Longitudinal LiNGAM

Model

This method [2] performs causal discovery on paired samples based on longitudinal data that collects samples over time. Their algorithm can analyze causal structures, including topological causal orders, that may change over time. Similarly to the basic LiNGAM model [1], this method makes the following assumptions:

  1. Linearity
  2. Non-Gaussian continuous error variables (except at most one)
  3. Acyclicity
  4. No hidden common causes

References

[1]S. Shimizu, P. O. Hoyer, A. Hyvärinen, and A. J. Kerminen. A linear non-gaussian acyclic model for causal discovery. Journal of Machine Learning Research, 7:2003-2030, 2006.
[2]K. Kadowaki, S. Shimizu, and T. Washio. Estimation of causal structures in longitudinal data using non-Gaussianity. In Proc. 23rd IEEE International Workshop on Machine Learning for Signal Processing (MLSP2013), pp. 1–6, Southampton, United Kingdom, 2013.

Import and settings

In this example, we need to import numpy, pandas, and graphviz in addition to lingam.

import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import graphviz
import lingam
from lingam.utils import print_causal_directions, print_dagc, make_dot

import warnings
warnings.filterwarnings('ignore')

print([np.__version__, pd.__version__, graphviz.__version__, lingam.__version__])

np.set_printoptions(precision=3, suppress=True)
np.random.seed(0)
['1.16.2', '0.24.2', '0.11.1', '1.5.2']

Test data

We create test data consisting of 5 variables. The causal model at each timepoint is as follows.

# setting
n_features = 5
n_samples = 200
n_lags = 1
n_timepoints = 3

causal_orders = []
B_t_true = np.empty((n_timepoints, n_features, n_features))
B_tau_true = np.empty((n_timepoints, n_lags, n_features, n_features))
X_t = np.empty((n_timepoints, n_samples, n_features))
# B(0,0)
B_t_true[0] = np.array([[0.0, 0.5,-0.3, 0.0, 0.0],
                        [0.0, 0.0,-0.3, 0.4, 0.0],
                        [0.0, 0.0, 0.0, 0.3, 0.0],
                        [0.0, 0.0, 0.0, 0.0, 0.0],
                        [0.1,-0.7, 0.0, 0.0, 0.0]])
causal_orders.append([3, 2, 1, 0, 4])
make_dot(B_t_true[0], labels=[f'x{i}(0)' for i in range(5)])
../_images/longitudinal_dag1.svg
# B(1,1)
B_t_true[1] = np.array([[0.0, 0.2,-0.1, 0.0,-0.5],
                        [0.0, 0.0, 0.0, 0.4, 0.0],
                        [0.0, 0.3, 0.0, 0.0, 0.0],
                        [0.0, 0.0, 0.0, 0.0, 0.0],
                        [0.0,-0.4, 0.0, 0.0, 0.0]])
causal_orders.append([3, 1, 2, 4, 0])
make_dot(B_t_true[1], labels=[f'x{i}(1)' for i in range(5)])
../_images/longitudinal_dag2.svg
# B(2,2)
B_t_true[2] = np.array([[0.0, 0.0, 0.0, 0.0, 0.0],
                        [0.0, 0.0,-0.7, 0.0, 0.5],
                        [0.2, 0.0, 0.0, 0.0, 0.0],
                        [0.0, 0.0,-0.4, 0.0, 0.0],
                        [0.3, 0.0, 0.0, 0.0, 0.0]])
causal_orders.append([0, 2, 4, 3, 1])
make_dot(B_t_true[2], labels=[f'x{i}(2)' for i in range(5)])
../_images/longitudinal_dag3.svg
# create B(t,t-τ) and X
for t in range(n_timepoints):
    # external influence
    expon = 0.1
    ext = np.empty((n_features, n_samples))
    for i in range(n_features):
        ext[i, :] = np.random.normal(size=(1, n_samples));
        ext[i, :] = np.multiply(np.sign(ext[i, :]), abs(ext[i, :]) ** expon);
        ext[i, :] = ext[i, :] - np.mean(ext[i, :]);
        ext[i, :] = ext[i, :] / np.std(ext[i, :]);

