I am getting KeyError:0 when running this code in python:
full_pipeline.fit(X_train, y_train)
Here is the completed code:
from gensim.sklearn_api import D2VTransformer
from sklearn.pipeline import FeatureUnion, Pipeline
from sklearn.model_selection import train_test_split
from sklearn.linear_model import LogisticRegression
name_pipeline = Pipeline( steps = [
( 'feature_selector', FeatureSelector(['name']) ),
( 'feature_transformer', D2VTransformer() ) ] )
description_pipeline = Pipeline( steps = [
( 'feature_selector', FeatureSelector(['description']) ),
( 'feature_transformer', D2VTransformer() ) ] )
X_pipeline = FeatureUnion( transformer_list = [
( 'name_pipeline', name_pipeline ),
( 'description_pipeline', description_pipeline ) ] )
#Split up the train and test data
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.1)
clf = LogisticRegression(random_state=0, class_weight='balanced', solver='lbfgs', max_iter=1000, multi_class='multinomial')
full_pipeline = Pipeline( steps =
[ ( 'pipeline', X_pipeline),
( 'model', clf ) ] )
full_pipeline.fit(X_train, y_train)
And here is the error I'm getting:
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
/usr/local/lib/python3.6/dist-packages/pandas/core/indexes/base.py in get_loc(self, key, method, tolerance)
2896 try:
-> 2897 return self._engine.get_loc(key)
2898 except KeyError:
pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()
pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()
pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.PyObjectHashTable.get_item()
pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.PyObjectHashTable.get_item()
KeyError: 0
During handling of the above exception, another exception occurred:
KeyError Traceback (most recent call last)
19 frames
<ipython-input-14-0ddbaedffb67> in <module>()
25 ( 'model', clf ) ] )
26
---> 27 full_pipeline.fit(X_train, y_train)
/usr/local/lib/python3.6/dist-packages/sklearn/pipeline.py in fit(self, X, y, **fit_params)
350 This estimator
351 """
--> 352 Xt, fit_params = self._fit(X, y, **fit_params)
353 with _print_elapsed_time('Pipeline',
354 self._log_message(len(self.steps) - 1)):
/usr/local/lib/python3.6/dist-packages/sklearn/pipeline.py in _fit(self, X, y, **fit_params)
315 message_clsname='Pipeline',
316 message=self._log_message(step_idx),
--> 317 **fit_params_steps[name])
318 # Replace the transformer of the step with the fitted
319 # transformer. This is necessary when loading the transformer
/usr/local/lib/python3.6/dist-packages/joblib/memory.py in __call__(self, *args, **kwargs)
353
354 def __call__(self, *args, **kwargs):
--> 355 return self.func(*args, **kwargs)
356
357 def call_and_shelve(self, *args, **kwargs):
/usr/local/lib/python3.6/dist-packages/sklearn/pipeline.py in _fit_transform_one(transformer, X, y, weight, message_clsname, message, **fit_params)
714 with _print_elapsed_time(message_clsname, message):
715 if hasattr(transformer, 'fit_transform'):
--> 716 res = transformer.fit_transform(X, y, **fit_params)
717 else:
718 res = transformer.fit(X, y, **fit_params).transform(X)
/usr/local/lib/python3.6/dist-packages/sklearn/pipeline.py in fit_transform(self, X, y, **fit_params)
910 sum of n_components (output dimension) over transformers.
911 """
--> 912 results = self._parallel_func(X, y, fit_params, _fit_transform_one)
913 if not results:
914 # All transformers are None
/usr/local/lib/python3.6/dist-packages/sklearn/pipeline.py in _parallel_func(self, X, y, fit_params, func)
940 message=self._log_message(name, idx, len(transformers)),
941 **fit_params) for idx, (name, transformer,
--> 942 weight) in enumerate(transformers, 1))
943
944 def transform(self, X):
/usr/local/lib/python3.6/dist-packages/joblib/parallel.py in __call__(self, iterable)
1001 # remaining jobs.
1002 self._iterating = False
-> 1003 if self.dispatch_one_batch(iterator):
1004 self._iterating = self._original_iterator is not None
1005
/usr/local/lib/python3.6/dist-packages/joblib/parallel.py in dispatch_one_batch(self, iterator)
832 return False
833 else:
--> 834 self._dispatch(tasks)
835 return True
836
/usr/local/lib/python3.6/dist-packages/joblib/parallel.py in _dispatch(self, batch)
751 with self._lock:
752 job_idx = len(self._jobs)
--> 753 job = self._backend.apply_async(batch, callback=cb)
754 # A job can complete so quickly than its callback is
755 # called before we get here, causing self._jobs to
/usr/local/lib/python3.6/dist-packages/joblib/_parallel_backends.py in apply_async(self, func, callback)
199 def apply_async(self, func, callback=None):
200 """Schedule a func to be run"""
--> 201 result = ImmediateResult(func)
202 if callback:
203 callback(result)
/usr/local/lib/python3.6/dist-packages/joblib/_parallel_backends.py in __init__(self, batch)
580 # Don't delay the application, to avoid keeping the input
581 # arguments in memory
--> 582 self.results = batch()
583
584 def get(self):
/usr/local/lib/python3.6/dist-packages/joblib/parallel.py in __call__(self)
254 with parallel_backend(self._backend, n_jobs=self._n_jobs):
255 return [func(*args, **kwargs)
--> 256 for func, args, kwargs in self.items]
257
258 def __len__(self):
/usr/local/lib/python3.6/dist-packages/joblib/parallel.py in <listcomp>(.0)
254 with parallel_backend(self._backend, n_jobs=self._n_jobs):
255 return [func(*args, **kwargs)
--> 256 for func, args, kwargs in self.items]
257
258 def __len__(self):
/usr/local/lib/python3.6/dist-packages/sklearn/pipeline.py in _fit_transform_one(transformer, X, y, weight, message_clsname, message, **fit_params)
714 with _print_elapsed_time(message_clsname, message):
715 if hasattr(transformer, 'fit_transform'):
--> 716 res = transformer.fit_transform(X, y, **fit_params)
717 else:
718 res = transformer.fit(X, y, **fit_params).transform(X)
/usr/local/lib/python3.6/dist-packages/sklearn/pipeline.py in fit_transform(self, X, y, **fit_params)
391 return Xt
392 if hasattr(last_step, 'fit_transform'):
--> 393 return last_step.fit_transform(Xt, y, **fit_params)
394 else:
395 return last_step.fit(Xt, y, **fit_params).transform(Xt)
/usr/local/lib/python3.6/dist-packages/sklearn/base.py in fit_transform(self, X, y, **fit_params)
554 else:
555 # fit method of arity 2 (supervised transformation)
--> 556 return self.fit(X, y, **fit_params).transform(X)
557
558
/usr/local/lib/python3.6/dist-packages/gensim/sklearn_api/d2vmodel.py in fit(self, X, y)
158
159 """
--> 160 if isinstance(X[0], doc2vec.TaggedDocument):
161 d2v_sentences = X
162 else:
/usr/local/lib/python3.6/dist-packages/pandas/core/frame.py in __getitem__(self, key)
2993 if self.columns.nlevels > 1:
2994 return self._getitem_multilevel(key)
-> 2995 indexer = self.columns.get_loc(key)
2996 if is_integer(indexer):
2997 indexer = [indexer]
/usr/local/lib/python3.6/dist-packages/pandas/core/indexes/base.py in get_loc(self, key, method, tolerance)
2897 return self._engine.get_loc(key)
2898 except KeyError:
-> 2899 return self._engine.get_loc(self._maybe_cast_indexer(key))
2900 indexer = self.get_indexer([key], method=method, tolerance=tolerance)
2901 if indexer.ndim > 1 or indexer.size > 1:
pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()
pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()
pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.PyObjectHashTable.get_item()
pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.PyObjectHashTable.get_item()
KeyError: 0
Does anyone know why might this happen? I think it has to do with D2VTransformer because when I'm running the code below I'm getting the same error:
model = D2VTransformer(min_count=1, size=5)
docvecs = model.fit_transform(X_train)
But when trying to select only one column from the dataframe:
docvecs = model.fit_transform(X_train['name'])
it doesn't throw an error and that is why when I created the pipelines I've only used one column, but still getting the error.
