Entropy of observations metric (#2340)

Summary:
Pull Request resolved: #2340

This commit introduces `entropy_of_observations` as a model fit metric. It quantifies the entropy of the outcomes `y_obs` using a kernel density estimator. This metric can be useful in detecting datasets in which the outcomes are clustered (implying a low entropy), rather than uniformly distributed in the outcome space (high entropy).

Reviewed By: saitcakmak

Differential Revision: D55930954

fbshipit-source-id: e2f839e6856879bae7268637966ca160aa8d6b74

ax/modelbridge/cross_validation.py

@@ -535,7 +535,6 @@ def compute_model_fit_metrics_from_modelbridge(
         if generalization
         else _predict_on_training_data(model_bridge=model_bridge, experiment=experiment)
     )
-
     if fit_metrics_dict is None:
         fit_metrics_dict = {
             "coefficient_of_determination": coefficient_of_determination,

ax/modelbridge/tests/test_model_fit_metrics.py

@@ -9,17 +9,23 @@
 import warnings
 from typing import cast, Dict
 
+import numpy as np
+
 from ax.core.experiment import Experiment
 from ax.core.objective import Objective
 from ax.core.optimization_config import OptimizationConfig
 from ax.metrics.branin import BraninMetric
-from ax.modelbridge.cross_validation import compute_model_fit_metrics_from_modelbridge
+from ax.modelbridge.cross_validation import (
+    _predict_on_cross_validation_data,
+    compute_model_fit_metrics_from_modelbridge,
+)
 from ax.modelbridge.generation_strategy import GenerationStep, GenerationStrategy
 from ax.modelbridge.registry import Models
 from ax.runners.synthetic import SyntheticRunner
 from ax.service.scheduler import get_fitted_model_bridge, Scheduler, SchedulerOptions
 from ax.utils.common.constants import Keys
 from ax.utils.common.testutils import TestCase
+from ax.utils.stats.model_fit_stats import _entropy_via_kde, entropy_of_observations
 from ax.utils.testing.core_stubs import get_branin_search_space
 
 NUM_SOBOL = 5
@@ -83,6 +89,29 @@ def test_model_fit_metrics(self) -> None:
         std_branin = std["branin"]
         self.assertIsInstance(std_branin, float)
 
+        # checking non-default model-fit-metric
+        untransform = False
+        fit_metrics = compute_model_fit_metrics_from_modelbridge(
+            model_bridge=model_bridge,
+            experiment=scheduler.experiment,
+            generalization=True,
+            untransform=untransform,
+            fit_metrics_dict={"Entropy": entropy_of_observations},
+        )
+        entropy = fit_metrics.get("Entropy")
+        self.assertIsInstance(entropy, dict)
+        entropy = cast(Dict[str, float], entropy)
+        self.assertTrue("branin" in entropy)
+        entropy_branin = entropy["branin"]
+        self.assertIsInstance(entropy_branin, float)
+
+        y_obs, _, _ = _predict_on_cross_validation_data(
+            model_bridge=model_bridge, untransform=untransform
+        )
+        y_obs_branin = np.array(y_obs["branin"])[:, np.newaxis]
+        entropy_truth = _entropy_via_kde(y_obs_branin)
+        self.assertAlmostEqual(entropy_branin, entropy_truth)
+
         # testing with empty metrics
         empty_metrics = compute_model_fit_metrics_from_modelbridge(
             model_bridge=model_bridge,

ax/utils/stats/model_fit_stats.py

@@ -9,6 +9,7 @@
 
 import numpy as np
 from scipy.stats import fisher_exact, norm, pearsonr, spearmanr
+from sklearn.neighbors import KernelDensity
 
 """
 ################################ Model Fit Metrics ###############################
@@ -127,6 +128,50 @@ def std_of_the_standardized_error(
     return ((y_obs - y_pred) / se_pred).std()
 