    # create B(t,t-τ)
    for tau in range(n_lags):
        value = np.random.uniform(low=0.01, high=0.5, size=(n_features, n_features))
        sign = np.random.choice([-1, 1], size=(n_features, n_features))
        B_tau_true[t, tau] = np.multiply(value, sign)

    # create X(t)
    X = np.zeros((n_features, n_samples))
    for co in causal_orders[t]:
        X[co] = np.dot(B_t_true[t][co, :], X) + ext[co]
        if t > 0:
            for tau in range(n_lags):
                X[co] = X[co] + np.dot(B_tau_true[t, tau][co, :], X_t[t-(tau+1)].T)

    X_t[t] = X.T

Causal Discovery

To run causal discovery, we create a LongitudinalLiNGAM object by specifying the n_lags parameter. Then, we call the fit() method.

model = lingam.LongitudinalLiNGAM(n_lags=n_lags)
model = model.fit(X_t)

Using the causal_orders_ property, we can see the causal ordering in time-points as a result of the causal discovery. All elements are nan because the causal order of B(t,t) at t=0 is not calculated. So access to the time points above t=1.

print(model.causal_orders_[0]) # nan at t=0
print(model.causal_orders_[1])
print(model.causal_orders_[2])
[nan, nan, nan, nan, nan]
[3, 1, 2, 4, 0]
[0, 4, 2, 3, 1]

Also, using the adjacency_matrices_ property, we can see the adjacency matrix as a result of the causal discovery. As with the causal order, all elements are nan because the B(t,t) and B(t,t-τ) at t=0 is not calculated. So access to the time points above t=1. Also, if we run causal discovery with n_lags=2, B(t,t-τ) at t=1 is also not computed, so all the elements are nan.

t = 0 # nan at t=0
print('B(0,0):')
print(model.adjacency_matrices_[t, 0])
print('B(0,-1):')
print(model.adjacency_matrices_[t, 1])

t = 1
print('B(1,1):')
print(model.adjacency_matrices_[t, 0])
print('B(1,0):')
print(model.adjacency_matrices_[t, 1])

t = 2
print('B(2,2):')
print(model.adjacency_matrices_[t, 0])
print('B(2,1):')
print(model.adjacency_matrices_[t, 1])
B(0,0):
[[nan nan nan nan nan]
 [nan nan nan nan nan]
 [nan nan nan nan nan]
 [nan nan nan nan nan]
 [nan nan nan nan nan]]
B(0,-1):
[[nan nan nan nan nan]
 [nan nan nan nan nan]
 [nan nan nan nan nan]
 [nan nan nan nan nan]
 [nan nan nan nan nan]]
B(1,1):
[[ 0.     0.099  0.     0.    -0.52 ]
 [ 0.     0.     0.     0.398  0.   ]
 [ 0.     0.384  0.    -0.162  0.   ]
 [ 0.     0.     0.     0.     0.   ]
 [ 0.    -0.249 -0.074  0.     0.   ]]
B(1,0):
[[ 0.025  0.116 -0.202  0.054 -0.216]
 [ 0.139 -0.211 -0.43   0.558  0.051]
 [-0.135  0.178  0.421  0.173  0.031]
 [ 0.384 -0.083 -0.495 -0.072 -0.323]
 [-0.206 -0.354 -0.199 -0.293  0.468]]
B(2,2):
[[ 0.     0.     0.     0.     0.   ]
 [ 0.     0.    -0.67   0.     0.46 ]
 [ 0.187  0.     0.     0.     0.   ]
 [ 0.     0.    -0.341  0.     0.   ]
 [ 0.25   0.     0.     0.     0.   ]]
B(2,1):
[[ 0.194  0.2    0.031 -0.473 -0.002]
 [-0.384 -0.037  0.158  0.255  0.095]
 [ 0.126  0.275 -0.048  0.502 -0.019]
 [ 0.238 -0.469  0.475 -0.029 -0.176]
 [-0.177  0.309 -0.112  0.295 -0.273]]
for t in range(1, n_timepoints):
    B_t, B_tau = model.adjacency_matrices_[t]
    plt.figure(figsize=(7, 3))