This is how X_train looks.
name description
9107 way great entrepreneur push limit help succeed way great entrepreneur push limit
7706 dit het team week week dit het team week week
3995 decorate home jewel tone feel bold colour choice inspire fill home abun...
5220 attic meat district attic meat district
3412 tee apparel choose design item clothe accessory piece inde...
... ... ...
3830 marque web designer mode marque web designer
3261 design holiday rest bite try lear magazine dai... design holiday rest bite try lear
2415 hallucinatory house father spirit music room hold tower season rug produce early...
7223 jacket rise jacket rise
4697 cupcake bake explorer love love chocolate cupcake top kind easy foll...
And some more details about X_train:
X_train.shape
(7159, 2)
X_train.dtypes
name object
description object
dtype: object
It looks like there was a recent bug and fix in gensim (October 2019, and not yet in any official release) to make D2VTransformer more tolerant of some Pandas Series as data sources, to resolve exactly the same exception as you've hit.
The line of code changed is exactly the one shown in your extended error-stack - line 160 of d2vmodel.py, testing X[0].
I would suggest grabbing the raw source of the latest version of d2vmodel.py to use locally (instead of importing from gensim.sklearn_api), and check if that resolves your issue. See:
https://github.com/RaRe-Technologies/gensim/blob/develop/gensim/sklearn_api/d2vmodel.py
Related
I am trying to train a StackingClassifier in Sklearn, but I keep running into this error where the fit method seems to be complaining about me having passed it numpy arrays. To my knowledge, this is how all the fit methods in sklearn are supposed to work. I read and followed the example from the documentation and expanded on it to include a more complex and comprehensive pipeline that would process categorical, ordinal, scalar, and text data.
Sorry in advance for the lengthy code sample, but I felt it was necessary to provide a complete reproducible example. Simply breaking down the pipeline into its constituent estimators and test those individually did not raise any exceptions, so I figure that the error somehow comes from the gestalt estimator.
Select Features
categorical_data = [
"race",
"gender",
"admission_type_id",
"discharge_disposition_id",
"admission_source_id",
"insulin",
"diabetesMed",
"change",
"payer_code",
"A1Cresult",
"metformin",
"repaglinide",
"nateglinide",
"chlorpropamide",
"glimepiride",
"glipizide",
"glyburide",
"tolbutamide",
"pioglitazone",
"rosiglitazone",
"acarbose",
"miglitol",
"tolazamide",
"glyburide.metformin",
"glipizide.metformin",
]
ordinal_data = [
"age"
]
scalar_data = [
"num_medications",
"time_in_hospital",
"num_lab_procedures",
"num_procedures",
"number_outpatient",
"number_emergency",
"number_inpatient",
"number_diagnoses",
]
text_data = [
"diag_1_desc",
"diag_2_desc",
"diag_3_desc"
]
Create Column Transformers
impute_trans = compose.make_column_transformer(
(
impute.SimpleImputer(
strategy="constant",
fill_value="missing"
),
categorical_data
)
)
encode_trans = compose.make_column_transformer(
(
preprocessing.OneHotEncoder(
sparse=False,
handle_unknown="ignore"
),
categorical_data
),
(
preprocessing.OrdinalEncoder(),
ordinal_data
)
)
scalar_trans = compose.make_column_transformer(
(preprocessing.StandardScaler(), scalar_data),
)
text_trans = compose.make_column_transformer(
(TfidfVectorizer(ngram_range=(1,2)), "diag_1_desc"),
(TfidfVectorizer(ngram_range=(1,2)), "diag_2_desc"),
(TfidfVectorizer(ngram_range=(1,2)), "diag_3_desc"),
)
Create Estimators
cat_pre_pipe = make_pipeline(impute_trans, encode_trans)
logreg = LogisticRegression(
solver = "saga",
penalty="elasticnet",
l1_ratio=0.5,
max_iter=1000
)
text_pipe = make_pipeline(text_trans, logreg)
scalar_pipe = make_pipeline(scalar_trans, logreg)
cat_pipe = make_pipeline(cat_pre_pipe, logreg)
estimators = [
("cat", cat_pipe),
("text", text_pipe),
("scalar", scalar_pipe)
]
Create Stacking Classifier
stack_clf = StackingClassifier(
estimators=estimators,
final_estimator=logreg
)
diabetes_data = pd.read_csv("8k_diabetes.csv", delimiter=',')
x_train, x_test, y_train, y_test = train_test_split(
pd.concat([
preprocess_dataframe(diabetes_data[text_data]),
diabetes_data[categorical_data + scalar_data]
], axis=1),
diabetes_data["readmitted"].astype(int)
)
stack_clf.fit(x_train, y_train)
Complete Stack Trace
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
File ~/anaconda3/envs/assignment2/lib/python3.8/site-packages/sklearn/utils/__init__.py:409, in _get_column_indices(X, key)
408 try:
--> 409 all_columns = X.columns
410 except AttributeError:
AttributeError: 'numpy.ndarray' object has no attribute 'columns'
During handling of the above exception, another exception occurred:
ValueError Traceback (most recent call last)
Input In [19], in <cell line: 1>()
----> 1 stack_clf.fit(x_train, y_train)
File ~/anaconda3/envs/assignment2/lib/python3.8/site-packages/sklearn/ensemble/_stacking.py:488, in StackingClassifier.fit(self, X, y, sample_weight)
486 self._le = LabelEncoder().fit(y)
487 self.classes_ = self._le.classes_
--> 488 return super().fit(X, self._le.transform(y), sample_weight)
File ~/anaconda3/envs/assignment2/lib/python3.8/site-packages/sklearn/ensemble/_stacking.py:158, in _BaseStacking.fit(self, X, y, sample_weight)
153 stack_method = [self.stack_method] * len(all_estimators)
155 # Fit the base estimators on the whole training data. Those
156 # base estimators will be used in transform, predict, and
157 # predict_proba. They are exposed publicly.
