Learning from Data to Predict

Key themes

  • The prediction task

  • Supervised learning

  • Machine learning tasks — e.g., regression (continuous) and classification (binary)

  • Building and evaluation of simple prediction models

  • The problem of model overfitting and strategies to avoid it:

    • Splitting the data into training set and testing set

    • Cross-validation

  • Introduction to supervised machine learning algorithms, including k-Nearest Neighbors and Logistic Regression

Learning resources

Predictability of life trajectories by Matthew Salganik

Introduction to Machine Learning Methods by Susan Athey

Machine Learning with Scikit Learn by Jake VanderPlas

M Molina & F Garip. 2019. Machine learning for sociology. Annual Review of Sociology. Link to an open-access version of the article available at the Open Science Framework.

Ian Foster, Rayid Ghani, Ron S. Jarmin, Frauke Kreuter, Julia Lane. 2021. Chapter 7: Machine Learning. In Big Data and Social Science (2nd edition).

Aurélien Géron. 2019. Chapter 2: End-to-end Machine Learning project. In Hands-On Machine Learning with Scikit-Learn, Keras, and TensorFlow (2nd Edition). O’Reilly.

The Prediction task

Prediction is a data science task among other data science tasks, including description and causal inference. Prediction is the use of data to map some input (X) to an output (Y). The prediction task is called classification when the output variable is categorical (or discrete), and regression when it is continuous. Our focus in this session will be on classification.

Prediction tasks in social sciences

There are many prediction problems in social sciences (summarised in Kleinberg et al. 2015) that can benefit from (supervised) machine learning, for example:

  • In child protection, predicting when kids are in danger;

  • In the criminal justice system, predicting whether to detain or release arrestees as they await adjudication of their case (e.g., Kleinberg et al. 2015);

  • In population health, predicting suicides;

  • In education, predicting which teacher will have the greatest value add (e.g., Rockoff et al., 2011);

  • In higher education, predicting earlier university dropouts;

  • In labor market policy, predicting unemployment spell length to help workers decide on savings rates and job search strategies;

  • In social policy, predicting highest risk youth for targeting interventions (e.g., Chandler et al., 2011);

  • In sociology, predicting life outcomes (Salganik et al. 2020).

Predictions gone wrong

Prediction and machine learning models went wrong in a few occasions in different domains, including public health, education, the criminal justice system, and healthcare:

Regardless of whether you use or not machine learning in your research, knowledge about prediction and machine learning techniques can help you evaluate how those techniques are used across domains and possibly identify ethical challenges and potential biases in those applications. Importantly, such data ethics challenges are found to reside not only in the machine learning algorithms themselves but in the entire data science ‘pipeline’ or ecosystem.

Supervised learning

Learn a model from labeled training data or outcome variable that would enable us to make predictions about unseen or future data. The learning is called supervised because the labels (e.g., email Spam or Ham where ‘Ham’ is e-mail that is not Spam) of the outcome variable (Y) that guide the learning process are already known.

Research problem: vaccine hesitancy

We will aim to predict people who are unlikely to take a coronavirus vaccine (Y) from socio-demographic and health input features (X). An unbiased prediction of individuals who are unlikely to vaccinate can inform targeted public health interventions, including information campaigns disseminating evidence-based information about Covid-19 vaccines.

Data: Understanding Society COVID-19

We will use data from The Understanding Society: Covid-19 Study. The survey asks participants across the UK about their experiences during the COVID-19 outbreak. We will use Wave 6 (November 2020) of the survey.

The data are safeguarded and can be downloaded from the UK Data Service.

Accessing data from your Google Drive

After you obtain access to the Understanding Society: Covid-19 Study, 2020, you can upload the Wave 6 (November 2020) data set into your Google Drive. Then you will need to connect your Google Drive to your Google Colab using the code below:

# Import the Drive helper
from google.colab import drive

# This will prompt for authorization. Enter your authorisation code and rerun the cell. 
drive.mount('/content/drive')
---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
<ipython-input-1-9b2f03ff29d8> in <module>
      1 # Import the Drive helper
----> 2 from google.colab import drive
      3 
      4 # This will prompt for authorization. Enter your authorisation code and rerun the cell.
      5 drive.mount('/content/drive')

ModuleNotFoundError: No module named 'google'

Loading the Understanding Society Covid-19 Study (Wave 6, November 2020)

import pandas as pd
import numpy as np

USocietyCovid = pd.read_csv('/content/drive/My Drive/Understanding_Society_Covid19_Wave6_November2020.csv')
# Display all columns in the Understanding Society: COVID-19 Study 
pd.options.display.max_columns = None

