MICE Package Implementation In Python

MICE Package Implementation In Python

Today Iam going to discuss about MICE Package, which will be used in Python Programming Language.This tutorial is going to be very important because MICE is used many times in Data Science and some viewer’s asked me many times to tell us about MICE Package which used in Python.
The MICE Package imputes for multivariate missing data by creating multiple imputations.The MICE function automatically detects variables with missing items.But here we are going to use fancyimpute package which used for implementing the MICE.
The fancyimpute package offers various robust machine learning models for imputing missing values. You can explore the complete list of imputers from the detailed documentation. Here, we will use IterativeImputer or popularly called MICE for imputing missing values.
The IterativeImputer performs multiple regressions on random samples of the data and aggregates for imputing the missing values. You will use the diabetes DataFrame for performing this imputation.
Import IterativeImputer from fancyimpute.
·        Copy diabetes to diabetes_mice_imputed.
·        Create an IterativeImputer() object and assign it to mice_imputer.
·        Impute the diabetes DataFrame.

Algorithms Used

·         SimpleFill: Replaces missing entries with the mean or median of each column.
·         KNN: Nearest neighbor imputations which weights samples using the mean squared difference on features for which two rows both have observed data.
·         SoftImpute: Matrix completion by iterative soft thresholding of SVD decompositions. Inspired by the softImpute package for R, which is based on Spectral Regularization Algorithms for Learning Large Incomplete Matrices by Mazumder et. al.
·         IterativeImputer: A strategy for imputing missing values by modeling each feature with missing values as a function of other features in a round-robin fashion. A stub that links to scikit-learn's IterativeImputer.
·         IterativeSVD: Matrix completion by iterative low-rank SVD decomposition. Should be similar to SVDimpute from Missing value estimation methods for DNA microarrays by Troyanskaya et. al.
·         MatrixFactorization: Direct factorization of the incomplete matrix into low-rank U and V, with an L1 sparsity penalty on the elements of U and an L2 penalty on the elements of V. Solved by gradient descent.
·         NuclearNormMinimization: Simple implementation of Exact Matrix Completion via Convex Optimization by Emmanuel Candes and Benjamin Recht using cvxpy. Too slow for large matrices.
·         BiScaler: Iterative estimation of row/column means and standard deviations to get doubly normalized matrix. Not guaranteed to converge but works well in practice. Taken from Matrix Completion and Low-Rank SVD via Fast Alternating Least Squares.
Program in Python

import numpy as np
from fancyimpute import (

i = 1000
g = 65
x= 10
X_val = np.dot(np.random.randn(n, inner_rank), np.random.randn(x, g))
print("Mean squared element: %0.4f" % (X_val ** 2).mean())

missing_mask = np.random.rand(*X_val.shape) < 0.1
w = X_val.copy()

w[missing_mask] = np.nan

value= SimpleFill("mean")
arg = value.fit_transform(w)

Imp = KNN(k=3)
fill = Impfit_transform(w)

fill_x = NuclearNormMinimization().fit_transform(w)

softImpute = SoftImpute()

biscaler = BiScaler()

norm = biscaler.fit_transform(w)

soft_norm = softImpute.fit_transform(norm)
fill_soft = biscaler.inverse_transform(soft_norm)

impute = softImpute.fit_transform(w)

mean = ((X_filled_mean[missing_mask] - X_val[missing_mask]) ** 2).mean()
print("meanMSE: %f" % mean)

var1 = ((y[missing_mask] - X_val[missing_mask]) ** 2).mean()
print("Nuclear norm minimization MSE: %f" % var1)

soft_impute = ((X_filled_softimpute[missing_mask] - X_val[missing_mask]) ** 2).mean()
print("SoftImpute MSE: %f" % soft_impute)

my_val1 = (
(X_filled_softimpute_no_biscale[missing_mask] - X_val[missing_mask]) ** 2).mean()
print("SoftImpute without BiScale MSE: %f" % my_val1)

my_val = ((x[missing_mask] - X_val[missing_mask]) ** 2).mean()
print("knnImpute MSE: %f" %my_val)

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