ENH add support for array API to various metric (scikit-learn#29709)

virchan · OmarManzoor · adrinjalali · web-flow · commit e92dd4009269 · 2024-09-27T17:03:37.000+02:00
Co-authored-by: Omar Salman &lt;omar.salman2007@gmail.com&gt;
Co-authored-by: Adrin Jalali &lt;adrin.jalali@gmail.com&gt;
diff --git a/doc/modules/array_api.rst b/doc/modules/array_api.rst
@@ -121,6 +121,7 @@ Metrics
 - :func:`sklearn.metrics.mean_gamma_deviance`
 - :func:`sklearn.metrics.mean_poisson_deviance` (requires `enabling array API support for SciPy <https://docs.scipy.org/doc/scipy/dev/api-dev/array_api.html#using-array-api-standard-support>`_)
 - :func:`sklearn.metrics.mean_squared_error`
+- :func:`sklearn.metrics.mean_squared_log_error`
 - :func:`sklearn.metrics.mean_tweedie_deviance`
 - :func:`sklearn.metrics.pairwise.additive_chi2_kernel`
 - :func:`sklearn.metrics.pairwise.chi2_kernel`
@@ -134,6 +135,8 @@ Metrics
 - :func:`sklearn.metrics.pairwise.rbf_kernel` (see :ref:`device_support_for_float64`)
 - :func:`sklearn.metrics.pairwise.sigmoid_kernel`
 - :func:`sklearn.metrics.r2_score`
+- :func:`sklearn.metrics.root_mean_squared_error`
+- :func:`sklearn.metrics.root_mean_squared_log_error`
 - :func:`sklearn.metrics.zero_one_loss`
 
 Tools
diff --git a/doc/whats_new/v1.6.rst b/doc/whats_new/v1.6.rst
@@ -55,7 +55,10 @@ See :ref:`array_api` for more details.
 - :func:`sklearn.metrics.mean_gamma_deviance` :pr:`29239` by :user:`Emily Chen <EmilyXinyi>`;
 - :func:`sklearn.metrics.mean_poisson_deviance` :pr:`29227` by :user:`Emily Chen <EmilyXinyi>`;
 - :func:`sklearn.metrics.mean_squared_error` :pr:`29142` by :user:`Yaroslav Korobko <Tialo>`;
+- :func:`sklearn.metrics.mean_squared_log_error` :pr:`29709` by :user:`Virgil Chan <virchan>`;
 - :func:`sklearn.metrics.mean_tweedie_deviance` :pr:`28106` by :user:`Thomas Li <lithomas1>`;
+- :func:`sklearn.metrics.root_mean_squared_error` :pr:`29709` by :user:`Virgil Chan <virchan>`;
+- :func:`sklearn.metrics.root_mean_squared_log_error` :pr:`29709` by :user:`Virgil Chan <virchan>`;
 - :func:`sklearn.metrics.pairwise.additive_chi2_kernel` :pr:`29144` by :user:`Yaroslav Korobko <Tialo>`;
 - :func:`sklearn.metrics.pairwise.chi2_kernel` :pr:`29267` by :user:`Yaroslav Korobko <Tialo>`;
 - :func:`sklearn.metrics.pairwise.cosine_distances` :pr:`29265` by :user:`Emily Chen <EmilyXinyi>`;
@@ -313,6 +316,19 @@ Changelog
   is renamed into `ensure_all_finite`. `force_all_finite` will be removed in 1.8.
   :pr:`29404` by :user:`Jérémie du Boisberranger <jeremiedb>`.
 
+- |Fix| the functions :func:`metrics.mean_squared_log_error` and
+  :func:`metrics.root_mean_squared_log_error` now check whether
+  the inputs are within the correct domain for the function
+  :math:`y=\log(1+x)`, rather than :math:`y=\log(x)`.
+  :pr:`29709` by :user:`Virgil Chan <virchan>`.
+
+- |Fix| the functions :func:`metrics.mean_absolute_error`,
+  :func:`metrics.mean_absolute_percentage_error`, :func:`metrics.mean_squared_error`
+  and :func:`metrics.root_mean_squared_error` now explicitly check whether a scalar
+  will be returned when `multioutput=uniform_average`.
+  :pr:`29709` by :user:`Virgil Chan <virchan>`.
+
+
 :mod:`sklearn.model_selection`
 ..............................
 
diff --git a/sklearn/metrics/_regression.py b/sklearn/metrics/_regression.py
@@ -217,13 +217,12 @@ def mean_absolute_error(
             multioutput = None
 
     # Average across the outputs (if needed).
+    # The second call to `_average` should always return
+    # a scalar array that we convert to a Python float to
+    # consistently return the same eager evaluated value.
+    # Therefore, `axis=None`.
     mean_absolute_error = _average(output_errors, weights=multioutput)
 
