Examples

The code used to generate these examples can be found here as an iPython Notebook.

Symbolic Regressor

This example demonstrates using the SymbolicRegressor to fit a symbolic relationship.

Let’s create some synthetic data based on the relationship \(y = X_0^{2} - X_1^{2} + X_1 - 1\):

x0 = np.arange(-1, 1, 1/10.)
x1 = np.arange(-1, 1, 1/10.)
x0, x1 = np.meshgrid(x0, x1)
y_truth = x0**2 - x1**2 + x1 - 1

ax = plt.figure().gca(projection='3d')
ax.set_xlim(-1, 1)
ax.set_ylim(-1, 1)
surf = ax.plot_surface(x0, x1, y_truth, rstride=1, cstride=1,
                       color='green', alpha=0.5)
plt.show()
_images/ex1_fig1.png

We can create some random training and test data that lies on this surface too:

rng = check_random_state(0)

# Training samples
X_train = rng.uniform(-1, 1, 100).reshape(50, 2)
y_train = X_train[:, 0]**2 - X_train[:, 1]**2 + X_train[:, 1] - 1

# Testing samples
X_test = rng.uniform(-1, 1, 100).reshape(50, 2)
y_test = X_test[:, 0]**2 - X_test[:, 1]**2 + X_test[:, 1] - 1

Now let’s consider how to fit our SymbolicRegressor to this data. Since it’s a fairly small dataset, we can probably use a large population since training time will still be pretty fast. We’ll evolve 20 generations unless the error falls below 0.01. Examining the equation, it looks like the default function set of addition, subtraction, multiplication and division will cover us. Let’s bump up the amount of mutation and subsample so that we can watch the OOB error evolve. We’ll also increase the parsimony coefficient to keep our solutions small, since we know the truth is a pretty simple equation:

est_gp = SymbolicRegressor(population_size=5000,
                           generations=20, stopping_criteria=0.01,
                           p_crossover=0.7, p_subtree_mutation=0.1,
                           p_hoist_mutation=0.05, p_point_mutation=0.1,
                           max_samples=0.9, verbose=1,
                           parsimony_coefficient=0.01, random_state=0)
est_gp.fit(X_train, y_train)

    |    Population Average   |             Best Individual              |
---- ------------------------- ------------------------------------------ ----------
 Gen   Length          Fitness   Length          Fitness      OOB Fitness  Time Left
   0    38.13     458.57768152        5   0.320665972828   0.556763539274      1.28m
   1     9.97    1.70232723129        5   0.320201761523   0.624787148042     57.78s
   2     7.72    1.94456344674       11   0.239536660154   0.533148180489     46.35s
   3     5.41   0.990156815469        7   0.235676349446   0.719906258051     37.93s
   4     4.66   0.894443363616       11   0.103946413589   0.103946413589     32.20s
   5     5.41   0.940242380405       11   0.060802040427   0.060802040427     28.15s
   6     6.78     1.0953592564       11   0.000781474035   0.000781474035     24.85s

The evolution process stopped early as the error of the best program in the 9th generation was better than 0.01. It also appears that the parsimony coefficient was just about right as the average length of the programs fluctuated around a bit before settling on a pretty reasonable size. Let’s look at what our solution was:

print(est_gp._program)

sub(add(-0.999, X1), mul(sub(X1, X0), add(X0, X1)))

Interestingly, this does not have the same structure as our target function. But let’s expand the mathematics out:

\[y = (-0.999 + X_1) - ((X_1 - X_0) \times (X_0 + X_1))\]
\[y = X_1 - 0.999 - (X_1 X_0 + X_1^{2} - X_0^{2} - X_0 X_1)\]
\[y = X_0^{2} - X_1^{2} + X_1 - 0.999\]

Despite representing an interaction of \(X_0\) and \(X_1\), these terms cancel and we’re left with the (almost) exact relationship we were seeking!

Great, but let’s compare with some other non-linear models to see how they do:

est_tree = DecisionTreeRegressor()
est_tree.fit(X_train, y_train)
est_rf = RandomForestRegressor()
est_rf.fit(X_train, y_train)

We can plot the decision surfaces of all three to visualize each one:

y_gp = est_gp.predict(np.c_[x0.ravel(), x1.ravel()]).reshape(x0.shape)
score_gp = est_gp.score(X_test, y_test)
y_tree = est_tree.predict(np.c_[x0.ravel(), x1.ravel()]).reshape(x0.shape)
score_tree = est_tree.score(X_test, y_test)
y_rf = est_rf.predict(np.c_[x0.ravel(), x1.ravel()]).reshape(x0.shape)
score_rf = est_rf.score(X_test, y_test)

fig = plt.figure(figsize=(12, 10))

for i, (y, score, title) in enumerate([(y_truth, None, "Ground Truth"),
                                       (y_gp, score_gp, "SymbolicRegressor"),
                                       (y_tree, score_tree, "DecisionTreeRegressor"),
                                       (y_rf, score_rf, "RandomForestRegressor")]):

    ax = fig.add_subplot(2, 2, i+1, projection='3d')
    ax.set_xlim(-1, 1)
    ax.set_ylim(-1, 1)
    surf = ax.plot_surface(x0, x1, y, rstride=1, cstride=1, color='green', alpha=0.5)
    points = ax.scatter(X_train[:, 0], X_train[:, 1], y_train)
    if score is not None:
        score = ax.text(-.7, 1, .2, "$R^2 =\/ %.6f$" % score, 'x', fontsize=14)
    plt.title(title)
plt.show()
_images/ex1_fig2.png

Not bad SymbolicRegressor! We were able to fit a very smooth function to the data, while the tree-based estimators created very “blocky” decision surfaces. The Random Forest appears to have smoothed out some of the wrinkles but in both cases the tree models have fit very well to the training data, but done worse on out-of-sample data.

