256 lines
9.7 KiB
Python
256 lines
9.7 KiB
Python
"""
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Health Information Privacy Lab
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Brad. Malin, Weiyi Xia, Steve L. Nyemba
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This framework computes re-identification risk of a dataset assuming the data being shared can be loaded into a dataframe (pandas)
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The framework will compute the following risk measures:
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- marketer
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- prosecutor
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- pitman
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References :
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https://www.scb.se/contentassets/ff271eeeca694f47ae99b942de61df83/applying-pitmans-sampling-formula-to-microdata-disclosure-risk-assessment.pdf
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This framework integrates pandas (for now) as an extension and can be used in two modes :
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Experimental mode
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Here the assumption is that we are not sure of the attributes to be disclosed, the framework will explore a variety of combinations and associate risk measures every random combinations
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Evaluation mode
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The evaluation mode assumes the set of attributes given are known and thus will evaluate risk for a subset of attributes.
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features :
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- determine viable fields (quantifiable in terms of uniqueness). This is a way to identify fields that can act as identifiers.
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- explore and evaluate risk of a sample dataset against a known population dataset
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- explore and evaluate risk on a sample dataset
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Usage:
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from pandas_risk import *
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mydataframe = pd.DataFrame('/myfile.csv')
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resp = mydataframe.risk.evaluate(id=<name of patient field>,num_runs=<number of runs>,cols=[])
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resp = mydataframe.risk.explore(id=<name of patient field>,num_runs=<number of runs>,cols=[])
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@TODO:
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- Provide a selected number of fields and risk will be computed for those fields.
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- include journalist risk
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"""
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import pandas as pd
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import numpy as np
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import logging
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import json
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from datetime import datetime
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import sys
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@pd.api.extensions.register_dataframe_accessor("risk")
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class deid :
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"""
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This class is a deidentification class that will compute risk (marketer, prosecutor) given a pandas dataframe
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"""
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def __init__(self,df):
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self._df = df.fillna(' ')
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def explore(self,**args):
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"""
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This function will perform experimentation by performing a random policies (combinations of attributes)
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This function is intended to explore a variety of policies and evaluate their associated risk.
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@param pop|sample data-frame with popublation reference
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@param id key field that uniquely identifies patient/customer ...
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"""
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pop= args['pop'] if 'pop' in args else None
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if 'pop_size' in args :
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pop_size = np.float64(args['pop_size'])
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else:
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pop_size = -1
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#
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# Policies will be generated with a number of runs
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#
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RUNS = args['num_runs'] if 'num_runs' in args else 5
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sample = args['sample'] if 'sample' in args else pd.DataFrame(self._df)
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k = sample.columns.size -1 if 'field_count' not in args else int(args['field_count'])
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if 'id' in args :
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id = args['id']
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columns = list(set(sample.columns.tolist()) - set([id]))
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else:
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columns = sample.columns.tolist()
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o = pd.DataFrame()
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for i in np.arange(RUNS):
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n = np.random.randint(2,k)
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cols = np.random.choice(columns,n,replace=False).tolist()
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params = {'sample':sample,'cols':cols}
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if pop is not None :
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params['pop'] = pop
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if pop_size > 0 :
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params['pop_size'] = pop_size
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r = self.evaluate(**params)
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#
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# let's put the policy in place
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p = pd.DataFrame(1*sample.columns.isin(cols)).T
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p.columns = sample.columns
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o = o.append(r.join(p))
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o.index = np.arange(o.shape[0]).astype(np.int64)
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return o
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def evaluate(self, **args):
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"""
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This function has the ability to evaluate risk associated with either a population or a sample dataset
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:sample sample dataset
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:pop population dataset
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:cols list of columns of interest or policies
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:flag user provided flag for the context of the evaluation
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"""
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if 'sample' in args :
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sample = pd.DataFrame(args['sample'])
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else:
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sample = pd.DataFrame(self._df)
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if not args or 'cols' not in args:
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cols = sample.columns.tolist()
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elif args and 'cols' in args:
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cols = args['cols']
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flag = 'UNFLAGGED' if 'flag' not in args else args['flag']
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#
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# @TODO: auto select the columns i.e removing the columns that will have the effect of an identifier
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#
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# if 'population' in args :
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# pop = pd.DataFrame(args['population'])
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r = {"flag":flag}
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# if sample :
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handle_sample = Sample()
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xi = sample.groupby(cols,as_index=False).size().values
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handle_sample.set('groups',xi)
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if 'pop_size' in args :
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pop_size = np.float64(args['pop_size'])
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else:
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pop_size = -1
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#
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#-- The following conditional line is to address the labels that will be returned
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# @TODO: Find a more elegant way of doing this.