-    # Since `y_pred.ndim <= 2` and `y_true.ndim <= 2`, the second call to _average
-    # should always return a scalar array that we convert to a Python float to
-    # consistently return the same eager evaluated value, irrespective of the
-    # Array API implementation.
-    assert mean_absolute_error.shape == ()
     return float(mean_absolute_error)
 
 
@@ -416,8 +415,13 @@ def mean_absolute_percentage_error(
             # pass None as weights to _average: uniform mean
             multioutput = None
 
+    # Average across the outputs (if needed).
+    # The second call to `_average` should always return
+    # a scalar array that we convert to a Python float to
+    # consistently return the same eager evaluated value.
+    # Therefore, `axis=None`.
     mean_absolute_percentage_error = _average(output_errors, weights=multioutput)
-    assert mean_absolute_percentage_error.shape == ()
+
     return float(mean_absolute_percentage_error)
 
 
@@ -524,12 +528,16 @@ def mean_squared_error(
         if multioutput == "raw_values":
             return output_errors
         elif multioutput == "uniform_average":
-            # pass None as weights to np.average: uniform mean
+            # pass None as weights to _average: uniform mean
             multioutput = None
 
-    # See comment in mean_absolute_error
+    # Average across the outputs (if needed).
+    # The second call to `_average` should always return
+    # a scalar array that we convert to a Python float to
+    # consistently return the same eager evaluated value.
+    # Therefore, `axis=None`.
     mean_squared_error = _average(output_errors, weights=multioutput)
-    assert mean_squared_error.shape == ()
+
     return float(mean_squared_error)
 
 
@@ -585,13 +593,16 @@ def root_mean_squared_error(
     >>> y_true = [3, -0.5, 2, 7]
     >>> y_pred = [2.5, 0.0, 2, 8]
     >>> root_mean_squared_error(y_true, y_pred)
-    np.float64(0.612...)
+    0.612...
     >>> y_true = [[0.5, 1],[-1, 1],[7, -6]]
     >>> y_pred = [[0, 2],[-1, 2],[8, -5]]
     >>> root_mean_squared_error(y_true, y_pred)
-    np.float64(0.822...)
+    0.822...
     """
-    output_errors = np.sqrt(
+
+    xp, _ = get_namespace(y_true, y_pred, sample_weight, multioutput)
+
+    output_errors = xp.sqrt(
         mean_squared_error(
             y_true, y_pred, sample_weight=sample_weight, multioutput="raw_values"
         )
@@ -601,10 +612,17 @@ def root_mean_squared_error(
         if multioutput == "raw_values":
             return output_errors
         elif multioutput == "uniform_average":
-            # pass None as weights to np.average: uniform mean
+            # pass None as weights to _average: uniform mean
             multioutput = None
 
-    return np.average(output_errors, weights=multioutput)
+    # Average across the outputs (if needed).
+    # The second call to `_average` should always return
+    # a scalar array that we convert to a Python float to
+    # consistently return the same eager evaluated value.
+    # Therefore, `axis=None`.
+    root_mean_squared_error = _average(output_errors, weights=multioutput)
+
+    return float(root_mean_squared_error)
 
 
 @validate_params(
@@ -700,20 +718,22 @@ def mean_squared_log_error(
                 y_true, y_pred, sample_weight=sample_weight, multioutput=multioutput
             )
 
-    y_type, y_true, y_pred, multioutput = _check_reg_targets(
-        y_true, y_pred, multioutput
+    xp, _ = get_namespace(y_true, y_pred)
+    dtype = _find_matching_floating_dtype(y_true, y_pred, xp=xp)
+
+    _, y_true, y_pred, _ = _check_reg_targets(
+        y_true, y_pred, multioutput, dtype=dtype, xp=xp
     )
-    check_consistent_length(y_true, y_pred, sample_weight)
 
-    if (y_true < 0).any() or (y_pred < 0).any():
+    if xp.any(y_true <= -1) or xp.any(y_pred <= -1):
         raise ValueError(
             "Mean Squared Logarithmic Error cannot be used when "
-            "targets contain negative values."
+            "targets contain values less than or equal to -1."
         )
 
     return mean_squared_error(
-        np.log1p(y_true),
-        np.log1p(y_pred),
+        xp.log1p(y_true),
+        xp.log1p(y_pred),
         sample_weight=sample_weight,
         multioutput=multioutput,
     )
@@ -773,20 +793,24 @@ def root_mean_squared_log_error(
     >>> y_true = [3, 5, 2.5, 7]
     >>> y_pred = [2.5, 5, 4, 8]
     >>> root_mean_squared_log_error(y_true, y_pred)
-    np.float64(0.199...)
+    0.199...
     """
-    _, y_true, y_pred, multioutput = _check_reg_targets(y_true, y_pred, multioutput)
-    check_consistent_length(y_true, y_pred, sample_weight)
+    xp, _ = get_namespace(y_true, y_pred)
+    dtype = _find_matching_floating_dtype(y_true, y_pred, xp=xp)
+
+    _, y_true, y_pred, multioutput = _check_reg_targets(
+        y_true, y_pred, multioutput, dtype=dtype, xp=xp
+    )
 
