scikit-learn · ogrisel · Sep 6, 2024 · Jul 5, 2024 · Jul 9, 2024 · Aug 8, 2024
diff --git a/doc/whats_new/v1.6.rst b/doc/whats_new/v1.6.rst
@@ -229,6 +229,10 @@ Changelog
 :mod:`sklearn.linear_model`
 ...........................
 
+- |Fix| :class:`linear_model.LogisticRegressionCV` corrects sample weight handling
+  for the calculation of test scores.
+  :pr:`29419` by :user:`Shruti Nath <snath-xoc>`.
+
 - |API| Deprecates `copy_X` in :class:`linear_model.TheilSenRegressor` as the parameter
   has no effect. `copy_X` will be removed in 1.8.
   :pr:`29105` by :user:`Adam Li <adam2392>`.

diff --git a/sklearn/linear_model/_logistic.py b/sklearn/linear_model/_logistic.py
@@ -736,9 +736,11 @@ def _log_reg_scoring_path(
     y_train = y[train]
     y_test = y[test]
 
+    sw_train, sw_test = None, None
     if sample_weight is not None:
         sample_weight = _check_sample_weight(sample_weight, X)
-        sample_weight = sample_weight[train]
+        sw_train = sample_weight[train]
+        sw_test = sample_weight[test]
 
     coefs, Cs, n_iter = _logistic_regression_path(
         X_train,
@@ -759,7 +761,7 @@ def _log_reg_scoring_path(
         random_state=random_state,
         check_input=False,
         max_squared_sum=max_squared_sum,
-        sample_weight=sample_weight,
+        sample_weight=sw_train,
     )
 
     log_reg = LogisticRegression(solver=solver, multi_class=multi_class)
@@ -793,12 +795,11 @@ def _log_reg_scoring_path(
             log_reg.intercept_ = 0.0
 
         if scoring is None:
-            scores.append(log_reg.score(X_test, y_test))
+            scores.append(log_reg.score(X_test, y_test, sample_weight=sw_test))
         else:
             score_params = score_params or {}
             score_params = _check_method_params(X=X, params=score_params, indices=test)
             scores.append(scoring(log_reg, X_test, y_test, **score_params))
-
     return coefs, Cs, np.array(scores), n_iter
 
 

diff --git a/sklearn/linear_model/tests/test_logistic.py b/sklearn/linear_model/tests/test_logistic.py
@@ -31,6 +31,7 @@
 from sklearn.metrics import get_scorer, log_loss
 from sklearn.model_selection import (
     GridSearchCV,
+    LeaveOneGroupOut,
     StratifiedKFold,
     cross_val_score,
     train_test_split,
@@ -775,86 +776,167 @@ def test_logistic_regressioncv_class_weights(weight, class_weight, global_random
         )
 
 
-def test_logistic_regression_sample_weights():
+@pytest.mark.parametrize("problem", ("single", "cv"))
+@pytest.mark.parametrize(
+    "solver", ("lbfgs", "liblinear", "newton-cg", "newton-cholesky", "sag", "saga")
+)
+def test_logistic_regression_sample_weights(problem, solver, global_random_seed):
+    n_samples_per_cv_group = 200
+    n_cv_groups = 3
+
     X, y = make_classification(
-        n_samples=20, n_features=5, n_informative=3, n_classes=2, random_state=0
+        n_samples=n_samples_per_cv_group * n_cv_groups,
+        n_features=5,
+        n_informative=3,
+        n_classes=2,
+        n_redundant=0,
+        random_state=global_random_seed,
     )
+    rng = np.random.RandomState(global_random_seed)
+    sw = np.ones(y.shape[0])
+
+    kw_weighted = {
+        "random_state": global_random_seed,
+        "fit_intercept": False,
+        "max_iter": 100_000 if solver.startswith("sag") else 1_000,
+        "tol": 1e-8,
+    }
+    kw_repeated = kw_weighted.copy()
+    sw[:n_samples_per_cv_group] = rng.randint(0, 5, size=n_samples_per_cv_group)
+    X_repeated = np.repeat(X, sw.astype(int), axis=0)
+    y_repeated = np.repeat(y, sw.astype(int), axis=0)
+
+    if problem == "single":
+        LR = LogisticRegression
+    elif problem == "cv":
+        LR = LogisticRegressionCV
+        # We weight the first fold 2 times more.
+        groups_weighted = np.concatenate(
+            [
+                np.full(n_samples_per_cv_group, 0),
+                np.full(n_samples_per_cv_group, 1),
+                np.full(n_samples_per_cv_group, 2),
+            ]
+        )
+        splits_weighted = list(LeaveOneGroupOut().split(X, groups=groups_weighted))
+        kw_weighted.update({"Cs": 100, "cv": splits_weighted})
+
+        groups_repeated = np.repeat(groups_weighted, sw.astype(int), axis=0)
+        splits_repeated = list(
+            LeaveOneGroupOut().split(X_repeated, groups=groups_repeated)
+        )
+        kw_repeated.update({"Cs": 100, "cv": splits_repeated})
+
+    clf_sw_weighted = LR(solver=solver, **kw_weighted)
+    clf_sw_repeated = LR(solver=solver, **kw_repeated)
+
+    if solver == "lbfgs":
+        # lbfgs has convergence issues on the data but this should not impact
+        # the quality of the results.
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore", ConvergenceWarning)
+            clf_sw_weighted.fit(X, y, sample_weight=sw)
+            clf_sw_repeated.fit(X_repeated, y_repeated)
+
+    else:
+        clf_sw_weighted.fit(X, y, sample_weight=sw)
+        clf_sw_repeated.fit(X_repeated, y_repeated)
+
+    if problem == "cv":
+        assert_allclose(clf_sw_weighted.scores_[1], clf_sw_repeated.scores_[1])
+    assert_allclose(clf_sw_weighted.coef_, clf_sw_repeated.coef_, atol=1e-5)
+
+
+@pytest.mark.parametrize(
+    "solver", ("lbfgs", "newton-cg", "newton-cholesky", "sag", "saga")
+)
+def test_logistic_regression_solver_class_weights(solver, global_random_seed):
+    # Test that passing class_weight as [1, 2] is the same as
+    # passing class weight = [1,1] but adjusting sample weights
+    # to be 2 for all instances of class 1.
+
+    X, y = make_classification(
+        n_samples=300,
+        n_features=5,
+        n_informative=3,
+        n_classes=2,
+        random_state=global_random_seed,
+    )
+
     sample_weight = y + 1
 