 
+def entropy_of_observations(
+    y_obs: np.ndarray,
+    y_pred: np.ndarray,
+    se_pred: np.ndarray,
+    bandwidth: float = 0.1,
+) -> float:
+    """Computes the entropy of the observations y_obs using a kernel density estimator.
+    This can be used to quantify how "clustered" the outcomes are. NOTE: y_pred and
+    se_pred are not used, but are required for the API.
+
+    Args:
+        y_obs: An array of observations for a single metric.
+        y_pred: An array of the predicted values corresponding to y_obs.
+        se_pred: An array of the standard errors of the predicted values.
+        bandwidth: The kernel bandwidth. Defaults to 0.1, which is a reasonable value
+            for standardized outcomes y_obs. The rank ordering of the results on a set
+            of y_obs data sets is not generally sensitive to the bandwidth, if it is
+            held fixed across the data sets. The absolute value of the results however
+            changes significantly with the bandwidth.
+
+    Returns:
+        The scalar entropy of the observations.
+    """
+    if y_obs.ndim == 1:
+        y_obs = y_obs[:, np.newaxis]
+    return _entropy_via_kde(y_obs, bandwidth=bandwidth)
+
+
+def _entropy_via_kde(y: np.ndarray, bandwidth: float = 0.1) -> float:
+    """Computes the entropy of the kernel density estimate of the input data.
+
+    Args:
+        y: An (n x m) array of observations.
+        bandwidth: The kernel bandwidth.
+
+    Returns:
+        The scalar entropy of the kernel density estimate.
+    """
+    kde = KernelDensity(kernel="gaussian", bandwidth=bandwidth)
+    kde.fit(y)
+    log_p = kde.score_samples(y)  # computes the log probability of each data point
+    return -np.sum(np.exp(log_p) * log_p)  # compute entropy, the negated sum of p log p
+
+
 def _mean_prediction_ci(
     y_obs: np.ndarray, y_pred: np.ndarray, se_pred: np.ndarray
 ) -> float:

ax/utils/stats/tests/test_model_fit_stats.py

@@ -6,20 +6,56 @@
 
 import numpy as np
 from ax.utils.common.testutils import TestCase
-from ax.utils.stats.model_fit_stats import _fisher_exact_test_p
+from ax.utils.stats.model_fit_stats import _fisher_exact_test_p, entropy_of_observations
 from scipy.stats import fisher_exact
 
 
-class FisherExactTestTest(TestCase):
+class TestModelFitStats(TestCase):
+    def test_entropy_of_observations(self) -> None:
+        np.random.seed(1234)
+        n = 16
+        yc = np.ones(n)
+        yc[: n // 2] = -1
+        yc += np.random.randn(n) * 0.05
+        yr = np.random.randn(n)
+
+        # standardize both observations
+        yc = yc / yc.std()
+        yr = yr / yr.std()
+
+        ones = np.ones(n)
+
+        # compute entropy of observations
+        ec = entropy_of_observations(y_obs=yc, y_pred=ones, se_pred=ones, bandwidth=0.1)
+        er = entropy_of_observations(y_obs=yr, y_pred=ones, se_pred=ones, bandwidth=0.1)
+
+        # testing that the Gaussian distributed data has a much larger entropy than
+        # the clustered distribution
+        self.assertTrue(er - ec > 10.0)
+
+        ec2 = entropy_of_observations(
+            y_obs=yc, y_pred=ones, se_pred=ones, bandwidth=0.2
+        )
+        er2 = entropy_of_observations(
+            y_obs=yr, y_pred=ones, se_pred=ones, bandwidth=0.2
+        )
+        # entropy increases with larger bandwidth
+        self.assertGreater(ec2, ec)
+        self.assertGreater(er2, er)
+
+        # ordering of entropies stays the same, though the difference is smaller
+        self.assertTrue(er2 - ec2 > 3)
+
     def test_contingency_table_construction(self) -> None:
         # Create a dummy set of observations and predictions
         y_obs = np.array([1, 3, 2, 5, 7, 3])
         y_pred = np.array([2, 4, 1, 6, 8, 2.5])
+        se_pred = np.full(len(y_obs), np.nan)  # not used for fisher exact
 
         # Compute ground truth contingency table
         true_table = np.array([[2, 1], [1, 2]])
 
         scipy_result = fisher_exact(true_table, alternative="greater")[1]
-        ax_result = _fisher_exact_test_p(y_obs, y_pred, se_pred=None)
+        ax_result = _fisher_exact_test_p(y_obs, y_pred, se_pred=se_pred)
 
         self.assertEqual(scipy_result, ax_result)