How can I apply a sklearn scaler to all rows of a pandas dataframe. The question is related to pandas dataframe columns scaling with sklearn. How can I apply a sklearn scaler to all values of a row?
NOTE: I know that for feature scaling it's normal to have features in columns and scaling features column wise like in the refenced other question. However I'd like to use sklearn scalers for preprocessing data for visualization where it's reasonable to scale row wise in my case.
Sklearn works both with panda dataframes and numpy arrays, and numpy arrays allow some basic matrix transformations when dataframes don't.
You can transform the dataframe to a numpy array, vectors = df.values. Then transpose the array, scale the transposed array columnwise, transpose it back
scaled_rows = scaler.fit_transform(vectors.T).T
and convert it to dataframe scaled_df = pd.DataFrame(data = scaled_rows, columns = df.columns)
Related
I want to apply MinmaxScaler on a number of pandas DataFrame 'together'. Meaning that I want the scaler to perform on all data in those columns, not separately on each column.
My DataFrame has 20 columns. I want to apply the scaler on 12 of the columns at the same time. I have already read this. But it does not solve my problem since it acts on each column separately.
IIUC, you want the sklearn scaler to fit and transform multiple columns with the same criteria (in this case min and max definitions). Here is one way you can do this -
You can save the initial shape of the columns and then transform the numpy array of those columns into a 1D array from a 2D array.
Next you can fit your scaler and transform this 1D array
Finally you can use the old shape to reshape the array back into the n columns you need and save them
The advantage of this approach is that this works with any of the sklearn scalers you need to use, MinMaxScaler, StandardScaler etc.
import pandas as pd
from sklearn.preprocessing import MinMaxScaler
scaler = MinMaxScaler()
dfTest = pd.DataFrame({'A':[14.00,90.20,90.95,96.27,91.21],
'B':[103.02,107.26,110.35,114.23,114.68],
'C':['big','small','big','small','small']})
cols = ['A','B']
old_shape = dfTest[cols].shape #(5,2)
dfTest[cols] = scaler.fit_transform(dfTest[cols].to_numpy().reshape(-1,1)).reshape(old_shape)
print(dfTest)
A B C
0 0.000000 0.884188 big
1 0.756853 0.926301 small
2 0.764303 0.956992 big
3 0.817143 0.995530 small
4 0.766885 1.000000 small
you can extract the "min" and "max" statistics from those columns and perform the scaling yourself:
# columns of interest
cols = [...]
# get the minimum and maximum values in that region
vals = df[cols].to_numpy()
min_val = vals.min()
max_val = vals.max()
# scale the region using them
df[cols] = df[cols].sub(min_val).div(max_val - min_val)
(sub is method way of doing "-" and div is for "/".)
Above, df is your training dataframe; to scale the testing dataframe, you replace df with that in the last line, e.g.,
test_df[cols] = test_df[cols].sub(min_val).div(max_val - min_val)
instead of extracting min/max of it separately which would leak information from the test set.
I am trying to impute some missing values in a Dataframe using the scikit-learn IterativeImputer(). The problem is that the imputer will take the pandas dataframe as an input, but will return a numpy array instead of the original dataframe. Here is a simple example taken from this post.
# Create an empty dataset
df = pd.DataFrame()
# Create two variables called x0 and x1. Make the first value of x1 a missing value
df['x0'] = [0.3051,0.4949,0.6974,0.3769,0.2231,0.341,0.4436,0.5897,0.6308,0.5]
df['x1'] = [np.nan,0.2654,0.2615,0.5846,0.4615,0.8308,0.4962,0.3269,0.5346,0.6731]
imputer = IterativeImputer(max_iter=10, random_state=42)
imputer.fit(df)
imputed_df = imputer.transform(df)
imputed_df
The problem is that when the numpy array is returned, the column names are removed and other metadata. I can of course manually extract that metadata from the original dataframe and then reapply it, but that seems a bit hacky. Pandas has its own imputer in terms of Dataframe.fillna() but the algorithms are not as sophisticated as the scikit ones.
So is there a way to fit the imputer to a dataframe and return a dataframe from the result.
Yes you can , just assign the values back
df[:]= imputer.transform(df)
Assuming we have a Pandas dataframe and a scikit-learn model, trained (fit) using that dataframe. Is there a way to do row-wise prediction? The use case is to use the predict function to fill in empty values in the dataframe, using an sklearn model.