USocietyCovid.head(0) # display headings only as the data is safeguarded
pidp psu strata birthy racel_dv bornuk_dv i_hidp j_hidp k_hidp i_ioutcome j_ioutcome k_ioutcome cf_welsh cf_dobchk cf_age cf_sex_cv cf_addrchk cf_couplewsh cf_hhnum cf_personsexa cf_personsexb cf_personsexc cf_personsexd cf_personsexe cf_personsexf cf_personsexg cf_personsexh cf_personsexi cf_personsexj cf_personsexk cf_personagea cf_personageb cf_personagec cf_personaged cf_personagee cf_personagef cf_personageg cf_personageh cf_personagei cf_personagej cf_personagek cf_relationa cf_relationb cf_relationc cf_relationd cf_relatione cf_relationf cf_relationg cf_relationh cf_relationi cf_relationj cf_relationk cf_couple cf_hhcompa cf_hhcompb cf_hhcompc cf_hhcompd cf_hhcompe cf_parent0plus cf_parent5plus cf_parent015 cf_parent1619 cf_parent511 cf_parent1217 cf_parent418 cf_scsf1 cf_ff_hadsymp cf_clinvuln_dv cf_hadsymp cf_hassymp cf_symptoms1 cf_symptoms2 cf_symptoms23 cf_symptoms24 cf_symptoms25 cf_symptoms3 cf_symptoms4 cf_symptoms5 cf_symptoms6 cf_symptoms7 cf_symptoms8 cf_symptoms9 cf_symptoms10 cf_symptoms12 cf_symptoms13 cf_symptoms14 cf_symptoms15 cf_symptoms16 cf_symptoms17 cf_symptoms18 cf_symptoms19 cf_symptoms20 cf_symptoms21 cf_symptoms22 cf_symptoms11 cf_cv19treat cf_cv19trwhat1 cf_cv19trwhat2 cf_cv19trwhat3 cf_cv19trwhat4 cf_cv19trwhat5 cf_cv19trwhat6 cf_cv19trwhat7 cf_cv19trwhat8 cf_cv19trwhat9 cf_cv19trwhat10 cf_cv19trwhat11 cf_longcovid cf_lgcvsymp1 cf_lgcvsymp23 cf_lgcvsymp24 cf_lgcvsymp25 cf_lgcvsymp3 cf_lgcvsymp4 cf_lgcvsymp5 cf_lgcvsymp6 cf_lgcvsymp7 cf_lgcvsymp8 cf_lgcvsymp9 cf_lgcvsymp10 cf_lgcvsymp12 cf_lgcvsymp13 cf_lgcvsymp14 cf_lgcvsymp15 cf_lgcvsymp16 cf_lgcvsymp17 cf_lgcvsymp18 cf_lgcvsymp19 cf_lgcvsymp20 cf_lgcvsymp21 cf_lgcvsymp22 cf_lgcvsymp26 cf_lgcvsymp_oth cf_tested cf_testresult cf_testwhen_d cf_testwhen_m cf_testwhen_y cf_hadcovid cf_testtrace cf_traceinfo cf_traceinfoeng cf_traced cf_contactcv19t1 cf_contactcv19t5 cf_contactcv19t2 cf_contactcv19t3 cf_contactcv19t4 cf_riskcv19 cf_smartphone cf_smarttype cf_smartmodel cf_covidapp cf_whynotapp1 cf_whynotapp2 cf_whynotapp3 cf_whynotapp4 cf_whynotapp5 cf_whynotapp6 cf_whynotapp7 cf_whynotapp8 cf_whynotapp9 cf_whynotapp10 cf_whynotapp11 cf_whynotapp_oth cf_whynotapporder cf_covidappon cf_covidappnot1 cf_covidappnot2 cf_covidappnot3 cf_covidappnot_oth cf_hhsymp cf_hhsympwho_persona cf_hhsympwho_personb cf_hhsympwho_personc cf_hhsympwho_persond cf_hhsympwho_persone cf_hhsympwho_personf cf_hhsympwho_persong cf_hhsympwho_personh cf_hhsympwho_personi cf_hhsympwho_personj cf_hhsympwho_personk cf_hhsympwho_personl cf_hhsympwho_personm cf_hhsympwho_personn cf_hhsympwho_persono cf_hhsympwho_personp cf_hhsympwho_personq cf_hhsympwho_personr cf_hhsympwho_persons cf_hhsympwho_persont cf_hhsympwho_personu cf_hhsympwho_personv cf_hhsympwho_personw cf_hhsympwho_personx cf_hhsympwho_persony cf_hhsympwho_none cf_hhtest cf_hhtestwho_persona cf_hhtestwho_personb cf_hhtestwho_personc cf_hhtestwho_persond cf_hhtestwho_persone cf_hhtestwho_personf cf_hhtestwho_persong cf_hhtestwho_personh cf_hhtestwho_personi cf_hhtestwho_personj cf_hhtestwho_personk cf_hhtestwho_personl cf_hhtestwho_personm cf_hhtestwho_personn cf_hhtestwho_persono cf_hhtestwho_personp cf_hhtestwho_personq cf_hhtestwho_personr cf_hhtestwho_persons cf_hhtestwho_persont cf_hhtestwho_personu cf_hhtestwho_personv cf_hhtestwho_personw cf_hhtestwho_personx cf_hhtestwho_persony cf_hhtestwho_none cf_hhresult_persona cf_hhresult_personb cf_hhresult_personc cf_hhresult_persond cf_hhresult_persone cf_hhresult_personf cf_hhresult_persong cf_hhresult_personh cf_hhresult_personi cf_hhresult_personj cf_hhresult_personk cf_hhresult_personl cf_hhresult_personm cf_hhresult_personn cf_hhresult_persono cf_hhresult_personp cf_hhresult_personq cf_hhresult_personr cf_hhresult_persons cf_hhresult_persont cf_hhresult_personu cf_hhresult_personv cf_hhresult_personw cf_hhresult_personx cf_hhresult_persony cf_hhtestwhen_d_persona cf_hhtestwhen_m_persona cf_hhtestwhen_y_persona cf_hhtestwhen_d_personb cf_hhtestwhen_m_personb cf_hhtestwhen_y_personb cf_hhtestwhen_d_personc cf_hhtestwhen_m_personc cf_hhtestwhen_y_personc cf_hhtestwhen_d_persond cf_hhtestwhen_m_persond cf_hhtestwhen_y_persond cf_hhtestwhen_d_persone cf_hhtestwhen_m_persone cf_hhtestwhen_y_persone cf_hhtestwhen_d_personf cf_hhtestwhen_m_personf cf_hhtestwhen_y_personf cf_hhtestwhen_d_persong cf_hhtestwhen_m_persong cf_hhtestwhen_y_persong cf_hhtestwhen_d_personh cf_hhtestwhen_m_personh cf_hhtestwhen_y_personh cf_hhtestwhen_d_personi cf_hhtestwhen_m_personi cf_hhtestwhen_y_personi cf_hhtestwhen_d_personj cf_hhtestwhen_m_personj cf_hhtestwhen_y_personj cf_hhtestwhen_d_personk cf_hhtestwhen_m_personk cf_hhtestwhen_y_personk cf_hhtestwhen_d_personl cf_hhtestwhen_m_personl cf_hhtestwhen_y_personl cf_hhtestwhen_d_personm cf_hhtestwhen_m_personm cf_hhtestwhen_y_personm cf_hhtestwhen_d_personn cf_hhtestwhen_m_personn cf_hhtestwhen_y_personn cf_hhtestwhen_d_persono