--> 158 self.estimators_ = Parallel(n_jobs=self.n_jobs)(
159 delayed(_fit_single_estimator)(clone(est), X, y, sample_weight)
160 for est in all_estimators
161 if est != "drop"
162 )
164 self.named_estimators_ = Bunch()
165 est_fitted_idx = 0
File ~/anaconda3/envs/assignment2/lib/python3.8/site-packages/joblib/parallel.py:1043, in Parallel.__call__(self, iterable)
1034 try:
1035 # Only set self._iterating to True if at least a batch
1036 # was dispatched. In particular this covers the edge
(...)
1040 # was very quick and its callback already dispatched all the
1041 # remaining jobs.
1042 self._iterating = False
-> 1043 if self.dispatch_one_batch(iterator):
1044 self._iterating = self._original_iterator is not None
1046 while self.dispatch_one_batch(iterator):
File ~/anaconda3/envs/assignment2/lib/python3.8/site-packages/joblib/parallel.py:861, in Parallel.dispatch_one_batch(self, iterator)
859 return False
860 else:
--> 861 self._dispatch(tasks)
862 return True
File ~/anaconda3/envs/assignment2/lib/python3.8/site-packages/joblib/parallel.py:779, in Parallel._dispatch(self, batch)
777 with self._lock:
778 job_idx = len(self._jobs)
--> 779 job = self._backend.apply_async(batch, callback=cb)
780 # A job can complete so quickly than its callback is
781 # called before we get here, causing self._jobs to
782 # grow. To ensure correct results ordering, .insert is
783 # used (rather than .append) in the following line
784 self._jobs.insert(job_idx, job)
File ~/anaconda3/envs/assignment2/lib/python3.8/site-packages/joblib/_parallel_backends.py:208, in SequentialBackend.apply_async(self, func, callback)
206 def apply_async(self, func, callback=None):
207 """Schedule a func to be run"""
--> 208 result = ImmediateResult(func)
209 if callback:
210 callback(result)
File ~/anaconda3/envs/assignment2/lib/python3.8/site-packages/joblib/_parallel_backends.py:572, in ImmediateResult.__init__(self, batch)
569 def __init__(self, batch):
570 # Don't delay the application, to avoid keeping the input
571 # arguments in memory
--> 572 self.results = batch()
File ~/anaconda3/envs/assignment2/lib/python3.8/site-packages/joblib/parallel.py:262, in BatchedCalls.__call__(self)
258 def __call__(self):
259 # Set the default nested backend to self._backend but do not set the
260 # change the default number of processes to -1
261 with parallel_backend(self._backend, n_jobs=self._n_jobs):
--> 262 return [func(*args, **kwargs)
263 for func, args, kwargs in self.items]
File ~/anaconda3/envs/assignment2/lib/python3.8/site-packages/joblib/parallel.py:262, in <listcomp>(.0)
258 def __call__(self):
259 # Set the default nested backend to self._backend but do not set the
260 # change the default number of processes to -1
261 with parallel_backend(self._backend, n_jobs=self._n_jobs):
--> 262 return [func(*args, **kwargs)
263 for func, args, kwargs in self.items]
File ~/anaconda3/envs/assignment2/lib/python3.8/site-packages/sklearn/utils/fixes.py:216, in _FuncWrapper.__call__(self, *args, **kwargs)
214 def __call__(self, *args, **kwargs):
215 with config_context(**self.config):
--> 216 return self.function(*args, **kwargs)
File ~/anaconda3/envs/assignment2/lib/python3.8/site-packages/sklearn/ensemble/_base.py:42, in _fit_single_estimator(estimator, X, y, sample_weight, message_clsname, message)
40 else:
41 with _print_elapsed_time(message_clsname, message):
---> 42 estimator.fit(X, y)
43 return estimator
File ~/anaconda3/envs/assignment2/lib/python3.8/site-packages/sklearn/pipeline.py:390, in Pipeline.fit(self, X, y, **fit_params)
364 """Fit the model.
365
366 Fit all the transformers one after the other and transform the
(...)
387 Pipeline with fitted steps.
388 """
389 fit_params_steps = self._check_fit_params(**fit_params)
--> 390 Xt = self._fit(X, y, **fit_params_steps)
391 with _print_elapsed_time("Pipeline", self._log_message(len(self.steps) - 1)):
392 if self._final_estimator != "passthrough":
File ~/anaconda3/envs/assignment2/lib/python3.8/site-packages/sklearn/pipeline.py:348, in Pipeline._fit(self, X, y, **fit_params_steps)
346 cloned_transformer = clone(transformer)
347 # Fit or load from cache the current transformer
--> 348 X, fitted_transformer = fit_transform_one_cached(
349 cloned_transformer,
350 X,
351 y,
352 None,
353 message_clsname="Pipeline",
354 message=self._log_message(step_idx),
355 **fit_params_steps[name],
356 )
357 # Replace the transformer of the step with the fitted
358 # transformer. This is necessary when loading the transformer
359 # from the cache.
360 self.steps[step_idx] = (name, fitted_transformer)
File ~/anaconda3/envs/assignment2/lib/python3.8/site-packages/joblib/memory.py:349, in NotMemorizedFunc.__call__(self, *args, **kwargs)
348 def __call__(self, *args, **kwargs):
--> 349 return self.func(*args, **kwargs)
File ~/anaconda3/envs/assignment2/lib/python3.8/site-packages/sklearn/pipeline.py:893, in _fit_transform_one(transformer, X, y, weight, message_clsname, message, **fit_params)
891 with _print_elapsed_time(message_clsname, message):
892 if hasattr(transformer, "fit_transform"):
--> 893 res = transformer.fit_transform(X, y, **fit_params)
894 else:
895 res = transformer.fit(X, y, **fit_params).transform(X)
File ~/anaconda3/envs/assignment2/lib/python3.8/site-packages/sklearn/pipeline.py:434, in Pipeline.fit_transform(self, X, y, **fit_params)
432 fit_params_last_step = fit_params_steps[self.steps[-1][0]]
433 if hasattr(last_step, "fit_transform"):
--> 434 return last_step.fit_transform(Xt, y, **fit_params_last_step)
435 else:
436 return last_step.fit(Xt, y, **fit_params_last_step).transform(Xt)
File ~/anaconda3/envs/assignment2/lib/python3.8/site-packages/sklearn/compose/_column_transformer.py:672, in ColumnTransformer.fit_transform(self, X, y)
670 self._check_n_features(X, reset=True)
671 self._validate_transformers()
--> 672 self._validate_column_callables(X)
673 self._validate_remainder(X)
675 result = self._fit_transform(X, y, _fit_transform_one)
File ~/anaconda3/envs/assignment2/lib/python3.8/site-packages/sklearn/compose/_column_transformer.py:352, in ColumnTransformer._validate_column_callables(self, X)
350 columns = columns(X)
351 all_columns.append(columns)
--> 352 transformer_to_input_indices[name] = _get_column_indices(X, columns)
354 self._columns = all_columns
355 self._transformer_to_input_indices = transformer_to_input_indices
File ~/anaconda3/envs/assignment2/lib/python3.8/site-packages/sklearn/utils/__init__.py:411, in _get_column_indices(X, key)
409 all_columns = X.columns
410 except AttributeError:
--> 411 raise ValueError(
412 "Specifying the columns using strings is only "
413 "supported for pandas DataFrames"
414 )
415 if isinstance(key, str):
416 columns = [key]
ValueError: Specifying the columns using strings is only supported for pandas DataFrames
Full Pipeline Diagram
Your categorical pipeline chains two column transformers together. After the first one, the output is a numpy array, but then the second one cannot select transformers by column name as you've requested. Notice the final error message is more informative here, ValueError: Specifying the columns using strings is only supported for pandas DataFrames.
