From 549f74302420e3042a9cd82261dad6db6ed74c85 Mon Sep 17 00:00:00 2001
From: Riku-Laine <28960190+Riku-Laine@users.noreply.github.com>
Date: Mon, 20 Jan 2020 11:53:19 +0200
Subject: [PATCH] Updated stan script
---
.../stan_modelling_empirical.py | 297 ++++++++++--------
1 file changed, 167 insertions(+), 130 deletions(-)
diff --git a/analysis_and_scripts/stan_modelling_empirical.py b/analysis_and_scripts/stan_modelling_empirical.py
index 5423a56..2b62c3c 100644
--- a/analysis_and_scripts/stan_modelling_empirical.py
+++ b/analysis_and_scripts/stan_modelling_empirical.py
@@ -1,19 +1,19 @@
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
-# Author: Riku Laine
-# Date: 12AUG2019
-# Project name: Potential outcomes in model evaluation
-# Description: This script creates the figures and results used
-# in empirical data experiments with COMPAS data.
-#
-# Parameters:
-# -----------
-# (1) save_name : file path and prefix for saving the created figures.
-# (2) group_amount : How many groups if the non-linear model is used.
-# (3) stan_code_file_name : Name of file containing the stan model code.
-# (4) sigma_tau : Values of prior variance for the Jung-inspired model.
-# (5) data_path : Path to data file.
+Author: Riku Laine
+Date: 12AUG2019 / Modified 30DEC2019
+Project name: Potential outcomes in model evaluation
+Description: This script creates the figures and results used
+ in empirical data experiments with COMPAS data.
+
+Parameters:
+-----------
+(1) save_name : file path and prefix for saving the created figures.
+(2) stan_code_file_name : Name of file containing the stan model code.
+(3) sigma_tau : Values of prior variance for the Jung-inspired model.
+(4) data_path : Path to data file.
+(5) nJudges_M : Number of judges in simulations.
"""
import numpy as np
@@ -35,31 +35,33 @@ plt.rcParams.update({'figure.figsize': (10, 6)})
import sys
# Seed for reproducibility
-npr.seed(123)
+npr.seed(111)
# figure storage name
-save_name = sys.argv[1] + "sl_compas"
-
-# How many groups if jung model is used
-group_amount = int(sys.argv[2])
+save_name = sys.argv[1] + "sl_compas_"
# Name of stan model code file
-stan_code_file_name = sys.argv[3]
+stan_code_file_name = sys.argv[2]
# Variance prior
-sigma_tau = float(sys.argv[4])
+sigma_tau = float(sys.argv[3])
# figure storage name
-data_path = sys.argv[5]
+data_path = sys.argv[4]
+
+nJudges_M = int(sys.argv[5])
# Prefix for the figures and log files
print("These results have been obtained with the following settings:")
-print("Number of groups:", group_amount)
-
print("Prior for the variances:", sigma_tau)
+def standardize(x):
+ '''Standardization function'''
+
+ return (x - np.mean(x)) / np.std(x, ddof=1)
+
##########################
# ## Evaluator modules
@@ -68,19 +70,19 @@ print("Prior for the variances:", sigma_tau)
def fitPredictiveModel(x_train, y_train, x_test, class_value, model_type=None):
'''
- Fit a predictive model (default logistic regression) with given training
- instances and return probabilities for test instances to obtain a given
+ Fit a predictive model (default logistic regression) with given training
+ instances and return probabilities for test instances to obtain a given
class label.
-
+
Arguments:
----------
-
+
x_train -- x values of training instances
y_train -- y values of training instances
x_test -- x values of test instances
class_value -- class label for which the probabilities are counted for.
model_type -- type of model to be fitted.
-
+
Returns:
--------
(1) Trained predictive model
@@ -130,13 +132,13 @@ def fitPredictiveModel(x_train, y_train, x_test, class_value, model_type=None):
def getProbabilityForClass(x, model, class_value):
'''
- Function (wrapper) for obtaining the probability of a class given x and a
+ Function (wrapper) for obtaining the probability of a class given x and a
predictive model.
Arguments:
-----------
x -- individual features, an array of shape (observations, features)
- model -- a trained sklearn model. Predicts probabilities for given x.
+ model -- a trained sklearn model. Predicts probabilities for given x.
Should accept input of shape (observations, features)
class_value -- the resulting class to predict (usually 0 or 1).