    plt.subplot(1,2,1)
    plt.plot([-1, 1],[-1, 1], marker="", color="blue", label="support")
    plt.scatter(B_t_true[t], B_t, facecolors='none', edgecolors='black')
    plt.xlim(-1, 1)
    plt.ylim(-1, 1)
    plt.xlabel('True')
    plt.ylabel('Estimated')
    plt.title(f'B({t},{t})')

    plt.subplot(1,2,2)
    plt.plot([-1, 1],[-1, 1], marker="", color="blue", label="support")
    plt.scatter(B_tau_true[t], B_tau, facecolors='none', edgecolors='black')
    plt.xlim(-1, 1)
    plt.ylim(-1, 1)
    plt.xlabel('True')
    plt.ylabel('Estimated')
    plt.title(f'B({t},{t-1})')

    plt.tight_layout()
    plt.show()
../_images/longitudinal_scatter1.png ../_images/longitudinal_scatter2.png

Independence between error variables

To check if the LiNGAM assumption is broken, we can get p-values of independence between error variables. The value in the i-th row and j-th column of the obtained matrix shows the p-value of the independence of the error variables \(e_i\) and \(e_j\).

p_values_list = model.get_error_independence_p_values()
t = 1
print(p_values_list[t])
[[0.    0.167 0.107 0.534 0.313]
 [0.167 0.    0.195 0.821 0.204]
 [0.107 0.195 0.    0.005 0.105]
 [0.534 0.821 0.005 0.    0.049]
 [0.313 0.204 0.105 0.049 0.   ]]
t = 2
print(p_values_list[2])
[[0.    0.723 0.596 0.579 0.564]
 [0.723 0.    0.612 0.688 0.412]
 [0.596 0.612 0.    0.267 0.636]
 [0.579 0.688 0.267 0.    0.421]
 [0.564 0.412 0.636 0.421 0.   ]]

Bootstrapping

We call bootstrap() method instead of fit(). Here, the second argument specifies the number of bootstrap sampling.

model = lingam.LongitudinalLiNGAM()
result = model.bootstrap(X_t, n_sampling=100)

Causal Directions

Since LongitudinalBootstrapResult object is returned, we can get the ranking of the causal directions extracted by get_causal_direction_counts() method. In the following sample code, n_directions option is limited to the causal directions of the top 8 rankings, and min_causal_effect option is limited to causal directions with a coefficient of 0.01 or more.

cdc_list = result.get_causal_direction_counts(n_directions=12, min_causal_effect=0.01, split_by_causal_effect_sign=True)
t = 1
labels = [f'x{i}({u})' for u in [t, t-1] for i in range(5)]
print_causal_directions(cdc_list[t], 100, labels=labels)
x4(1) <--- x4(0) (b>0) (100.0%)
x2(1) <--- x0(0) (b<0) (100.0%)
x3(1) <--- x0(0) (b>0) (100.0%)
x1(1) <--- x3(0) (b>0) (100.0%)
x1(1) <--- x2(0) (b<0) (100.0%)
x3(1) <--- x2(0) (b<0) (100.0%)
x3(1) <--- x4(0) (b<0) (100.0%)
x1(1) <--- x3(1) (b>0) (100.0%)
x0(1) <--- x4(1) (b<0) (100.0%)
x4(1) <--- x1(0) (b<0) (100.0%)
x4(1) <--- x1(1) (b<0) (100.0%)
x2(1) <--- x2(0) (b>0) (100.0%)
t = 2
labels = [f'x{i}({u})' for u in [t, t-1] for i in range(5)]
print_causal_directions(cdc_list[t], 100, labels=labels)
x0(2) <--- x0(1) (b>0) (100.0%)
x4(2) <--- x1(1) (b>0) (100.0%)
x3(2) <--- x2(1) (b>0) (100.0%)
x3(2) <--- x1(1) (b<0) (100.0%)
x3(2) <--- x0(1) (b>0) (100.0%)
x3(2) <--- x2(2) (b<0) (100.0%)
x2(2) <--- x3(1) (b>0) (100.0%)
x2(2) <--- x1(1) (b>0) (100.0%)
x4(2) <--- x3(1) (b>0) (100.0%)
x1(2) <--- x3(1) (b>0) (100.0%)
x1(2) <--- x2(1) (b>0) (100.0%)
x1(2) <--- x0(1) (b<0) (100.0%)