cf_hhtestwhen_m_persono cf_hhtestwhen_y_persono cf_hhtestwhen_d_personp cf_hhtestwhen_m_personp cf_hhtestwhen_y_personp cf_hhtestwhen_d_personq cf_hhtestwhen_m_personq cf_hhtestwhen_y_personq cf_hhtestwhen_d_personr cf_hhtestwhen_m_personr cf_hhtestwhen_y_personr cf_hhtestwhen_d_persons cf_hhtestwhen_m_persons cf_hhtestwhen_y_persons cf_hhtestwhen_d_persont cf_hhtestwhen_m_persont cf_hhtestwhen_y_persont cf_hhtestwhen_d_personu cf_hhtestwhen_m_personu cf_hhtestwhen_y_personu cf_hhtestwhen_d_personv cf_hhtestwhen_m_personv cf_hhtestwhen_y_personv cf_hhtestwhen_d_personw cf_hhtestwhen_m_personw cf_hhtestwhen_y_personw cf_hhtestwhen_d_personx cf_hhtestwhen_m_personx cf_hhtestwhen_y_personx cf_hhtestwhen_d_persony cf_hhtestwhen_m_persony cf_hhtestwhen_y_persony cf_fluinvite cf_hadflujab cf_noflujab cf_nofluinvite cf_fluinvite50 cf_flusoon cf_vaxxer cf_vaxno cf_vaxwhy cf_vaxpush1 cf_vaxpush2 cf_vaxpush3 cf_ff_hcond1 cf_ff_hcond2 cf_ff_hcond3 cf_ff_hcond4 cf_ff_hcond5 cf_ff_hcond6 cf_ff_hcond7 cf_ff_hcond8 cf_ff_hcond10 cf_ff_hcond11 cf_ff_hcond12 cf_ff_hcond13 cf_ff_hcond14 cf_ff_hcond15 cf_ff_hcond16 cf_ff_hcond18 cf_ff_hcond19 cf_ff_hcond21 cf_ff_hcond22 cf_ff_hcond23 cf_ff_hcond24 cf_ff_hcond27 cf_ff_hcondhas cf_ff_pregnow cf_ff_stillpreg cf_hcondnew_cv1 cf_hcondnew_cv2 cf_hcondnew_cv3 cf_hcondnew_cv4 cf_hcondnew_cv5 cf_hcondnew_cv6 cf_hcondnew_cv7 cf_hcondnew_cv8 cf_hcondnew_cv11 cf_hcondnew_cv21 cf_hcondnew_cv10 cf_hcondnew_cv12 cf_hcondnew_cv13 cf_hcondnew_cv14 cf_hcondnew_cv15 cf_hcondnew_cv16 cf_hcondnew_cv22 cf_hcondnew_cv19 cf_hcondnew_cv23 cf_hcondnew_cv24 cf_hcondnew_cv27 cf_hcondnew_cv18 cf_hcondnew_cv96 cf_arthtypn cf_cancertypn_cv1 cf_cancertypn_cv2 cf_cancertypn_cv3 cf_cancertypn_cv4 cf_cancertypn_cv5 cf_cancertypn_cv6 cf_cancertypn_cv8 cf_cancertypn_cv7 cf_mhealthtypn_cv2 cf_mhealthtypn_cv3 cf_mhealthtypn_cv4 cf_mhealthtypn_cv5 cf_mhealthtypn_cv6 cf_mhealthtypn_cv8 cf_mhealthtypn_cv9 cf_mhealthtypn_cv10 cf_mhealthtypn_cv11 cf_mhealthtypn_cv12 cf_mhealthtypn_cv13 cf_mhealthtypn_cv14 cf_mhealthtypn_cv15 cf_mhealthtypn_cv16 cf_mhealthtypn_cv17 cf_mhealthtypn_cv18 cf_mhealthtypn_cv19 cf_mhealthtypn_cv20 cf_hcond_treat1 cf_hcond_treat2 cf_hcond_treat3 cf_hcond_treat4 cf_hcond_treat5 cf_hcond_treat6 cf_treatment1 cf_treatment2 cf_treatment3 cf_treatment4 cf_treatment5 cf_canceltreat cf_nhsnowgp2 cf_nhsnowpm2 cf_nhsnowop2 cf_nhsnowip2 cf_nhsnow1112 cf_chscnowpharm2 cf_chscnowotcm2 cf_chscnowcarer2 cf_chscnowpsy2 cf_pregnow cf_stillpreg cf_pregscan cf_pregmidwife cf_pregantenatal cf_aidhh cf_aidnum cf_carehhc1 cf_carehhc2 cf_carehhc3 cf_carehhc4 cf_carehhc5 cf_carehhc6 cf_carehhwho1 cf_carehhwho2 cf_carehhwho3 cf_carehhwho4 cf_carehhwho5 cf_carehhwho6 cf_carehhwho7 cf_carehhwho8 cf_carehhsh cf_aidhrs_cv cf_respitenow cf_caring cf_carehow1 cf_carehow2 cf_carehow3 cf_carehow4 cf_carehow5 cf_carehow6 cf_carehow7 cf_carehow8 cf_carehow9 cf_carehow10 cf_carewho1 cf_carewho2 cf_carewho3 cf_carewho4 cf_carewho5 cf_carewho6 cf_carewho7 cf_carewho8 cf_help cf_helpwhat1 cf_helpwhat2 cf_helpwhat3 cf_helpwhat4 cf_helpwhat5 cf_helpwhat6 cf_helpwhat7 cf_helpwhat8 cf_helpwhat9 cf_helpwhat10 cf_helpwho1 cf_helpwho2 cf_helpwho3 cf_helpwho4 cf_helpwho5 cf_helpwho6 cf_helpwho7 cf_helpwho8 cf_sclonely_cv cf_f2fcontact cf_f2fcontfreq cf_phcontact cf_smcontact cf_whymove1 cf_whymove2 cf_whymove3 cf_whymove4 cf_whymove5 cf_whymove6 cf_whymove7 cf_whymove8 cf_whymove9 cf_whymove10 cf_whymove11 cf_whymove12 cf_whymove13 cf_hsownd_cv cf_garden1 cf_garden2 cf_garden3 cf_garden4 cf_garden5 cf_garden6 cf_deskspace cf_pcnet cf_expmove cf_whyexpmove1 cf_whyexpmove2 cf_whyexpmove3 cf_whyexpmove4 cf_whyexpmove5 cf_whyexpmove6 cf_whyexpmove7 cf_whyexpmove8 cf_whyexpmove9 cf_whyexpmove10 cf_whyexpmove11 cf_whyexpmove12 cf_whyexpmove13 cf_ff_semp cf_ff_sempderived cf_ff_hours cf_ff_furlough cf_ff_stillfurl cf_ff_sempgovt cf_ff_blwork cf_sempchk cf_semp cf_sempderived cf_hours cf_hrschange112 cf_hrschange11 cf_hrschange12 cf_hrschange13 cf_hrschange14 cf_hrschange15 cf_hrschange116 cf_hrschange16 cf_hrschange113 cf_hrschange17 cf_hrschange18 cf_hrschange19 cf_hrschange114 cf_hrschange110 cf_hrschange115 cf_hrschange111 cf_hrschange28 cf_hrschange21 cf_hrschange22 cf_hrschange23 cf_hrschange24 cf_hrschange25 cf_hrschange29 cf_hrschange26 cf_hrschange210 cf_hrschange27 cf_hrschange315 cf_hrschange31 cf_hrschange32 cf_hrschange33 cf_hrschange34 cf_hrschange35 cf_hrschange319 cf_hrschange36 cf_hrschange316 cf_hrschange37 cf_hrschange38 cf_hrschange39 cf_hrschange310 cf_hrschange311 cf_hrschange312 cf_hrschange317 cf_hrschange313 cf_hrschange318 cf_hrschange314 cf_hrschangeup11 cf_hrschangeup12 cf_hrschangeup13 cf_hrschangeup14 cf_hrschangeup15 cf_hrschangeup16 cf_hrschangeup17 cf_hrschangeup18 cf_hrschangeup19 cf_hrschangeup110 cf_hrschangeup111 cf_hrschangeup112 cf_hrschangeup113 cf_stillfurl cf_supprob6 cf_supprob8 cf_sempgovt2 cf_netpay_amount cf_netpay_period cf_grosspay_amount cf_grosspay_period cf_hhearners cf_hhearn_amount