
graph.plot_2d([test_res],"test_residual")
#calculate mean square error
print "Train MSE", mse(train_out, data[100:])
print "Test MSE", mse(test_out, data)
def graph_fields(self):
"""for all companies"""
for key in self.fields:
results_list = []
for record in self.table:
result = []
for column in self.fields[key]:
result.append(record[column])
results_list.append(result)
graph.plot_2d(results_list, key)
def main():
"""comparison code"""
import random
random.seed(1)
genome = [random.randint(0, 1) for _ in range(0, 5000)]
results, conc_list = run_grn(genome, delta=1, syncsize=1, offset=10)
if len(conc_list) > 1:
graph.plot_2d(conc_list, "testdata" + str(1))
def main():
"""comparison code"""
import random
random.seed(1)
genome = [random.randint(0, 1) for _ in range(0, 5000)]
results, conc_list = run_grn(genome, delta=1, syncsize=1, offset=10)
if len(conc_list) > 1:
graph.plot_2d(conc_list, "testdata"+str(1))
def main():
"""comparison code"""
import random
random.seed(1)
genome = [random.randint(0, 1) for _ in range(0, 5000)]
results, conc_list = run_grn(genome, delta=1, syncsize=100, offset=10)
minresult = 126 - max(results)
print "bestfit:", minresult
if len(conc_list) > 1:
graph.plot_2d(conc_list, "sinedata"+str(1))
def train(self, target, inputs, trim=100):
"""Calculate weights between hidden layer and output layer for
a given time series, uses pseudo-inverse training step"""
acts = zeros((len(target), self.hidden_size))
summed_acts = []
#create initial state for the hidden nodes
for i in range(len(acts[0])):
acts[0][i] = (random()*2)-1
# create the activations
for i in range(1, len(target)):
# turn target into array
targ, inp = array([target[i-1]]), array([inputs[i-1]])
# dotting target with back weights as the teacher signal
activation = tanh(dot(acts[i-1], self.weights['hidden'])+
dot(self.weights['back'], targ)+
dot(self.weights['input'], inp))
# leaky integrator: prev state effects current state
acts[i] = ((1-self.alpha) * acts[i-1])
acts[i] += self.alpha * activation
#trim out the initial 100 activations as they are unstable
target = target[trim:]
inputs = inputs[trim:]
acts = acts[trim:, :]
#store activations and plot
self.acts = acts
graph.plot_2d(acts.T, "training_activations")
#add the inputs to the activations
acts = vstack((acts.T, inputs)).T
# Pseudo-inverse to train the output and setting weights
tinv = arctanh(target)
clf = linear_model.RidgeCV(alphas=[0.01, 0.1, 1.0, 10.0])
#clf = linear_model.Ridge(alpha=0.5)
#clf = linear_model.LassoCV()
clf.fit(acts, tinv)
self.weights['out'] = linear_model.ridge_regression(acts, tinv,
alpha=.15)
self.weights['out'] = clf.coef_
#self.weights['out'] = linalg.lstsq(acts, tinv)[0]
#residual = dot(acts, self.weights['out']) - tinv
graph.bar_plot(self.weights['out'], "weights")
# checking the output against previous activations
train_out = []
for act in acts:
output = tanh(dot(act, self.weights['out']))
train_out.append(output)
return train_out
def graph_fields(table, fields):
for field in fields:
print "graphing", field['name']
results_list = []
for record in table:
result = []
for column in field['cols']:
result.append(record[column])
results_list.append(result)
graph.plot_2d(results_list, "graphs/"+field['name'])
def main():
"""comparison code"""
import random
random.seed(1)
genome = [random.randint(0, 1) for _ in range(0, 5000)]
results, conc_list = run_grn(genome, delta=1, syncsize=100, offset=10)
minresult = 126 - max(results)
print "bestfit:", minresult
if len(conc_list) > 1:
graph.plot_2d(conc_list, "sinedata" + str(1))
def train(self, target, inputs, trim=100):
"""Calculate weights between hidden layer and output layer for
a given time series, uses pseudo-inverse training step"""