We can also inspect the program that the SymbolicRegressor found:

dot_data = est_gp._program.export_graphviz()
graph = graphviz.Source(dot_data)
graph
_images/ex1_child.png

And check out who its parents were:

print(est_gp._program.parents)

{'method': 'Crossover',
 'parent_idx': 1555,
 'parent_nodes': [1, 2, 3],
 'donor_idx': 78,
 'donor_nodes': []}

This dictionary tells us what evolution operation was performed to get our new individual, as well as the parents from the prior generation, and any nodes that were removed from them during, in this case, Crossover.

Plotting the parents shows how the genetic material from them combined to form our winning program:

idx = est_gp._program.parents['donor_idx']
fade_nodes = est_gp._program.parents['donor_nodes']
dot_data = est_gp._programs[-2][idx].export_graphviz(fade_nodes=fade_nodes)
graph = graphviz.Source(dot_data)
graph
_images/ex1_fig3.png

Symbolic Transformer

This example demonstrates using the SymbolicTransformer to generate new non-linear features automatically.

Let’s load up the Boston housing dataset and randomly shuffle it:

rng = check_random_state(0)
boston = load_boston()
perm = rng.permutation(boston.target.size)
boston.data = boston.data[perm]
boston.target = boston.target[perm]

We’ll use Ridge Regression for this example and train our regressor on the first 300 samples, and see how it performs on the unseen final 200 samples. The benchmark to beat is simply Ridge running on the dataset as-is:

est = Ridge()
est.fit(boston.data[:300, :], boston.target[:300])
print(est.score(boston.data[300:, :], boston.target[300:]))

0.759145222183

So now we’ll train our transformer on the same first 300 samples to generate some new features. Let’s use a large population of 2000 individuals over 20 generations. We’ll select the best 100 of these for the hall_of_fame, and then use the least-correlated 10 as our new features. A little parsimony should control bloat, but we’ll leave the rest of the evolution options at their defaults. The default metric='pearson' is appropriate here since we are using a linear model as the estimator. If we were going to use a tree-based estimator, the Spearman correlation might be interesting to try out too:

function_set = ['add', 'sub', 'mul', 'div',
                'sqrt', 'log', 'abs', 'neg', 'inv',
                'max', 'min']
gp = SymbolicTransformer(generations=20, population_size=2000,
                         hall_of_fame=100, n_components=10,
                         function_set=function_set,
                         parsimony_coefficient=0.0005,
                         max_samples=0.9, verbose=1,
                         random_state=0, n_jobs=3)
gp.fit(boston.data[:300, :], boston.target[:300])

We will then apply our trained transformer to the entire Boston dataset (remember, it still hasn’t seen the final 200 samples) and concatenate this to the original data:

gp_features = gp.transform(boston.data)
new_boston = np.hstack((boston.data, gp_features))

Now we train the Ridge regressor on the first 300 samples of the transformed dataset and see how it performs on the final 200 again:

est = Ridge()
est.fit(new_boston[:300, :], boston.target[:300])
print(est.score(new_boston[300:, :], boston.target[300:]))

0.841750404385

Great! We have improved the \(R^{2}\) score by a significant margin. It looks like the linear model was able to take advantage of some new non-linear features to fit the data even better.

Symbolic Classifier

Continuing the scikit-learn classifier comparison example to include the SymbolicClassifier we can see what types of decision boundaries could be found using genetic programming.

_images/ex4_comparison.png

As we can see, the SymbolicClassifier was able to find non-linear decision boundaries. Individual tweaks to the function sets and other parameters to better suit each dataset may also improve the fits.

As with scikit-learn’s disclaimer, this should be taken with a grain of salt for use with real-world datasets in multi-dimensional spaces. In order to look at that, let’s load the Wisconsin breast cancer dataset and shuffle it:

rng = check_random_state(0)
cancer = load_breast_cancer()
perm = rng.permutation(cancer.target.size)
cancer.data = cancer.data[perm]
cancer.target = cancer.target[perm]

We will use the base function sets and increase the parsimony in order to find a small solution to the problem, and fit to the first 400 samples:

est = SymbolicClassifier(parsimony_coefficient=.01,
                         feature_names=cancer.feature_names,
                         random_state=1)
est.fit(cancer.data[:400], cancer.target[:400])

Testing the estimator on the remaining samples shows that it found a very good solution:

y_true = cancer.target[400:]
y_score = est.predict_proba(cancer.data[400:])[:,1]
roc_auc_score(y_true, y_score)

0.96937869822485212

We can then also visualise the solution with Graphviz:

dot_data = est._program.export_graphviz()
graph = graphviz.Source(dot_data)
graph
_images/ex4_tree.png

It is important to note that the results of this formula are passed through the sigmoid function in order to transform the solution into class probabilities.

Next up, explore the full API reference or just skip ahead install the package!