SSA Webinar report, 17th August

The  1-hour webinar covered in compressed format the challenge of researching economic disadvantage in Australia given data constraints. The speakers, Anders Holmberg, Chief Methodologist at the ABS and Rajeev Samarage, Senior Data Analyst at the Melbourne Institute, representing respectively producers and users of official statistics, built the case for an entirely new approach to assembling analytical datasets applicable to the economic debates that are being brought on by a rapidly changing economic climate.

This approach is organised around the framework presented by Li Chun Zhang in a 2012 Statistica Neerlandica paper. The Total Survey Error Model had been maturing for a generation from its introduction by Torre Dalenius and co-workers in Sweden to the succession of publications and transatlantic conferences organised by Robert Groves and associates at Maryland as a way of organising the business of population survey taking that had become the central activity of national statistical offices.

The 2012 paper reinterpreted TSE - expressed in terms of the diad of measurement processes and representational units - as stepped generation of errors into the survey dataset - in more general terms palatable to analytical workers: a common conceptual parcel of variables; and objects from a variety of sources.

By this means the statistical task becomes forward looking: to align analytical measures and statistical units brought together into an integrated secondary microdata set, fully documented, and with a level of quality assured.

By allowing the Zhang construction to carry through time we can bring further statistical tools to bear to deliver a credible longitudinal dataset from which the impact of external shocks can be demonstrated, within robust statistical constraints. Equally the fully constructive nature of this process allows for cross jurisdictional conceptual datasets leading into aggregate and comparative study.

The most valuable point however made in the course of the presentation was drawing attention to the contrasting, and legitimate, perspectives of producers and users - so much so that it had been difficult in the past to retrieve a common interest between the two communities:

On the one hand is concern with integrity and an industrialised process at public expense subject to narrow legislative restraints concerning the release of any information that can relate to any one respondents, even though the furnishing of information to the statistical office is privileged over any other producer;

On the other hand analysts have struggled with data access and data fluency issues, with interpreting the specificity of survey designs and underlying limitations in official census sources, with misalignment between official measurement base and that used in other sources where the design is not as transparent or absent, as for some administrative data troves. 

A common model means a shared vocabulary, where the methodology used in collection design and production is converted to strengthened analytical reach, meeting the rigour required for research publication, and the lucidity and authority required of political communication.

That ABS and MI are working in harness is encouraging for the future of official statistics and business analytics; whether the answer to the question posed is at best highly qualified or not.

The presenters have given a limited set of references; other sources are output of workshops on survey nonresponse from the 1990s that mutated into European Conferences on Quality in Official Statistics and their offshoots in international fora; the working papers from the ABS’ long term Data Integration project; and technical papers documenting the design and adaptation of HILDA - since its launch by the MI on behalf of the Department of Social Security in 2001 - and its sister longitudinal studies of economic disadvantage in Europe and North America. It will be interesting to see where this goes in the future.  

Stephen Horn

Chair, Official Statistics Section, Statistical Society of Australia

Unlocking the secrets in your DNA USING machine learning and cloud-computing

Dr Natalie Twine is team leader of the CSIRO Transformational Bioinformatics Group and gave a talk to the SA members in July. The groups’ vision is to improve health care through digital technology.

The potential information held in within an individual is huge. A genome contains DNA which holds the blueprint for every cell in the human body and is like a fingerprint- unique to an individual. CSIRO have developed technology platforms around using cloud computing to investigate DNA, for example, VariantSpark and TRIBES.