I'd suggest using one column transformer with separate pipelines instead of one pipeline with multiple columntransformers for this reason.
I am building a model using customized transformers (KeyError: "None of [Index([('A','B','C')] , dtype='object')] are in the [columns]).
When I run the below code, I get an error because of .fit:
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-165-289e1d466eb9> in <module>
10
11 # fit on the complete pipeline
---> 12 training = full_pipeline.fit(X, y)
13
14 # metrics
~/opt/anaconda3/lib/python3.8/site-packages/sklearn/pipeline.py in fit(self, X, y, **fit_params)
339 """
340 fit_params_steps = self._check_fit_params(**fit_params)
--> 341 Xt = self._fit(X, y, **fit_params_steps)
342 with _print_elapsed_time('Pipeline',
343 self._log_message(len(self.steps) - 1)):
~/opt/anaconda3/lib/python3.8/site-packages/sklearn/pipeline.py in _fit(self, X, y, **fit_params_steps)
301 cloned_transformer = clone(transformer)
302 # Fit or load from cache the current transformer
--> 303 X, fitted_transformer = fit_transform_one_cached(
304 cloned_transformer, X, y, None,
305 message_clsname='Pipeline',
~/opt/anaconda3/lib/python3.8/site-packages/joblib/memory.py in __call__(self, *args, **kwargs)
350
351 def __call__(self, *args, **kwargs):
--> 352 return self.func(*args, **kwargs)
353
354 def call_and_shelve(self, *args, **kwargs):
~/opt/anaconda3/lib/python3.8/site-packages/sklearn/pipeline.py in _fit_transform_one(transformer, X, y, weight, message_clsname, message, **fit_params)
752 with _print_elapsed_time(message_clsname, message):
753 if hasattr(transformer, 'fit_transform'):
--> 754 res = transformer.fit_transform(X, y, **fit_params)
755 else:
756 res = transformer.fit(X, y, **fit_params).transform(X)
~/opt/anaconda3/lib/python3.8/site-packages/sklearn/pipeline.py in fit_transform(self, X, y, **fit_params)
385 fit_params_last_step = fit_params_steps[self.steps[-1][0]]
386 if hasattr(last_step, 'fit_transform'):
--> 387 return last_step.fit_transform(Xt, y, **fit_params_last_step)
388 else:
389 return last_step.fit(Xt, y,
~/opt/anaconda3/lib/python3.8/site-packages/sklearn/pipeline.py in fit_transform(self, X, y, **fit_params)
978 sum of n_components (output dimension) over transformers.
979 """
--> 980 results = self._parallel_func(X, y, fit_params, _fit_transform_one)
981 if not results:
982 # All transformers are None
~/opt/anaconda3/lib/python3.8/site-packages/sklearn/pipeline.py in _parallel_func(self, X, y, fit_params, func)
1000 transformers = list(self._iter())
1001
-> 1002 return Parallel(n_jobs=self.n_jobs)(delayed(func)(
1003 transformer, X, y, weight,
1004 message_clsname='FeatureUnion',
~/opt/anaconda3/lib/python3.8/site-packages/joblib/parallel.py in __call__(self, iterable)
1042 self._iterating = self._original_iterator is not None
1043
-> 1044 while self.dispatch_one_batch(iterator):
1045 pass
1046
~/opt/anaconda3/lib/python3.8/site-packages/joblib/parallel.py in dispatch_one_batch(self, iterator)
857 return False
858 else:
--> 859 self._dispatch(tasks)
860 return True
861
~/opt/anaconda3/lib/python3.8/site-packages/joblib/parallel.py in _dispatch(self, batch)
775 with self._lock:
776 job_idx = len(self._jobs)
--> 777 job = self._backend.apply_async(batch, callback=cb)
778 # A job can complete so quickly than its callback is
779 # called before we get here, causing self._jobs to
~/opt/anaconda3/lib/python3.8/site-packages/joblib/_parallel_backends.py in apply_async(self, func, callback)
206 def apply_async(self, func, callback=None):
207 """Schedule a func to be run"""
--> 208 result = ImmediateResult(func)
209 if callback:
210 callback(result)
~/opt/anaconda3/lib/python3.8/site-packages/joblib/_parallel_backends.py in __init__(self, batch)
570 # Don't delay the application, to avoid keeping the input
571 # arguments in memory
--> 572 self.results = batch()
573
574 def get(self):
~/opt/anaconda3/lib/python3.8/site-packages/joblib/parallel.py in __call__(self)
260 # change the default number of processes to -1
261 with parallel_backend(self._backend, n_jobs=self._n_jobs):
--> 262 return [func(*args, **kwargs)
263 for func, args, kwargs in self.items]
264
~/opt/anaconda3/lib/python3.8/site-packages/joblib/parallel.py in <listcomp>(.0)
260 # change the default number of processes to -1
261 with parallel_backend(self._backend, n_jobs=self._n_jobs):
--> 262 return [func(*args, **kwargs)
263 for func, args, kwargs in self.items]
264
~/opt/anaconda3/lib/python3.8/site-packages/sklearn/utils/fixes.py in __call__(self, *args, **kwargs)
220 def __call__(self, *args, **kwargs):
221 with config_context(**self.config):
--> 222 return self.function(*args, **kwargs)
~/opt/anaconda3/lib/python3.8/site-packages/sklearn/pipeline.py in _fit_transform_one(transformer, X, y, weight, message_clsname, message, **fit_params)
752 with _print_elapsed_time(message_clsname, message):
753 if hasattr(transformer, 'fit_transform'):
--> 754 res = transformer.fit_transform(X, y, **fit_params)
755 else:
756 res = transformer.fit(X, y, **fit_params).transform(X)
~/opt/anaconda3/lib/python3.8/site-packages/sklearn/pipeline.py in fit_transform(self, X, y, **fit_params)
385 fit_params_last_step = fit_params_steps[self.steps[-1][0]]
386 if hasattr(last_step, 'fit_transform'):
--> 387 return last_step.fit_transform(Xt, y, **fit_params_last_step)
388 else:
389 return last_step.fit(Xt, y,
~/opt/anaconda3/lib/python3.8/site-packages/sklearn/feature_extraction/text.py in fit_transform(self, raw_documents, y)
1200 max_features = self.max_features
1201
-> 1202 vocabulary, X = self._count_vocab(raw_documents,
1203 self.fixed_vocabulary_)
1204
~/opt/anaconda3/lib/python3.8/site-packages/sklearn/feature_extraction/text.py in _count_vocab(self, raw_documents, fixed_vocab)
1112 for doc in raw_documents:
1113 feature_counter = {}
-> 1114 for feature in analyze(doc):
1115 try:
1116 feature_idx = vocabulary[feature]
~/opt/anaconda3/lib/python3.8/site-packages/sklearn/feature_extraction/text.py in _analyze(doc, analyzer, tokenizer, ngrams, preprocessor, decoder, stop_words)
102 else:
103 if preprocessor is not None:
--> 104 doc = preprocessor(doc)
105 if tokenizer is not None:
106 doc = tokenizer(doc)
~/opt/anaconda3/lib/python3.8/site-packages/sklearn/feature_extraction/text.py in _preprocess(doc, accent_function, lower)
67 """
68 if lower:
---> 69 doc = doc.lower()
70 if accent_function is not None:
71 doc = accent_function(doc)
AttributeError: 'numpy.ndarray' object has no attribute 'lower'
The code is
# MODEL
from sklearn import tree
# Decision Tree
decision_tree = tree.DecisionTreeClassifier()
# define full pipeline --> preprocessing + model
full_pipeline = Pipeline(steps=[
('preprocess_pipeline', preprocess_pipeline),
('model', decision_tree)])
# fit on the complete pipeline
training = full_pipeline.fit(X, y) # <- this step returns the error
# metrics
score_test = \
round(training.score(X, y) * 100, 2)
print(f"\nTraining Accuracy: {score_test}")
I have also tried with .fit_transform but I get the same error.