cf_hhearn_period cf_hhincome_amount cf_hhincome_period cf_ghhincome_amount cf_ghhincome_period cf_wah cf_wktrv_cv1 cf_wktrv_cv2 cf_wktrv_cv3 cf_wktrv_cv4 cf_wktrv_cv5 cf_wktrv_cv6 cf_wktrv_cv7 cf_wktrv_cv8 cf_wktrv_cv9 cf_wktrv_cv10 cf_wktrv_cv11 cf_wktrv_cv12 cf_wktrvfar_cv cf_trcarfq_cv cf_trbikefq_cv cf_trwalkfq cf_trbusfq_cv cf_trtrnfq_cv cf_trtubefq cf_ff_ucredit cf_ff_morhol cf_ff_hsownd_cv cf_ff_credithol cf_ucreditb65 cf_ucredit2b65 cf_ucreditadvance65 cf_benefitsamt65 cf_transfers cf_transfmade1 cf_transfmade2 cf_transfmade3 cf_transfmade4 cf_transfmade5 cf_transfmade6 cf_transfmade7 cf_transfrec1 cf_transfrec2 cf_transfrec3 cf_transfrec4 cf_transfrec5 cf_transfrec6 cf_transfrec7 cf_transfout cf_transfin cf_xphs_cv cf_morhol3 cf_renthol cf_xpbills_cv cf_credithol cf_creditholend cf_creditholwhich1 cf_creditholwhich2 cf_creditholwhich3 cf_creditholwhich4 cf_creditholwhich5 cf_inoutflows1 cf_inoutflows2 cf_inoutflows9 cf_inoutflows3 cf_inoutflows4 cf_inoutflows5 cf_inoutflows6 cf_inoutflows10 cf_inoutflows7 cf_inoutflows8 cf_save_cv cf_saved_cv cf_debtnonmort cf_debtamt cf_debt2 cf_debt3 cf_spend cf_ff_mpcalloc cf_finnow cf_finfut_cv3 cf_jobsec cf_finsec cf_mpc1 cf_mpc2 cf_mpc31 cf_mpc32 cf_mpc33 cf_mpc34 cf_mpc35 cf_mpc1b cf_mpc2b cf_mpc3b1 cf_mpc3b2 cf_mpc3b3 cf_mpc3b4 cf_scopngbhh_cv cf_nbrcoh3 cf_nbrcoh2 cf_nbrcoh4 cf_scopngbhg cf_crrace_cv cf_num418 cf_ch418doba_y cf_ch418dobb_y cf_ch418dobc_y cf_ch418dobd_y cf_ch418dobe_y cf_childage_childa cf_childage_childb cf_childage_childc cf_childage_childd cf_childage_childe cf_schoollw_childa cf_schoollw_childb cf_schoollw_childc cf_schoollw_childd cf_schoollw_childe cf_schoollwdys_childa cf_schoollwdys_childb cf_schoollwdys_childc cf_schoollwdys_childd cf_schoollwdys_childe cf_schoollwhrs_childa cf_schoollwhrs_childb cf_schoollwhrs_childc cf_schoollwhrs_childd cf_schoollwhrs_childe cf_schoollwgo_childa cf_schoollwgo_childb cf_schoollwgo_childc cf_schoollwgo_childd cf_schoollwgo_childe cf_schoolgodys_childa cf_schoolgodys_childb cf_schoolgodys_childc cf_schoolgodys_childd cf_schoolgodys_childe cf_schoolgohrs_childa cf_schoolgohrs_childb cf_schoolgohrs_childc cf_schoolgohrs_childd cf_schoolgohrs_childe cf_schoolwork_childa cf_schoolwork_childb cf_schoolwork_childc cf_schoolwork_childd cf_schoolwork_childe cf_lessonsoff_childa cf_lessonsoff_childb cf_lessonsoff_childc cf_lessonsoff_childd cf_lessonsoff_childe cf_lessonson_childa cf_lessonson_childb cf_lessonson_childc cf_lessonson_childd cf_lessonson_childe cf_hstime2_childa cf_hstime2_childb cf_hstime2_childc cf_hstime2_childd cf_hstime2_childe cf_hshelp2_childa cf_hshelp2_childb cf_hshelp2_childc cf_hshelp2_childd cf_hshelp2_childe cf_tutoring1_childa cf_tutoring2_childa cf_tutoring3_childa cf_tutoring1_childb cf_tutoring2_childb cf_tutoring3_childb cf_tutoring1_childc cf_tutoring2_childc cf_tutoring3_childc cf_tutoring1_childd cf_tutoring2_childd cf_tutoring3_childd cf_tutoring1_childe cf_tutoring2_childe cf_tutoring3_childe cf_remedials_childa cf_remedials_childb cf_remedials_childc cf_remedials_childd cf_remedials_childe cf_academprg_childa cf_academprg_childb cf_academprg_childc cf_academprg_childd cf_academprg_childe cf_cospace1_childa cf_cospace1_childb cf_cospace1_childc cf_cospace1_childd cf_cospace1_childe cf_cospace2_childa cf_cospace2_childb cf_cospace2_childc cf_cospace2_childd cf_cospace2_childe cf_cospace3_childa cf_cospace3_childb cf_cospace3_childc cf_cospace3_childd cf_cospace3_childe cf_cospace4_childa cf_cospace4_childb cf_cospace4_childc cf_cospace4_childd cf_cospace4_childe cf_cospace5_childa cf_cospace5_childb cf_cospace5_childc cf_cospace5_childd cf_cospace5_childe cf_sclfsato_cv cf_scghqa cf_scghqb cf_scghqc cf_scghqd cf_scghqe cf_scghqf cf_scghqg cf_scghqh cf_scghqi cf_scghqj cf_scghqk cf_scghql cf_incentives cf_noemailvoucher cf_scghq1_dv cf_scghq2_dv cf_outcome cf_lastq cf_lastmodule cf_link cf_surveystart cf_surveyend cf_surveytime cf_tsidcheckst cf_tsidcheckend cf_tshhrelst cf_tshhrelend cf_tssahst cf_tssahend cf_tscovidst cf_tscovidend cf_tshhcvst cf_tshhcvend cf_tsflust cf_tsfluend cf_tslthealthst cf_tslthealthend cf_tscaringhhst cf_tscaringhhend cf_tscareexhhst cf_tscareexhhend cf_tslonelyst cf_tslonelyend cf_tscffst cf_tscffend cf_tshsingst cf_tshsingend cf_tsempst cf_tsempend cf_tsttwst cf_tsttwend cf_tstranspst cf_tstranspend cf_tsfinst cf_tsfinend cf_tsfinsecst cf_tsfinsecend cf_tsnbhdst cf_tsnbhdend cf_tsnovschst cf_tsnovschend cf_tslfsatst cf_tslfsatend cf_tsghqst cf_tsghqend cf_tsclosest cf_tscloseend cf_screenres cf_browserres cf_useragentstring cf_ff_prevsurv cf_ff_intd cf_ff_intm cf_ff_inty cf_ff_country cf_gor_dv cf_aid_dv cf_betaindin_xw cf_betaindin_xw_t cf_betaindin_lw cf_betaindin_lw_t1 cf_betaindin_lw_t2
USocietyCovid.shape
(12035, 916)
USocietyCovid.info()
<class 'pandas.core.frame.DataFrame'>
RangeIndex: 12035 entries, 0 to 12034
Columns: 916 entries, pidp to cf_betaindin_lw_t2
dtypes: float64(10), int64(855), object(51)
memory usage: 84.1+ MB