@@ -155,8 +157,8 @@ def getProbabilityForClass(x, model, class_value):
# ### Contraction algorithm
-#
-# Below is an implementation of Lakkaraju's team's algorithm presented in
+#
+# Below is an implementation of Lakkaraju's team's algorithm presented in
# [their paper](https://helka.finna.fi/PrimoRecord/pci.acm3098066). Relevant
# parameters to be passed to the function are presented in the description.
@@ -164,7 +166,7 @@ def contraction(df, judgeIDJ_col, decisionT_col, resultY_col, modelProbS_col,
accRateR_col, r):
'''
This is an implementation of the algorithm presented by Lakkaraju
- et al. in their paper "The Selective Labels Problem: Evaluating
+ et al. in their paper "The Selective Labels Problem: Evaluating
Algorithmic Predictions in the Presence of Unobservables" (2017).
Arguments:
@@ -177,7 +179,7 @@ def contraction(df, judgeIDJ_col, decisionT_col, resultY_col, modelProbS_col,
resultY_col -- String, the name of the column containing the realization
modelProbS_col -- String, the name of the column containing the probability
scores from the black-box model B.
- accRateR_col -- String, the name of the column containing the judges'
+ accRateR_col -- String, the name of the column containing the judges'
acceptance rates
r -- Float between 0 and 1, the given acceptance rate.
@@ -192,25 +194,28 @@ def contraction(df, judgeIDJ_col, decisionT_col, resultY_col, modelProbS_col,
D_q = df[df[judgeIDJ_col] == most_lenient_ID_q].copy()
##### Agreement rate computation begins #######
-
- max_leniency = max(df[accRateR_col])
-
+
+ Q_leniency = max(df[accRateR_col])
+
+ if Q_leniency < r:
+ return np.nan, np.nan
+
# Sort D_q
# "Observations deemed as high risk by B are at the top of this list"
D_sort_q = D_q.sort_values(by=modelProbS_col, ascending=False)
-
+
# The agreement rate is now computed as the percentage of all the positive
# decisions given by q in the 1-r % of the most dangerous subjects.
all_negatives = np.sum(D_sort_q[decisionT_col] == 0)
-
- n_most_dangerous = int(round(D_q.shape[0] * (1-max_leniency)))
-
- agreed_decisions = np.sum(D_sort_q[decisionT_col][0:n_most_dangerous])
+
+ n_most_dangerous = int(round(D_q.shape[0] * (1-Q_leniency)))
+
+ agreed_decisions = np.sum(D_sort_q[decisionT_col][0:n_most_dangerous] == 0)
print("The agreement rate of contraction is:", agreed_decisions/all_negatives)
-
+
##### Agreement rate computation ends #######
-
+
# All observations of R_q have observed outcome labels.
# "R_q is the set of observations in D_q with observed outcome labels."
R_q = D_q[D_q[decisionT_col] == 1].copy()
@@ -236,7 +241,7 @@ def trueEvaluationEvaluator(df, resultY_col, r):
df.sort_values(by='B_prob_0_model', inplace=True, ascending=True)
to_release = int(round(df.shape[0] * r))
-
+
failed = df[resultY_col][0:to_release] == 0
return np.sum(failed) / df.shape[0], df.shape[0]
@@ -251,7 +256,7 @@ def labeledOutcomesEvaluator(df, decisionT_col, resultY_col, r, adjusted=False):
ascending=True)
to_release = int(round(df_observed.shape[0] * r))
-
+
failed = df_observed[resultY_col][0:to_release] == 0
if adjusted:
@@ -266,13 +271,12 @@ def labeledOutcomesEvaluator(df, decisionT_col, resultY_col, r, adjusted=False):
compas_raw = pd.read_csv(data_path)
# Select columns
-compas = compas_raw[[
- 'age', 'c_charge_degree', 'race', 'age_cat', 'score_text', 'sex',
- 'priors_count', 'days_b_screening_arrest', 'decile_score', 'is_recid',
- 'two_year_recid', 'c_jail_in', 'c_jail_out'
-]]
+compas = compas_raw[['age', 'c_charge_degree', 'race', 'age_cat', 'score_text',
+ 'sex','priors_count', 'days_b_screening_arrest',
+ 'decile_score', 'is_recid', 'two_year_recid', 'c_jail_in',
+ 'c_jail_out']]
-# Subset values, see reasons in ProPublica methodology.
