def test_event_find_first_change_from_inital_conditions_3(self): data = me.Data('data_init') assert ( (True, 1.0) == me.Data.event_find_first_change_from_inital_conditions( data, np.array([[0.0, 0.0, 1.0, 0.0], [0.0, 1.0, 0.0, 1.0]]), np.array([0.0, 1.0, 2.0, 3.0])))
def test_gamma_compute_bin_probabilities_sum(self): data = me.Data('data_init') data_time_values = [0.0, 1.0, 2.0, 3.0, 4.0, 5.0] data.gamma_fit_bins = np.concatenate( ([-np.inf], data_time_values, [np.inf])) assert (0.9999 < sum(data.gamma_compute_bin_probabilities([4.0, 0.5])) < 1.0001)
def test_bootstrap_count_data_to_summary_stats_shape(self): count_data = np.array([[[ 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 1., 1., 1., 1., 1., 1., 2., 2., 2., 2., 2., 3., 3. ], [ 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0. ]], [[ 0., 0., 0., 0., 0., 0., 0., 0., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 2., 2., 3., 4., 4., 5., 5. ], [ 1., 1., 1., 1., 1., 1., 1., 1., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0. ]]]) data_name = 'test_data' data = me.Data(data_name) data.load(['A', 'B'], np.linspace(0.0, 54.0, num=28, endpoint=True), count_data, bootstrap_samples=10) data_mean, data_var, data_cov = me.Data.bootstrap_count_data_to_summary_stats( data, data.data_num_time_values, data.data_mean_order, data.data_variance_order, data.data_covariance_order, data.data_counts, data.data_bootstrap_samples) assert ((data_mean.shape, data_var.shape, data_cov.shape) == ((2, 2, 28), (2, 2, 28), (2, 1, 28)))
def test_event_find_first_cell_count_increase_after_cell_type_conversion_4( self): data = me.Data('data_init') assert ( (False, None) == me.Data. event_find_first_cell_count_increase_after_cell_type_conversion( data, np.array([[4.0, 4.0, 5.0, 6.0], [1.0, 1.0, 1.0, 1.0]]), np.array([0.0, 1.0, 2.0, 3.0])))
def test_bootstrap_count_data_to_summary_stats_stat_values(self): count_data = np.array([[[ 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 1., 1., 1., 1., 1., 1., 2., 2., 2., 2., 2., 3., 3. ], [ 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0. ]], [[ 0., 0., 0., 0., 0., 0., 0., 0., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 2., 2., 3., 4., 4., 5., 5. ], [ 1., 1., 1., 1., 1., 1., 1., 1., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0. ]]]) data_name = 'test_data' data = me.Data(data_name) data.load(['A', 'B'], np.linspace(0.0, 54.0, num=28, endpoint=True), count_data, bootstrap_samples=10) data_mean, data_var, data_cov = me.Data.bootstrap_count_data_to_summary_stats( data, data.data_num_time_values, data.data_mean_order, data.data_variance_order, data.data_covariance_order, data.data_counts, data.data_bootstrap_samples) assert (np.all( data_mean[0, :, :] == np.array([[ 0., 0., 0., 0., 0., 0., 0., 0., 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 1., 1., 1., 1., 1., 1., 2., 2., 2.5, 3., 3., 4., 4. ], [ 1., 1., 1., 1., 1., 1., 1., 1., 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0. ]])) == True) assert (np.all( data_var[0, :, :] == np.array([[ 0., 0., 0., 0., 0., 0., 0., 0., 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0., 0., 0., 0., 0., 0., 0., 0., 0.5, 2., 2., 2., 2. ], [ 0., 0., 0., 0., 0., 0., 0., 0., 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0. ]])) == True) assert (np.all(data_cov[0, :, :] == np.array([[ 0., 0., 0., 0., 0., 0., 0., 0., -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0. ]])) == True)