-    for LR in [LogisticRegression, LogisticRegressionCV]:
-        kw = {"random_state": 42, "fit_intercept": False}
-        if LR is LogisticRegressionCV:
-            kw.update({"Cs": 3, "cv": 3})
-
-        # Test that passing sample_weight as ones is the same as
-        # not passing them at all (default None)
-        for solver in ["lbfgs", "liblinear"]:
-            clf_sw_none = LR(solver=solver, **kw)
-            clf_sw_ones = LR(solver=solver, **kw)
-            clf_sw_none.fit(X, y)
-            clf_sw_ones.fit(X, y, sample_weight=np.ones(y.shape[0]))
-            assert_allclose(clf_sw_none.coef_, clf_sw_ones.coef_, rtol=1e-4)
-
-        # Test that sample weights work the same with the lbfgs,
-        # newton-cg, newton-cholesky and 'sag' solvers
-        clf_sw_lbfgs = LR(**kw, tol=1e-5)
-        clf_sw_lbfgs.fit(X, y, sample_weight=sample_weight)
-        for solver in set(SOLVERS) - set(["lbfgs"]):
-            clf_sw = LR(solver=solver, tol=1e-10 if solver == "sag" else 1e-5, **kw)
-            # ignore convergence warning due to small dataset with sag
-            with ignore_warnings():
-                clf_sw.fit(X, y, sample_weight=sample_weight)
-            assert_allclose(clf_sw_lbfgs.coef_, clf_sw.coef_, rtol=1e-4)
-
-        # Test that passing class_weight as [1,2] is the same as
-        # passing class weight = [1,1] but adjusting sample weights
-        # to be 2 for all instances of class 2
-        for solver in ["lbfgs", "liblinear"]:
-            clf_cw_12 = LR(solver=solver, class_weight={0: 1, 1: 2}, **kw)
-            clf_cw_12.fit(X, y)
-            clf_sw_12 = LR(solver=solver, **kw)
-            clf_sw_12.fit(X, y, sample_weight=sample_weight)
-            assert_allclose(clf_cw_12.coef_, clf_sw_12.coef_, rtol=1e-4)
+    kw_weighted = {
+        "random_state": global_random_seed,
+        "fit_intercept": False,
+        "max_iter": 100_000,
+        "tol": 1e-8,
+    }
+    clf_cw_12 = LogisticRegression(
+        solver=solver, class_weight={0: 1, 1: 2}, **kw_weighted
+    )
+    clf_cw_12.fit(X, y)
+    clf_sw_12 = LogisticRegression(solver=solver, **kw_weighted)
+    clf_sw_12.fit(X, y, sample_weight=sample_weight)
+    assert_allclose(clf_cw_12.coef_, clf_sw_12.coef_, atol=1e-6)
+
 
+def test_sample_and_class_weight_equivalence_liblinear(global_random_seed):
     # Test the above for l1 penalty and l2 penalty with dual=True.
     # since the patched liblinear code is different.
+
+    X, y = make_classification(
+        n_samples=300,
+        n_features=5,
+        n_informative=3,
+        n_classes=2,
+        random_state=global_random_seed,
+    )
+
+    sample_weight = y + 1
+
     clf_cw = LogisticRegression(
         solver="liblinear",
         fit_intercept=False,
         class_weight={0: 1, 1: 2},
         penalty="l1",
-        tol=1e-5,
-        random_state=42,
+        max_iter=10_000,
+        tol=1e-12,
+        random_state=global_random_seed,
     )
     clf_cw.fit(X, y)
     clf_sw = LogisticRegression(
         solver="liblinear",
         fit_intercept=False,
         penalty="l1",
-        tol=1e-5,
-        random_state=42,
+        max_iter=10_000,
+        tol=1e-12,
+        random_state=global_random_seed,
     )
     clf_sw.fit(X, y, sample_weight)
-    assert_array_almost_equal(clf_cw.coef_, clf_sw.coef_, decimal=4)
+    assert_allclose(clf_cw.coef_, clf_sw.coef_, atol=1e-10)
 
     clf_cw = LogisticRegression(
         solver="liblinear",
         fit_intercept=False,
         class_weight={0: 1, 1: 2},
         penalty="l2",
+        max_iter=10_000,
+        tol=1e-12,
         dual=True,
-        random_state=42,
+        random_state=global_random_seed,
     )
     clf_cw.fit(X, y)
     clf_sw = LogisticRegression(
         solver="liblinear",
         fit_intercept=False,
         penalty="l2",
+        max_iter=10_000,
+        tol=1e-12,
         dual=True,
-        random_state=42,
+        random_state=global_random_seed,
     )
     clf_sw.fit(X, y, sample_weight)
-    assert_array_almost_equal(clf_cw.coef_, clf_sw.coef_, decimal=4)
+    assert_allclose(clf_cw.coef_, clf_sw.coef_, atol=1e-10)
 
 
 def _compute_class_weight_dictionary(y):