I read this: AttributeError: 'numpy.ndarray' object has no attribute 'lower' fitting logistic model data but it seems that I am not passing X or y in the Decision tree like in that example, but maybe I am wrong.
Adding
# Defining the steps in the text pipeline
text_pipeline = Pipeline(steps=[
('text_transformer', TextTransformer()),
('cv', CountVectorizer(analyzer='word', ngram_range=(2, 2), lowercase=False))])
I get this new error:
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-159-289e1d466eb9> in <module>
10
11 # fit on the complete pipeline
---> 12 training = full_pipeline.fit(X, y)
13
14 # metrics
~/opt/anaconda3/lib/python3.8/site-packages/sklearn/pipeline.py in fit(self, X, y, **fit_params)
339 """
340 fit_params_steps = self._check_fit_params(**fit_params)
--> 341 Xt = self._fit(X, y, **fit_params_steps)
342 with _print_elapsed_time('Pipeline',
343 self._log_message(len(self.steps) - 1)):
~/opt/anaconda3/lib/python3.8/site-packages/sklearn/pipeline.py in _fit(self, X, y, **fit_params_steps)
301 cloned_transformer = clone(transformer)
302 # Fit or load from cache the current transformer
--> 303 X, fitted_transformer = fit_transform_one_cached(
304 cloned_transformer, X, y, None,
305 message_clsname='Pipeline',
~/opt/anaconda3/lib/python3.8/site-packages/joblib/memory.py in __call__(self, *args, **kwargs)
350
351 def __call__(self, *args, **kwargs):
--> 352 return self.func(*args, **kwargs)
353
354 def call_and_shelve(self, *args, **kwargs):
~/opt/anaconda3/lib/python3.8/site-packages/sklearn/pipeline.py in _fit_transform_one(transformer, X, y, weight, message_clsname, message, **fit_params)
752 with _print_elapsed_time(message_clsname, message):
753 if hasattr(transformer, 'fit_transform'):
--> 754 res = transformer.fit_transform(X, y, **fit_params)
755 else:
756 res = transformer.fit(X, y, **fit_params).transform(X)
~/opt/anaconda3/lib/python3.8/site-packages/sklearn/pipeline.py in fit_transform(self, X, y, **fit_params)
385 fit_params_last_step = fit_params_steps[self.steps[-1][0]]
386 if hasattr(last_step, 'fit_transform'):
--> 387 return last_step.fit_transform(Xt, y, **fit_params_last_step)
388 else:
389 return last_step.fit(Xt, y,
~/opt/anaconda3/lib/python3.8/site-packages/sklearn/pipeline.py in fit_transform(self, X, y, **fit_params)
978 sum of n_components (output dimension) over transformers.
979 """
--> 980 results = self._parallel_func(X, y, fit_params, _fit_transform_one)
981 if not results:
982 # All transformers are None
~/opt/anaconda3/lib/python3.8/site-packages/sklearn/pipeline.py in _parallel_func(self, X, y, fit_params, func)
1000 transformers = list(self._iter())
1001
-> 1002 return Parallel(n_jobs=self.n_jobs)(delayed(func)(
1003 transformer, X, y, weight,
1004 message_clsname='FeatureUnion',
~/opt/anaconda3/lib/python3.8/site-packages/joblib/parallel.py in __call__(self, iterable)
1042 self._iterating = self._original_iterator is not None
1043
-> 1044 while self.dispatch_one_batch(iterator):
1045 pass
1046
~/opt/anaconda3/lib/python3.8/site-packages/joblib/parallel.py in dispatch_one_batch(self, iterator)
857 return False
858 else:
--> 859 self._dispatch(tasks)
860 return True
861
~/opt/anaconda3/lib/python3.8/site-packages/joblib/parallel.py in _dispatch(self, batch)
775 with self._lock:
776 job_idx = len(self._jobs)
--> 777 job = self._backend.apply_async(batch, callback=cb)
778 # A job can complete so quickly than its callback is
779 # called before we get here, causing self._jobs to
~/opt/anaconda3/lib/python3.8/site-packages/joblib/_parallel_backends.py in apply_async(self, func, callback)
206 def apply_async(self, func, callback=None):
207 """Schedule a func to be run"""
--> 208 result = ImmediateResult(func)
209 if callback:
210 callback(result)
~/opt/anaconda3/lib/python3.8/site-packages/joblib/_parallel_backends.py in __init__(self, batch)
570 # Don't delay the application, to avoid keeping the input
571 # arguments in memory
--> 572 self.results = batch()
573
574 def get(self):
~/opt/anaconda3/lib/python3.8/site-packages/joblib/parallel.py in __call__(self)
260 # change the default number of processes to -1
261 with parallel_backend(self._backend, n_jobs=self._n_jobs):
--> 262 return [func(*args, **kwargs)
263 for func, args, kwargs in self.items]
264
~/opt/anaconda3/lib/python3.8/site-packages/joblib/parallel.py in <listcomp>(.0)
260 # change the default number of processes to -1
261 with parallel_backend(self._backend, n_jobs=self._n_jobs):
--> 262 return [func(*args, **kwargs)
263 for func, args, kwargs in self.items]
264
~/opt/anaconda3/lib/python3.8/site-packages/sklearn/utils/fixes.py in __call__(self, *args, **kwargs)
220 def __call__(self, *args, **kwargs):
221 with config_context(**self.config):
--> 222 return self.function(*args, **kwargs)
~/opt/anaconda3/lib/python3.8/site-packages/sklearn/pipeline.py in _fit_transform_one(transformer, X, y, weight, message_clsname, message, **fit_params)
752 with _print_elapsed_time(message_clsname, message):
753 if hasattr(transformer, 'fit_transform'):
--> 754 res = transformer.fit_transform(X, y, **fit_params)
755 else:
756 res = transformer.fit(X, y, **fit_params).transform(X)
~/opt/anaconda3/lib/python3.8/site-packages/sklearn/pipeline.py in fit_transform(self, X, y, **fit_params)
385 fit_params_last_step = fit_params_steps[self.steps[-1][0]]
386 if hasattr(last_step, 'fit_transform'):
--> 387 return last_step.fit_transform(Xt, y, **fit_params_last_step)