VariantSpark

This can be used to explore differences in genes between sick and healthy individuals. Often diseases are controlled by more than a single gene, such that genes interact each with a variable contribution. An example is motor neurone disease or ALS which is a serious condition leading to death within 2 years of diagnosis. There is a data set of the genomes of 22K individuals of healthy and sick individuals that can be used to investigate the genes underlying this disease. The genome of one individual covers over 80 million gene variants for each individual so it is a large data set. Using VariantSpark on this data set, a machine learning (ML) approach using Random Forests was implemented to investigate interacting genes. Where traditional bioinformatics tools are underpowered, VariantSpark uses using an apache spark cluster which is parallelised with capacity for adding extra computing power. This approach can be implemented in various platforms such as AWS or Microsoft Azure. There is an example on AWS marketplace in demo notebooks

https://databricks-prod-cloudfront.cloud.databricks.com/public/4027ec902e239c93eaaa8714f173bcfc/8497971343024764/53198984527781/2559267461126367/latest.html

TRIBES

Disease is often inherited. With genetic ancestry it is becoming possible as more genome data becomes available to find genes underlying disease. Determining whether there is distant ancestry between people with the disease is important as it enables the identification of DNA that they have inherited from a common ancestor. These segments of DNA are known as identical by descent (IBD) segments. By exploring these IBD segments it narrows the research and enables potential drivers of the disease to be targeted. TRIBES which is available from GITHUB, is a pairwise classifier and very accurate compared to other tools. It enables the identification of new disease genes, it is also able to connect different families through these IBD regions. In an ALS example, it was able to connect 19 families from 25 and identify 5 independent or different mutations associated with ALS. The identification of different mutation is particularly important as it means that drug therapy can be targeted. The identification of novel genes was also possible.

COVID-19

A final example using technology was in the fight against the corona virus or COVID-19. CSIRO has been involved in replicating the virus, sequencing the genome, developing animal models and preclinical vaccine testing. They have found that the virus mutates approximately 25 times a year compared to influenza which mutates around 50 times per year. Identifying COVID-19 strains for vaccine testing is important. From the original host of the virus it may have mutated multiple times but its only possible to capture those virus in people that are tested so intermediate strains are lost. CSIRO have used ML to compare the virus genome isolated from people who have been tested and to identify how identical they are. This can aid in determining the most appropriate strain for vaccine testing. 

CSIRO have developed a web service which monitors new genome sequences of COVID-19. Data from around the world can be uploaded to an AWS platform and each day an analysis can be run comparing strains with results available on a website. This is enabled by using serverless powered computing which is agile, such that resources are able to be shared when it’s not used, its good if software is used sporadically.

The final impact is detecting community spread of the virus, where the different strains are monitored. They are able to track mutations to see how they may effect transmission, virulence and symptoms.

The take home message from the talk was that there is a massive explosion in data. IT technology can make a big difference in the fight against disease.

By Helena Oakey

MEDIA RELEASE - Science & Technology Australia

12 August 2020

Results of a nationwide survey of over 1,000 professional scientists and researchers shows COVID-19 has had a dramatic impact on the science workforce in Australia.

In a first snapshot of the impact of the pandemic on scientists’ jobs and wages, a survey by Professional Scientists Australia and Science & Technology Australia found despite the frontline role of scientists in the pandemic, they too had been hit by job losses and wage freezes.

In The Initial Employment Impact Of The Covid-19 Pandemic On Australia's Science Workforce, scientists reported job losses, pay freezes, changes to job roles, and limitations on their ability to work due to juggling working from home while caring for children.

At the same time, as an indicator of the central role science is playing in Australia’s response to the pandemic, the survey found almost six in 10 scientists said Australians now placed greater value in science and our nation’s professional scientific workforce as a result of the COVID-19 pandemic.

Even at that early stage, key findings in the report include:

• One in 20 scientists in the survey had taken a pay cut, and one in 10 said their paid work hours had fallen.
• Around 7 in 10 had been instructed to work from home, and almost one in three said physical distancing and home isolation had limited their work.
• One in seven scientists surveyed said their work role had changed during the pandemic, and nearly one in four said anxiety/ mental distress caused by the pandemic was affecting their ability to work.
• One in five said caring for children/home schooling had limited their ability to work.
• A lack of job security was a key source of stress affecting mental health and well-being.