acts = zeros((len(target), self.hidden_size))
summed_acts = []
#create initial state for the hidden nodes
for i in range(len(acts[0])):
acts[0][i] = (random()*2)-1
# create the activations
for i in range(1, len(target)):
# turn target into array
targ, inp = array([target[i-1]]), array([inputs[i-1]])
# dotting target with back weights as the teacher signal
activation = tanh(dot(acts[i-1],self.weights['hidden'])+
dot(self.weights['back'], targ)+
dot(self.weights['input'], inp))
# leaky integrator: prev state effects current state
acts[i] = ((1-self.alpha) * acts[i-1])
acts[i] += self.alpha * activation
#trim out the initial 100 activations as they are unstable
target = target[trim:]
inputs = inputs[trim:]
acts = acts[trim:, :]
#store activations and plot
self.acts = acts
graph.plot_2d(acts.T, "training_activations")
#add the inputs to the activations
acts = vstack((acts.T,inputs)).T
# Pseudo-inverse to train the output and setting weights
tinv = arctanh(target)
clf = linear_model.RidgeCV(alphas=[0.01, 0.1, 1.0, 10.0])
#clf = linear_model.Ridge(alpha=0.5)
#clf = linear_model.LassoCV()
clf.fit(acts, tinv)
self.weights['out'] = linear_model.ridge_regression(acts, tinv,alpha=.15)
self.weights['out'] = clf.coef_
#self.weights['out'] = linalg.lstsq(acts, tinv)[0]
#residual = dot(acts, self.weights['out']) - tinv
graph.bar_plot(self.weights['out'], "weights")
# checking the output against previous activations
train_out = []
for act in acts:
output = tanh(dot(act, self.weights['out']))
train_out.append(output)
return train_out
def graph_attrib(table, fields):
for field in fields:
print "graphing", field['name']
results_list = []
for record in table:
result = []
for column in field['cols']:
result.append(record[column])
results_list.append(result)
graph.plot_2d(results_list, field['name'])
graph.plot_ave(results_list, field['name'])
graph.boxplot_data(results_list, field['name'])
def test_damping(esn, iterations):
"""Checking if the network stabilises"""
acts = zeros((iterations, esn.hidden_size))
#set them to random initial activations
for i in range(len(acts[0])):
acts[0][i] = (random()*2)-1
# lets see if it dampens out
for i in range(1, iterations):
acts[i] = ((1-esn.alpha) * acts[i-1])
acts[i] += esn.alpha * tanh(dot(acts[i-1],
esn.weights['hidden']))
graph.plot_2d(acts.T, "damped_activations")
def test_damping(esn, iterations):
"""Checking if the network stabilises"""
acts = zeros((iterations, esn.hidden_size))
#set them to random initial activations
for i in range(len(acts[0])):
acts[0][i] = (random()*2)-1
# lets see if it dampens out
for i in range(1, iterations):
acts[i] = ((1-esn.alpha) * acts[i-1])
acts[i] += esn.alpha * tanh(dot(acts[i-1],
esn.weights['hidden']))
graph.plot_2d(acts.T, "damped_activations")
def main():
# input not used yet
esn = ESN(input_size=1, hidden_size=20, output_size=1)
esn.test_damping(200)
#gendata = datagen.sine(600) * 0.5
data = loadtxt('sine2.dat')
train_data = data[:300]
test_data = data[:50]
train_out = esn.train(train_data)
test_out = esn.test(test_data)
graph.plot_2d([train_out, data[100:300]], "train_out")
graph.plot_2d([test_out, data[:50]], "test_out")
#plot residuals
train_res = residual(train_out, train_data[100:])
test_res = residual(test_out, test_data)
graph.plot_2d([train_res], "train_residual")
graph.plot_2d([test_res], "test_residual")
#calculate mse
train_error = mse(train_out, train_data[100:])
test_error = mse(test_out, test_data)
print "Train MSE", train_error
print "Test MSE", test_error
def multicore(filename, delta, popsize, generations):
#set up the evo strategy
evo = popstrat.Evostrategy(5000, popsize)
children = evo.iterate(evo.pop)
nodes = ("*", )
