Reshape error when using mutual_info regression fo

Question

I am trying to do some feature selection using mutual_info_regression with SelectKBest wrapper. However I keep running into an error indicating that my list of features needs to be reshaped into a 2D array, not quite sure why I keep getting this message-

#feature selection before linear regression benchmark test
import sklearn
from sklearn.feature_selection import mutual_info_regression, SelectKBest
features = list(housing_data[housing_data.columns.difference(['sale_price'])])
target = 'sale_price'
new = SelectKBest(mutual_info_regression, k=20).fit_transform(features, target)

This is my traceback:

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-18-8c778124066c> in <module>()
      3 features = list(housing_data[housing_data.columns.difference(['sale_price'])])
      4 target = 'sale_price'
----> 5 new = SelectKBest(mutual_info_regression, k=20).fit_transform(features, target)

/usr/local/lib/python3.6/dist-packages/sklearn/base.py in fit_transform(self, X, y, **fit_params)
    463         else:
    464             # fit method of arity 2 (supervised transformation)
--> 465             return self.fit(X, y, **fit_params).transform(X)
    466 
    467 

/usr/local/lib/python3.6/dist-packages/sklearn/feature_selection/univariate_selection.py in fit(self, X, y)
    339         self : object
    340         """
--> 341         X, y = check_X_y(X, y, ['csr', 'csc'], multi_output=True)
    342 
    343         if not callable(self.score_func):

/usr/local/lib/python3.6/dist-packages/sklearn/utils/validation.py in check_X_y(X, y, accept_sparse, accept_large_sparse, dtype, order, copy, force_all_finite, ensure_2d, allow_nd, multi_output, ensure_min_samples, ensure_min_features, y_numeric, warn_on_dtype, estimator)
    754                     ensure_min_features=ensure_min_features,
    755                     warn_on_dtype=warn_on_dtype,
--> 756                     estimator=estimator)
    757     if multi_output:
    758         y = check_array(y, 'csr', force_all_finite=True, ensure_2d=False,

/usr/local/lib/python3.6/dist-packages/sklearn/utils/validation.py in check_array(array, accept_sparse, accept_large_sparse, dtype, order, copy, force_all_finite, ensure_2d, allow_nd, ensure_min_samples, ensure_min_features, warn_on_dtype, estimator)
    550                     "Reshape your data either using array.reshape(-1, 1) if "
    551                     "your data has a single feature or array.reshape(1, -1) "
--> 552                     "if it contains a single sample.".format(array))
    553 
    554         # in the future np.flexible dtypes will be handled like object dtypes

ValueError: Expected 2D array, got 1D array instead:
array=['APPBBL' 'APPDate' 'Address' 'AreaSource' 'AssessLand' 'AssessTot' 'BBL'
 'BldgArea' 'BldgClass' 'BldgDepth' 'BldgFront' 'BoroCode' 'Borough'
 'BsmtCode' 'BuiltFAR' 'CB2010' 'CD' 'CT2010' 'ComArea' 'CommFAR'
 'CondoNo' 'Council' 'EDesigNum' 'Easements' 'ExemptLand' 'ExemptTot'
 'Ext' 'FIRM07_FLA' 'FacilFAR' 'FactryArea' 'FireComp' 'GarageArea'
 'HealthArea' 'HealthCent' 'HistDist' 'IrrLotCode' 'LandUse' 'Landmark'
 'LotArea' 'LotDepth' 'LotFront' 'LotType' 'LtdHeight' 'MAPPLUTO_F'
 'NumBldgs' 'NumFloors' 'OfficeArea' 'OtherArea' 'Overlay1' 'Overlay2'
 'OwnerName' 'OwnerType' 'PFIRM15_FL' 'PLUTOMapID' 'PolicePrct' 'ProxCode'
 'ResArea' 'ResidFAR' 'RetailArea' 'SHAPE_Area' 'SHAPE_Leng' 'SPDist1'
 'SPDist2' 'SPDist3' 'Sanborn' 'SanitBoro' 'SanitDistr' 'SanitSub'
 'SchoolDist' 'SplitZone' 'StrgeArea' 'TaxMap' 'Tract2010' 'UnitsRes'
 'UnitsTotal' 'Unnamed: 0' 'Version' 'XCoord' 'YCoord' 'YearAlter1'
 'YearAlter2' 'YearBuilt' 'ZMCode' 'ZipCode' 'ZoneDist1' 'ZoneDist2'
 'ZoneDist3' 'ZoneDist4' 'ZoneMap' 'address' 'apartment_number' 'block'
 'borough' 'building_class' 'building_class_at_sale'
 'building_class_category' 'commercial_units' 'easement' 'gross_sqft'
 'land_sqft' 'lot' 'neighborhood' 'price_range' 'residential_units'
 'sale_date' 'tax_class' 'tax_class_at_sale' 'total_units' 'year_built'
 'year_of_sale' 'zip_code'].
Reshape your data either using array.reshape(-1, 1) if your data has a single feature or array.reshape(1, -1) if it contains a single sample.