-    if (y_true < 0).any() or (y_pred < 0).any():
+    if xp.any(y_true <= -1) or xp.any(y_pred <= -1):
         raise ValueError(
             "Root Mean Squared Logarithmic Error cannot be used when "
-            "targets contain negative values."
+            "targets contain values less than or equal to -1."
         )
 
     return root_mean_squared_error(
-        np.log1p(y_true),
-        np.log1p(y_pred),
+        xp.log1p(y_true),
+        xp.log1p(y_pred),
         sample_weight=sample_weight,
         multioutput=multioutput,
     )
diff --git a/sklearn/metrics/tests/test_common.py b/sklearn/metrics/tests/test_common.py
@@ -37,6 +37,7 @@
     mean_pinball_loss,
     mean_poisson_deviance,
     mean_squared_error,
+    mean_squared_log_error,
     mean_tweedie_deviance,
     median_absolute_error,
     multilabel_confusion_matrix,
@@ -47,6 +48,8 @@
     recall_score,
     roc_auc_score,
     roc_curve,
+    root_mean_squared_error,
+    root_mean_squared_log_error,
     top_k_accuracy_score,
     zero_one_loss,
 )
@@ -120,11 +123,14 @@
     "max_error": max_error,
     "mean_absolute_error": mean_absolute_error,
     "mean_squared_error": mean_squared_error,
+    "mean_squared_log_error": mean_squared_log_error,
     "mean_pinball_loss": mean_pinball_loss,
     "median_absolute_error": median_absolute_error,
     "mean_absolute_percentage_error": mean_absolute_percentage_error,
     "explained_variance_score": explained_variance_score,
     "r2_score": partial(r2_score, multioutput="variance_weighted"),
+    "root_mean_squared_error": root_mean_squared_error,
+    "root_mean_squared_log_error": root_mean_squared_log_error,
     "mean_normal_deviance": partial(mean_tweedie_deviance, power=0),
     "mean_poisson_deviance": mean_poisson_deviance,
     "mean_gamma_deviance": mean_gamma_deviance,
@@ -458,7 +464,10 @@ def precision_recall_curve_padded_thresholds(*args, **kwargs):
     "mean_absolute_error",
     "median_absolute_error",
     "mean_squared_error",
+    "mean_squared_log_error",
     "r2_score",
+    "root_mean_squared_error",
+    "root_mean_squared_log_error",
     "explained_variance_score",
     "mean_absolute_percentage_error",
     "mean_pinball_loss",
@@ -482,6 +491,9 @@ def precision_recall_curve_padded_thresholds(*args, **kwargs):
     "micro_f1_score",
     "macro_f1_score",
     "weighted_recall_score",
+    "mean_squared_log_error",
+    "root_mean_squared_error",
+    "root_mean_squared_log_error",
     # P = R = F = accuracy in multiclass case
     "micro_f0.5_score",
     "micro_f1_score",
@@ -551,6 +563,12 @@ def precision_recall_curve_padded_thresholds(*args, **kwargs):
     "d2_tweedie_score",
 }
 
+# Metrics involving y = log(1+x)
+METRICS_WITH_LOG1P_Y = {
+    "mean_squared_log_error",
+    "root_mean_squared_log_error",
+}
+
 
 def _require_positive_targets(y1, y2):
     """Make targets strictly positive"""
@@ -560,6 +578,16 @@ def _require_positive_targets(y1, y2):
     return y1, y2
 
 
+def _require_log1p_targets(y1, y2):
+    """Make targets strictly larger than -1"""
+    offset = abs(min(y1.min(), y2.min())) - 0.99
+    y1 = y1.astype(float)
+    y2 = y2.astype(float)
+    y1 += offset
+    y2 += offset
+    return y1, y2
+
+
 def test_symmetry_consistency():
     # We shouldn't forget any metrics
     assert (
@@ -582,6 +610,9 @@ def test_symmetric_metric(name):
     if name in METRICS_REQUIRE_POSITIVE_Y:
         y_true, y_pred = _require_positive_targets(y_true, y_pred)
 
