Select Page

Research digital skills training 2021

Bayesian additive regression trees vs logistic regression – estimation of propensity scores

Samuel Passmore, Department of Statistics

Home • Projects • Bayesian additive regression trees vs logistic regression – estimation of propensity scores

Accurate comparison of hospital performance is crucial to the allocation of funding in New Zealand hospitals.

A problem for such comparisons is that patients and conditions are not randomly spread across hospitals. A range of factors, such as the economic environment surrounding the hospital, or a specialty unit within the hospital, mean that there may be disproportionate groups of demographics within any one hospital. When comparing hospitals’ performance, the non-random spread of patients can be accounted for through the use of propensity scores. Propensity scores weigh the importance of patients so that the demographics are balanced between hospitals. A number of methods can be used to estimate propensity scores.

My Honours project research compared the performance of Bayesian additive regression trees (BART) to a logistic regression. BART is a sum of trees model where the growth of a tree is constrained by its priors, then using an iterative Markov-chain Monte-Carlo algorithm, back fits the model for optimal fit. This method is computationally expensive.

 Analysing propensity scores

The NeSI Pan cluster allowed me to perform a parameter sweep to optimise the performance of BART and compare the results to a logistic regression. Results showed that a tailored BART performed marginally better than logistic regression in the estimation of propensity scores across the 9 hospitals. Figure 1 shows the difference in the proportion of patients in each age category of Hospital 17 when compared to all other hospitals. This result was fairly typical across the hospital comparisons.

Pan allowed me to run my analyses across 15 hospitals, with a sweep of parameter settings, in parallel. Considering a single run of a BART model would take between 10 –16 hours, being able to run this in parallel saved me weeks in time and allowed me to focus on the results of the analyses rather than waiting for the calculation to complete. For a project that only had a year time-frame this was very helpful. The staff at the Centre for eResearch were very helpful in helping me set up the analyses to run in the most efficient way which saved a lot of time and effort.

 

Figure 1: shows for hospital 17 the Mean Squared Covariate Balance score (MSCOB) for both the Default BART and Logistic regression models across the 10 propensity score bins. Propensity scores are continuous values from 0 – 1; however, to compare between hospitals we computed the mean-squared difference for each decile calling each a bin.
Figure 2: shows the MSCOB for deprivation score across the deciled bins. Deprivation score is a poverty scale ranging from 1, most impoverished, to 10, least impoverished. A perfect balance would show a matrix of squares. We can see from this graph that the balance is not perfect particularly in the first bin with a deprivation score of 9. This indicates there are a disproportionate number of wealthy people who have a 0 – 10% chance of attending this hospital.

See more case study projects

Data maturity project in High Value Nutrition, National Science Challenge

Data maturity project in High Value Nutrition, National Science Challenge

Haka on the move: sport circuits and cultural performance 

Haka on the move: sport circuits and cultural performance 

Proteins under a computational microscope: designing in-silico strategies to understand and develop molecular functionalities in Life Sciences and Engineering

Proteins under a computational microscope: designing in-silico strategies to understand and develop molecular functionalities in Life Sciences and Engineering

Remote temperature monitoring to reduce the spread of COVID-19

Remote temperature monitoring to reduce the spread of COVID-19

COVID-19 exponential growth visualisation

COVID-19 exponential growth visualisation

Developing virtual capabilities for the Science Payload Operations Centre

Developing virtual capabilities for the Science Payload Operations Centre

Hosting visualisation and analytics tools for COVID-19 studies

Hosting visualisation and analytics tools for COVID-19 studies

Exploring perceptions towards climate change over time on Twitter

Exploring perceptions towards climate change over time on Twitter

Coastal image classification and nalysis based on convolutional neural betworks and pattern recognition

Coastal image classification and nalysis based on convolutional neural betworks and pattern recognition

Calcium signalling in salivary gland acinar cells

Calcium signalling in salivary gland acinar cells

Anti-corruption regulations for promoting socially responsible practices

Anti-corruption regulations for promoting socially responsible practices

Determinants of translation efficiency in the evolutionarily-divergent protist Trichomonas vaginalis

Determinants of translation efficiency in the evolutionarily-divergent protist Trichomonas vaginalis