def test_get_credible_interval(self): net = me.Network('net_test') data = me.Data('data_test') est = me.Estimation('est_test', net, data) samples = np.array([[0.2, 3.4], [0.4, 3.2], [0.25, 3.65]]) params_cred_res = np.array(est.get_credible_interval(samples)) params_cred_sol = np.array([[0.25, 0.2025, 0.3925], [3.4, 3.21, 3.6375]]) np.testing.assert_allclose(params_cred_sol, params_cred_res)
def test_plots_est_corner_weight_plot(self): net = me.Network('net_div_g5') net.structure([{'start': 'X_t', 'end': 'X_t', 'rate_symbol': 'l', 'type': 'S -> S + S', 'reaction_steps': 5}]) num_iter = 5 initial_values_type = 'synchronous' initial_values = {'X_t': 1} theta_values = {'l': 0.22} time_values = np.array([0.0, 10.0]) variables = {'X_t': ('X_t', )} sim = me.Simulation(net) res_list = list() for __ in range(num_iter): res_list.append(sim.simulate('gillespie', variables, theta_values, time_values, initial_values_type, initial_gillespie=initial_values)[1]) sims = np.array(res_list) data = me.Data('data_test_select_models') data.load(['X_t',], time_values, sims, bootstrap_samples=5, basic_sigma=0.01) # overwrite with known values (from a num_iter=100 simulation) data.data_mean = np.array([[[1. , 3.73 ]], [[0.01 , 0.15406761]]]) data.data_variance = np.array([[[0. , 2.36070707]], [[0.01 , 0.32208202]]]) ### define model(s) for selection net2 = me.Network('net_div_g2') net2.structure([{'start': 'X_t', 'end': 'X_t', 'rate_symbol': 'l', 'type': 'S -> S + S', 'reaction_steps': 2}, {'start': 'X_t', 'end': 'env', 'rate_symbol': 'd', 'type': 'S ->', 'reaction_steps': 1}]) # important note: theta_bounds are reduced here to # prevent odeint warning at high steps networks = [net2] variables = [{'X_t': ('X_t', )}]*1 initial_values_types = ['synchronous']*1 initial_values = [{('X_t',): 1.0, ('X_t', 'X_t'): 0.0}]*1 theta_bounds = [{'l': (0.0, 0.3), 'd': (0.0, 0.1)}]*1 ### run selection (sequentially) est_res = me.selection.select_models(networks, variables, initial_values_types, initial_values, theta_bounds, data, parallel=False) me.plots.est_corner_weight_plot(est_res[0], show=False) plt.close('all')
def test_gamma_fit_binned_waiting_times(self): data = me.Data('data_init') data.data_time_values = [0.0, 1.0, 2.0, 3.0, 4.0, 5.0] theta = [4.0, 0.5] waiting_times_arr = np.random.gamma(theta[0], theta[1], 100000) data.gamma_fit_binned_waiting_times(waiting_times_arr) theta_fit = data.gamma_fit_theta assert (3.8 < theta_fit[0] < 4.2) assert (0.4 < theta_fit[1] < 0.6)
def simple_est_setup_mean_only_summary(self): # see jupyter notebook ex_docs_tests for more info and plots ### define network net = me.Network('net_min_2_4') net.structure([{ 'start': 'X_t', 'end': 'Y_t', 'rate_symbol': 'd', 'type': 'S -> E', 'reaction_steps': 2 }, { 'start': 'Y_t', 'end': 'Y_t', 'rate_symbol': 'l', 'type': 'S -> S + S', 'reaction_steps': 4 }]) ### create data with known values time_values = np.array([0.0, 20.0, 40.0]) data_mean = np.array([[[1., 0.67, 0.37], [0., 0.45, 1.74]], [[0.01, 0.0469473, 0.04838822], [0.01, 0.07188642, 0.1995514]]]) data_variance = np.array([[[0., 0.22333333, 0.23545455], [0., 0.51262626, 4.03272727]], [[0.01, 0.01631605, 0.01293869], [0.01, 0.08878719, 0.68612036]]]) data_covariance = np.array([[[0., -0.30454545, -0.65030303]], [[0.01, 0.0303608, 