LogisticRegression convert to float64 (for SAG solver) (scikit-learn#…

…13243)

* Remove unused code

* Squash all the PR 9040 commits

initial PR commit

seq_dataset.pyx generated from template

seq_dataset.pyx generated from template scikit-learn#2

rename variables

fused types consistency test for seq_dataset

a

sklearn/utils/tests/test_seq_dataset.py

new if statement

add doc

sklearn/utils/seq_dataset.pyx.tp

minor changes

minor changes

typo fix

check numeric accuracy only up 5th decimal

Address oliver's request for changing test name

add test for make_dataset and rename a variable in test_seq_dataset

* FIX tests

* TST more numerically stable test_sgd.test_tol_parameter

* Added benchmarks to compare SAGA 32b and 64b

* Fixing gael's comments

* fix

* solve some issues

* PEP8

* Address lesteve comments

* fix merging

* avoid using assert_equal

* use all_close

* use explicit ArrayDataset64 and CSRDataset64

* fix: remove unused import

* Use parametrized to cover ArrayDaset-CSRDataset-32-64 matrix

* for consistency use 32 first then 64 + add 64 suffix to variables

* it would be cool if this worked !!!

* more verbose version

* revert SGD changes as much as possible.

* Add solvers back to bench_saga

* make 64 explicit in the naming

* remove checking native python type + add comparison between 32 64

* Add whatsnew with everyone with commits

* simplify a bit the testing

* simplify the parametrize

* update whatsnew

* fix pep8

.gitignore

@@ -71,3 +71,8 @@ _configtest.o.d
 
 # Used by mypy
 .mypy_cache/
+
+# files generated from a template
+sklearn/utils/seq_dataset.pyx
+sklearn/utils/seq_dataset.pxd
+sklearn/linear_model/sag_fast.pyx

benchmarks/bench_saga.py

@@ -1,11 +1,11 @@
-"""Author: Arthur Mensch
+"""Author: Arthur Mensch, Nelle Varoquaux
 
 Benchmarks of sklearn SAGA vs lightning SAGA vs Liblinear. Shows the gain
 in using multinomial logistic regression in term of learning time.
 """
 import json
 import time
-from os.path import expanduser
+import os
 
 from joblib import delayed, Parallel, Memory
 import matplotlib.pyplot as plt
@@ -21,7 +21,7 @@
 
 
 def fit_single(solver, X, y, penalty='l2', single_target=True, C=1,
-               max_iter=10, skip_slow=False):
+               max_iter=10, skip_slow=False, dtype=np.float64):
     if skip_slow and solver == 'lightning' and penalty == 'l1':
         print('skip_slowping l1 logistic regression with solver lightning.')
         return
@@ -37,7 +37,8 @@ def fit_single(solver, X, y, penalty='l2', single_target=True, C=1,
         multi_class = 'ovr'
     else:
         multi_class = 'multinomial'
-
+    X = X.astype(dtype)
+    y = y.astype(dtype)
     X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=42,
                                                         stratify=y)
     n_samples = X_train.shape[0]
@@ -69,11 +70,15 @@ def fit_single(solver, X, y, penalty='l2', single_target=True, C=1,
                                     multi_class=multi_class,
                                     C=C,
                                     penalty=penalty,
-                                    fit_intercept=False, tol=1e-24,
+                                    fit_intercept=False, tol=0,
                                     max_iter=this_max_iter,
                                     random_state=42,
                                     )
+
+        # Makes cpu cache even for all fit calls
+        X_train.max()
         t0 = time.clock()
+
         lr.fit(X_train, y_train)
         train_time = time.clock() - t0
 
@@ -106,9 +111,13 @@ def _predict_proba(lr, X):
     return softmax(pred)
 
 
-def exp(solvers, penalties, single_target, n_samples=30000, max_iter=20,
+def exp(solvers, penalty, single_target,
+        n_samples=30000, max_iter=20,
         dataset='rcv1', n_jobs=1, skip_slow=False):
-    mem = Memory(cachedir=expanduser('~/cache'), verbose=0)
+    dtypes_mapping = {
+        "float64": np.float64,
+        "float32": np.float32,
+    }
 
     if dataset == 'rcv1':
         rcv1 = fetch_rcv1()
@@ -151,21 +160,24 @@ def exp(solvers, penalties, single_target, n_samples=30000, max_iter=20,
     X = X[:n_samples]
     y = y[:n_samples]
 
-    cached_fit = mem.cache(fit_single)
     out = Parallel(n_jobs=n_jobs, mmap_mode=None)(
-        delayed(cached_fit)(solver, X, y,
+        delayed(fit_single)(solver, X, y,
                             penalty=penalty, single_target=single_target,
+                            dtype=dtype,
                             C=1, max_iter=max_iter, skip_slow=skip_slow)
         for solver in solvers
-        for penalty in penalties)
+        for dtype in dtypes_mapping.values())
 
     res = []
     idx = 0
-    for solver in solvers:
-        for penalty in penalties:
-            if not (skip_slow and solver == 'lightning' and penalty == 'l1'):
+    for dtype_name in dtypes_mapping.keys():
+        for solver in solvers:
+            if not (skip_slow and
+                    solver == 'lightning' and
+                    penalty == 'l1'):
                 lr, times, train_scores, test_scores, accuracies = out[idx]
                 this_res = dict(solver=solver, penalty=penalty,
+                                dtype=dtype_name,
                                 single_target=single_target,
                                 times=times, train_scores=train_scores,
                                 test_scores=test_scores,
@@ -177,68 +189,117 @@ def exp(solvers, penalties, single_target, n_samples=30000, max_iter=20,
         json.dump(res, f)
 