388 else:
389 return last_step.fit(Xt, y,
~/opt/anaconda3/lib/python3.8/site-packages/sklearn/feature_extraction/text.py in fit_transform(self, raw_documents, y)
1200 max_features = self.max_features
1201
-> 1202 vocabulary, X = self._count_vocab(raw_documents,
1203 self.fixed_vocabulary_)
1204
~/opt/anaconda3/lib/python3.8/site-packages/sklearn/feature_extraction/text.py in _count_vocab(self, raw_documents, fixed_vocab)
1112 for doc in raw_documents:
1113 feature_counter = {}
-> 1114 for feature in analyze(doc):
1115 try:
1116 feature_idx = vocabulary[feature]
~/opt/anaconda3/lib/python3.8/site-packages/sklearn/feature_extraction/text.py in _analyze(doc, analyzer, tokenizer, ngrams, preprocessor, decoder, stop_words)
104 doc = preprocessor(doc)
105 if tokenizer is not None:
--> 106 doc = tokenizer(doc)
107 if ngrams is not None:
108 if stop_words is not None:
TypeError: cannot use a string pattern on a bytes-like object
If I remove text_pipeline, the error does not occur, so it seems that something is going wrong because of the way to use countVectorizer.
An example of text is
an example
example number 1
this is another small example
I have other columns that are numerical and categorical.
Have you experienced a similar issue? If yes, how did you handle it?
A common error in text transformers of sklearn involves the shape of the data: unlike most other sklearn preprocessors, text transformers generally expect a one-dimensional input, and python's duck-typing causes weird errors from both arrays and strings being iterables.
Your TextTransformer.transform returns X[['Tweet']], which is 2-dimensional, and will cause problems with the subsequent CountVectorizer. (Converting to a numpy array with .values doesn't change the dimensionality problem, but there's also no compelling reason to do that conversion.) Returning X['Tweet'] instead should cure that problem.
could you help me with the problem below? Many thanks in advance.
Without fit_params=fit_params, the code below works fine, but I want to try early stopping with lgbm.
I did try to search for clues but found limited resources but some github issues from lightgbm and BayesSearchCV.
lg = lgb.LGBMClassifier(random_state=42, n_jobs=-1, objective='multiclass', n_estimators=5000)
fullPipeline = Pipeline(steps=[
('scaler', StandardScaler()),
('model', lg)
])
param_space = {'model__max_depth': [2, 63],
'model__num_leaves': [7, 4095],
}
fit_params = {
'early_stopping_rounds':30,
'eval_metric':'accuracy',
'eval_set':[(xValid, yValid)],
}
BSLGB = BayesSearchCV(fullPipeline, param_space, random_state=42, scoring='accuracy', cv=5, n_iter=50, verbose=3, n_jobs=-1,
fit_params=fit_params)
%time BSLGB.fit(xTrain.astype(float), yTrain)
Exception:
ValueError Traceback (most recent call last)
<timed eval> in <module>
C:\Anaconda3x64\envs\ml\lib\site-packages\skopt\searchcv.py in fit(self, X, y, groups, callback)
652 optim_result = self._step(
653 X, y, search_space, optimizer,
--> 654 groups=groups, n_points=n_points_adjusted
655 )
656 n_iter -= n_points
C:\Anaconda3x64\envs\ml\lib\site-packages\skopt\searchcv.py in _step(self, X, y, search_space, optimizer, groups, n_points)
548 refit = self.refit
549 self.refit = False
--> 550 self._fit(X, y, groups, params_dict)
551 self.refit = refit
552
C:\Anaconda3x64\envs\ml\lib\site-packages\skopt\searchcv.py in _fit(self, X, y, groups, parameter_iterable)
401 error_score=self.error_score
402 )
--> 403 for parameters in parameter_iterable
404 for train, test in cv_iter)
405
C:\Anaconda3x64\envs\ml\lib\site-packages\sklearn\externals\joblib\parallel.py in __call__(self, iterable)
928
929 with self._backend.retrieval_context():
--> 930 self.retrieve()
931 # Make sure that we get a last message telling us we are done
932 elapsed_time = time.time() - self._start_time
C:\Anaconda3x64\envs\ml\lib\site-packages\sklearn\externals\joblib\parallel.py in retrieve(self)
831 try:
832 if getattr(self._backend, 'supports_timeout', False):
--> 833 self._output.extend(job.get(timeout=self.timeout))
834 else:
835 self._output.extend(job.get())
C:\Anaconda3x64\envs\ml\lib\site-packages\sklearn\externals\joblib\_parallel_backends.py in wrap_future_result(future, timeout)
519 AsyncResults.get from multiprocessing."""
520 try:
--> 521 return future.result(timeout=timeout)
522 except LokyTimeoutError:
523 raise TimeoutError()
C:\Anaconda3x64\envs\ml\lib\concurrent\futures\_base.py in result(self, timeout)
430 raise CancelledError()
431 elif self._state == FINISHED:
--> 432 return self.__get_result()
433 else:
434 raise TimeoutError()
C:\Anaconda3x64\envs\ml\lib\concurrent\futures\_base.py in __get_result(self)
382 def __get_result(self):
383 if self._exception:
--> 384 raise self._exception
385 else:
386 return self._result
ValueError: not enough values to unpack (expected 2, got 1)
The root cause of this issue is I passed a pipeline, not a model into BayesSearchCV. Meanwhile, my fit_params do not have a prefix. To fix:
fit_params = {
'model__early_stopping_rounds':30,
'model__eval_metric':'multi_logloss',
'model__eval_set':[(xValid, yValid)],
}
I am using GridSearchCV in order to find the best parameters for my pipeline.
My pipeline seems to work well as I can apply:
pipeline.fit(X_train, y_train)
preds = pipeline.predict(X_test)
And I get a decent result.
But GridSearchCV obviously doesn't like something, and I cannot figure it out.