Directed Acyclic Graphs

Also, using the get_directed_acyclic_graph_counts() method, we can get the ranking of the DAGs extracted. In the following sample code, n_dags option is limited to the dags of the top 3 rankings, and min_causal_effect option is limited to causal directions with a coefficient of 0.01 or more.

dagc_list = result.get_directed_acyclic_graph_counts(n_dags=3, min_causal_effect=0.01, split_by_causal_effect_sign=True)
t = 1
labels = [f'x{i}({u})' for u in [t, t-1] for i in range(5)]
print_dagc(dagc_list[t], 100, labels=labels)
DAG[0]: 2.0%
    x0(1) <--- x4(1) (b<0)
    x0(1) <--- x0(0) (b>0)
    x0(1) <--- x1(0) (b>0)
    x0(1) <--- x2(0) (b<0)
    x0(1) <--- x3(0) (b>0)
    x0(1) <--- x4(0) (b<0)
    x1(1) <--- x3(1) (b>0)
    x1(1) <--- x0(0) (b>0)
    x1(1) <--- x1(0) (b<0)
    x1(1) <--- x2(0) (b<0)
    x1(1) <--- x3(0) (b>0)
    x1(1) <--- x4(0) (b>0)
    x2(1) <--- x1(1) (b>0)
    x2(1) <--- x0(0) (b<0)
    x2(1) <--- x1(0) (b>0)
    x2(1) <--- x2(0) (b>0)
    x2(1) <--- x3(0) (b>0)
    x2(1) <--- x4(0) (b>0)
    x3(1) <--- x0(0) (b>0)
    x3(1) <--- x1(0) (b<0)
    x3(1) <--- x2(0) (b<0)
    x3(1) <--- x4(0) (b<0)
    x4(1) <--- x1(1) (b<0)
    x4(1) <--- x0(0) (b<0)
    x4(1) <--- x1(0) (b<0)
    x4(1) <--- x2(0) (b<0)
    x4(1) <--- x3(0) (b<0)
    x4(1) <--- x4(0) (b>0)
DAG[1]: 1.0%
    x0(1) <--- x2(1) (b<0)
    x0(1) <--- x4(1) (b<0)
    x0(1) <--- x0(0) (b>0)
    x0(1) <--- x1(0) (b<0)
    x0(1) <--- x2(0) (b<0)
    x0(1) <--- x3(0) (b>0)
    x0(1) <--- x4(0) (b<0)
    x1(1) <--- x3(1) (b>0)
    x1(1) <--- x0(0) (b>0)
    x1(1) <--- x1(0) (b<0)
    x1(1) <--- x2(0) (b<0)
    x1(1) <--- x3(0) (b>0)
    x1(1) <--- x4(0) (b>0)
    x2(1) <--- x1(1) (b>0)
    x2(1) <--- x0(0) (b<0)
    x2(1) <--- x2(0) (b>0)
    x2(1) <--- x3(0) (b>0)
    x2(1) <--- x4(0) (b>0)
    x3(1) <--- x0(0) (b>0)
    x3(1) <--- x1(0) (b>0)
    x3(1) <--- x2(0) (b<0)
    x3(1) <--- x3(0) (b<0)
    x3(1) <--- x4(0) (b<0)
    x4(1) <--- x1(1) (b<0)
    x4(1) <--- x2(1) (b<0)
    x4(1) <--- x3(1) (b>0)
    x4(1) <--- x0(0) (b<0)
    x4(1) <--- x1(0) (b<0)
    x4(1) <--- x2(0) (b>0)
    x4(1) <--- x3(0) (b>0)
    x4(1) <--- x4(0) (b>0)
DAG[2]: 1.0%
    x0(1) <--- x1(1) (b>0)
    x0(1) <--- x4(1) (b<0)
    x0(1) <--- x1(0) (b>0)
    x0(1) <--- x2(0) (b<0)
    x0(1) <--- x3(0) (b>0)
    x0(1) <--- x4(0) (b<0)
    x1(1) <--- x3(1) (b>0)
    x1(1) <--- x0(0) (b>0)
    x1(1) <--- x1(0) (b<0)
    x1(1) <--- x2(0) (b<0)
    x1(1) <--- x3(0) (b>0)
    x1(1) <--- x4(0) (b>0)
    x2(1) <--- x1(1) (b>0)
    x2(1) <--- x0(0) (b<0)
    x2(1) <--- x1(0) (b>0)
    x2(1) <--- x2(0) (b>0)
    x2(1) <--- x3(0) (b>0)
    x2(1) <--- x4(0) (b>0)
    x3(1) <--- x0(0) (b>0)
    x3(1) <--- x1(0) (b<0)
    x3(1) <--- x2(0) (b<0)
    x3(1) <--- x3(0) (b<0)