Defining Output and Input variables

Here are the Output and Input data features we will use in this session.

Outcome: Output (Y)

Description

Variable

Values

Likelihood of taking up a coronavirus vaccination

cf_vaxxer

1 = Very likely, 2 = Likely, 3 = Unlikely, 4 = Very unlikely

Predictors: Input features (X)

We select 4 (demographic and health-related) variables as examples only, no prior literature or expert knowledge is considered. We will discuss the role of prior literature and expert knowledge in the process of variable selection when we learn causal inference approaches.

Description

Variable

Values

Age

cf_age

Integer values (whole numbers)

Respondent sex

cf_sex_cv

1 = Male, 2 = Female, 3 = Prefer not to say

General health

cf_scsf1

1 = Excellent, 2 = Very good, 3 = Good, 4 = Fair, 5 = Poor

At risk of serious illness from Covid-19

cf_clinvuln_dv

0 = no risk (not clinically vulnerable), 1 = moderate risk (clinically vulnerable), 2 = high risk (clinically extremely vulnerable)

Data wrangling

# Select output y and input X variables
USocietyCovid = USocietyCovid[['cf_vaxxer', 'cf_age','cf_sex_cv','cf_scsf1', 'cf_clinvuln_dv']]
USocietyCovid.head()
cf_vaxxer cf_age cf_sex_cv cf_scsf1 cf_clinvuln_dv
0 2 37 2 2 0
1 3 35 1 4 0
2 3 55 2 2 0
3 1 38 1 3 1
4 1 67 2 2 0
import seaborn as sns
sns.set_context("notebook", font_scale=1.5)
%matplotlib inline

fig = sns.catplot(x="cf_vaxxer", 
            kind = "count",
            height=6, aspect=1.5, palette="ch:.25",
            data = USocietyCovid)

# Tweak the plot 
(fig.set_axis_labels("Likelihood of taking up a coronavirus vaccination", "Frequency")
    .set_xticklabels(["missing", "inapplicable", "refusal", "don't know", "Very likely","Likely","Unlikely","Very unlikely"])
    .set_xticklabels(rotation=45))
<seaborn.axisgrid.FacetGrid at 0x7f9209efc670>
_images/prediction_supervised_learning_20_1.png

Missing observations in Understanding Society are indicated by negative values. Let’s convert negative values to NaN using the function mask in pandas. An alternative approach would be to reload the data using the Pandas read_csv() function and provide the negative values as an argument to the parameter na_values, as a result of which Pandas will recognise these values as NaN.

# The function 'mask' in pandas replaces values where a condition is met.
USocietyCovid = USocietyCovid.mask(USocietyCovid < 0)
# Alternatively, you could replace negative values with another value, e.g., 0, using the code USocietyCovid.mask(USocietyCovid < 0, 0)
USocietyCovid
cf_vaxxer cf_age cf_sex_cv cf_scsf1 cf_clinvuln_dv
0 2.0 37 2 2.0 0.0
1 3.0 35 1 4.0 0.0
2 3.0 55 2 2.0 0.0
3 1.0 38 1 3.0 1.0
4 1.0 67 2 2.0 0.0
... ... ... ... ... ...
12030 1.0 57 1 2.0 0.0
12031 2.0 70 2 3.0 1.0
12032 2.0 64 1 2.0 0.0
12033 4.0 31 1 1.0 0.0
12034 3.0 41 2 3.0 0.0

12035 rows × 5 columns

# Remove NaN
USocietyCovid = USocietyCovid[['cf_vaxxer', 'cf_age', 'cf_sex_cv', 'cf_scsf1', 'cf_clinvuln_dv']].dropna()

USocietyCovid
cf_vaxxer cf_age cf_sex_cv cf_scsf1 cf_clinvuln_dv
0 2.0 37 2 2.0 0.0
1 3.0 35 1 4.0 0.0
2 3.0 55 2 2.0 0.0
3 1.0 38 1 3.0 1.0
4 1.0 67 2 2.0 0.0
... ... ... ... ... ...
12030 1.0 57 1 2.0 0.0
12031 2.0 70 2 3.0 1.0
12032 2.0 64 1 2.0 0.0
12033 4.0 31 1 1.0 0.0
12034 3.0 41 2 3.0 0.0

11930 rows × 5 columns

# Plot the new cf_vaxxer (vaccination likelihood) variable

fig = sns.catplot(x="cf_vaxxer",
            kind = "count",
            height=6, aspect=1.5, palette="ch:.25",
            data = USocietyCovid)

# Tweak the plot
(fig.set_axis_labels("Likelihood of taking up a coronavirus vaccination", "Frequency")
    .set_xticklabels(["Very likely","Likely","Unlikely","Very unlikely"])
    .set_xticklabels(rotation=45))
<seaborn.axisgrid.FacetGrid at 0x7f92284700d0>
_images/prediction_supervised_learning_24_1.png

To simplify the problem, we will recode cf_vaxxer (vaccination likelihood) variable into a binary variable where 1 refers to ‘Likely to take up a Covid-19 vaccine’ and 2 refers to ‘Unlikely to take up a Covid-19 vaccine’. To achieve this, we use the replace() method which replaces a set of values we specify (in our case, [1,2,3,4]) with another set of values we specify (in our case, [1,1,0,0]).