Here is a sample of my data:

housing_data = pd.DataFrame({'Unnamed: 0': {0: 1, 1: 2, 2: 3, 3: 4}, 'borough': {0: 3, 1: 3, 2: 3, 3: 3}, 'neighborhood': {0: 'DOWNTOWN-METROTECH', 1: 'DOWNTOWN-FULTON FERRY', 2: 'BROOKLYN HEIGHTS', 3: 'MILL BASIN'}, 'building_class_category': {0: '28  COMMERCIAL CONDOS', 1: '29  COMMERCIAL GARAGES', 2: '21  OFFICE BUILDINGS', 3: '22  STORE BUILDINGS'}, 'tax_class': {0: '4', 1: '4', 2: '4', 3: '4'}, 'block': {0: 140, 1: 54, 2: 204, 3: 8470}, 'lot': {0: 1001, 1: 1, 2: 1, 3: 55}, 'easement': {0: nan, 1: nan, 2: nan, 3: nan}, 'building_class': {0: 'R5', 1: 'G7', 2: 'O6', 3: 'K6'}, 'address': {0: '330 JAY STREET', 1: '85 JAY STREET', 2: '29 COLUMBIA HEIGHTS', 3: '5120 AVENUE U'}, 'apartment_number': {0: 'COURT', 1: nan, 2: nan, 3: nan}, 'zip_code': {0: 11201, 1: 11201, 2: 11201, 3: 11234}, 'residential_units': {0: 0, 1: 0, 2: 0, 3: 0}, 'commercial_units': {0: 1, 1: 0, 2: 0, 3: 123}, 'total_units': {0: 1, 1: 0, 2: 0, 3: 123}, 'land_sqft': {0: 0.0, 1: 134988.0, 2: 32000.0, 3: 905000.0}, 'gross_sqft': {0: 0.0, 1: 0.0, 2: 304650.0, 3: 2548000.0}, 'year_built': {0: 2002, 1: 0, 2: 1924, 3: 1970}, 'tax_class_at_sale': {0: 4, 1: 4, 2: 4, 3: 4}, 'building_class_at_sale': {0: 'R5', 1: 'G7', 2: 'O6', 3: 'K6'}, 'sale_price': {0: 499401179.0, 1: 345000000.0, 2: 340000000.0, 3: 276947000.0}, 'sale_date': {0: '2008-04-23', 1: '2016-12-20', 2: '2016-08-03', 3: '2012-11-28'}, 'year_of_sale': {0: 2008, 1: 2016, 2: 2016, 3: 2012}, 'Borough': {0: nan, 1: 'BK', 2: 'BK', 3: 'BK'}, 'CD': {0: nan, 1: 302.0, 2: 302.0, 3: 318.0}, 'CT2010': {0: nan, 1: 21.0, 2: 1.0, 3: 698.0}, 'CB2010': {0: nan, 1: 3017.0, 2: 1003.0, 3: 2005.0}, 'SchoolDist': {0: nan, 1: 13.0, 2: 13.0, 3: 22.0}, 'Council': {0: nan, 1: 33.0, 2: 33.0, 3: 46.0}, 'ZipCode': {0: nan, 1: 11201.0, 2: 11201.0, 3: 11234.0}, 'FireComp': {0: nan, 1: 'L118', 2: 'E205', 3: 'E323'}, 'PolicePrct': {0: nan, 1: 84.0, 2: 84.0, 3: 63.0}, 'HealthCent': {0: nan, 1: 36.0, 2: 38.0, 3: 35.0}, 'HealthArea': {0: nan, 1: 1000.0, 2: 2300.0, 3: 8822.0}, 'SanitBoro': {0: nan, 1: 3.0, 2: 3.0, 3: 3.0}, 'SanitDistr': {0: nan, 1: 2.0, 2: 2.0, 3: 18.0}, 'SanitSub': {0: nan, 1: '1B', 2: '1A', 3: '4E'}, 'Address': {0: nan, 1: '87 JAY STREET', 2: '29 COLUMBIA HEIGHTS', 3: '5120 AVENUE U'}, 'ZoneDist1': {0: nan, 1: 'M1-2/R8', 2: 'M2-1', 3: 'M3-1'}, 'ZoneDist2': {0: nan, 1: nan, 2: nan, 3: nan}, 'ZoneDist3': {0: nan, 1: nan, 2: nan, 3: nan}, 'ZoneDist4': {0: nan, 1: nan, 2: nan, 3: nan}, 'Overlay1': {0: nan, 1: nan, 2: nan, 3: nan}, 'Overlay2': {0: nan, 1: nan, 2: nan, 3: nan}, 'SPDist1': {0: nan, 1: 'MX-2', 2: nan, 3: nan}, 'SPDist2': {0: nan, 1: nan, 2: nan, 3: nan}, 'SPDist3': {0: nan, 1: nan, 2: nan, 3: nan}, 'LtdHeight': {0: nan, 1: nan, 2: nan, 3: nan}, 'SplitZone': {0: nan, 1: 'N', 2: 'N', 3: 'N'}, 'BldgClass': {0: nan, 1: 'G7', 2: 'O6', 3: 'K6'}, 'LandUse': {0: nan, 1: 10.0, 2: 5.0, 3: 5.0}, 'Easements': {0: nan, 1: 0.0, 2: 0.0, 3: 1.0}, 'OwnerType': {0: nan, 1: 'P', 2: nan, 3: nan}, 'OwnerName': {0: nan, 1: '85 JAY STREET BROOKLY', 2: '25-30 COLUMBIA HEIGHT', 