Analysing text data by time-series feature engineering

Analysing text data by time-series feature engineering

An investigation into Leap Motion device for “gesture-as-sign”

An investigation into Leap Motion device for “gesture-as-sign”

Antibiotic resistance and the “end of modern medicine ”

Antibiotic resistance and the “end of modern medicine ”

Develop short-term eruption warning systems for Whakaari and other volcanoes

Develop short-term eruption warning systems for Whakaari and other volcanoes

Evenly spaced observation fields from irregularly sampled data in the Southern Ocean

Evenly spaced observation fields from irregularly sampled data in the Southern Ocean

Measuring impact of entrepreneurship activities on students’ mindset, capabilities and entrepreneurial intentions

Measuring impact of entrepreneurship activities on students’ mindset, capabilities and entrepreneurial intentions

Using Zebra Finch data and deep learning classification to identify individual bird calls from audio recordings

Using Zebra Finch data and deep learning classification to identify individual bird calls from audio recordings

NETwork! analysis in cancer – managing genomics research data and building a repository workflow

NETwork! analysis in cancer – managing genomics research data and building a repository workflow

The Coronary Atlas – data processing workflow optimisation

The Coronary Atlas – data processing workflow optimisation

3D visualisation of indigenous burial site in Roonka

3D visualisation of indigenous burial site in Roonka

Automated measurement of intracranial cerebrospinal fluid volume and outcome after endovascular thrombectomy for ischemic stroke

Automated measurement of intracranial cerebrospinal fluid volume and outcome after endovascular thrombectomy for ischemic stroke

A new ‘stratigraphy’: interpreting object relationships with 3D point densities

A new ‘stratigraphy’: interpreting object relationships with 3D point densities

Towards the use of deep learning techniques for storm surge prediction

Towards the use of deep learning techniques for storm surge prediction

Using simple models to explore complex dynamics: A case study of macomona liliana (wedge-shell) and nutrient variations

Using simple models to explore complex dynamics: A case study of macomona liliana (wedge-shell) and nutrient variations

Development of Machine Learning methodology for genomic research

Development of Machine Learning methodology for genomic research

An Archaeological database for threatened North Island rock art in New Zealand

An Archaeological database for threatened North Island rock art in New Zealand

Presence: distributed mixed reality learning environment

Presence: distributed mixed reality learning environment

Digital video and the early learning lab

Digital video and the early learning lab

Publishing the Bay of Island Bottlenose dolphin catalogue

Publishing the Bay of Island Bottlenose dolphin catalogue

Modelling the diurnal cycle* of winds and clouds

Modelling the diurnal cycle* of winds and clouds

Presence: distributed mixed reality learning environment

Presence: distributed mixed reality learning environment

Using research virtual machines to analyse fMRI datasets

Using research virtual machines to analyse fMRI datasets

Genomic Virtual Lab (GVL) as a bioinformatics training platform

Genomic Virtual Lab (GVL) as a bioinformatics training platform

SwiftLaTeX- Exploring web-based true WYSIWYG editing for digital publishing

SwiftLaTeX- Exploring web-based true WYSIWYG editing for digital publishing

Climate change impacts on weather-related hazards

Climate change impacts on weather-related hazards

Understanding tumour evolution through augmented reality

Understanding tumour evolution through augmented reality

Myocardial motion tracking and strain calculation using Deep Learning networks

Myocardial motion tracking and strain calculation using Deep Learning networks

OnTask pilot at the Centre for Learning and Research in Higher Education

OnTask pilot at the Centre for Learning and Research in Higher Education

Visualising the University campus in 3D

Visualising the University campus in 3D

Visualising protein interaction

Visualising protein interaction

Biological heritage National Science Challenge eDNA virtual hub

Biological heritage National Science Challenge eDNA virtual hub

Interactive AR art – Project Gordon

Interactive AR art – Project Gordon

1-D numerical models of post-glacial river evolution

1-D numerical models of post-glacial river evolution

Mathematically modelling gastrointestinal electrical activity

Mathematically modelling gastrointestinal electrical activity

3D Cryo-EM reconstructions of macromolecular complexes

3D Cryo-EM reconstructions of macromolecular complexes

Engine knock in a spark-ignition engine with hydrogen supplementation

Engine knock in a spark-ignition engine with hydrogen supplementation

The complex unsteady flow within a fluid-filled annulus and its transition to turbulence