# Recode cf_vaxxer into a binary variable
USocietyCovid['cf_vaxxer'] = USocietyCovid['cf_vaxxer'].replace([1,2,3,4],[1,1,0,0])
USocietyCovid.head()
cf_vaxxer cf_age cf_sex_cv cf_scsf1 cf_clinvuln_dv
0 1.0 37 2 2.0 0.0
1 0.0 35 1 4.0 0.0
2 0.0 55 2 2.0 0.0
3 1.0 38 1 3.0 1.0
4 1.0 67 2 2.0 0.0
# Plot the binary cf_vaxxer (vaccination likelihood) variable
fig = sns.catplot(x="cf_vaxxer", 
            kind = "count",
            height=6, aspect=1.5, palette="ch:.25",
            data = USocietyCovid)

# Tweak the plot 
(fig.set_axis_labels("Likelihood of taking up a coronavirus vaccination", "Frequency")
    .set_xticklabels(["Unlikely","Likely"])
    .set_xticklabels(rotation=45))
<seaborn.axisgrid.FacetGrid at 0x7f92586612b0>
_images/prediction_supervised_learning_27_1.png
USocietyCovid.groupby('cf_vaxxer').count()
cf_age cf_sex_cv cf_scsf1 cf_clinvuln_dv
cf_vaxxer
0.0 1837 1837 1837 1837
1.0 10093 10093 10093 10093
USocietyCovid.shape[0]
11930
# 84.6% of respondents very likely or likely to take up a Covid vaccine and 15.4% very unlikely or unlikely  
USocietyCovid.groupby('cf_vaxxer').count()/USocietyCovid.shape[0]
cf_age cf_sex_cv cf_scsf1 cf_clinvuln_dv
cf_vaxxer
0.0 0.153982 0.153982 0.153982 0.153982
1.0 0.846018 0.846018 0.846018 0.846018

So far, we have described our outcome variable to make sense of the task but we have neither looked at the predictor variables nor examined any relationships between predictor variables and outcomes. It is a good practice to first split the data into training set and test set and only then explore predictors and relationships in the training set.

Overfitting and data splitting

The problem of model overfitting

Overfitting occurs when model captures ‘noise’ in a specific sample while failing to recognise general patterns across samples. As a result of overfitting, the model produces accurate predictions for examples from the sample at hand but will predict poorly new examples the model has never seen.

Training set, Validation set, and Test set

To avoid overfitting, data is typically split into three groups:

  • Training set — used to train models

  • Validation set — used to tune the model and estimate model performance/accuracy for best model selection

  • Test set - used to evaluate the generalisability of the model to new observations the model has never seen

If your data set is not large enough, a possible strategy, which we will use here, is to split the data into training set and test set, and use cross-validation on the training set to evaluate our models’ performance/accuracy. We will use 2/3 of the data to train the predictive model and the remaining 1/3 to create the test set.

# Split train and test data

from sklearn.model_selection import train_test_split

# Outcome variable
y = USocietyCovid[['cf_vaxxer']]

# Predictor variables
X = USocietyCovid[['cf_age', 'cf_sex_cv', 'cf_scsf1', 'cf_clinvuln_dv']]

# Split data into training set and test set
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.33, stratify=y, random_state=0)
print('Train data', X_train.shape, '\n''Test data', X_test.shape)
Train data (7993, 4) 
Test data (3937, 4)

Preprocessing the training data set

Categorical predictors — dummy variables

Categorical variables are often encoded using numeric values. For example, Respondent sex is recorded as 1 = Men, 2 = Female, 3 = Prefer not to say. The numeric values can be ‘misinterpreted’ by the algorithms — the value of 1 is obviously less than the value of 3 but that does not correspond to real-world numerical differences.

A solution is to convert categorical predictors into dummy variables. Basically, each category value is converted into a new column and assigns a 1 or 0 (True/False) values using the function get_dummies in pandas. The function creates dummy/indicator variables that contain value of 1 or 0.

The Respondent sex variable is converted below is three columns of 1s or 0s corresponding to the respective value.

# Use get_dummies to convert the Respondent sex categorical variable into 3 dummy/indicator variables
X_train_predictors = pd.get_dummies(X_train, columns=["cf_sex_cv"])
X_train_predictors.head()
cf_age cf_scsf1 cf_clinvuln_dv cf_sex_cv_1 cf_sex_cv_2 cf_sex_cv_3
994 28 2.0 0.0 0 1 0
11376 41 5.0 0.0 0 1 0
9730 77 3.0 1.0 0 1 0
8235 41 3.0 2.0 0 1 0
1406 60 2.0 0.0 0 1 0
# Create two DataFrames, one for numerical variables and one for categorical variables
X_train_predictors_cat = X_train_predictors[['cf_sex_cv_1', 'cf_sex_cv_2', 'cf_sex_cv_3']]
X_train_predictors_cont = X_train_predictors[['cf_age', 'cf_scsf1', 'cf_clinvuln_dv']]

Continuous predictors — standardisation

We standardise the continuous input variables.

# Standardise the predictors using the StandardScaler function in sklearn
from sklearn.preprocessing import StandardScaler  # For standartising data
scaler = StandardScaler() # Initialising the scaler using the default arguments 
X_train_predictors_cont_scale = scaler.fit_transform(X_train_predictors_cont) # Fit to continuous input variables and return the standardised dataset 
X_train_predictors_cont_scale
array([[-1.65608796, -0.56081614, -0.80754698],
       [-0.84497135,  2.64868513, -0.80754698],
       [ 1.40119771,  0.50901761,  0.81873748],
       ...,
       [-0.96975852, -1.6306499 , -0.80754698],
       [ 0.46529394,  0.50901761,  2.44502193],
       [ 0.77726186,  0.50901761,  0.81873748]])

Combine categorical and continuous predictors into one data array

# Use the concatenate function in Numpy to combine all variables — both categorical and continuous predictors — in one array
X_train_preprocessed = np.concatenate([X_train_predictors_cont_scale,X_train_predictors_cat], axis = 1)
X_train_preprocessed
array([[-1.65608796, -0.56081614, -0.80754698,  0.        ,  1.        ,
         0.        ],
       [-0.84497135,  2.64868513, -0.80754698,  0.        ,  1.        ,
         0.        ],
       [ 1.40119771,  0.50901761,  0.81873748,  0.        ,  1.        ,
         0.        ],
       ...,
       [-0.96975852, -1.6306499 , -0.80754698,  0.        ,  1.        ,
         0.        ],
       [ 0.46529394,  0.50901761,  2.44502193,  0.        ,  1.        ,
         0.        ],
       [ 0.77726186,  0.50901761,  0.81873748,  1.        ,  0.        ,
         0.        ]])
X_train_preprocessed.shape
(7993, 6)

Unbalance class problem

In the case of the vaccination likelihood question, one of the classes (likely to vaccinate) has a significantly greater proportion of cases (84.6%) than the other case (unlikely to vaccinate) (15.4%). We therefore face an unbalanced class problem.