My pipeline:
feats = FeatureUnion([('age', age),
('education_num', education_num),
('is_education_favo', is_education_favo),
('is_marital_status_favo', is_marital_status_favo),
('hours_per_week', hours_per_week),
('capital_diff', capital_diff),
('sex', sex),
('race', race),
('native_country', native_country)
])
pipeline = Pipeline([
('adhocFC',AdHocFeaturesCreation()),
('imputers', KnnImputer(target = 'native-country', n_neighbors = 5)),
('features',feats),('clf',LogisticRegression())])
My GridSearch:
hyperparameters = {'imputers__n_neighbors' : [5,21,41], 'clf__C' : [1.0, 2.0]}
GSCV = GridSearchCV(pipeline, hyperparameters, cv=3, scoring = 'roc_auc' , refit = False) #change n_jobs = 2, refit = False
GSCV.fit(X_train, y_train)
I receive 11 similar warnings:
/home/jo/anaconda2/envs/py35/lib/python3.5/site-packages/ipykernel/main.py:11:
SettingWithCopyWarning: A value is trying to be set on a copy of a
slice from a DataFrame. Try using .loc[row_indexer,col_indexer] =
value instead
and this is the error message:
/home/jo/anaconda2/envs/py35/lib/python3.5/site-packages/ipykernel/main.py:11:
SettingWithCopyWarning: A value is trying to be set on a copy of a
slice from a DataFrame. Try using .loc[row_indexer,col_indexer] =
value instead
See the caveats in the documentation:
http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
/home/jo/anaconda2/envs/py35/lib/python3.5/site-packages/ipykernel/main.py:12:
SettingWithCopyWarning: A value is trying to be set on a copy of a
slice from a DataFrame. Try using .loc[row_indexer,col_indexer] =
value instead
See the caveats in the documentation:
http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
/home/jo/anaconda2/envs/py35/lib/python3.5/site-packages/ipykernel/main.py:14:
SettingWithCopyWarning: A value is trying to be set on a copy of a
slice from a DataFrame. Try using .loc[row_indexer,col_indexer] =
value instead
See the caveats in the documentation:
http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
--------------------------------------------------------------------------- ValueError Traceback (most recent call
last) in ()
3 GSCV = GridSearchCV(pipeline, hyperparameters, cv=3, scoring = 'roc_auc' ,refit = False) #change n_jobs = 2, refit = False
4
----> 5 GSCV.fit(X_train, y_train)
/home/jo/anaconda2/envs/py35/lib/python3.5/site-packages/sklearn/model_selection/_search.py
in fit(self, X, y, groups)
943 train/test set.
944 """
--> 945 return self._fit(X, y, groups, ParameterGrid(self.param_grid))
946
947
/home/jo/anaconda2/envs/py35/lib/python3.5/site-packages/sklearn/model_selection/_search.py
in _fit(self, X, y, groups, parameter_iterable)
562 return_times=True, return_parameters=True,
563 error_score=self.error_score)
--> 564 for parameters in parameter_iterable
565 for train, test in cv_iter)
566
/home/jo/anaconda2/envs/py35/lib/python3.5/site-packages/sklearn/externals/joblib/parallel.py
in call(self, iterable)
756 # was dispatched. In particular this covers the edge
757 # case of Parallel used with an exhausted iterator.
--> 758 while self.dispatch_one_batch(iterator):
759 self._iterating = True
760 else:
/home/jo/anaconda2/envs/py35/lib/python3.5/site-packages/sklearn/externals/joblib/parallel.py
in dispatch_one_batch(self, iterator)
606 return False
607 else:
--> 608 self._dispatch(tasks)
609 return True
610
/home/jo/anaconda2/envs/py35/lib/python3.5/site-packages/sklearn/externals/joblib/parallel.py
in _dispatch(self, batch)
569 dispatch_timestamp = time.time()
570 cb = BatchCompletionCallBack(dispatch_timestamp, len(batch), self)
--> 571 job = self._backend.apply_async(batch, callback=cb)
572 self._jobs.append(job)
573
/home/jo/anaconda2/envs/py35/lib/python3.5/site-packages/sklearn/externals/joblib/_parallel_backends.py
in apply_async(self, func, callback)
107 def apply_async(self, func, callback=None):
108 """Schedule a func to be run"""
--> 109 result = ImmediateResult(func)
110 if callback:
111 callback(result)
/home/jo/anaconda2/envs/py35/lib/python3.5/site-packages/sklearn/externals/joblib/_parallel_backends.py
in init(self, batch)
324 # Don't delay the application, to avoid keeping the input
325 # arguments in memory
--> 326 self.results = batch()
327
328 def get(self):
/home/jo/anaconda2/envs/py35/lib/python3.5/site-packages/sklearn/externals/joblib/parallel.py
in call(self)
129
130 def call(self):
--> 131 return [func(*args, **kwargs) for func, args, kwargs in self.items]
132
133 def len(self):
/home/jo/anaconda2/envs/py35/lib/python3.5/site-packages/sklearn/externals/joblib/parallel.py
in (.0)
129
130 def call(self):
--> 131 return [func(*args, **kwargs) for func, args, kwargs in self.items]
132
133 def len(self):
/home/jo/anaconda2/envs/py35/lib/python3.5/site-packages/sklearn/model_selection/_validation.py
in _fit_and_score(estimator, X, y, scorer, train, test, verbose,
parameters, fit_params, return_train_score, return_parameters,
return_n_test_samples, return_times, error_score)
236 estimator.fit(X_train, **fit_params)
237 else:
--> 238 estimator.fit(X_train, y_train, **fit_params)
239
240 except Exception as e:
/home/jo/anaconda2/envs/py35/lib/python3.5/site-packages/sklearn/pipeline.py
in fit(self, X, y, **fit_params)
266 This estimator
267 """
--> 268 Xt, fit_params = self._fit(X, y, **fit_params)
269 if self._final_estimator is not None:
270 self._final_estimator.fit(Xt, y, **fit_params)
/home/jo/anaconda2/envs/py35/lib/python3.5/site-packages/sklearn/pipeline.py
in _fit(self, X, y, **fit_params)
232 pass
233 elif hasattr(transform, "fit_transform"):
--> 234 Xt = transform.fit_transform(Xt, y, **fit_params_steps[name])
235 else:
236 Xt = transform.fit(Xt, y, **fit_params_steps[name]) \
/home/jo/anaconda2/envs/py35/lib/python3.5/site-packages/sklearn/base.py
in fit_transform(self, X, y, **fit_params)
495 else:
496 # fit method of arity 2 (supervised transformation)
--> 497 return self.fit(X, y, **fit_params).transform(X)
498
499
in fit(self, X, y)
16 self.ohe.fit(X_full)
17 #Create a Dataframe that does not contain any nulls, categ variables are OHE, with all each rows
---> 18 X_ohe_full = self.ohe.transform(X_full[~X[self.col].isnull()].drop(self.col,
axis=1))
19
20 #Fit the classifier on lines where col is null
/home/jo/anaconda2/envs/py35/lib/python3.5/site-packages/pandas/core/frame.py
in getitem(self, key) 2057 return
self._getitem_multilevel(key) 2058 else:
-> 2059 return self._getitem_column(key) 2060 2061 def _getitem_column(self, key):
/home/jo/anaconda2/envs/py35/lib/python3.5/site-packages/pandas/core/frame.py
in _getitem_column(self, key) 2064 # get column 2065
if self.columns.is_unique:
-> 2066 return self._get_item_cache(key) 2067 2068 # duplicate columns & possible reduce dimensionality
/home/jo/anaconda2/envs/py35/lib/python3.5/site-packages/pandas/core/generic.py
in _get_item_cache(self, item) 1384 res = cache.get(item)
1385 if res is None:
-> 1386 values = self._data.get(item) 1387 res = self._box_item_values(item, values) 1388
cache[item] = res
/home/jo/anaconda2/envs/py35/lib/python3.5/site-packages/pandas/core/internals.py
in get(self, item, fastpath) 3550 loc =
indexer.item() 3551 else:
-> 3552 raise ValueError("cannot label index with a null key") 3553 3554 return self.iget(loc,
fastpath=fastpath)
ValueError: cannot label index with a null key
Without additional information I believe it is because your X_train and y_train variables are pandas dataframe, the basic sci-kit learn library isn't comparable with these: e.g., the .fit method of a classifier is expecting an array like object.