The complex unsteady flow within a fluid-filled annulus and its transition to turbulence

Using data mining for digital ink recognition

Using data mining for digital ink recognition

The landscape costs of brushtail possum dispersal

The landscape costs of brushtail possum dispersal

Accelerating the discovery of natural products made by orphan megasynthases

Accelerating the discovery of natural products made by orphan megasynthases

Improving the short term precipitation forecasts for New Zealand

Improving the short term precipitation forecasts for New Zealand

Finding genetic variants responsible  for human disease hiding in the universe of benign variants

Finding genetic variants responsible for human disease hiding in the universe of benign variants

Revealing key processes in enzyme efficiency through high performance computing

Revealing key processes in enzyme efficiency through high performance computing

3D Electromagnetic modeling and simulation using heterogeneous computing

3D Electromagnetic modeling and simulation using heterogeneous computing

Hemodynamics in the microcirculation

Hemodynamics in the microcirculation

Putting turbulence to work

Putting turbulence to work

Why are some molecules drugs?

Why are some molecules drugs?

Bayesian additive regression trees  vs logistic regression – estimation of propensity scores

Bayesian additive regression trees vs logistic regression – estimation of propensity scores

Fully coupled thermo-hydro-mechanical modelling of permeability enhancement by the finite element method

Fully coupled thermo-hydro-mechanical modelling of permeability enhancement by the finite element method

Modelling dispersal and ecological competition in a statistical phylogeographic framework

Modelling dispersal and ecological competition in a statistical phylogeographic framework

Studying the shape and the size of the universe

Studying the shape and the size of the universe

Planet hunting

Planet hunting

Simulating quantum mechanics on high performance computing cluster

Simulating quantum mechanics on high performance computing cluster

Multiscale modelling of saliva secretion

Multiscale modelling of saliva secretion

Modelling dual reflux pressure swing adsorption (DR-PSA) units for gas separation in natural gas processing

Modelling dual reflux pressure swing adsorption (DR-PSA) units for gas separation in natural gas processing

Improving the treatment of heart disease

Improving the treatment of heart disease

Estimating migration rates in the budding yeast Saccharomyces cerevisiae

Estimating migration rates in the budding yeast Saccharomyces cerevisiae

Number theoretic algorithms in cryptography

Number theoretic algorithms in cryptography

Molecular phylogenetics uses genetic data to reconstruct the evolutionary history of individuals, populations or species

Molecular phylogenetics uses genetic data to reconstruct the evolutionary history of individuals, populations or species

Phylogeny and phylogeography of the family kyphosidae (Perciformes: teleostei)

Phylogeny and phylogeography of the family kyphosidae (Perciformes: teleostei)

Testing what cosmic inflation really predicts

Testing what cosmic inflation really predicts

Multigene environmental DNA data analysis for New Zealand genomic observatory

Multigene environmental DNA data analysis for New Zealand genomic observatory

Finding genetic variants responsible for human disease hiding in universe of benign variants

Finding genetic variants responsible for human disease hiding in universe of benign variants

BEAST, Bayesian evolutionary analysis sampling trees

BEAST, Bayesian evolutionary analysis sampling trees

The formation of surface archaeological deposits in arid Australia

The formation of surface archaeological deposits in arid Australia

Statistical modelling of carryover effects after cessation of treatments

Statistical modelling of carryover effects after cessation of treatments

High-resolution cryo-electron microscopy of protein complexes and machines

High-resolution cryo-electron microscopy of protein complexes and machines

ARCI, archaeology eResearch collaboration initiative

ARCI, archaeology eResearch collaboration initiative

Optimisation of blades on large wind turbines with individual pitch control and trailing edge flaps

Optimisation of blades on large wind turbines with individual pitch control and trailing edge flaps