Different methods to mitigate the problem exist. We will use a method called ADASYN: Adaptive Synthetic Sampling Method for Imbalanced Data. The method oversamples the minority class in the training data set until both classes have an equal number of observations. Hence, the data set we use to train our models contains two balanced classes.

from imblearn.over_sampling import ADASYN

# Initialization of the ADASYN resampling method; set random_state for reproducibility
adasyn = ADASYN(random_state=0)

# Fit the ADASYN resampling method to the train data  
X_train_balance, y_train_balance = adasyn.fit_resample(X_train_preprocessed, y_train)

The resulting X_train_balance and y_train_balance now include both the original data and the resampled data. The y_train_balance now includes an almost equal number of labels for each class.

# Now that the two classes are balanced, the train data is ~14K observations, greater than the original ~8K.   
X_train_balance.shape
(13611, 6)

Hands-on mini-exercise

Verify that after the oversampling the y_train_balance data object contains indeed approximately equal number of observations for both classes, those likely to vaccinate (1) and those unlikely to vaccinate (0).

Note that y_train_balance is a NumPy array. You can check that on your own using the function type(), for example: type(y_train).

(y_train_balance == 0).sum()
cf_vaxxer    6849
dtype: int64
(y_train_balance == 1).sum()
cf_vaxxer    6762
dtype: int64

Train models on training data

We fit two classifiers — k-Nearest Neighbours (k-NN) and Logistic Regression — on the training data. The k-Nearest Neighbours classifier (k-NN) and Logistic Regression classifier are two widely used classifiers. Our focus is on the end-to-end workflow so we do not discuss the workings of the two classifiers in detail. To learn more about the two classifiers, see Python Data Science Handbook by Jake VanderPlas (on k-NN) and the DataCamp course Supervised Learning with scikit-learn.

In the models below, we use the default hyperparameters (hyperparameter are parameters that are not learned from data but are set by the researcher to guide the learning process) for both classifiers.

from sklearn.neighbors import KNeighborsClassifier
from sklearn.linear_model import LogisticRegression

# Create an instance of k-nearest neighbors (k-NN) classifier.
# We set the hyperparameter n_neighbors=5 meaning that the label of an unknown respondent (0 or 1) is a function of the labels of its five closest training respondents.
kNN_Classifier =  KNeighborsClassifier(n_neighbors = 5)

# Create an instance of Logistic Regression Classifier
LogReg_Classifier =  LogisticRegression()

# Fit both models to the training data
kNN_Classifier.fit(X_train_balance, y_train_balance.cf_vaxxer)
LogReg_Classifier.fit(X_train_balance, y_train_balance.cf_vaxxer)
LogisticRegression()

Model evaluation using Cross-validation

Now that your two models are fitted, you can evaluate the accuracy of their prediction. In older approaches, the prediction accuracy is often calculated on the same set of training data used to fit the model. The problem of such an approach is that the model can ‘memorise’ the training data and show high prediction accuracy on that data set while failing to perform well on new data. For this reason, approaches in data science, and machine learning in particular, prefer to evaluate the prediction accuracy of a model on new data that has not been used in training the model.

The cross-validation technique

Cross-Validation is a methodology to assess accuracy of model prediction without relying on in-sample prediction. We will split our training set into k equal folds or parts. The number of folds can differ but for simplicity we will consider 5-fold cross-validation. How does 5-fold cross-validation work? While keeping aside one fold (or part), we fit the model with the remaining four folds and use the fitted model to predict outcomes of observations in fold one and on this basis compute model prediction accuracy. We repeat the procedure for all 5 folds or parts of the data and compute the average prediction accuracy.

Metrics to evaluate model performance

Many metrics to evaluate model performance exist. We evaluate model performance using the accuracy score. The accuracy score is the simplest metric for evaluating classification models. Simply put, accuracy is the proportion of predictions our model got right. Keep in mind, however, that because of the unbalanced class problem, accuracy may not be the best metric in our case. Because one of our classes accounts for 84.6% of the cases, even a model that uniformly predicts that all respondents are likely to take up the vaccine will obtain very high accuracy of 0.846 while being useless for identifying respondents who are unlikely to take up the vaccine. We will return to this problem shortly.

# Import the function cross_val_score() which performs cross-validation and evaluates the model using a score
# Many scores are available to evaluate a classification mdoel, we select the simplest one called accuracy
from sklearn.model_selection import cross_val_score

# Evaluate the kNN_Classifier model via 5-fold cross-validation
kNN_score = cross_val_score(kNN_Classifier, X_train_balance, y_train_balance.cf_vaxxer, cv=5, scoring='accuracy')
kNN_score
array([0.6232097 , 0.65686995, 0.64070536, 0.65980896, 0.64731815])
# Take the mean across the five accuracy scores
kNN_score.mean()*100
64.55824239753719
# Repeat for our logistic regression model
LogReg_score = cross_val_score(LogReg_Classifier, X_train_balance, y_train_balance.cf_vaxxer, cv=5, scoring='accuracy')
LogReg_score.mean()*100
62.21431553077533

The output from the cross-validation technique shows that the performance of our two models is comparable as measured by the accuracy score.

At this stage, we could fine-tune model hyperparameters — i.e., parameters that the model does not learn from data, e.g., the number of k neighbours in the k-NN algorithm — and re-evaluate model performance. During the process of model validation, we do not use the test data. Once we are happy with how our model(s) perform, we test the model on unseen data.

Testing model accuracy on new data

Before we test the accuracy of our model on the test data set, we preprocess the test data set using the same procedure we used to preprocess the training data.

