def run_sims_from_prior():
"""
Runs several simulations with parameters sampled from the prior. Saves the parameters, summary statistics and
distances with the observed summary statistic. Intention is to use the data for rejection abc and to train mdns.
"""
n_files = 10
n_sims_per_file = 10**6
_, obs_stats = helper.load(datadir + 'observed_data.pkl')
for j in xrange(n_files):
ps = np.empty([n_sims_per_file, 3])
stats = np.empty([n_sims_per_file, n_percentiles])
dist = np.empty(n_sims_per_file)
for i in xrange(n_sims_per_file):
ps[i] = sim_prior()
_, _, _, idts, _ = sim_likelihood(*ps[i])
stats[i] = calc_summary_stats(idts)
dist[i] = calc_dist(stats[i], obs_stats)
print 'simulation {0}, distance = {1}'.format(
j * n_sims_per_file + i, dist[i])
# save data
filename = datadir + 'sims_from_prior_{0}.pkl'.format(j)
helper.save((ps, stats, dist), filename)
def run_sims_from_prior():
"""
Runs several simulations with parameters sampled from the prior. Saves the parameters, summary statistics and
distances with the observed summary statistic. Intention is to use the data for rejection abc and to train mdns.
"""
n_sims = 10 ** 7
# load observed data and prior
_, x, obs_data = helper.load(datadir + 'observed_data.pkl')
prior = get_prior()
# generate new data
ws = np.empty([n_sims, n_dim])
data = np.empty([n_sims, n_data])
dist = np.empty(n_sims)
for i in xrange(n_sims):
w = prior.gen()[0]
this_data = gen_y_data(w, x)
ws[i] = w
data[i] = this_data
dist[i] = calc_dist(this_data, obs_data)
print 'simulation {0}, distance = {1}'.format(i, dist[i])
helper.save((ws, data, dist), datadir + 'sims_from_prior.pkl')
def run_sims_from_prior():
"""
Runs several simulations with parameters sampled from the prior. Saves the parameters, normalized summary statistics
and distances with the observed summary statistic. Intention is to use the data for rejection abc and to train mdns.
"""
num_sims = 100000
pilot_means, pilot_stds = helper.load(datadir + 'pilot_run_results.pkl')
obs_stats = helper.load(datadir + 'obs_stats.pkl')
obs_stats -= pilot_means
obs_stats /= pilot_stds
params = []
stats = []
dist = []
for i in xrange(num_sims):
prop_params = sim_prior_params()
lv = mjp.LotkaVolterra(init, prop_params)
try:
states = lv.sim_time(dt, duration, max_n_steps=max_n_steps)
except mjp.SimTooLongException:
continue
sum_stats = calc_summary_stats(states)
sum_stats -= pilot_means
sum_stats /= pilot_stds
params.append(prop_params)
stats.append(sum_stats)
dist.append(calc_dist(sum_stats, obs_stats))
print 'simulation {0}, distance = {1}'.format(i, dist[-1])
params = np.array(params)
stats = np.array(stats)
dist = np.array(dist)
filename = datadir + 'sims_from_prior_{0}.pkl'.format(time.time())
helper.save((params, stats, dist), filename)
def show_true_posterior():
"""Calculates analytically and shows the true posterior."""
w, x, y = helper.load(datadir + 'observed_data.pkl')
prior = get_prior()
posterior = calc_posterior(prior, x, y)
helper.plot_pdf_marginals(pdf=prior, lims=[-3.0, 3.0], gt=w)
helper.plot_pdf_marginals(pdf=posterior, lims=[-3.0, 3.0], gt=w)
def calc_summary_stats(data, whiten=True):
"""Given observations, calculate summary statistics."""
perc = np.linspace(0.0, 100.0, n_percentiles)
stats = np.percentile(data, perc)
if whiten:
# whiten stats
means, U, istds = helper.load(datadir + 'pilot_run_results.pkl')
stats -= means
stats = np.dot(stats, U)
stats *= istds
return stats
def load_sims_from_prior(n_files=10):
"""Loads the huge file(s) that store the results from simulations from the prior."""
ws = np.empty([0, n_dim])
data = np.empty([0, n_data])
dist = np.empty([0])
for i in xrange(n_files):
ws_i, data_i, dist_i = helper.load(datadir + 'sims_from_prior_{0}.pkl'.format(i))
ws = np.concatenate([ws, ws_i], axis=0)
data = np.concatenate([data, data_i], axis=0)
dist = np.concatenate([dist, dist_i], axis=0)
n_sims = ws.shape[0]
assert n_sims == data.shape[0]
assert n_sims == dist.shape[0]
return ws, data, dist
def load_sims_from_prior(n_files=12):
"""Loads the huge file(s) that store the results from simulations from the prior."""
params = np.empty([0, 4])
stats = np.empty([0, 9])
dist = np.empty([0])
for i in xrange(n_files):
params_i, stats_i, dist_i = helper.load(
datadir + 'sims_from_prior_{0}.pkl'.format(i))
params = np.concatenate([params, params_i], axis=0)
stats = np.concatenate([stats, stats_i], axis=0)
dist = np.concatenate([dist, dist_i], axis=0)
n_sims = params.shape[0]
assert n_sims == stats.shape[0]
assert n_sims == dist.shape[0]
return params, stats, dist
def show_histograms(n_samples=1000):
"""Simulates from joint and shows histograms of simulations."""
true_ps, obs_stats = helper.load(datadir + 'observed_data.pkl')
ps = np.empty([n_samples, 3])
stats = np.empty([n_samples, n_percentiles])
for i in xrange(n_samples):
ps[i] = sim_prior()
_, _, _, idts, _ = sim_likelihood(*ps[i])
stats[i] = calc_summary_stats(idts)
# plot prior parameter histograms
helper.plot_hist_marginals(ps, lims=disp_lims, gt=true_ps)
plt.gcf().suptitle('p(thetas)')
# plot stats histograms
helper.plot_hist_marginals(stats, gt=obs_stats)
plt.gcf().suptitle('p(stats)')
plt.show(block=False)
def sum_stats_hist():
"""
Runs several simulations with given parameters and plots a histogram of the resulting normalized summary statistics.
"""
n_sims = 1000
sum_stats = []
i = 1
pilot_means, pilot_stds = helper.load(datadir + 'pilot_run_results.pkl')
while i <= n_sims:
lv = mjp.LotkaVolterra(init, true_params)
try:
states = lv.sim_time(dt, duration, max_n_steps=max_n_steps)
except mjp.SimTooLongException:
continue
sum_stats.append(calc_summary_stats(states))
print 'simulation {0}'.format(i)
i += 1
sum_stats = np.array(sum_stats)
sum_stats -= pilot_means
sum_stats /= pilot_stds
_, axs = plt.subplots(3, 3)
nbins = int(np.sqrt(n_sims))
for i, ax in enumerate(axs.flatten()):
ax.hist(sum_stats[:, i], nbins, normed=True)
ax.set_title('stat ' + str(i + 1))
plt.show()