    x3(1) <--- x4(0) (b<0)
    x4(1) <--- x1(1) (b<0)
    x4(1) <--- x2(1) (b<0)
    x4(1) <--- x3(1) (b>0)
    x4(1) <--- x0(0) (b<0)
    x4(1) <--- x1(0) (b<0)
    x4(1) <--- x2(0) (b<0)
    x4(1) <--- x3(0) (b<0)
    x4(1) <--- x4(0) (b>0)
t = 2
labels = [f'x{i}({u})' for u in [t, t-1] for i in range(5)]
print_dagc(dagc_list[t], 100, labels=labels)
DAG[0]: 3.0%
    x0(2) <--- x0(1) (b>0)
    x0(2) <--- x1(1) (b>0)
    x0(2) <--- x2(1) (b>0)
    x0(2) <--- x3(1) (b<0)
    x0(2) <--- x4(1) (b>0)
    x1(2) <--- x2(2) (b<0)
    x1(2) <--- x4(2) (b>0)
    x1(2) <--- x0(1) (b<0)
    x1(2) <--- x1(1) (b<0)
    x1(2) <--- x2(1) (b>0)
    x1(2) <--- x3(1) (b>0)
    x1(2) <--- x4(1) (b>0)
    x2(2) <--- x0(2) (b>0)
    x2(2) <--- x0(1) (b>0)
    x2(2) <--- x1(1) (b>0)
    x2(2) <--- x2(1) (b<0)
    x2(2) <--- x3(1) (b>0)
    x2(2) <--- x4(1) (b<0)
    x3(2) <--- x2(2) (b<0)
    x3(2) <--- x0(1) (b>0)
    x3(2) <--- x1(1) (b<0)
    x3(2) <--- x2(1) (b>0)
    x3(2) <--- x3(1) (b>0)
    x3(2) <--- x4(1) (b<0)
    x4(2) <--- x0(2) (b>0)
    x4(2) <--- x0(1) (b<0)
    x4(2) <--- x1(1) (b>0)
    x4(2) <--- x2(1) (b<0)
    x4(2) <--- x3(1) (b>0)
    x4(2) <--- x4(1) (b<0)
DAG[1]: 2.0%
    x0(2) <--- x0(1) (b>0)
    x0(2) <--- x1(1) (b>0)
    x0(2) <--- x2(1) (b>0)
    x0(2) <--- x3(1) (b<0)
    x0(2) <--- x4(1) (b>0)
    x1(2) <--- x2(2) (b<0)
    x1(2) <--- x4(2) (b>0)
    x1(2) <--- x0(1) (b<0)
    x1(2) <--- x1(1) (b<0)
    x1(2) <--- x2(1) (b>0)
    x1(2) <--- x3(1) (b>0)
    x1(2) <--- x4(1) (b<0)
    x2(2) <--- x0(2) (b>0)
    x2(2) <--- x0(1) (b>0)
    x2(2) <--- x1(1) (b>0)
    x2(2) <--- x2(1) (b<0)
    x2(2) <--- x3(1) (b>0)
    x2(2) <--- x4(1) (b>0)
    x3(2) <--- x2(2) (b<0)
    x3(2) <--- x0(1) (b>0)
    x3(2) <--- x1(1) (b<0)
    x3(2) <--- x2(1) (b>0)
    x3(2) <--- x3(1) (b<0)
    x3(2) <--- x4(1) (b<0)
    x4(2) <--- x0(2) (b>0)
    x4(2) <--- x0(1) (b<0)
    x4(2) <--- x1(1) (b>0)
    x4(2) <--- x2(1) (b<0)
    x4(2) <--- x3(1) (b>0)
    x4(2) <--- x4(1) (b<0)
DAG[2]: 2.0%
    x0(2) <--- x0(1) (b>0)
    x0(2) <--- x1(1) (b>0)
    x0(2) <--- x2(1) (b<0)
    x0(2) <--- x3(1) (b<0)
    x0(2) <--- x4(1) (b<0)
    x1(2) <--- x2(2) (b<0)
    x1(2) <--- x4(2) (b>0)
    x1(2) <--- x0(1) (b<0)
    x1(2) <--- x1(1) (b<0)
    x1(2) <--- x2(1) (b>0)
    x1(2) <--- x3(1) (b>0)
    x1(2) <--- x4(1) (b>0)
    x2(2) <--- x0(1) (b>0)
    x2(2) <--- x1(1) (b>0)
    x2(2) <--- x2(1) (b<0)
    x2(2) <--- x3(1) (b>0)
    x2(2) <--- x4(1) (b<0)
    x3(2) <--- x2(2) (b<0)
    x3(2) <--- x0(1) (b>0)
    x3(2) <--- x1(1) (b<0)
    x3(2) <--- x2(1) (b>0)
    x3(2) <--- x3(1) (b<0)
    x3(2) <--- x4(1) (b<0)
    x4(2) <--- x0(2) (b>0)
    x4(2) <--- x0(1) (b<0)
    x4(2) <--- x1(1) (b>0)
    x4(2) <--- x2(1) (b<0)
    x4(2) <--- x3(1) (b>0)
    x4(2) <--- x4(1) (b<0)