job_server = pp.Server(8, ppservers=nodes)
print "Starting pp with", job_server.get_ncpus(), "workers"
start_time = time.time()
for i in range(generations):
run_time = time.time()
jobs = [(child,
job_server.submit(run_grn, (child['genome'], delta), (),
("cgrn as grn", "numpy", "math")))
for child in children]
for child, result in jobs:
results, conclist = result()
bestidx = results.index(max(results))
child['fitness'] = results[bestidx]
#plotting the best with colors
children = evo.iterate(children)
bestgenome = evo.pop[-1]['genome']
bestresult, conclist = run_grn(bestgenome, delta)
bestidx = bestresult.index(max(bestresult))
colors = []
simplist = []
for idx, result in enumerate(bestresult):
if idx == len(bestresult) - 1:
simplist.append(conclist[idx])
colors.append('k')
elif idx == bestidx:
colors.append('g')
simplist.append(conclist[idx])
else:
simplist.append(conclist[idx])
colors.append('r')
graph.plot_2d(simplist, filename, colors)
print "gen:", evo.gen_count, "fitness:", evo.pop[-1]['fitness']
if evo.adaptive:
evo.adapt_mutation()
res_file = open(filename, "a")
res_file.write(str(evo.pop[-1]) + '\n')
res_file.close()
def main():
grn = GRN()
grn.read_genome("eoinseed1.txt")
grn.build_genes()
#grn.add_gene(0.0, "EXTRA")
grn.precalc_matrix()
grn.regulate_matrix(10000, False)
# for i in range(0,3):
# init_concs = []
# for conc in grn.conc_list:
# init_concs.append(conc[i])
# print "ROUND ", i
# print init_concs
graph.plot_2d(grn.conc_list, 0)
def simple_grn(graphname):
size = 5
iterations = 10
edges = np.zeros([size, size])
nodes = np.empty([size])
result_array = [[] for i in range(size)]
"""
Initialise the nodes to have equal concentrations and
initialise the weight array with vals between -1,1
with stepsize 1
"""
nodes.fill(1.0 / size)
weightvals = np.arange(-1, 1.1, 0.1)
for x in np.nditer(edges, op_flags=['readwrite']):
#x[...] = float(random.randint(-1,1)) / (size)
x[...] = round(random.choice(weightvals), 2)
print "nodes\n", nodes, "\nedges\n", edges
for itr in range(iterations):
#nudge a node halfway through
#if itr == (iterations/2):
# nodes[0] = nodes[0] * 0.2
#calculate concentration changes for the nodes
change = np.empty(size)
for i in range(len(nodes)):
change[i] = np.dot(nodes, edges[i])
# alter concs and prevent it from going below zero
print "iter:", itr, "conc:", nodes, "change:", change
nodes = np.add(nodes, change)
nodes[nodes < 0] = 0.000001
#normalize
# total = sum(nodes)
# nodes = np.divide(nodes,total)
#record concentrations
for i in range(size):
result_array[i].append(nodes[i])
graph.plot_2d(result_array, "graph" + str(graphname))
def main():
import time
if(len(sys.argv) != 2):
print "Usage: " + sys.argv[0] + " <rseed>"
sys.exit(1)
seed = int(sys.argv[1])
random.seed(seed)
#read in the compustat data for given companies
delta = 20
companies = []
company_list = ['ARCHER-DANIELS-MIDLAND CO', 'ARTHUR J GALLAGHER & CO',
'ASCENA RETAIL GROUP INC', 'ASTEC INDUSTRIES INC', 'ASTORIA FINANCIAL CORP',
'BLACKBAUD INC', 'BMC SOFTWARE INC','BOSTON BEER INC -CL A', 'BRADY CORP',
'BRIGGS & STRATTON']
database = csvreader.CSVReader('compustat.csv')
for company in company_list:
companies.append(database.get_company(company))
#set up the evo strategy
best_list, mut_list = [], []
evo = popstrat.Evostrategy(5000,50)
children = evo.iterate(evo.pop)
for i in range(50):
for child in children:
start_time = time.time()
fitness = run_grn(child['genome'], companies, delta)
child['fitness'] = fitness
print "fitness:",child['fitness'],"time taken", str(time.time()-start_time)
children = evo.iterate(children)
if evo.adaptive:
evo.adapt_mutation()
best_list.append(evo.pop[-1]['fitness'])
mut_list.append(evo.mut_rate)