I expected that this would be possible using the pandas apply function (with axis=1), but I keep getting dimensionality errors.
Using Pandas version '0.22.0' and sklearn version '0.19.1'.
Simple example:
import pandas as pd
from sklearn.cluster import kmeans
data = [[x,y,x*y] for x in range(1,10) for y in range(10,15)]
df = pd.DataFrame(data,columns=['input1','input2','output'])
model = kmeans()
model.fit(df[['input1','input2']],df['output'])
df['predictions'] = df[['input1','input2']].apply(model.predict,axis=1)
The resulting dimensionality error:
ValueError: ('Expected 2D array, got 1D array instead:\narray=[ 1.
10.].\nReshape 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.',
'occurred at index 0')
Running predict on the whole column works fine:
df['predictions'] = model.predict(df[['input1','input2']])
However, I want the flexibility to use this row-wise.
I've tried various approaches to reshape the data first, for example:
def reshape_predict(df):
return model.predict(np.reshape(df.values,(1,-1)))
df[['input1','input2']].apply(reshape_predict,axis=1)
Which just returns the input with no error, whereas I expect it to return a single column of output values (as an array).
SOLUTION:
Thanks to Yakym for providing a working solution! Trying a few variants based on his suggestion, the easiest solution was to simply wrap the row values in square brackets (I tried this previously, but without the 0 index for the prediction, with no luck).
df['predictions'] = df[['input1','input2']].apply(lambda x: model.predict([x])[0],axis=1)
Slightly more verbose, you can turn each row into 2D array by adding new a new axis to the values. You will then have to access the prediction with 0 index:
df["predictions"] = df[["input1", "input2"]].apply(
lambda s: model.predict(s.values[None])[0], axis=1
)
Suppose I have 2 pandas series, which I perceive as column vector in linear algebra x1 and x2
I want to do the operation x1 * x2^T, which is a column vector multiply with a row vector to produce a matrix (pandas dataframe).
What is the best procedure for this?
You want to import numpy and call:
pandas.DataFrame(numpy.outer(x1, x2))
Inside of pandas, you can go back to data frames to do it, e.g.
x1.to_frame().dot(x2.to_frame().T)
How do I create a sparse matrix in CSR/COO format for a huge feature vector (50000 x 100000) from categorical data stored in Pandas DataFrame? I am creating the feature vector using Pandas get_dummies() function, but it returns a MemoryError. How do I avoid that and rather generate it in a sparse matrix CSR format?
Possibly useful links:
Populate a Pandas SparseDataFrame from a SciPy Sparse Matrix
http://pandas.pydata.org/pandas-docs/stable/sparse.html
http://pandas.pydata.org/pandas-docs/stable/generated/pandas.SparseSeries.to_coo.html#pandas.SparseSeries.to_coo
Pandas sparse dataFrame to sparse matrix, without generating a dense matrix in memory
Use:
scipy.sparse.coo_matrix(df_dummies)
but do not forget to create df_dummies sparse in the first place...
df_dummies = pandas.get_dummies(df, sparse=True)
This answer will keep the data as sparse as possible and avoids memory issues when using Pandas get_dummies.
import pandas as pd
import numpy as np
from sklearn.preprocessing import OneHotEncoder
from sklearn.preprocessing import LabelEncoder
from scipy import sparse
df = pd.DataFrame({'rowid':[1,2,3,4,5], 'category':['c1', 'c2', 'c1', 'c3', 'c1']})
print 'Input data frame\n{0}'.format(df)
print 'Encode column category as numerical variables'
print LabelEncoder().fit_transform(df.category)
print 'Encode column category as dummy matrix'
print OneHotEncoder().fit_transform(LabelEncoder().fit_transform(df.category).reshape(-1,1)).todense()
print 'Concat with the original data frame as a matrix'
dummy_matrix = OneHotEncoder().fit_transform(LabelEncoder().fit_transform(df.category).reshape(-1,1))
df_as_sparse = sparse.csr_matrix(df.drop(labels=['category'], axis=1).as_matrix())
sparse_combined = sparse.hstack((df_as_sparse, dummy_matrix), format='csr')
print sparse_combined.todense()