Probability

Using the get_probabilities() method, we can get the probability of bootstrapping.

probs = result.get_probabilities(min_causal_effect=0.01)
print(probs[1])
[[[0.   0.51 0.09 0.15 1.  ]
  [0.   0.   0.   1.   0.  ]
  [0.02 0.99 0.   0.52 0.3 ]
  [0.   0.   0.   0.   0.  ]
  [0.   1.   0.23 0.3  0.  ]]

 [[0.92 0.97 1.   0.94 0.99]
  [0.99 0.99 1.   1.   0.94]
  [1.   0.97 1.   0.99 0.87]
  [1.   0.98 1.   0.92 1.  ]
  [1.   1.   1.   1.   1.  ]]]
t = 1
print('B(1,1):')
print(probs[t, 0])
print('B(1,0):')
print(probs[t, 1])

t = 2
print('B(2,2):')
print(probs[t, 0])
print('B(2,1):')
print(probs[t, 1])
B(1,1):
[[0.   0.51 0.09 0.15 1.  ]
 [0.   0.   0.   1.   0.  ]
 [0.02 0.99 0.   0.52 0.3 ]
 [0.   0.   0.   0.   0.  ]
 [0.   1.   0.23 0.3  0.  ]]
B(1,0):
[[0.92 0.97 1.   0.94 0.99]
 [0.99 0.99 1.   1.   0.94]
 [1.   0.97 1.   0.99 0.87]
 [1.   0.98 1.   0.92 1.  ]
 [1.   1.   1.   1.   1.  ]]
B(2,2):
[[0.   0.   0.   0.   0.  ]
 [0.1  0.   1.   0.06 1.  ]
 [0.78 0.   0.   0.   0.13]
 [0.13 0.   1.   0.   0.16]
 [0.88 0.   0.   0.   0.  ]]
B(2,1):
[[1.   1.   0.91 1.   0.92]
 [1.   0.86 1.   1.   0.95]
 [0.95 1.   0.96 1.   0.8 ]
 [1.   1.   1.   0.92 1.  ]
 [0.99 1.   0.96 1.   1.  ]]