graph.plot_2d([best_list], 'bestfit')
graph.plot_2d([mut_list], 'mutrate')
def main():
best_list, mut_list = [], []
evo = Evostrategy(5000)
fitness = evo.onemax_fitness(evo.parent['genome'])
indiv = {'genome':evo.parent['genome'], 'fitness':fitness}
child = evo.iterate(indiv)
for i in range(100):
child['fitness'] = evo.onemax_fitness(child['genome'])
child = evo.iterate(child)
print evo.parent['fitness']
if evo.parent['fitness'] == 5000:
break
if evo.adaptive:
evo.adapt_mutation()
best_list.append(evo.parent['fitness'])
mut_list.append(evo.mut_rate)
graph.plot_2d([best_list], 'bestfit')
graph.plot_2d([mut_list], 'mutrate')
def singlecore(filename, delta, popsize, generations):
"""Run serially"""
#set up the evo strategy
best_list, mut_list = [], []
evo = popstrat.Evostrategy(5000, popsize)
children = evo.iterate(evo.pop)
for i in range(generations):
for child in children:
results, conclist = run_grn(child['genome'], delta)
bestidx = results.index(max(results))
child['fitness'] = results[bestidx]
print "fitness:", child['fitness']
children = evo.iterate(children)
bestgenome = evo.pop[-1]['genome']
results, conclist = run_grn(bestgenome, delta)
filename = "best_gen_"+str(i)
graph.plot_2d(conclist, filename)
if evo.adaptive:
evo.adapt_mutation()
best_list.append(evo.pop[-1]['fitness'])
mut_list.append(evo.mut_rate)
print "best overall fitness", evo.pop[-1]['fitness']
graph.plot_2d([best_list], 'bestfit')
graph.plot_2d([mut_list], 'mutrate')
def main():
# random.seed(2)
# grn = GRN(delta=1)
# grn.build_genes()
# grn.add_extra("EXTRA_sineval", 0.0, [0]*32)
# grn.precalc_matrix()
# grn.regulate_matrix(5)
import time
start_time = time.time()
for seed in range(10):
random.seed(seed)
stabiter = 10000
runiter = 1000
grn = GRN(delta=1)
grn.build_genes()
grn.add_extra("EXTRA_sineval", 0.0, [0]*32)
grn.precalc_matrix()
grn.regulate_matrix(stabiter)
onff = 0
for i in range(0, 50):
if i % 10 == 0:
if onff == 1:
onff = 0
else:
onff = 1
inputval = onff
extra_vals = {'sineval': inputval}
grn.set_extras(extra_vals)
grn.regulate_matrix(runiter)
for conc in grn.conc_list:
print conc[-1]
filename = "demo"+str(seed)
graph.plot_2d(grn.conc_list, filename)
print "took", str(time.time() - start_time)
def singlecore(filename, delta, popsize, generations):
"""Run serially"""
#set up the evo strategy
best_list, mut_list = [], []
evo = popstrat.Evostrategy(5000, popsize)
children = evo.iterate(evo.pop)
for i in range(generations):
for child in children:
results, conclist = run_grn(child['genome'], delta)
bestidx = results.index(max(results))
child['fitness'] = results[bestidx]
print "fitness:", child['fitness']
children = evo.iterate(children)
bestgenome = evo.pop[-1]['genome']
results, conclist = run_grn(bestgenome, delta)
filename = "best_gen_" + str(i)
graph.plot_2d(conclist, filename)
if evo.adaptive:
evo.adapt_mutation()
best_list.append(evo.pop[-1]['fitness'])
mut_list.append(evo.mut_rate)
print "best overall fitness", evo.pop[-1]['fitness']
graph.plot_2d([best_list], 'bestfit')
graph.plot_2d([mut_list], 'mutrate')
def test_damping(self, iterations):
"""Checking if the network stabilises"""
numpy.set_printoptions(precision=4, linewidth=2000)
acts = zeros((iterations, self.hidden_size))
acts[0] = [
0.949029602769840, -0.195694633071382, -0.737442723592159,
0.449467774003339, 0.799036414715420, -0.658597370832685,
-0.913942617588595, -0.0416815501470254, -0.812127430489660,
0.300099663301922, 0.904555077842031, -0.0845746012151277,
0.0737612940120569, -0.867025708396808, -0.0122598328349043,
-0.164918055240550, -0.415485899463317, -0.420672124930247,
0.507691993375378, -0.806408576103972
]
# lets see if it dampens out
for i in range(1, iterations):