0.06645246]]]) data = me.Data('data_test_est_min_2_4') data.load(['X_t', 'Y_t'], time_values, None, 'summary', mean_data=data_mean, var_data=data_variance, cov_data=data_covariance) ### run estimation and return object variables = {'X_t': ('X_t', ), 'Y_t': ('Y_t', )} initial_values_type = 'synchronous' initial_values = {('X_t', ): 1.0, ('Y_t', ): 0.0} theta_bounds = {'d': (0.0, 0.15), 'l': (0.0, 0.15)} time_values = None sim_mean_only = True fit_mean_only = True nlive = 1000 # 250 # 1000 tolerance = 0.01 # 0.1 (COARSE) # 0.05 # 0.01 (NORMAL) bound = 'multi' sample = 'unif' est = me.Estimation('est_min_2_4', net, data) est.estimate(variables, initial_values_type, initial_values, theta_bounds, time_values, sim_mean_only, fit_mean_only, nlive, tolerance, bound, sample) return est
def test_event_find_first_cell_count_increase_after_cell_type_conversion_3( self): data = me.Data('data_init') assert ( (True, 3.0) == me.Data. event_find_first_cell_count_increase_after_cell_type_conversion( data, np.array([[4.0, 3.0, 3.0, 3.0], [1.0, 2.0, 2.0, 3.0]]), np.array([0.0, 1.0, 2.0, 3.0]), diff=False))
def test_check_bin_digitalisation(self): data = me.Data('data_init') data_time_values = [0.0, 1.0, 2.0, 3.0, 4.0, 5.0] data.gamma_fit_bins = np.concatenate( ([-np.inf], data_time_values, [np.inf])) assert (np.all( np.array([0, 1, 1, 2, 2, 6]) == np.digitize([0.0, 0.1, 1.0, 1.8, 2.0, 5.2], data.gamma_fit_bins, right=True) - 1) == True)
def test_event_find_third_cell_count_increase_after_first_and_second_cell_count_increase_after_cell_type_conversion_1( self): data = me.Data('data_init') assert ( (True, 1.0) == me.Data. event_find_third_cell_count_increase_after_first_and_second_cell_count_increase_after_cell_type_conversion( data, np.array([[4.0, 3.0, 3.0, 4.0, 5.0, 5.0], [1.0, 2.0, 2.0, 2.0, 2.0, 3.0]]), np.array([0.0, 1.0, 2.0, 3.0, 4.0, 5.0]), diff=True))
def test_compute_bayesian_information_criterion(self): net = me.Network('net_test') data = me.Data('data_test') est = me.Estimation('est_test', net, data) bic = est.compute_bayesian_information_criterion(15, 2, 35.49) np.testing.assert_allclose(-65.56389959779558, bic) bic = est.compute_bayesian_information_criterion(15.0, 2, 35.49) np.testing.assert_allclose(-65.56389959779558, bic) bic = est.compute_bayesian_information_criterion(15, 2.0, 35.49) np.testing.assert_allclose(-65.56389959779558, bic) bic = est.compute_bayesian_information_criterion(15.0, 2.0, 35.49) np.testing.assert_allclose(-65.56389959779558, bic)
def data_setup(self): count_data = np.array([[[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 1., 1., 1., 1., 1., 1., 2., 2., 2., 2., 2., 3., 3.], [1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.]], [[0., 0., 0., 0., 0., 0., 0., 0., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 2., 2., 3., 4., 4., 5., 5.], [1., 1., 1., 1., 1., 1., 1., 1., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.]]]) data_name = 'test_data' data = me.Data(data_name) data.load(['A', 'B'], np.linspace(0.0, 54.0, num=28, endpoint=True), count_data, bootstrap_samples=10) return data
def test_initialise_net_theta_bounds(self): net = me.Network('net_test') data = me.Data('data_test') est = me.Estimation('est_test', net, data) net_theta_bounds_res = est.initialise_net_theta_bounds( ['theta_0', 'theta_1', 'theta_2'], { 'theta_2': 'p3', 'theta_0': 'p1', 'theta_1': 'p2' }, { 'p2': (0.0, 0.1), 'p3': (0.0, 0.2), 'p1': (0.0, 0.3) }) net_theta_bounds_sol = np.array([[0., 0.3], [0., 0.1], [0., 0.2]]) np.testing.assert_allclose(net_theta_bounds_sol, net_theta_bounds_res)