+    elif name in METRICS_WITH_LOG1P_Y:
+        y_true, y_pred = _require_log1p_targets(y_true, y_pred)
+
     y_true_bin = random_state.randint(0, 2, size=(20, 25))
     y_pred_bin = random_state.randint(0, 2, size=(20, 25))
 
@@ -631,6 +662,8 @@ def test_sample_order_invariance(name):
 
     if name in METRICS_REQUIRE_POSITIVE_Y:
         y_true, y_pred = _require_positive_targets(y_true, y_pred)
+    elif name in METRICS_WITH_LOG1P_Y:
+        y_true, y_pred = _require_log1p_targets(y_true, y_pred)
 
     y_true_shuffle, y_pred_shuffle = shuffle(y_true, y_pred, random_state=0)
 
@@ -698,6 +731,8 @@ def test_format_invariance_with_1d_vectors(name):
 
     if name in METRICS_REQUIRE_POSITIVE_Y:
         y1, y2 = _require_positive_targets(y1, y2)
+    elif name in METRICS_WITH_LOG1P_Y:
+        y1, y2 = _require_log1p_targets(y1, y2)
 
     y1_list = list(y1)
     y2_list = list(y2)
@@ -986,6 +1021,8 @@ def check_single_sample(name):
     # assert that no exception is thrown
     if name in METRICS_REQUIRE_POSITIVE_Y:
         values = [1, 2]
+    elif name in METRICS_WITH_LOG1P_Y:
+        values = [-0.7, 1]
     else:
         values = [0, 1]
     for i, j in product(values, repeat=2):
@@ -2017,6 +2054,10 @@ def check_array_api_metric_pairwise(metric, array_namespace, device, dtype_name)
         check_array_api_regression_metric,
         check_array_api_regression_metric_multioutput,
     ],
+    mean_squared_log_error: [
+        check_array_api_regression_metric,
+        check_array_api_regression_metric_multioutput,
+    ],
     d2_tweedie_score: [
         check_array_api_regression_metric,
     ],
@@ -2036,6 +2077,14 @@ def check_array_api_metric_pairwise(metric, array_namespace, device, dtype_name)
     linear_kernel: [check_array_api_metric_pairwise],
     polynomial_kernel: [check_array_api_metric_pairwise],
     rbf_kernel: [check_array_api_metric_pairwise],
+    root_mean_squared_error: [
+        check_array_api_regression_metric,
+        check_array_api_regression_metric_multioutput,
+    ],
+    root_mean_squared_log_error: [
+        check_array_api_regression_metric,
+        check_array_api_regression_metric_multioutput,
+    ],
     sigmoid_kernel: [check_array_api_metric_pairwise],
 }
 
diff --git a/sklearn/metrics/tests/test_regression.py b/sklearn/metrics/tests/test_regression.py
@@ -245,29 +245,33 @@ def test_regression_metrics_at_limits():
         assert_almost_equal(s([1, 1], [1, 1]), 1.0)
         assert_almost_equal(s([1, 1], [1, 1], force_finite=False), np.nan)
     msg = (
-        "Mean Squared Logarithmic Error cannot be used when targets "
-        "contain negative values."
+        "Mean Squared Logarithmic Error cannot be used when "
+        "targets contain values less than or equal to -1."
     )
     with pytest.raises(ValueError, match=msg):
         mean_squared_log_error([-1.0], [-1.0])
     msg = (
-        "Mean Squared Logarithmic Error cannot be used when targets "
-        "contain negative values."
+        "Mean Squared Logarithmic Error cannot be used when "
+        "targets contain values less than or equal to -1."
     )
     with pytest.raises(ValueError, match=msg):
         mean_squared_log_error([1.0, 2.0, 3.0], [1.0, -2.0, 3.0])
     msg = (
-        "Mean Squared Logarithmic Error cannot be used when targets "
-        "contain negative values."
+        "Mean Squared Logarithmic Error cannot be used when "
+        "targets contain values less than or equal to -1."
     )
     with pytest.raises(ValueError, match=msg):
         mean_squared_log_error([1.0, -2.0, 3.0], [1.0, 2.0, 3.0])
     msg = (
-        "Root Mean Squared Logarithmic Error cannot be used when targets "
-        "contain negative values."
+        "Mean Squared Logarithmic Error cannot be used when "
+        "targets contain values less than or equal to -1."
     )
     with pytest.raises(ValueError, match=msg):
         root_mean_squared_log_error([1.0, -2.0, 3.0], [1.0, 2.0, 3.0])
+    msg = (
+        "Root Mean Squared Logarithmic Error cannot be used when "
+        "targets contain values less than or equal to -1."
+    )
 
     # Tweedie deviance error
     power = -1.2
diff --git a/sklearn/metrics/tests/test_score_objects.py b/sklearn/metrics/tests/test_score_objects.py