#acts[i] = ((1-self.alpha) * acts[i-1])
#acts[i] += self.alpha * tanh(dot(acts[i-1],
# self.weights['hidden']))
product = dot(acts[i - 1], self.weights['hidden'].T)
# print "product",product
# print "tanh", tanh(product)
graph.plot_2d(acts.T, "damped_activations")
def multicore(filename, syncsize, offset, delta, popsize, generations):
""" Uses parallel python to evaluate, PP can also be used to
distribute evaluations to machines accross the network"""
#set up the evo strategy
evo = popstrat.Evostrategy(5000, popsize)
children = evo.iterate(evo.pop)
nodes = ("*",)
job_server = pp.Server(ncpus=8, ppservers=nodes)
print "Starting pp with", job_server.get_ncpus(), "workers"
for _ in range(generations):
jobs = [(child, job_server.submit(run_grn,
(child['genome'], delta,
syncsize, offset),
(),
("cgrn as grn","numpy","math")))
for child in children]
for child, result in jobs:
results, conclist = result()
bestidx = results.index(max(results))
child['fitness'] = results[bestidx]
print "gen:", evo.gen_count, "fitness:", evo.pop[-1]['fitness']
children = evo.iterate(children)
if evo.adaptive:
evo.adapt_mutation()
res_file = open(filename,"a")
res_file.write(str(evo.pop[-1])+'\n')
res_file.close()
restopname = filename+".rest"
#plotting the best with colors
bestgenome = evo.pop[-1]['genome']
bestresult, conclist = run_grn(bestgenome, delta, syncsize, offset, restopname)
bestidx = bestresult.index(max(bestresult))
fitness = round(max(bestresult), 1)
colors = []
for idx, result in enumerate(bestresult):
# draw the input in black
if idx == len(bestresult)-1:
colors.append('k')
# draw the best in green
elif idx == bestidx:
colors.append('g')
# draw p_genes in red
elif result > 0:
colors.append('r')
# draw TFs in blue
else:
colors.append('b')
print "colors", colors
graphname = filename.split('/')[2]
graphname = graphname[:-4] + "-F" + str(fitness)
graph.plot_2d(conclist, graphname, colors, (0, 1))
def train(self, target, trim=100):
"""Calculate weights between hidden layer and output layer for
a given time series, uses pseudo-inverse training step"""
acts = zeros((len(target), self.hidden_size))
summed_acts = []
acts[0] = [
0.949029602769840, -0.195694633071382, -0.737442723592159,
0.449467774003339, 0.799036414715420, -0.658597370832685,
-0.913942617588595, -0.0416815501470254, -0.812127430489660,
0.300099663301922, 0.904555077842031, -0.0845746012151277,
0.0737612940120569, -0.867025708396808, -0.0122598328349043,
-0.164918055240550, -0.415485899463317, -0.420672124930247,
0.507691993375378, -0.806408576103972
]
# create the activations
self.weights['back'] = self.weights['back'].T
for i in range(1, len(target)):
# turn target into array, should it be -1?
t = array([target[i - 1]])
# dotting target with back weights as the teacher signal
activation = tanh(
dot(acts[i - 1], self.weights['hidden'].T) +
dot(self.weights['back'], t))
#decay activation by alpha
acts[i] = ((1 - self.alpha) * acts[i - 1])
acts[i] += self.alpha * activation
#print i-1, acts[i-1]
#trim out the initial activations as they are unstable
target = target[trim:]
acts = acts[trim:, :]
#store activations and plot
self.acts = acts
graph.plot_2d(acts.T, "sample_activations")
#print "last",acts[-1]
# Pseudo-inverse to train the output and setting weights
tinv = arctanh(target)
pinv = linalg.pinv(acts)
aconj = acts.conjugate()
tconj = tinv.conjugate()
pinvaconj = linalg.pinv(aconj)
numpy.set_printoptions(precision=4, linewidth=2000)
# print "Pseudo inverse"
#for row in aconj:
# print row
print "acts", aconj.shape, "targ", tconj.shape
#self.weights['out'] = dot(pinv, tinv)
#self.weights['out'] = dot(pinvaconj,tconj)
self.weights['out'] = linalg.lstsq(aconj, tconj)[0]