def test_gamma_compute_bin_probabilities_values(self): data = me.Data('data_init') data_time_values = [0.0, 1.0, 2.0, 3.0, 4.0, 5.0] data.gamma_fit_bins = np.concatenate( ([-np.inf], data_time_values, [np.inf])) res = np.array([ 0., 0.14287654, 0.42365334, 0.28226624, 0.10882377, 0.03204406, 0.01033605 ]) lower_res = res - 0.0001 uppper_res = res + 0.0001 assert (np.all([ np.all( lower_res < data.gamma_compute_bin_probabilities([4.0, 0.5])), np.all( data.gamma_compute_bin_probabilities([4.0, 0.5]) < uppper_res) ]) == True)
def test_compute_log_likelihood_norm_mean_only_true(self): net = me.Network('net_test') data = me.Data('data_test') est = me.Estimation('est_test', net, data) mean_data = np.array([[[1., 0.67, 0.37], [0., 0.45, 1.74]], [[0.01, 0.0469473, 0.04838822], [0.01, 0.07188642, 0.1995514]]]) var_data = np.array([[[0., 0.22333333, 0.23545455], [0., 0.51262626, 4.03272727]], [[0.01, 0.01631605, 0.01293869], [0.01, 0.08878719, 0.68612036]]]) cov_data = np.array([[[0., -0.30454545, -0.65030303]], [[0.01, 0.0303608, 0.06645246]]]) norm_res = est.compute_log_likelihood_norm(mean_data, var_data, cov_data, True) norm_sol = 14.028288976285737 np.testing.assert_allclose(norm_sol, norm_res)
def test_prior_transform(self): net = me.Network('net_test') data = me.Data('data_test') est = me.Estimation('est_test', net, data) est.net_theta_bounds = np.array([[0., 0.15], [0., 0.15]]) theta_unit = np.array([0.03 / 0.15, 0.075 / 0.15]) theta_orig_res = est.prior_transform(theta_unit) theta_orig_sol = np.array([0.03, 0.075]) np.testing.assert_allclose(theta_orig_sol, theta_orig_res) est.net_theta_bounds = np.array([[0.5, 2.0], [0.1, 4.0]]) theta_unit = np.array([0.8, 0.2]) theta_orig_res = est.prior_transform(theta_unit) theta_orig_sol = np.array( [0.8 * (2.0 - 0.5) + 0.5, 0.2 * (4.0 - 0.1) + 0.1]) np.testing.assert_allclose(theta_orig_sol, theta_orig_res)
def test_load_summary_data_mean_only_1(self): variables = ['A', 'B'] time_values = np.linspace(0.0, 4.0, num=5) sol_mean = np.array([[[0., 0.5, 1.25, 3., 4.], [1., 0.75, 0.25, 0.25, 0.]], [[0., 0.25096378, 0.41313568, 0.50182694, 0.], [0., 0.21847682, 0.21654396, 0.21624184, 0.]]]) sol_var = np.empty((2, 0, 5)) sol_cov = np.empty((2, 0, 5)) data = me.Data('data_init') data.load(variables, time_values, None, data_type='summary', mean_data=sol_mean, var_data=sol_var, cov_data=sol_cov) np.testing.assert_allclose(sol_mean, data.data_mean) np.testing.assert_allclose(sol_var, data.data_variance) np.testing.assert_allclose(sol_cov, data.data_covariance) assert (data.data_mean_exists_only == True) assert (data.data_num_variables == 2) assert (data.data_num_time_values == 5) assert (data.data_mean_order == [{ 'variables': 'A', 'summary_indices': 0, 'count_indices': (0, ) }, { 'variables': 'B', 'summary_indices': 1, 'count_indices': (1, ) }]) assert (data.data_variance_order == []) assert (data.data_covariance_order == []) assert (data.data_type == 'summary') assert (data.data_num_values == 10) assert (data.data_num_values_mean_only == 10)