3: 'BROOKLYN KINGS PLAZA'}, 'LotArea': {0: nan, 1: 134988.0, 2: 32000.0, 3: 905000.0}, 'BldgArea': {0: nan, 1: 0.0, 2: 304650.0, 3: 2548000.0}, 'ComArea': {0: nan, 1: 0.0, 2: 304650.0, 3: 2548000.0}, 'ResArea': {0: nan, 1: 0.0, 2: 0.0, 3: 0.0}, 'OfficeArea': {0: nan, 1: 0.0, 2: 264750.0, 3: 0.0}, 'RetailArea': {0: nan, 1: 0.0, 2: 0.0, 3: 1263000.0}, 'GarageArea': {0: nan, 1: 0.0, 2: 0.0, 3: 1285000.0}, 'StrgeArea': {0: nan, 1: 0.0, 2: 0.0, 3: 0.0}, 'FactryArea': {0: nan, 1: 0.0, 2: 0.0, 3: 0.0}, 'OtherArea': {0: nan, 1: 0.0, 2: 39900.0, 3: 0.0}, 'AreaSource': {0: nan, 1: 7.0, 2: 2.0, 3: 2.0}, 'NumBldgs': {0: nan, 1: 0.0, 2: 1.0, 3: 4.0}, 'NumFloors': {0: nan, 1: 0.0, 2: 13.0, 3: 2.0}, 'UnitsRes': {0: nan, 1: 0.0, 2: 0.0, 3: 0.0}, 'UnitsTotal': {0: nan, 1: 0.0, 2: 0.0, 3: 123.0}, 'LotFront': {0: nan, 1: 490.5, 2: 92.42, 3: 930.0}, 'LotDepth': {0: nan, 1: 275.33, 2: 335.92, 3: 859.0}, 'BldgFront': {0: nan, 1: 0.0, 2: 335.0, 3: 0.0}, 'BldgDepth': {0: nan, 1: 0.0, 2: 92.0, 3: 0.0}, 'Ext': {0: nan, 1: nan, 2: nan, 3: nan}, 'ProxCode': {0: nan, 1: 0.0, 2: 0.0, 3: 0.0}, 'IrrLotCode': {0: nan, 1: 'N', 2: 'Y', 3: 'Y'}, 'LotType': {0: nan, 1: 5.0, 2: 3.0, 3: 3.0}, 'BsmtCode': {0: nan, 1: 5.0, 2: 5.0, 3: 5.0}, 'AssessLand': {0: nan, 1: 1571850.0, 2: 1548000.0, 3: 36532350.0}, 'AssessTot': {0: nan, 1: 1571850.0, 2: 25463250.0, 3: 149792400.0}, 'ExemptLand': {0: nan, 1: 1571850.0, 2: 0.0, 3: 0.0}, 'ExemptTot': {0: nan, 1: 1571850.0, 2: 0.0, 3: 0.0}, 'YearBuilt': {0: nan, 1: 0.0, 2: 1924.0, 3: 1970.0}, 'YearAlter1': {0: nan, 1: 0.0, 2: 1980.0, 3: 0.0}, 'YearAlter2': {0: nan, 1: 0.0, 2: 0.0, 3: 0.0}, 'HistDist': {0: nan, 1: nan, 2: nan, 3: nan}, 'Landmark': {0: nan, 1: nan, 2: nan, 3: nan}, 'BuiltFAR': {0: nan, 1: 0.0, 2: 9.52, 3: 2.82}, 'ResidFAR': {0: nan, 1: 7.2, 2: 0.0, 3: 0.0}, 'CommFAR': {0: nan, 1: 2.0, 2: 2.0, 3: 2.0}, 'FacilFAR': {0: nan, 1: 6.5, 2: 0.0, 3: 0.0}, 'BoroCode': {0: nan, 1: 3.0, 2: 3.0, 3: 3.0}, 'BBL': {0: nan, 1: 3000540001.0, 2: 3002040001.0, 3: 3084700055.0}, 'CondoNo': {0: nan, 1: 0.0, 2: 0.0, 3: 0.0}, 'Tract2010': {0: nan, 1: 21.0, 2: 1.0, 3: 698.0}, 'XCoord': {0: nan, 1: 988208.0, 2: 985952.0, 3: 1006597.0}, 'YCoord': {0: nan, 1: 195011.0, 2: 195007.0, 3: 161424.0}, 'ZoneMap': {0: nan, 1: '12d', 2: '12d', 3: '23b'}, 'ZMCode': {0: nan, 1: nan, 2: nan, 3: nan}, 'Sanborn': {0: nan, 1: '302 016', 2: '302 004', 3: '319 077'}, 'TaxMap': {0: nan, 1: 30101.0, 2: 30106.0, 3: 32502.0}, 'EDesigNum': {0: nan, 1: nan, 2: nan, 3: nan}, 'APPBBL': {0: nan, 1: 3000540001.0, 2: 0.0, 3: 0.0}, 'APPDate': {0: nan, 1: '12/06/2002', 2: nan, 3: nan}, 'PLUTOMapID': {0: nan, 1: 1.0, 2: 1.0, 3: 1.0}, 'FIRM07_FLA': {0: nan, 1: nan, 2: nan, 3: 1.0}, 'PFIRM15_FL': {0: nan, 1: nan, 2: nan, 3: 1.0}, 'Version': {0: nan, 1: '17V1.1', 2: '17V1.1', 3: '17V1.1'}, 'MAPPLUTO_F': {0: nan, 1: 0.0, 2: 0.0, 3: 0.0}, 'SHAPE_Leng': {0: nan, 1: 1559.88914353, 2: 890.718521021, 3: 3729.78685686}, 'SHAPE_Area': {0: nan, 1: 140131.577176, 2: 34656.4472405, 3: 797554.847834}, 'price_range': {0: nan, 1: nan, 2: nan, 3: nan}})