+# Filter values, see ProPublica methodology.
compas = compas.query('days_b_screening_arrest <= 30 and \
days_b_screening_arrest >= -30 and \
is_recid != -1 and \
@@ -286,30 +290,39 @@ compas = compas[compas.score_text.notnull()]
compas['result_Y'] = np.where(compas['is_recid'] == 1, 0, 1)
# Convert string values to dummies, drop first to keep full rank.
-compas_dummy = pd.get_dummies(
- compas,
- columns=['c_charge_degree', 'race', 'age_cat', 'sex'],
- drop_first=True)
+compas_dummy = pd.get_dummies(compas,
+ columns=['c_charge_degree', 'race', 'age_cat', 'sex'],
+ drop_first=True)
-compas_dummy.drop(columns=[
- 'age', 'days_b_screening_arrest', 'c_jail_in', 'c_jail_out',
- 'two_year_recid', 'score_text', 'is_recid'
-],
- inplace=True)
+compas_dummy.drop(columns=['age', 'days_b_screening_arrest', 'c_jail_in',
+ 'c_jail_out', 'two_year_recid', 'score_text',
+ 'is_recid'], inplace=True)
# Shuffle rows for random judge assignment
compas_shuffled = compas_dummy.sample(frac=1)
-nJudges_M = 10
+# Decision assignment
+
+# Generate leniencies from U(0.1, 0.9) for all 16 judges. Then distribute the
+# observations evenly to all decision-makers and give positive decisions to
+# r% of subjects with the lowest COMPAS score.
+
+# nJudges_M = 16
+# nJudges_M = 12
# Assign judges as evenly as possible
judge_ID = pd.qcut(np.arange(len(compas_shuffled)), nJudges_M, labels=False)
-# Assign fixed leniencies from 0.1 to 0.9
-judge_leniency = np.array([0.1, 0.3, 0.5, 0.7, 0.9]*2)
+# Draw leniencies
+# judge_leniency = npr.uniform(0.1, 0.9, nJudges_M)
+# Assign leniencies
+judge_leniency = np.repeat([0.1, 0.5, 0.9], int(nJudges_M/3))
+
+# Replicate values for assignment
judge_leniency = judge_leniency[judge_ID]
+# Attach to data
compas_shuffled = compas_shuffled.assign(judge_ID=judge_ID,
judge_leniency=judge_leniency)
@@ -340,20 +353,27 @@ compas_unlabeled = compas_shuffled.copy()
# Hide unobserved
compas_labeled.loc[compas_labeled.decision_T == 0, 'result_Y'] = np.nan
-# Choose feature_columns
+# Choose feature_columns for the regression (priors, charge degree, race, age
+# and sex).
feature_cols = ~compas_labeled.columns.isin(
['result_Y', 'decile_score', 'judge_ID', 'judge_leniency', 'judge_index', 'decision_T'])
feature_cols = compas_labeled.columns[feature_cols]
+# Standardize priors count
+
+compas_labeled.priors_count = standardize(compas_labeled.priors_count)
####### Draw figures ###########
def drawDiagnostics(title, save_name, f_rates, titles):
-
+ '''
+ Draw boxplot figures. One panel for each method.
+ '''
+
cols = 2
rows = np.ceil(len(f_rates) / cols)
-
+
plt.figure(figsize=(16, 4.5*rows+1))
ax = plt.subplot(rows, cols, 1)
@@ -383,6 +403,8 @@ def drawDiagnostics(title, save_name, f_rates, titles):
plt.savefig(save_name + '_diagnostic_plot')
plt.show()
+ plt.close('all')
+
nIter = 10
@@ -398,87 +420,89 @@ f_rate_cf = np.zeros((nIter, 8))
sm = Model(stan_file=stan_code_file_name)
sm.compile()
+# Split the nJudges_M judges to two datasets nIter times.
+
for i in range(nIter):
-
- ids = np.arange(5)
- selected = ids + npr.choice([0, 5], 5)
-
+
+ # Split data using judge IDs.