def test_load_summary_data(self): variables = ['A', 'B'] time_values = np.linspace(0.0, 4.0, num=5) sol_mean = np.array([[[0., 0.5, 1.25, 3., 4.], [1., 0.75, 0.25, 0.25, 0.]], [[0., 0.25096378, 0.41313568, 0.50182694, 0.], [0., 0.21847682, 0.21654396, 0.21624184, 0.]]]) sol_var = np.array([[[ 0., 0.33333333, 0.91666667, 1.33333333, 0., ], [ 0., 0.25, 0.25, 0.25, 0., ]], [[ 0., 0.10247419, 0.39239737, 0.406103, 0., ], [ 0., 0.13197367, 0.13279328, 0.13272021, 0., ]]]) sol_cov = np.array([[[0., 0.16666667, 0.25, -0.33333333, 0.]], [[0., 0.11379549, 0.18195518, 0.22722941, 0.]]]) data = me.Data('data_init') data.load(variables, time_values, None, data_type='summary', mean_data=sol_mean, var_data=sol_var, cov_data=sol_cov) np.testing.assert_allclose(sol_mean, data.data_mean) np.testing.assert_allclose(sol_var, data.data_variance) np.testing.assert_allclose(sol_cov, data.data_covariance) assert (data.data_mean_exists_only == False) assert (data.data_num_variables == 2) assert (data.data_num_time_values == 5) assert (data.data_mean_order == [{ 'variables': 'A', 'summary_indices': 0, 'count_indices': (0, ) }, { 'variables': 'B', 'summary_indices': 1, 'count_indices': (1, ) }]) assert (data.data_variance_order == [{ 'variables': ('A', 'A'), 'summary_indices': 0, 'count_indices': (0, 0) }, { 'variables': ('B', 'B'), 'summary_indices': 1, 'count_indices': (1, 1) }]) assert (data.data_covariance_order == [{ 'variables': ('A', 'B'), 'summary_indices': 0, 'count_indices': (0, 1) }]) assert (data.data_type == 'summary') assert (data.data_num_values == 25) assert (data.data_num_values_mean_only == 10)
def test_event_find_first_cell_type_conversion_1(self): data = me.Data('data_init') assert ((True, 3.0) == me.Data.event_find_first_cell_type_conversion( data, np.array([[4.0, 4.0, 4.0, 3.0], [0.0, 0.0, 0.0, 1.0], [1.0, 1.0, 1.0, 1.0]]), np.array([0.0, 1.0, 2.0, 3.0])))
def test_division_model_sequential(self): ### create data from 5-steps model net = me.Network('net_div_g5') net.structure([{ 'start': 'X_t', 'end': 'X_t', 'rate_symbol': 'l', 'type': 'S -> S + S', 'reaction_steps': 5 }]) num_iter = 100 initial_values_type = 'synchronous' initial_values = {'X_t': 1} theta_values = {'l': 0.22} time_values = np.array([0.0, 10.0]) variables = {'X_t': ('X_t', )} sim = me.Simulation(net) res_list = list() for __ in range(num_iter): res_list.append( sim.simulate('gillespie', variables, theta_values, time_values, initial_values_type, initial_gillespie=initial_values)[1]) sims = np.array(res_list) data = me.Data('data_test_select_models') data.load([ 'X_t', ], time_values, sims, bootstrap_samples=10000, basic_sigma=1 / num_iter) # overwrite with known values (from a num_iter=100 simulation) data.data_mean = np.array([[[1., 3.73]], [[0.01, 0.15406761]]]) data.data_variance = np.array([[[0., 2.36070707]], [[0.01, 0.32208202]]]) ### define models for selection net2 = me.Network('net_div_g2') net2.structure([{ 'start': 'X_t', 'end': 'X_t', 'rate_symbol': 'l', 'type': 'S -> S + S', 'reaction_steps': 2 }]) net5 = me.Network('net_div_g5') net5.structure([{ 'start': 'X_t', 'end': 'X_t', 'rate_symbol': 'l', 'type': 'S -> S + S', 'reaction_steps': 5 }]) net15 = me.Network('net_div_g15') net15.structure([{ 'start': 'X_t', 'end': 'X_t', 'rate_symbol': 'l', 'type': 'S -> S + S', 'reaction_steps': 15 }]) # important note: theta_bounds are reduced here to # prevent odeint warning at high steps networks = [net2, net5, net15] variables = [{'X_t': ('X_t', )}] * 3 initial_values_types = ['synchronous'] * 3 initial_values = [{('X_t', ): 1.0, ('X_t', 'X_t'): 0.0}] * 3 theta_bounds = [{'l': (0.0, 0.5)}] * 3 ### run selection (sequentially) est_res = me.selection.select_models(networks, variables, initial_values_types, initial_values, theta_bounds, data, parallel=False) ### assert log evidence values evid_res = np.array([est.bay_est_log_evidence for est in est_res]) # expected solution evid_summary = np.array( [[-10.629916697804973, 4.7325886118420755, -5.956029975676918], [-10.707752281691006, 4.648483811563277, -5.904935097433867], [-10.660052905403797, 4.786992306046756, -5.865460195018101], [-10.560456631689906, 4.712198906183986, -6.024845876715448], [-10.67465188224791, 4.739031922471972, -5.832238436663494], [-10.688286571898711, 4.796078612214922, -5.866083545090796], [-10.674939299757629, 4.763798403008956, -5.869504378082593], [-10.706803542779763, 4.758241853964541, -5.921262356541525], [-10.55770560556853, 4.770112513127923, -5.9405505492747315], [-10.660075345658038, 4.832557590020761, -5.869471476946568]]) evid_sol = np.mean(evid_summary, axis=0) evid_tol = np.max(np.std(evid_summary, axis=0) * 6) np.testing.assert_allclose(evid_sol, evid_res, rtol=evid_tol, atol=evid_tol) ### assert maximal log likelihood value logl_max_res = np.array( [est.bay_est_log_likelihood_max for est in est_res]) logl_max_sol = np.array( [-6.655917426977538, 8.536409735755383, -2.583752295846338]) np.testing.assert_allclose(logl_max_sol, logl_max_res, rtol=1.0, atol=1.0) ### assert estimated parameter value (95% credible interval) theta_cred_res = np.array([est.bay_est_params_cred for est in est_res]) theta_cred_sol = [[[0.15403995, 0.14659241, 0.16079126]], [[0.21181266, 0.20239213, 0.22030757]], [[0.23227569, 0.21840278, 0.24577387]]] np.testing.assert_allclose(theta_cred_sol, theta_cred_res, rtol=0.02, atol=0.02)
def test_division_model_parallel_fit_mean_only_summary(self): ### create data from 5-steps model time_values = np.array([0.0, 10.0]) data_mean = np.array([[[1., 3.73]], [[0.01, 0.15406761]]]) data = me.Data('data_test_select_models') data.load([ 'X_t', ], time_values, None, 'summary', mean_data=data_mean) ### define models for selection net2 = me.Network('net_div_g2') net2.structure([{ 'start': 'X_t', 'end': 'X_t', 'rate_symbol': 'l', 'type': 'S -> S + S', 'reaction_steps': 2 }]) net5 = me.Network('net_div_g5') net5.structure([{ 'start': 'X_t', 'end': 'X_t', 'rate_symbol': 'l', 'type': 'S -> S + S', 'reaction_steps': 5 }]) net15 = me.Network('net_div_g15') net15.structure([{ 'start': 'X_t', 'end': 'X_t', 'rate_symbol': 'l', 'type': 'S -> S + S', 'reaction_steps': 15 }]) # important note: theta_bounds are reduced here to # prevent odeint warning at high steps networks = [net2, net5, net15] variables = [{'X_t': ('X_t', )}] * 3 initial_values_types = ['synchronous'] * 3 initial_values = [{('X_t', ): 1.0, ('X_t', 'X_t'): 0.0}] * 3 theta_bounds = [{'l': (0.0, 0.5)}] * 3 ### run selection (in parallel) est_res = me.selection.select_models(networks, variables, initial_values_types, initial_values, theta_bounds, data, sim_mean_only=False, fit_mean_only=True, parallel=True) ### assert log evidence values evid_res = np.array([est.bay_est_log_evidence for est in est_res]) # expected solution evid_summary = np.array( [[0.9419435322851446, 