print "\nnumpy lstsq", self.weights['out']
#self.weights['out'] = linalg.lstsq(aconj,tconj)[0]
#self.weights['out'] = scialg.lsqr(aconj,tconj)[0]
#self.weights['out'] = array([-2.62751866452261,0.911724638334178,0,0,0,-9.47053869171588,0,0,-3.90801067449960,0,7.05096786026327,11.5512880240272,7.35498461772589,-0.221961288369604,0,0,0.681830006046591,0,0,-0.458162995895149])
print "\nnew weights", self.weights['out']
graph.bar_plot(self.weights['out'], "weights")
# checking the output against previous activations
train_out = []
for act in acts:
output = tanh(dot(act, self.weights['out']))
train_out.append(output)
return train_out
def graph_company(self, company_name):
"""all fields for a given company"""
data = self.get_company(company_name)
for key in data:
graph.plot_2d([data[key]], company_name + ' ' + key)
def main():
# random.seed(2)
# stabiter = 10000
# runiter = 1000
# grn = GRN(delta=1)
# grn.build_genes()
# grn.add_extra("EXTRA_sineval", 0.0, [0]*32)
# grn.precalc_matrix()
# grn.regulate_matrix(stabiter)
# onff = 0
# for i in range(0, 10):
# if i % 10 == 0:
# if onff == 1:
# onff = 0
# else:
# onff = 1
# extra_vals = {'sineval': onff}
# grn.set_extras(extra_vals)
# grn.regulate_matrix(10)
# for i in range(len(grn.conc_list[0])):
# concs = []
# for j in range(len(grn.conc_list)):
# concs.append(grn.conc_list[j][i])
# print concs
import time
start_time = time.time()
for seed in range(10):
random.seed(seed)
stabiter = 10000
runiter = 1000
grn = GRN(delta=1)
grn.build_genes()
grn.add_extra("EXTRA_sineval", 0.0, [0] * 32)
grn.precalc_matrix()
grn.regulate_matrix(stabiter)
onff = 0
for i in range(0, 50):
if i % 10 == 0:
if onff == 1:
onff = 0
else:
onff = 1
inputval = onff
extra_vals = {'sineval': inputval}
grn.set_extras(extra_vals)
grn.regulate_matrix(runiter)
print "rows", len(grn.conc_list), "cols", len(grn.conc_list[0])
for conc in grn.conc_list:
print conc[-1]
filename = "demo" + str(seed)
graph.plot_2d(grn.conc_list, filename)
print "took", str(time.time() - start_time)
def multicore(filename, syncsize, offset, delta, popsize, generations):
""" Uses parallel python to evaluate, PP can also be used to
distribute evaluations to machines accross the network"""
#set up the evo strategy
evo = popstrat.Evostrategy(5000, popsize)
children = evo.iterate(evo.pop)
nodes = ("*", )
job_server = pp.Server(ncpus=8, ppservers=nodes)
print "Starting pp with", job_server.get_ncpus(), "workers"
for _ in range(generations):
jobs = [(child,
job_server.submit(run_grn,
(child['genome'], delta, syncsize, offset),
(), ("cgrn as grn", "numpy", "math")))
for child in children]
for child, result in jobs:
results, conclist = result()
bestidx = results.index(max(results))
child['fitness'] = results[bestidx]
print "gen:", evo.gen_count, "fitness:", evo.pop[-1]['fitness']
children = evo.iterate(children)
if evo.adaptive:
evo.adapt_mutation()
res_file = open(filename, "a")
res_file.write(str(evo.pop[-1]) + '\n')
res_file.close()
restopname = filename + ".rest"
#plotting the best with colors
bestgenome = evo.pop[-1]['genome']
bestresult, conclist = run_grn(bestgenome, delta, syncsize, offset,
restopname)
bestidx = bestresult.index(max(bestresult))
fitness = round(max(bestresult), 1)
colors = []
for idx, result in enumerate(bestresult):
# draw the input in black
if idx == len(bestresult) - 1:
colors.append('k')
# draw the best in green
elif idx == bestidx:
colors.append('g')
# draw p_genes in red
elif result > 0:
colors.append('r')
# draw TFs in blue
else:
colors.append('b')
print "colors", colors
graphname = filename.split('/')[2]
graphname = graphname[:-4] + "-F" + str(fitness)
graph.plot_2d(conclist, graphname, colors, (0, 1))