Python implementation of the R package synthpop
Project description
synthpop
Python implementation of the R package synthpop.
The R implementation of synthpop is a tool for producing synthetic versions of microdata containing confidential information so that they are safe to be released to users for exploratory analysis. The key objective of generating synthetic data is to replace sensitive original values with synthetic ones causing minimal distortion of the statistical information contained in the dataset. Variables, which can be categorical or continuous, are synthesised one-by-one using sequential modelling. Replacements are generated by drawing from conditional distributions fitted to the original data using parametric or classification and regression trees models.
This is a reimplementation in Python which allows synthetic data to be generated via the method .generate() after the algorithm had been fit to the original data via the method .fit(). The process can be largely automated, if default settings are used, or with methods defined by the user. Optional parameters can be used to influence the disclosure risk and the analytical quality of the synthetic data.
Development status and roadmap
This project is in Alpha status and the roadmap can be found here.
Installation from sources
git clone git@github.com:hazy/synthpop.git
cd synthpop
pip install -r requirements.txt
python setup.py install
Examples
Adult dataset
We will use the US adult census dataset, which is a freely available open dataset extracted from the US census bureau database. The dataset is initially designed for a binary classification problem and the task is to predict whether a person earns over $50,000 a year. The dataset is a mixture of discrete and continuous features, including age, working status (workclass), education, marital status, race, sex, relationship and hours worked per week.
In [1]: from datasets.adult import df
In [2]: df.head()
Out[2]:
age workclass fnlwgt education educational-num marital-status occupation relationship race gender capital-gain capital-loss hours-per-week native-country income
0 39 State-gov 77516 Bachelors 13 Never-married Adm-clerical Not-in-family White Male 2174 0 40 United-States <=50K
1 50 Self-emp-not-inc 83311 Bachelors 13 Married-civ-spouse Exec-managerial Husband White Male 0 0 13 United-States <=50K
2 38 Private 215646 HS-grad 9 Divorced Handlers-cleaners Not-in-family White Male 0 0 40 United-States <=50K
3 53 Private 234721 11th 7 Married-civ-spouse Handlers-cleaners Husband Black Male 0 0 40 United-States <=50K
4 28 Private 338409 Bachelors 13 Married-civ-spouse Prof-specialty Wife Black Female 0 0 40 Cuba <=50K
synthpop
- Use default parameters for the Adult dataset:
In [1]: from synthpop import Synthpop
In [2]: from datasets.adult import df, dtypes
In [3]: spop = Synthpop()
In [4]: spop.fit(df, dtypes)
train_age
train_workclass
train_fnlwgt
train_education
train_educational-num
train_marital-status
train_occupation
train_relationship
train_race
train_gender
train_capital-gain
train_capital-loss
train_hours-per-week
train_native-country
train_income
In [5]: synth_df = spop.generate(len(df))
generate_age
generate_workclass
generate_fnlwgt
generate_education
generate_educational-num
generate_marital-status
generate_occupation
generate_relationship
generate_race
generate_gender
generate_capital-gain
generate_capital-loss
generate_hours-per-week
generate_native-country
generate_income
In [6]: synth_df.head()
Out[6]:
age workclass fnlwgt education educational-num marital-status occupation relationship race gender capital-gain capital-loss hours-per-week native-country income
0 21 ? 213055 11th 7 Never-married ? Not-in-family Other Female 0 0 30 United-States <=50K
1 23 Private 150683 HS-grad 9 Never-married Adm-clerical Not-in-family White Female 0 0 40 United-States <=50K
2 61 Private 191417 10th 6 Widowed Sales Not-in-family Black Female 0 0 32 United-States <=50K
3 50 Private 190762 HS-grad 9 Divorced Sales Not-in-family White Male 0 0 60 United-States <=50K
4 42 Local-gov 255675 HS-grad 9 Married-civ-spouse Other-service Husband Black Male 0 0 40 United-States <=50K
In [7]: spop.method
Out[7]:
age sample
workclass cart
fnlwgt cart
education cart
educational-num cart
marital-status cart
occupation cart
relationship cart
race cart
gender cart
capital-gain cart
capital-loss cart
hours-per-week cart
native-country cart
income cart
dtype: object
In [8]: spop.visit_sequence
Out[8]:
age 0
workclass 1
fnlwgt 2
education 3
educational-num 4
marital-status 5
occupation 6
relationship 7
race 8
gender 9
capital-gain 10
capital-loss 11
hours-per-week 12
native-country 13
income 14
dtype: int64
In [9]: spop.predictor_matrix
Out[9]:
age workclass fnlwgt education educational-num marital-status occupation relationship race gender capital-gain capital-loss hours-per-week native-country income
age 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
workclass 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fnlwgt 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
education 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0
educational-num 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0
marital-status 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0
occupation 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0
relationship 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0
race 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0
gender 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0
capital-gain 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0
capital-loss 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0
hours-per-week 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0
native-country 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0
income 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0
- Define the visit sequence for the Adult dataset:
In [1]: from synthpop import Synthpop
In [2]: from datasets.adult import df, dtypes
In [3]: spop = Synthpop(visit_sequence=[0, 1, 5, 3, 2])
In [4]: spop.fit(df, dtypes)
train_age
train_workclass
train_marital-status
train_education
train_fnlwgt
In [5]: synth_df = spop.generate(len(df))
generate_age
generate_workclass
generate_marital-status
generate_education
generate_fnlwgt
In [6]: synth_df.head()
Out[6]:
age workclass fnlwgt education marital-status
0 57 Self-emp-not-inc 327901 Prof-school Married-civ-spouse
1 24 Private 34568 Assoc-voc Never-married
2 50 Private 256861 HS-grad Married-civ-spouse
3 28 Private 186239 Some-college Never-married
4 38 Private 216129 Bachelors Divorced
In [7]: spop.method
Out[7]:
age sample
workclass cart
fnlwgt cart
education cart
educational-num cart
marital-status cart
occupation cart
relationship cart
race cart
gender cart
capital-gain cart
capital-loss cart
hours-per-week cart
native-country cart
income cart
dtype: object
In [8]: spop.visit_sequence
Out[8]:
age 0
workclass 1
fnlwgt 4
education 3
marital-status 2
dtype: int64
In [9]: spop.predictor_matrix
Out[9]:
age workclass fnlwgt education marital-status
age 0 0 0 0 0
workclass 1 0 0 0 0
fnlwgt 1 1 0 1 1
education 1 1 0 0 1
marital-status 1 1 0 0 0
License
This project is being developed at Hazy Limited and is released under MIT license.
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