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Research digital skills training 2021

Data analytics and visualisation for improving
public health and transport planning

Professor Mark Gahegan, Computer Science; Assoc Professor Daniel Exeter, Epidemiology and Biostatistics; Professor David O’Sullivan,
Victoria University of Wellington; Nick Young, Sina Masoud-Ansari, Centre for eResearch

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Overview

Conventional ways of collecting data such as censuses and surveys are increasingly gathered at a micro-scale individual level. The improvements of collection methods designs and data integration across various government and service agencies, coupled with analytics, visualisation, and sophisticated Deep Learning methods to support assessments, projections, interventions and innovation, can bring meaningful social outcomes. The micro-simulations and mathematical models of citizen behaviour, mobilities, decision-making, and choices support the government on economic policy, social welfare, and public safety to build healthier lifestyles and smarter cities.

The transport project aims to harness both the new data and new analysis methods to provide better insights into public transport uptake, accessibility, planning and policy that will help in improving transport services. Auckland Transport (AT) now has some very accurate microdata on public transport via HOP card, which shows the date and time of travel, the journey’s origin and destination, and the bus route. The data can be used to map with demographics, place of employment and the geography of Auckland. The resulting datasets are rich with possibilities that provide better insights into public transport uptake, accessibility, planning and policy-making.

The health project is to help decision-makers to compare likely impacts and benefits on public health across the whole of New Zealand. To achieve this goal, the team worked with multiple government agencies to create an “e-Atlas” to facilitate the discovery of important trends over space and time and compare places and regions of interest at several aggregated levels. The project will create a sophisticated picture of lifestyles, deprivation, welfare and life courses, supported by best practices in data visualisation and analytical capability via collaboration between the Turing Aotearoa and Alan Turing Institute in the UK. We will look at some examples of work in the following sections.

Using visualisation to support the exploration of transport data

One body of work was to create a near real-time traffic visualisation map by collecting traffic camera images from the New Zealand Transport Agency (NZTA) website. (https://www.journeys.nzta.govt.nz/traffic-and-travel-information/traffic-cameras/). There were approximately >112M images collected from 297 cameras, summing to >5TB, which were run on the University of Auckland Nectar cloud with V100 GPU capacity. These images were processed with ImageAI (https://github.com/OlafenwaMoses/ImageAI) from the Python library with self-contained Deep Learning capability. The resulting code can capture and count the number of motorcycles, cars, buses and trucks present in each image. The visualisation map shows the vehicles detection and traffic flow pattern (Figure 1), which can be used, for example, to assist effective management of road traffic infrastructure and deployment of intelligent transportation systems.

 

Workflow analysis to determine location-based accessibility to essential services

Another exploration was to look at the relationship between accessibility to essential services via public transport and how they are related to the measurement of deprivation in the New Zealand population. We used data sourced from The General Transit Feed Specification (GTFS) feeds for Auckland,  Wellington and Christchurch and used OpenStreetMap (OSM) to build a walking, cycling and driving network. The New Zealand OSM data is sourced from GeoFabrik and  GDAM for region boundaries, and the travel time was calculated using OpenTripPlanner. We were looking at the possibility of finding the shortest path transit travel times between sets of origins and destinations in major cities (Figure 2) such as Auckland, Wellington and Christchurch etc., and exploring how easy it is to access essential services (such as hospitals) within these major cities.

 

Figure 1. An interactive map showing vehicle detections for a camera over time
Figure 2. Mean estimated travel time in minutes from Ponsonby to other locations in Auckland accessible within 1 hour using public transport. Coloured regions indicate at least one journey option meets the constraint.

Visual analytics laboratory to improve social policy design

We have extracted the demographical smoking data from the 2018 NZ Census and the relevant cancer data from the Ministry of Health. These data were integrated using an open source Geographic Information System QGIS (https://www.qgis.org/en/site/), and processed with Pandas tool from Python library, further mapped with JavaScript libraries Leaflet (https://leafletjs.com/). Finally, they plotted with the Plotly tool (https://plotly.com/javascript/). We also add analytics and Deep Learning capability to help identify trends, anomalies, hotspots and other features of interest. These tools could also be used to project into the future based on observed (learned) trends. The resulting source code is open source at (http://github.com/uoa-eResearch/cancermap). (Figure 3)

Collaboration

By linking together the latest data, visual analytic methods, spatial analysis techniques, and machine learning tools to create a collaborative visual analytics laboratory for public transport is the first of its kind in New Zealand.

 

We plan to create an ongoing partnership with the best researchers to help the government to address the most challenging problems to ensure the best research ideas are implemented in secure and robust systems. The simulation outcomes can be used reliably in real-world situations with well-designed interfaces and the most suitable platforms and services. The project partners include AT, researchers from the University of Auckland and the University of Canterbury, spanning the fields of data science, spatial analytical modelling and geo-visualisation, data infrastructure support and transportation planning. We will also invite government agency staff to explore their data collaboratively using the advanced visualisation facilities in the Centre for eResearch at the University of Auckland. There is an additional benefit of leveraging the considerable expertise and experience of researchers at the companion Alan Turing Institute in the UK, which already has a track record of success, and ongoing engagement with its government to create and evaluate better policies.

Figure 3. Visualisation of New Zealand cancer map

Note:
Turing Aotearoa is a direct collaboration with the Alan Turing Institute (ATI) in the UK. Both parties share ambitions and a version to deliver new training, research and data science leadership opportunities. This enduring collaboration aims to improve the data science and Al skills to support the next generation of data-intense research and recognise that data science and Al are rapidly developing disciplines drawing expertise from multiple sectors, industries and academic pathways. 

See more case study projects

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Automated stone artefacts classification using machine learning

Hands-on DNA: exploring the impact of virtual reality on teaching DNA structure and function

Hands-on DNA: exploring the impact of virtual reality on teaching DNA structure and function

Re-assess urban spaces under COVID-19 impact: sensing Auckland social ‘hotspots’ with mobile location data

Re-assess urban spaces under COVID-19 impact: sensing Auckland social ‘hotspots’ with mobile location data

Aotearoa New Zealand’s changing coastline – Resilience to Nature’s Challenges (National Science Challenge)

Aotearoa New Zealand’s changing coastline – Resilience to Nature’s Challenges (National Science Challenge)

Auckland housing and land use geo-data

Auckland housing and land use geo-data

Rapid monitoring of infrastructural health using remote sensing

Rapid monitoring of infrastructural health using remote sensing

Enhancing Spontaneous Recovery after Stroke Study (ESPRESSo)

Enhancing Spontaneous Recovery after Stroke Study (ESPRESSo)

Data analytics and visualisation for improving  public health and transport planning

Data analytics and visualisation for improving public health and transport planning

Data maturity project in High Value Nutrition (Phase 2) – National Science Challenge

Data maturity project in High Value Nutrition (Phase 2) – National Science Challenge

Supporting the airborne remote sensing mission – Rongowai

Supporting the airborne remote sensing mission – Rongowai

A collaborative extended reality tool to examine tumour evolution (Phase II)

A collaborative extended reality tool to examine tumour evolution (Phase II)

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

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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

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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

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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

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Why are some molecules drugs?

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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

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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

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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

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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

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

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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