+
+ # Get number of judges
+ id_max = np.max(compas_labeled.judge_ID) + 1
+
+ # Choose random judges by id
+ selected = npr.choice(np.arange(id_max), int(id_max/2), False)
+
test_labeled = compas_labeled[compas_labeled.judge_ID.isin(selected)]
train = compas_labeled[~compas_labeled.judge_ID.isin(selected)]
# Renew IDs
- test_labeled.loc[:, 'judge_ID'] = test_labeled.judge_ID % 5
-
+ test_labeled.loc[:, 'judge_ID'] = test_labeled.groupby('judge_ID').ngroup()
+
# Assign same observations to unlabeled data
test_unlabeled = compas_unlabeled.iloc[test_labeled.index.values]
-
-
+
# Train a logistic regression model
B_model, predictions = fitPredictiveModel(
train.loc[train['decision_T'] == 1, feature_cols],
train.loc[train['decision_T'] == 1, 'result_Y'], test_labeled[feature_cols], 0)
-
+
# Attach predictions to data
test_labeled = test_labeled.assign(B_prob_0_model=predictions)
test_unlabeled = test_unlabeled.assign(B_prob_0_model=predictions)
-
+
test_labeled.sort_values(by='B_prob_0_model', inplace=True, ascending=True)
-
- kk_array = pd.qcut(test_labeled['B_prob_0_model'], group_amount, labels=False)
-
+
# Find observed values
observed = test_labeled['decision_T'] == 1
-
+
# Assign data to the model
dat = dict(D=int(10),
N_obs=int(np.sum(observed)),
N_cens=int(np.sum(~observed)),
- K=int(group_amount),
sigma_tau=sigma_tau,
M=int(len(set(test_labeled['judge_ID']))),
jj_obs=test_labeled.loc[observed, 'judge_ID']+1,
jj_cens=test_labeled.loc[~observed, 'judge_ID']+1,
- kk_obs=kk_array[observed]+1,
- kk_cens=kk_array[~observed]+1,
dec_obs=test_labeled.loc[observed, 'decision_T'],
dec_cens=test_labeled.loc[~observed, 'decision_T'],
- X_obs=test_labeled.loc[observed, feature_cols.values],
- X_cens=test_labeled.loc[~observed, feature_cols.values],
+ X_obs=test_labeled.loc[observed, feature_cols.values].values,
+ X_cens=test_labeled.loc[~observed, feature_cols.values].values,
y_obs=test_labeled.loc[observed, 'result_Y'].astype(int))
-
- # Do the sampling
- fit = sm.sample(data=dat, chains=4, seed=123, warmup_iters=1500,
- sampling_iters=4500, adapt_delta=0.975)
+
+
+ # Do the sampling
+ fit = sm.sample(data=dat, chains=4, seed=123, warmup_iters=1500,
+ sampling_iters=4000, adapt_delta=0.975)
# Extract predictions
fit_colnames = fit.column_names
- print("Colnames", fit.column_names)
-
pred_cols = [s for s in fit_colnames if 'y_est' in s]
-
+
pars = fit.get_drawset(params=pred_cols)
-
+
fit.get_drawset(params=pred_cols)
- print("Drawset:", fit.get_drawset())
-
plt.close('all')
gc.collect()
gc.collect()
print(fit.diagnose(), file=open(save_name + '_stan_fit_diagnostics_' +
str(i) + '.txt', 'w'))
-
+
+ # Draw figures for every 5th iteration
+ if i % 5 == 0:
+ # Save fit object to csv
+ fit.save_csvfiles(dir=save_name, basename='fit_obj_i_' + str(i))
# Bayes
-
+
# Format matrix, each row is a sample of the posterior
# columns are observations
-
+
#y_imp = np.ones((pars['y_est'].shape[0], test_labeled.shape[0]))
y_imp = np.ones((pars.shape[0], test_labeled.shape[0]))
- # Impute the unobserved with the estimated
+ # Impute the unobserved with the estimated
# Reverse the binary coding to compute failures as sum. 0 == 0 = 1
#y_imp[:, ~observed] = 1 - pars['y_est']
y_imp[:, ~observed] = 1 - pars
@@ -491,53 +515,53 @@ for i in range(nIter):
gc.collect()
gc.collect()
-
+
process = psutil.Process(os.getpid())
- print("Memory use after deletion:", process.memory_info().rss) # in bytes
-
+ print("Memory use after deletion:", process.memory_info().rss) # in bytes
+
# Impute the observed
y_imp[:, observed] = 1 - test_labeled.loc[observed, 'result_Y']