Preprocessing the test data set

# Use get_dummies to convert the Respondent sex categorical variable into 3 dummy/indicator variables
X_test_predictors = pd.get_dummies(X_test, columns=["cf_sex_cv"])

# Create two DataFrames, one for quantitative variables and one for qualitative variables
X_test_predictors_cat = X_test_predictors[['cf_sex_cv_1', 'cf_sex_cv_2', 'cf_sex_cv_3']]
X_test_predictors_cont = X_test_predictors[['cf_age', 'cf_scsf1', 'cf_clinvuln_dv']]

# Standardise the predictors using the StandardScaler function in sklearn
scaler = StandardScaler() # Initialising the scaler using the default arguments 
X_test_predictors_cont_scale = scaler.fit_transform(X_test_predictors_cont) # Fit to continuous input variables and return the standardised dataset 

# Use the concatenate function in Numpy to combine all variables — both categorical and continuous predictors — in one array
X_test_preprocessed = np.concatenate([X_test_predictors_cont_scale,X_test_predictors_cat], axis = 1)
X_test_preprocessed
array([[ 0.44686144, -1.63480238, -0.82552056,  1.        ,  0.        ,
         0.        ],
       [-0.41738323, -0.58244513, -0.82552056,  0.        ,  1.        ,
         0.        ],
       [-0.35565147, -0.58244513, -0.82552056,  1.        ,  0.        ,
         0.        ],
       ...,
       [ 0.01473911, -0.58244513, -0.82552056,  1.        ,  0.        ,
         0.        ],
       [ 1.37283788,  0.46991213,  0.7914319 ,  0.        ,  1.        ,
         0.        ],
       [-0.47911499, -1.63480238, -0.82552056,  1.        ,  0.        ,
         0.        ]])

Predicting vaccine hesitancy

Use the predict function to predict who is likely to take up the COVID-19 vaccine or not using the test data.

y_pred_kNN = kNN_Classifier.predict(X_test_preprocessed)
y_pred_LogReg = LogReg_Classifier.predict(X_test_preprocessed)
y_pred_LogReg
array([1., 0., 1., ..., 1., 1., 1.])

Model evaluation on test data

Let’s evaluate the performance of our models predicting vaccination willingness using accuracy metric.

# Evaluate performance using the accuracy score for the logistic regresson model
from sklearn.metrics import accuracy_score
accuracy_score(y_test, y_pred_LogReg)
0.6245872491744984
# Evaluate performance using the accuracy score for the  k-nearest neighbors model
accuracy_score(y_test, y_pred_kNN)
0.5044450088900178

The accuracy scores are slightly lower on the test set compared to the accuracy score on the training set, indicating that the data split methodology mitigates the risk of overfitting.

Accuracy is a good metric when the positive class and the negative class are balanced. However, when one of the classes is a majority, as in our case, then a model can achieve a high accuracy by just predicting all observations to be the majority class. However, this is not what we want. In fact, in order to inform an information campaign about vaccination, we are more interested in predicting the minority class, people that are unlikely to take up the vaccine.

We can use a confusion matrix to further evaluate the performance of our classification models. The confusion matrix shows the number of respondents known to be in group 0 (unlikely to vaccinate) or 1 (likely to vaccinate) and predicted to be in group 0 or 1, respectively.

The confusion matrix below shows that the logistic model predicts 393 out of the 606 respondents who are unlikely to vaccinate. The model does much better job predicting respondents that are likely to vaccinate, 2066 out of 3331 respondents in the test data set.

# Confusion matrix for the logistic regression model plotted via Pandas crosstab() function

pd.crosstab(y_test.cf_vaxxer,y_pred_LogReg, rownames=['Actual'], colnames=['Predicted'], margins=True)
Predicted 0.0 1.0 All
Actual
0.0 393 213 606
1.0 1265 2066 3331
All 1658 2279 3937

What do the numbers in the confusion matrix mean?

  • True positive - our model correctly predicts the positive class (likely to vaccinate)

  • True negative - our model correctly predicts the negative class (unlikely to vaccinate)

  • False positive - our model incorrectly predicts the positive class

  • False negative - our model incorrectly predicts the negative class

# Here is another representation of the confusion matrix using the scikit-learn `confusion_matrix` function
from sklearn.metrics import confusion_matrix
confusion_matrix(y_test,y_pred_LogReg)
array([[ 393,  213],
       [1265, 2066]])
# The function ravel() flattens the confusion matrix
tn, fp, fn, tp = confusion_matrix(y_test,y_pred_LogReg).ravel()
print('True negative = ', tn, '\nFalse positive = ', fp, '\nFalse negative = ', fn, '\nTrue positive = ', tp)
True negative =  393 
False positive =  213 
False negative =  1265 
True positive =  2066

For the k-nearest neighbors model, the confusion matrix below shows that the k-NN model predicts 316 out of the 606 respondents who are unlikely to vaccinate (the logistic regression model predicts more accurately those unlikely to vaccinate). The model does not predicts well respondents that are likely to vaccinate, 1670 out of 3331 respondents in the test data set.

Recall that we are less interested in predicting the majority class (likely to vaccinate). Instead, we are interested in predicting the minority class (unlikely to vaccinate) so that the results can inform an information campaign among people that are unlikely to vaccinate.

# Confusion matrix for the k-nearest neighbors model plotted via pandas function crosstab
pd.crosstab(y_test.cf_vaxxer,y_pred_kNN, rownames=['Actual'], colnames=['Predicted'], margins=True)
Predicted 0.0 1.0 All
Actual
0.0 316 290 606
1.0 1661 1670 3331
All 1977 1960 3937

Instead of relying on a single metric, it is often helpful (if not confusing) to compare various metrics. You can use the scikit-learn function classification_report to calculate various classification metrics, including precision and recall.

from sklearn.metrics import classification_report

# Various metrics for the logistic regression model
print(classification_report(y_test,y_pred_LogReg))
              precision    recall  f1-score   support

         0.0       0.24      0.65      0.35       606
         1.0       0.91      0.62      0.74      3331

    accuracy                           0.62      3937
   macro avg       0.57      0.63      0.54      3937
weighted avg       0.80      0.62      0.68      3937
# Various metrics for the k-nearest neighbors model 
print(classification_report(y_test,y_pred_kNN))
              precision    recall  f1-score   support

         0.0       0.16      0.52      0.24       606
         1.0       0.85      0.50      0.63      3331

    accuracy                           0.50      3937
   macro avg       0.51      0.51      0.44      3937
weighted avg       0.75      0.50      0.57      3937

Overall, predicting accuracy of approximately 62% and 50% for the two models and the low predictive accuracy of the minority class (unlikely to vaccinate) indicate that the performance of our models is far from optimal. However, the purpose of this lab is not to build a well-performing model but to introduce you to an end-to-end machine learning workflow.

Keep in mind that it is not a good research practice to now — after you tested the models on the test data — go back and fine-tune the training models as this will introduce overfitting. A good research practice is to fine-tune and improve your model(s) at the stage of training and cross-validation (not after you tested your model on unseen data). Once you select your best performing model(s) at the cross-validation stage, you test the model using the test data and report the performance scores.

As part of your data analysis exercises, you will have another opportunity to build a new machine learning model and evaluate model performance.