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#
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if 'pop' in args :
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r['sample marketer'] = handle_sample.marketer()
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r['sample prosecutor'] = handle_sample.prosecutor()
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r['sample unique ratio'] = handle_sample.unique_ratio()
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r['sample group count'] = xi.size
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else:
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r['marketer'] = handle_sample.marketer()
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r['prosecutor'] = handle_sample.prosecutor()
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r['unique ratio'] = handle_sample.unique_ratio()
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r['group count'] = xi.size
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if pop_size > 0 :
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handle_sample.set('pop_size',pop_size)
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r['pitman risk'] = handle_sample.pitman()
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if 'pop' in args :
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xi = pd.DataFrame({"sample_group_size":sample.groupby(cols,as_index=False).size()}).reset_index()
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yi = pd.DataFrame({"population_group_size":args['pop'].groupby(cols,as_index=False).size()}).reset_index()
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merged_groups = pd.merge(xi,yi,on=cols,how='inner')
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handle_population= Population()
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handle_population.set('merged_groups',merged_groups)
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r['pop. marketer'] = handle_population.marketer()
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r['pitman risk'] = handle_population.pitman()
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r['pop. group size'] = np.unique(yi.population_group_size).size
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#
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# At this point we have both columns for either sample,population or both
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#
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r['field count'] = len(cols)
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return pd.DataFrame([r])
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class Risk :
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"""
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This class is an abstraction of how we chose to structure risk computation i.e in 2 sub classes:
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- Sample computes risk associated with a sample dataset only
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- Population computes risk associated with a population
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"""
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def __init__(self):
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self.cache = {}
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def set(self,key,value):
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if id not in self.cache :
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self.cache[id] = {}
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self.cache[key] = value
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class Sample(Risk):
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"""
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This class will compute risk for the sample dataset: the marketer and prosecutor risk are computed by default.
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This class can optionally add pitman risk if the population size is known.
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"""
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def __init__(self):
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Risk.__init__(self)
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def marketer(self):
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"""
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computing marketer risk for sample dataset
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"""
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groups = self.cache['groups']
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group_count = groups.size
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row_count = groups.sum()
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return group_count / np.float64(row_count)
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def prosecutor(self):
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"""
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The prosecutor risk consists in determining 1 over the smallest group size
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It identifies if there is at least one record that is unique
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"""
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groups = self.cache['groups']
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return 1 / np.float64(groups.min())
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def unique_ratio(self):
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groups = self.cache['groups']
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row_count = groups.sum()
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return groups[groups == 1].sum() / np.float64(row_count)
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def pitman(self):
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"""
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This function will approximate pitman de-identification risk based on pitman sampling
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"""
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groups = self.cache['groups']
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si = groups[groups == 1].size
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u = groups.size
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alpha = np.divide(si , np.float64(u) )
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f = np.divide(groups.sum(), np.float64(self.cache['pop_size']))
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return np.power(f,1-alpha)
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class Population(Sample):
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"""
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This class will compute risk for datasets that have population information or datasets associated with them.
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This computation includes pitman risk (it requires minimal information about population)
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"""
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def __init__(self,**args):
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Sample.__init__(self)
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def set(self,key,value):
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Sample.set(self,key,value)
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if key == 'merged_groups' :
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Sample.set(self,'pop_size',np.float64(value.population_group_size.sum()) )
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Sample.set(self,'groups',value.sample_group_size)
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"""
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This class will measure risk and account for the existance of a population
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:merged_groups {sample_group_size, population_group_size} is a merged dataset with group sizes of both population and sample
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"""
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def marketer(self):
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"""
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This function requires
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"""
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r = self.cache['merged_groups']
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sample_row_count = r.sample_group_size.sum()
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#
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# @TODO : make sure the above line is size (not sum)
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# sample_row_count = r.sample_group_size.size
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return r.apply(lambda row: (row.sample_group_size / np.float64(row.population_group_size)) /np.float64(sample_row_count) ,axis=1).sum()
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