 
-def plot():
+def plot(outname=None):
     import pandas as pd
     with open('bench_saga.json', 'r') as f:
         f = json.load(f)
     res = pd.DataFrame(f)
-    res.set_index(['single_target', 'penalty'], inplace=True)
+    res.set_index(['single_target'], inplace=True)
 
-    grouped = res.groupby(level=['single_target', 'penalty'])
+    grouped = res.groupby(level=['single_target'])
 
-    colors = {'saga': 'blue', 'liblinear': 'orange', 'lightning': 'green'}
+    colors = {'saga': 'C0', 'liblinear': 'C1', 'lightning': 'C2'}
+    linestyles = {"float32": "--", "float64": "-"}
+    alpha = {"float64": 0.5, "float32": 1}
 
     for idx, group in grouped:
-        single_target, penalty = idx
-        fig = plt.figure(figsize=(12, 4))
-        ax = fig.add_subplot(131)
-
-        train_scores = group['train_scores'].values
-        ref = np.min(np.concatenate(train_scores)) * 0.999
-
-        for scores, times, solver in zip(group['train_scores'], group['times'],
-                                         group['solver']):
-            scores = scores / ref - 1
-            ax.plot(times, scores, label=solver, color=colors[solver])
+        single_target = idx
+        fig, axes = plt.subplots(figsize=(12, 4), ncols=4)
+        ax = axes[0]
+
+        for scores, times, solver, dtype in zip(group['train_scores'],
+                                                group['times'],
+                                                group['solver'],
+                                                group["dtype"]):
+            ax.plot(times, scores, label="%s - %s" % (solver, dtype),
+                    color=colors[solver],
+                    alpha=alpha[dtype],
+                    marker=".",
+                    linestyle=linestyles[dtype])
+            ax.axvline(times[-1], color=colors[solver],
+                       alpha=alpha[dtype],
+                       linestyle=linestyles[dtype])
         ax.set_xlabel('Time (s)')
         ax.set_ylabel('Training objective (relative to min)')
         ax.set_yscale('log')
 
-        ax = fig.add_subplot(132)
+        ax = axes[1]
 
-        test_scores = group['test_scores'].values
-        ref = np.min(np.concatenate(test_scores)) * 0.999
+        for scores, times, solver, dtype in zip(group['test_scores'],
+                                                group['times'],
+                                                group['solver'],
+                                                group["dtype"]):
+            ax.plot(times, scores, label=solver, color=colors[solver],
+                    linestyle=linestyles[dtype],
+                    marker=".",
+                    alpha=alpha[dtype])
+            ax.axvline(times[-1], color=colors[solver],
+                       alpha=alpha[dtype],
+                       linestyle=linestyles[dtype])
 
-        for scores, times, solver in zip(group['test_scores'], group['times'],
-                                         group['solver']):
-            scores = scores / ref - 1
-            ax.plot(times, scores, label=solver, color=colors[solver])
         ax.set_xlabel('Time (s)')
         ax.set_ylabel('Test objective (relative to min)')
         ax.set_yscale('log')
 
-        ax = fig.add_subplot(133)
+        ax = axes[2]
+        for accuracy, times, solver, dtype in zip(group['accuracies'],
+                                                  group['times'],
+                                                  group['solver'],
+                                                  group["dtype"]):
+            ax.plot(times, accuracy, label="%s - %s" % (solver, dtype),
+                    alpha=alpha[dtype],
+                    marker=".",
+                    color=colors[solver], linestyle=linestyles[dtype])
+            ax.axvline(times[-1], color=colors[solver],
+                       alpha=alpha[dtype],
+                       linestyle=linestyles[dtype])
 
-        for accuracy, times, solver in zip(group['accuracies'], group['times'],
-                                           group['solver']):
-            ax.plot(times, accuracy, label=solver, color=colors[solver])
         ax.set_xlabel('Time (s)')
         ax.set_ylabel('Test accuracy')
         ax.legend()
         name = 'single_target' if single_target else 'multi_target'
         name += '_%s' % penalty
         plt.suptitle(name)
-        name += '.png'
+        if outname is None:
+            outname = name + '.png'
         fig.tight_layout()
         fig.subplots_adjust(top=0.9)
-        plt.savefig(name)
-        plt.close(fig)
+
+        ax = axes[3]
+        for scores, times, solver, dtype in zip(group['train_scores'],
+                                                group['times'],
+                                                group['solver'],
+                                                group["dtype"]):
+            ax.plot(np.arange(len(scores)),
+                    scores, label="%s - %s" % (solver, dtype),
+                    marker=".",
+                    alpha=alpha[dtype],
+                    color=colors[solver], linestyle=linestyles[dtype])
+
+        ax.set_yscale("log")
+        ax.set_xlabel('# iterations')
+        ax.set_ylabel('Objective function')
+        ax.legend()
+
+        plt.savefig(outname)
 