-
+
for r in range(1, 9):
-
+
to_release = np.round(test_labeled.shape[0] * (r / 10)).astype(int)
-
+
failed = np.sum(y_imp[:, 0:to_release], axis=1)
-
+
f_rate_cf[i, r - 1] = np.mean(failed / test_labeled.shape[0])
-
+
print(".", end="")
-
+
# True evaluation
-
- f_rate_true[i, r - 1], N = trueEvaluationEvaluator(test_unlabeled,
+
+ f_rate_true[i, r - 1], N = trueEvaluationEvaluator(test_unlabeled,
'result_Y', r / 10)
-
+
# Labeled outcomes only
-
- f_rate_label[i, r - 1], N = labeledOutcomesEvaluator(test_labeled,
+
+ f_rate_label[i, r - 1], N = labeledOutcomesEvaluator(test_labeled,
'decision_T', 'result_Y', r / 10)
-
+
# Contraction
-
- f_rate_cont[i, r - 1], N = contraction(test_labeled, 'judge_ID',
- 'decision_T', 'result_Y', 'B_prob_0_model',
+
+ f_rate_cont[i, r - 1], N = contraction(test_labeled, 'judge_ID',
+ 'decision_T', 'result_Y', 'B_prob_0_model',
'judge_leniency', r / 10)
-
-failure_rates[:, 0] = np.mean(f_rate_true, axis=0)
-failure_rates[:, 1] = np.mean(f_rate_label, axis=0)
-failure_rates[:, 2] = np.mean(f_rate_cont, axis=0)
-failure_rates[:, 3] = np.mean(f_rate_cf, axis=0)
-failure_stds[:, 0] = np.std(f_rate_true, axis=0)
-failure_stds[:, 1] = np.std(f_rate_label, axis=0)
-failure_stds[:, 2] = np.std(f_rate_cont, axis=0)
-failure_stds[:, 3] = np.std(f_rate_cf, axis=0)
+failure_rates[:, 0] = np.nanmean(f_rate_true, axis=0)
+failure_rates[:, 1] = np.nanmean(f_rate_label, axis=0)
+failure_rates[:, 2] = np.nanmean(f_rate_cont, axis=0)
+failure_rates[:, 3] = np.nanmean(f_rate_cf, axis=0)
+
+failure_stds[:, 0] = np.nanstd(f_rate_true, axis=0, ddof=1)
+failure_stds[:, 1] = np.nanstd(f_rate_label, axis=0, ddof=1)
+failure_stds[:, 2] = np.nanstd(f_rate_cont, axis=0, ddof=1)
+failure_stds[:, 3] = np.nanstd(f_rate_cf, axis=0, ddof=1)
x_ax = np.arange(0.1, 0.9, 0.1)
-labels = ['True Evaluation', 'Labeled outcomes', 'Contraction',
+labels = ['True Evaluation', 'Labeled outcomes', 'Contraction',
'Counterfactuals']
colours = ['g', 'magenta', 'b', 'r']
@@ -562,12 +586,14 @@ plt.savefig(save_name + '_all')
plt.show()
+plt.close('all')
+
# Plot error of the methods (contraction and counterfactual)
# w.r.t True evaluation
for i in range(2, failure_rates.shape[1]):
error = np.abs(failure_rates[:, 0] - failure_rates[:, i])
-
+
plt.errorbar(x_ax,
error,
label=labels[i],
@@ -575,6 +601,7 @@ for i in range(2, failure_rates.shape[1]):
linestyle=line_styles[i],
yerr=failure_stds[:, i])
+plt.axhline(y=0, c='k')
plt.xlabel('Acceptance rate')
plt.ylabel('Error w.r.t. True evaluation')
plt.legend()
@@ -584,12 +611,22 @@ plt.savefig(save_name + '_all_err')
plt.show()
+plt.close('all')
+
+print("\nSingle runs:")
+print(f_rate_true, f_rate_label, f_rate_cont, f_rate_cf)
+
print("\nFailure rates:")
print(np.array2string(failure_rates, formatter={'float_kind':lambda x: "%.5f" % x}))
print("\nStandard deviations:")
print(np.array2string(failure_stds, formatter={'float_kind':lambda x: "%.5f" % x}))
+# Save arrays
+np.save(save_name + "_true_FRs", f_rate_true)
+np.save(save_name + "_labeled_FRs", f_rate_label)
+np.save(save_name + "_contraction_FRs", f_rate_cont)
+np.save(save_name + "_counterfactuals_FRs", f_rate_cf)
print("\nMean absolute errors:")
for i in range(1, failure_rates.shape[1]):
@@ -601,4 +638,4 @@ for i in range(1, failure_rates.shape[1]):
drawDiagnostics(title="Variation of failure rate estimates by method\nCOMPAS data set",
save_name=save_name,
f_rates=[f_rate_true, f_rate_label, f_rate_cont, f_rate_cf],
- titles=labels)
\ No newline at end of file
+ titles=labels)
--
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