1.0106982945064, 1.1012240890675635], [0.9566246018872815, 1.0030070861382694, 1.185808337623029], [0.9907574912748793, 1.047671927169712, 1.19272285522771], [0.9344626373613755, 1.0150202141481144, 1.1356276897852824], [0.9957857383128643, 1.1147029967812334, 1.2813572453964095], [0.9224870435679013, 1.135816900454853, 1.2377276605741654], [0.9894778490215606, 1.0941277563587202, 1.1494814071976407], [0.9845703717052129, 1.2037659025849716, 1.1818061600496066], [0.9512176652730777, 1.0724397747692442, 1.2583570008429867], [0.8883984291598804, 1.003479199497773, 1.1824954558159297]]) evid_sol = np.mean(evid_summary, axis=0) evid_tol = np.max(np.std(evid_summary, axis=0) * 6) np.testing.assert_allclose(evid_sol, evid_res, rtol=evid_tol, atol=evid_tol) ### assert maximal log likelihood value logl_max_res = np.array( [est.bay_est_log_likelihood_max for est in est_res]) # expected solution logl_max_summary = np.array( [[4.637656866490975, 4.63765686651381, 4.637656866427406], [4.637656866313304, 4.63765686645764, 4.637656866472604], [4.637656866511199, 4.637656866434893, 4.637656866503798], [4.637656866478411, 4.637656866496112, 4.637656866472503], [4.637656866481246, 4.637656866487981, 4.637656866364033], [4.63765686651618, 4.637656866167647, 4.637656866000495], [4.6376568664946385, 4.637656866516615, 4.637656865509905], [4.637656866397452, 4.63765686646518, 4.637656866516921], [4.637656866513331, 4.637656866516135, 4.637656866481746], [4.6376568665054085, 4.637656866400874, 4.63765686645308]]) logl_max_sol = np.mean(logl_max_summary, axis=0) logl_max_tol = np.max(np.std(logl_max_summary, axis=0) * 6) np.testing.assert_allclose(logl_max_sol, logl_max_res, rtol=logl_max_tol, atol=logl_max_tol) ### assert estimated parameter value (95% credible interval) theta_cred_res = np.array([est.bay_est_params_cred for est in est_res]) # expected solution theta_cred_summary = np.array([ [[[0.17767525971322726, 0.16766484301297668, 0.1871859065530188]], [[0.2116378072993456, 0.19980784768361473, 0.22221378166000505]], [[0.22706308238730954, 0.21426688997969887, 0.23898897505750633]]], [[[0.17783574075135636, 0.16745234255033054, 0.18709129910629485]], [[0.21159566312843459, 0.20025740650972587, 0.22225069777450657]], [[0.22685131261479294, 0.2148889188053539, 0.23873886327930333]]], [[[0.17772495817619227, 0.16792866692656294, 0.18716373871632497]], [[0.21147737507817208, 0.20013138837338232, 0.2221836017996362]], [[0.22712942097758385, 0.21459786012153031, 0.239019411969675]]], [[[0.17765310186185357, 0.16737710709424608, 0.18699853276265388]], [[0.21152367704878855, 0.20017333735288512, 0.22195840272665873]], [[0.22739299020772027, 0.21494870304871327, 0.23871190646445717]]], [[[0.17774890954479852, 0.16785378992605757, 0.18692744095053854]], [[0.2117422771562304, 0.20033115893162734, 0.221744778476685]], [[0.22700636347057088, 0.21483175457317827, 0.23850802940459553]]], [[[0.17770323548026393, 0.16762338985697867, 0.18722030610380444]], [[0.21148199985918062, 0.20004025740164794, 0.22246417034066013]], [[0.22726641468296005, 0.21508239943597135, 0.23893200778722384]]], [[[0.17774638376606106, 0.16741064926107696, 0.18714861450676257]], [[0.211685981167947, 0.20044959549495348, 0.2218134914679289]], [[0.2272913418178502, 0.21488828222344508, 0.23918800766586332]]], [[[0.17786567511829948, 0.16774372529113826, 