 
 if __name__ == '__main__':
     solvers = ['saga', 'liblinear', 'lightning']
     penalties = ['l1', 'l2']
+    n_samples = [100000, 300000, 500000, 800000, None]
     single_target = True
-    exp(solvers, penalties, single_target, n_samples=None, n_jobs=1,
-        dataset='20newspaper', max_iter=20)
-    plot()
+    for penalty in penalties:
+        for n_sample in n_samples:
+            exp(solvers, penalty, single_target,
+                n_samples=n_sample, n_jobs=1,
+                dataset='rcv1', max_iter=10)
+            if n_sample is not None:
+                outname = "figures/saga_%s_%d.png" % (penalty, n_sample)
+            else:
+                outname = "figures/saga_%s_all.png" % (penalty,)
+            try:
+                os.makedirs("figures")
+            except OSError:
+                pass
+            plot(outname)

doc/whats_new/v0.21.rst

@@ -162,6 +162,11 @@ Support for Python 3.4 and below has been officially dropped.
 :mod:`sklearn.linear_model`
 ...........................
 
+- |Enhancement| :class:`linear_model.make_dataset` now preserves
+  ``float32`` and ``float64`` dtypes. :issues:`8769` and :issues:`11000` by
+  :user:`Nelle Varoquaux`_, :user:`Arthur Imbert <Henley13>`,
+  :user:`Guillaume Lemaitre <glemaitre>`, and :user:`Joan Massich <massich>`
+
 - |Feature| :class:`linear_model.LogisticRegression` and
   :class:`linear_model.LogisticRegressionCV` now support Elastic-Net penalty,
   with the 'saga' solver. :issue:`11646` by :user:`Nicolas Hug <NicolasHug>`.

sklearn/linear_model/base.py

@@ -32,7 +32,8 @@
 from ..utils.extmath import safe_sparse_dot
 from ..utils.sparsefuncs import mean_variance_axis, inplace_column_scale
 from ..utils.fixes import sparse_lsqr
-from ..utils.seq_dataset import ArrayDataset, CSRDataset
+from ..utils.seq_dataset import ArrayDataset32, CSRDataset32
+from ..utils.seq_dataset import ArrayDataset64, CSRDataset64
 from ..utils.validation import check_is_fitted
 from ..exceptions import NotFittedError
 from ..preprocessing.data import normalize as f_normalize
@@ -76,15 +77,22 @@ def make_dataset(X, y, sample_weight, random_state=None):
     """
 
     rng = check_random_state(random_state)
-    # seed should never be 0 in SequentialDataset
+    # seed should never be 0 in SequentialDataset64
     seed = rng.randint(1, np.iinfo(np.int32).max)
 
+    if X.dtype == np.float32:
+        CSRData = CSRDataset32
+        ArrayData = ArrayDataset32
+    else:
+        CSRData = CSRDataset64
+        ArrayData = ArrayDataset64
+
     if sp.issparse(X):
-        dataset = CSRDataset(X.data, X.indptr, X.indices, y, sample_weight,
-                             seed=seed)
+        dataset = CSRData(X.data, X.indptr, X.indices, y, sample_weight,
+                          seed=seed)
         intercept_decay = SPARSE_INTERCEPT_DECAY
     else:
-        dataset = ArrayDataset(X, y, sample_weight, seed=seed)
+        dataset = ArrayData(X, y, sample_weight, seed=seed)
         intercept_decay = 1.0
 
     return dataset, intercept_decay

sklearn/linear_model/logistic.py

@@ -964,7 +964,7 @@ def _logistic_regression_path(X, y, pos_class=None, Cs=10, fit_intercept=True,
 
         elif solver in ['sag', 'saga']:
             if multi_class == 'multinomial':
-                target = target.astype(np.float64)
+                target = target.astype(X.dtype, copy=False)
                 loss = 'multinomial'
             else:
                 loss = 'log'
@@ -1486,6 +1486,10 @@ def fit(self, X, y, sample_weight=None):
         Returns
         -------
         self : object
+
+        Notes
+        -----
+        The SAGA solver supports both float64 and float32 bit arrays.
         """
         solver = _check_solver(self.solver, self.penalty, self.dual)
 
@@ -1520,10 +1524,10 @@ def fit(self, X, y, sample_weight=None):
             raise ValueError("Tolerance for stopping criteria must be "
                              "positive; got (tol=%r)" % self.tol)
 
-        if solver in ['newton-cg']:
-            _dtype = [np.float64, np.float32]
-        else:
+        if solver in ['lbfgs', 'liblinear']:
             _dtype = np.float64
+        else:
+            _dtype = [np.float64, np.float32]
 
         X, y = check_X_y(X, y, accept_sparse='csr', dtype=_dtype, order="C",
                          accept_large_sparse=solver != 'liblinear')