Answer 1

The transformer expects a 2D array, of shape (n x m) where n is the number of samples and m the number of features and if you look at the shape of features I imagine it will display: (m,).

Reshaping arrays

In general for a feature array of shape (n,), you can do as the error code suggests and call .reshape(-1,1) on your feature array, the -1 lets it infer the additional dimension: The shape of the array will be (n,m), where for a 1 feature case m = 1.

Sklearn transformers

The above being said, I think there is additional errors with your code and understanding.

I would print features to screen and check it is what you want, it looks like you are printing a list of all the column names except sale_price. I am not familiar with SelectKBest but it requires an (n,m) feature array not a list of column names of the features.

Additionally, target should not be the name of the target column, but an array of shape (n,), where its values are the observed target values of the training instances.

I would suggest checking the documentation (previously referenced) while you are writing your code to make sure you are using the correct arguments and utilising the function as it is intended.

Extracting features

Your data seems in a strange format (dictionary's nested in a pandas DF). However is a explicit example of how I would extract features from a pd.DataFrame for use with functions from the SKlearn framework.

housing_data = pd.DataFrame({'age': [1,5,1,10], 'size':[0,1,2,0], 
                             'price':[190,100,50,100]
                            })

feature_arr = housing_data.drop('price', axis=1).values
target_values = housing_data['price']

Print feature_arr and you will hopefully see your issue. Normally you would then have to preprocess the data to, for example, drop NaN values or perform feature scaling.