0.18716669314766138]], [[0.21176955766928585, 0.2003380716254387, 0.2220132491656906]], [[0.2267721834898168, 0.2144859118131004, 0.23877758912985064]]], [[[0.17774477002988257, 0.16777800470913823, 0.186737513643131]], [[0.21140631049740677, 0.20034762799106276, 0.22201850676261048]], [[0.22699475212678594, 0.21520075443250175, 0.23875173560623902]]], [[[0.17768763634149626, 0.16748127097311355, 0.18726644765855052]], [[0.21158086725786138, 0.20022479235379922, 0.22237544704503034]], [[0.22692686604795786, 0.21503615490679384, 0.2388629470323908]]] ]) theta_cred_sol = np.mean(theta_cred_summary, axis=0) theta_cred_tol = np.max(np.std(theta_cred_summary, axis=0) * 6) np.testing.assert_allclose(theta_cred_sol, theta_cred_res, rtol=theta_cred_tol, atol=theta_cred_tol)
def test_event_find_first_cell_count_increase_3(self): data = me.Data('data_init') assert ((True, 2.0) == me.Data.event_find_first_cell_count_increase( data, np.array([[4.0, 4.0, 4.0, 4.0], [0.0, 0.0, 0.0, 1.0], [1.0, 1.0, 2.0, 3.0]]), np.array([0.0, 1.0, 2.0, 3.0])))
def simple_est_setup_mean_only(self): # see jupyter notebook ex_docs_tests for more info and plots ### define network net = me.Network('net_min_2_4') net.structure([{ 'start': 'X_t', 'end': 'Y_t', 'rate_symbol': 'd', 'type': 'S -> E', 'reaction_steps': 2 }, { 'start': 'Y_t', 'end': 'Y_t', 'rate_symbol': 'l', 'type': 'S -> S + S', 'reaction_steps': 4 }]) ### create data with known values num_iter = 100 initial_values_type = 'synchronous' initial_values = {'X_t': 1, 'Y_t': 0} theta_values = {'d': 0.03, 'l': 0.07} time_values = np.array([0.0, 20.0, 40.0]) variables = {'X_t': ('X_t', ), 'Y_t': ('Y_t', )} sim = me.Simulation(net) res_list = list() for __ in range(num_iter): res_list.append( sim.simulate('gillespie', variables, theta_values, time_values, initial_values_type, initial_gillespie=initial_values)[1]) sims = np.array(res_list) data = me.Data('data_test_est_min_2_4') data.load(['X_t', 'Y_t'], time_values, sims, bootstrap_samples=10000, basic_sigma=1 / num_iter) # overwrite with fixed values (from a num_iter = 100 simulation) data.data_mean = np.array([[[1., 0.67, 0.37], [0., 0.45, 1.74]], [[0.01, 0.0469473, 0.04838822], [0.01, 0.07188642, 0.1995514]]]) data.data_variance = np.array([[[0., 0.22333333, 0.23545455], [0., 0.51262626, 4.03272727]], [[0.01, 0.01631605, 0.01293869], [0.01, 0.08878719, 0.68612036]]]) data.data_covariance = np.array([[[0., -0.30454545, -0.65030303]], [[0.01, 0.0303608, 0.06645246]]]) ### run estimation and return object variables = {'X_t': ('X_t', ), 'Y_t': ('Y_t', )} initial_values_type = 'synchronous' initial_values = {('X_t', ): 1.0, ('Y_t', ): 0.0} theta_bounds = {'d': (0.0, 0.15), 'l': (0.0, 0.15)} time_values = None sim_mean_only = True fit_mean_only = True nlive = 1000 # 250 # 1000 tolerance = 0.01 # 0.1 (COARSE) # 0.05 # 0.01 (NORMAL) bound = 'multi' sample = 'unif' est = me.Estimation('est_min_2_4', net, data) est.estimate(variables, initial_values_type, initial_values, theta_bounds, time_values, sim_mean_only, fit_mean_only, nlive, tolerance, bound, sample) return est
def test_compute_log_evidence_from_bic(self): net = me.Network('net_test') data = me.Data('data_test') est = me.Estimation('est_test', net, data) log_evid_from_bic = est.compute_log_evidence_from_bic(-65.5) np.testing.assert_allclose(32.75, log_evid_from_bic)