By feeding in pandas dataframes you are inadvertently indexing them like numpy arrays, which is not that stable in pandas.
Try converting your training data to numpy arrays:
X_train_arr = X_train.to_numpy()
y_train_arr = y_train.to_numpy()
I am trying to find the best hyperparameters for my SVM using Grid Search. When doing it the following way:
from sklearn.model_selection import GridSearchCV
param_grid = {'coef0': [10, 5, 0.5, 0.001], 'C': [100, 50, 1, 0.001]}
poly_svm_search = SVC(kernel="poly", degree="2")
grid_search = GridSearchCV(poly_svm_search, param_grid, cv=5, scoring='f1')
grid_search.fit(train_data, train_labels)
I get this error:
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-72-dadf5782618c> in <module>
8
----> 9 grid_search.fit(train_data, train_labels)
~/.local/lib/python3.6/site-packages/sklearn/model_selection/_search.py in fit(self, X, y, groups, **fit_params)
720 return results_container[0]
721
--> 722 self._run_search(evaluate_candidates)
723
724 results = results_container[0]
~/.local/lib/python3.6/site-packages/sklearn/model_selection/_search.py in _run_search(self, evaluate_candidates)
1189 def _run_search(self, evaluate_candidates):
1190 """Search all candidates in param_grid"""
-> 1191 evaluate_candidates(ParameterGrid(self.param_grid))
1192
1193
~/.local/lib/python3.6/site-packages/sklearn/model_selection/_search.py in evaluate_candidates(candidate_params)
709 for parameters, (train, test)
710 in product(candidate_params,
--> 711 cv.split(X, y, groups)))
712
713 all_candidate_params.extend(candidate_params)
~/.local/lib/python3.6/site-packages/sklearn/externals/joblib/parallel.py in __call__(self, iterable)
981 # remaining jobs.
982 self._iterating = False
--> 983 if self.dispatch_one_batch(iterator):
984 self._iterating = self._original_iterator is not None
985
~/.local/lib/python3.6/site-packages/sklearn/externals/joblib/parallel.py in dispatch_one_batch(self, iterator)
823 return False
824 else:
--> 825 self._dispatch(tasks)
826 return True
827
~/.local/lib/python3.6/site-packages/sklearn/externals/joblib/parallel.py in _dispatch(self, batch)
780 with self._lock:
781 job_idx = len(self._jobs)
--> 782 job = self._backend.apply_async(batch, callback=cb)
783 # A job can complete so quickly than its callback is
784 # called before we get here, causing self._jobs to
~/.local/lib/python3.6/site-packages/sklearn/externals/joblib/_parallel_backends.py in apply_async(self, func, callback)
180 def apply_async(self, func, callback=None):
181 """Schedule a func to be run"""
--> 182 result = ImmediateResult(func)
183 if callback:
184 callback(result)
~/.local/lib/python3.6/site-packages/sklearn/externals/joblib/_parallel_backends.py in __init__(self, batch)
543 # Don't delay the application, to avoid keeping the input
544 # arguments in memory
--> 545 self.results = batch()
546
547 def get(self):
~/.local/lib/python3.6/site-packages/sklearn/externals/joblib/parallel.py in __call__(self)
259 with parallel_backend(self._backend):
260 return [func(*args, **kwargs)
--> 261 for func, args, kwargs in self.items]
262
263 def __len__(self):
~/.local/lib/python3.6/site-packages/sklearn/externals/joblib/parallel.py in <listcomp>(.0)
259 with parallel_backend(self._backend):
260 return [func(*args, **kwargs)
--> 261 for func, args, kwargs in self.items]
262
263 def __len__(self):
~/.local/lib/python3.6/site-packages/sklearn/model_selection/_validation.py in _fit_and_score(estimator, X, y, scorer, train, test, verbose, parameters, fit_params, return_train_score, return_parameters, return_n_test_samples, return_times, return_estimator, error_score)
526 estimator.fit(X_train, **fit_params)
527 else:
--> 528 estimator.fit(X_train, y_train, **fit_params)
529
530 except Exception as e:
~/.local/lib/python3.6/site-packages/sklearn/svm/base.py in fit(self, X, y, sample_weight)
210
211 seed = rnd.randint(np.iinfo('i').max)
--> 212 fit(X, y, sample_weight, solver_type, kernel, random_seed=seed)
213 # see comment on the other call to np.iinfo in this file
214
~/.local/lib/python3.6/site-packages/sklearn/svm/base.py in _sparse_fit(self, X, y, sample_weight, solver_type, kernel, random_seed)
291 sample_weight, self.nu, self.cache_size, self.epsilon,
292 int(self.shrinking), int(self.probability), self.max_iter,
--> 293 random_seed)
294
295 self._warn_from_fit_status()
sklearn/svm/libsvm_sparse.pyx in sklearn.svm.libsvm_sparse.libsvm_sparse_train()
TypeError: an integer is required
My train_labels variable contains a list of booleans, so I have a binary classification problem. train_data is a <class'scipy.sparse.csr.csr_matrix'>, basically containing all scaled and One-Hot encoded features.
What did I do wrong? It's hard for me to track down what the issue is here. I thank you for any help in advance ;).
When you initialize the SVC using this line:
poly_svm_search = SVC(kernel="poly", degree="2")
You are supplying degree param with a string, due to inverted commas around it. But according to the documentation, degree takes an integer as value.
degree : int, optional (default=3) Degree of the polynomial kernel
function (‘poly’). Ignored by all other kernels.
So you need to do this:
poly_svm_search = SVC(kernel="poly", degree=2)
Notice how I did not use inverted commas here.