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Research digital skills training 2021

Centre for eResearch machine learning service

Sina Masoud-Ansari, Research IT Specialist, Centre for eResearch

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Figure 1. Machine Learning as a Service (MLaaS) prototype website. Currently creates a Jupyter Notebook environment on request with all the tools required for popular deep learning workflows.

The initiative

There has been significant growth in interest around machine learning and its applications to research. This has largely been driven by advances in algorithms, particularly in neural networks where the use of Graphics Processing Units (GPUs) has reduced the time to train complex or ‘deep’ neural networks by orders of magnitude. With the rise of ‘big data’, researchers are increasingly finding opportunities to apply these methods to deliver new insights.

Machine learning is often useful when explicit formal models are difficult to develop, for example, a model to identify human faces. Whereas in the past, researchers would ‘tell’ the computer what features to look for, machine learning takes the opposite approach and attempts to ‘learn’ appropriate features based on successive attempts at guessing the correct answer and adjusting to reduce mistakes.

Examples of research in this area that the Centre of eResearch is supporting include using machine learning to improve modelling of financial markets, developing intelligent question/answer systems for understanding text and developing predictors of heart disease based on the shape of coronary arteries. In order to support these and future projects, CeR has initiated a Machine Learning Service to cater to a wide range of needs and experience levels at the University.

Powerful graphics cards are crucial to this type of research and can be difficult to get hold of in sufficient quantities. In addition, the software stack required to run these workflows can be barrier for researchers who are curious about using these tools but do not have the expertise or time to set up the required environment.

Self-service booking portal

To make it easier for researchers to experiment with machine learning and ‘deep learning’ in particular, we are developing a self service booking portal where researchers can request time on computers with powerful hardware and have a fully capable Jupyter Notebook environment available to them with all the required tools (Figure 1). Our self-service notebooks are hosted in the University’s Docker containers which allow each researcher to have an isolated computing environment on the shared system. This system was successfully trialled at the Winter Boot Camp in July where we ran an introduction to machine learning workshop with 40 participants working concurrently on the system (Figure 2). The benefit of using Docker containers in research is also in their reproducibility, where each instance has the same container operating system and libraries. This is helpful when researchers need to publish or replicate their workflows.

 

What more can CeR help with

For more experienced researchers or for those who would like require more control over their computing environment, we offer remote access to a shared Linux server with powerful GPUs and fast SSD based storage for demanding workflows. Researchers can customise this environment to suit their needs, and the Centre provides additional support in installing libraries and additional software required for machine learning. For researchers looking to run large scale projects using multiple GPUs, we are planning to offer access to the Nectar research cloud where we have a large memory server with four GPUs. Our plan is to allow researchers to request virtual machines on the Nectar system where they can select the number of GPUs they would like to use.

Figure 2. An example of a Jupyter Notebook running via the MLaaS prototype. The Notebook covers an introduction to neural networks for image recognition used as part of the Winter Bootcamp machine learning workshop in July this year.

For most demanding workflows, we offer training and advice for researchers to help them make use of NeSI Pan cluster and its array of 20 GPUs ready machines. The Centre also has the capacity to support researchers development of machine learning approaches to solving research problems. For example, working with Dr. Susann Beier from the Faculty of Medical and Health Sciences, the Centre has started on a project exploring the applications of machine learning to improve segmentation of coronary arteries from medical images and exploring the potential of assessing coronary disease risk from the resultant 3D structures.

 

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