Total Causal Effects

Using the get_total_causal_effects() method, we can get the list of total causal effect. The total causal effects we can get are dictionary type variable. We can display the list nicely by assigning it to pandas.DataFrame. Also, we have replaced the variable index with a label below.

causal_effects = result.get_total_causal_effects(min_causal_effect=0.01)

df = pd.DataFrame(causal_effects)

labels = [f'x{i}({t})' for t in range(3) for i in range(5)]
df['from'] = df['from'].apply(lambda x : labels[x])
df['to'] = df['to'].apply(lambda x : labels[x])
df
from to effect probability
0 x1(1) x0(1) 0.269441 1.00
1 x0(2) x4(2) 0.119620 1.00
2 x4(1) x4(2) -0.109855 1.00
3 x3(1) x4(2) 0.260481 1.00
4 x1(1) x4(2) 0.297682 1.00
5 x2(2) x3(2) -0.394208 1.00
6 x4(1) x3(2) -0.152984 1.00
7 x3(1) x3(2) -0.284373 1.00
8 x2(1) x3(2) 0.425542 1.00
9 x1(1) x3(2) -0.263069 1.00
10 x0(2) x2(2) 0.177046 1.00
11 x4(1) x2(2) -0.110188 1.00
12 x3(1) x2(2) 0.524608 1.00
13 x1(1) x2(2) 0.329232 1.00
14 x4(2) x1(2) 0.113916 1.00
15 x2(2) x1(2) -0.429614 1.00
16 x0(1) x2(2) 0.202225 1.00
17 x1(1) x0(2) 0.154852 1.00
18 x1(1) x1(2) -0.145485 1.00
19 x3(1) x0(1) 0.116298 1.00
20 x0(1) x1(2) -0.462228 1.00
21 x4(1) x0(1) -0.562721 1.00
22 x3(1) x0(2) -0.238794 1.00
23 x3(1) x1(1) 0.317693 1.00
24 x4(1) x1(2) 0.222208 1.00
25 x1(1) x2(1) 0.187445 1.00
26 x1(1) x4(1) -0.280015 1.00
27 x4(2) x3(2) -0.059277 0.92
28 x4(1) x0(2) -0.139972 0.91
29 x4(2) x2(2) 0.033740 0.69
30 x4(1) x2(1) -0.050954 0.54
31 x2(1) x4(1) -0.102010 0.46
32 x2(1) x0(2) 0.034217 0.35
33 x2(1) x1(2) 0.161172 0.34
34 x2(2) x4(2) 0.029630 0.31
35 x0(1) x3(2) 0.106614 0.19
36 x0(1) x0(2) 0.136141 0.15
37 x2(1) x2(2) -0.089162 0.12
38 x3(2) x4(2) -0.081235 0.08

We can easily perform sorting operations with pandas.DataFrame.

df.sort_values('effect', ascending=False).head()
from to effect probability
12 x3(1) x2(2) 0.524608 1.0
8 x2(1) x3(2) 0.425542 1.0
13 x1(1) x2(2) 0.329232 1.0
23 x3(1) x1(1) 0.317693 1.0
4 x1(1) x4(2) 0.297682 1.0

And with pandas.DataFrame, we can easily filter by keywords. The following code extracts the causal direction towards x0(2).

df[df['to']=='x0(2)'].head()
from to effect probability
17 x1(1) x0(2) 0.154852 1.00
22 x3(1) x0(2) -0.238794 1.00
28 x4(1) x0(2) -0.139972 0.91
32 x2(1) x0(2) 0.034217 0.35
36 x0(1) x0(2) 0.136141 0.15

Because it holds the raw data of the total causal effect (the original data for calculating the median), it is possible to draw a histogram of the values of the causal effect, as shown below.

import matplotlib.pyplot as plt
import seaborn as sns
sns.set()
%matplotlib inline

from_index = 5 # index of x0(1). (index:0)+(n_features:5)*(timepoint:1) = 5
to_index = 12 # index of x2(2). (index:2)+(n_features:5)*(timepoint:2) = 12
plt.hist(result.total_effects_[:, to_index, from_index])
../_images/longitudinal_hist.png