Quality of care and outcomes in children with cleft lip and/or palate

Quality of care and outcomes in children with cleft lip and/or palate

Geographic and temporal information retrieval on massive document collections

Geographic and temporal information retrieval on massive document collections

Homodynamics in the microcirculation

Homodynamics in the microcirculation

Processing structure-from-motion photogrammetry on the cluster

Processing structure-from-motion photogrammetry on the cluster

Computational investigation of catalysis mechanisms for polyurethane synthesis

Computational investigation of catalysis mechanisms for polyurethane synthesis

Virtual childhood obesity prevention laboratory

Virtual childhood obesity prevention laboratory

Giving Pacific research greater reach

Giving Pacific research greater reach

Development of novel waveguides  in the terahertz (THz) region

Development of novel waveguides in the terahertz (THz) region

Modelling of costs of diets  by INFORMAS

Modelling of costs of diets by INFORMAS

Foodback

Foodback

Finite element method code for  modelling biological cells

Finite element method code for modelling biological cells

The future of memory: Neuroimaging memory and imagination with functional MRI

The future of memory: Neuroimaging memory and imagination with functional MRI

Modelling and visualisation of calcium waves in parotid acinar cells

Modelling and visualisation of calcium waves in parotid acinar cells

Mapping donor contributions in the Pacific

Mapping donor contributions in the Pacific

Visualising humpback whale migration

Visualising humpback whale migration

Visualising the 2010 and 2011  Canterbury earthquakes

Visualising the 2010 and 2011 Canterbury earthquakes

Data management planning for MOA*

Data management planning for MOA*

Research data publishing  and preservation at COMPASS

Research data publishing and preservation at COMPASS

Centre for eResearch machine learning service

Centre for eResearch machine learning service

Building a discrete global  grid gazetteer service

Building a discrete global grid gazetteer service

The new Wanhal catalogue

The new Wanhal catalogue

Passive acoustic modelling

Passive acoustic modelling

Using GPUs to expand our understanding of the Solar System

Using GPUs to expand our understanding of the Solar System

Shedding new light on dark matter

Shedding new light on dark matter

Aerodynamics modelling paves the way for improved yacht designs

Aerodynamics modelling paves the way for improved yacht designs

Modernising models to help diagnose or treat disease and injury

Modernising models to help diagnose or treat disease and injury

Wandering around the molecular landscape: embracing virtual reality as a research showcasing outreach and teaching tool

Wandering around the molecular landscape: embracing virtual reality as a research showcasing outreach and teaching tool

ALTER: Between human and nonhuman – a VR art exhibition

ALTER: Between human and nonhuman – a VR art exhibition

Disposition of Microsoft HoloLenses for a Pop-Up Reality Shop to demonstrate the progress of a research project

Disposition of Microsoft HoloLenses for a Pop-Up Reality Shop to demonstrate the progress of a research project

Improving diagnosis for schistosomiasis by using the ‘metabolic footprint’ of urine samples from an animal model of Schistosoma infection to identify possible biomarkers

Improving diagnosis for schistosomiasis by using the ‘metabolic footprint’ of urine samples from an animal model of Schistosoma infection to identify possible biomarkers

Making stroke recovery prediction tools freely available

Making stroke recovery prediction tools freely available

MFT-ICR mass spectrometry data management and analysis workflow

MFT-ICR mass spectrometry data management and analysis workflow

Taking a ‘Big Data’ approach to find new clinical-omic associations in cancer

Taking a ‘Big Data’ approach to find new clinical-omic associations in cancer

Growing Up in New Zealand

Growing Up in New Zealand

Improving arrival time predictions for vehicles in a public transport network

Improving arrival time predictions for vehicles in a public transport network

Distributed and cloud-based control at field-level for systems interacting with soft bodies

Distributed and cloud-based control at field-level for systems interacting with soft bodies

Mobile Click Fraud Attack (MCFA)

Mobile Click Fraud Attack (MCFA)

Skin-omics: exploring the volatile organic compounds on human skin

Skin-omics: exploring the volatile organic compounds on human skin

New analytics tools for workload planning for the 2018 New Zealand Census

New analytics tools for workload planning for the 2018 New Zealand Census

Visualising the New Zealand Index of Multiple Deprivation

Visualising the New Zealand Index of Multiple Deprivation