Science & Technology Australia President Jeremy Brownlie said the report is a timely reminder that whilst Australians rely on our exceptional science sector to respond to crises such as the pandemic, the wellbeing of the science workforce needs to be a stronger priority.

“This report provides vital insight into the vulnerability of scientists and researchers as employees, as the economic impact of COVID-19 places significant strain on universities and research institutes, even as the demand for their skills had grown,” Associate Professor Brownlie said.

“Australia boasts incredible talent in scientific research, and we’ve drawn on this extensively amid COVID-19 – yet the job security and conditions of scientists and researchers are at risk.”

“We need to protect Australia’s scientific workforce so it can play its crucial role in Australia’s recovery from COVID-19 in job creation and economic growth.”

Science & Technology Australia CEO Misha Schubert noted the survey ran in May before major job losses started to be announced at universities

“Even at that early stage of the pandemic, almost one in 20 scientists surveyed said they had had their employment terminated, their contract not renewed, or had been stood down without pay,” she said.

“And since this survey was in the field, we’ve seen announcements of thousands more job losses at universities.”

 “Now is the time for a stronger investment in the science and technology workforce. This pandemic has highlighted how crucial our scientists are to the safety and security of all Australians.”

Please see the full report, The Initial Employment Impact Of The Covid-19 Pandemic On Australia's Science Workforce here. For interviews, please contact STA Communications Manager, Zoya Patel on 0406 249 786.

Science & Technology Australia, 3/8 Phipps Close, Deakin, Australian Capital Territory 2600, Australia
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Had 2020 been an ordinary year, ANZSC would already have been and gone. But 2020 is far from an ordinary year! Although ANZSC has been pushed back to July 5-9, 2021, this does not diminish the excitement that we, the Presidents of the Statistical Society of Australia and the New Zealand Statistical Association, have for this event. We can’t wait to see old friends and make new ones from around Australia and New Zealand in July 2021.

So why should you come along to the Gold Coast on July 5-9 2021 for ANZSC? Here are just a few reasons:

• Catch up on the latest in statistical theory and practice from our region;
• Hear from some leading statistical thinkers from around the world, including Professor Frauke Kreuter and Professor Iain Johnstone.
• Socialise with colleagues and enjoy delicious food at the conference dinner.
• See what the future of statistics has in store with presentations from our early career and student members.

2020 has been a challenging year for many of us, and we look forward to celebrating the resilience and strength of the Australian and New Zealand statistical communities at ANZSC 2021!

Jessica Kasza
President of the Statistical Society of Australia

Vanessa Cave
President of the New Zealand Statistical Association

On a chilly, wintery evening, SSA history was made last Tuesday when we held our first Society AGM via Zoom. As a result of these unprecedented times the ACT Government recently amended the Associations Incorporations ACT 1991, now allowing association AGMs to be held online rather than face-to-face only.

However, the history-making did not stop there. Counting over forty members at the Zoom meeting, the participation rate at this AGM exceeded any number previously recorded at an AGM held outside a Statistical Conference year. Thank you to everyone who joined in!

Our new President, Jess Kasza, took us through the agenda items in such an efficient way that the AGMs for SSA and ASPAI were completed within half an hour. After a brief break, attendees were then treated to a captivating talk by RSS President, Professor Deborah Ashby. Professor Ashby is the Director of the School of Public Health, Imperial College London, where she holds the Chair in Medical Statistics and Clinical Trials. She is a Founding Co-Director of Imperial Clinical Trials Unit. Her talk was titled

Florence Nightingale at 200: using data to improve health from the time of the Crimea to the time of the coronavirus

and the audience was taken on a journey through Florence Nightingale’s fascinating life. Many pieces have been written about Florence being recognised as a pioneering and passionate statistician. Coming from a background of privilege and with powerful connections, Florence chose a life of hard work and never-ending learning, using her - what we these days would call “network” - to try to improve the health situation in her country and abroad. She recognised the connection between statistics and health and used her influence to make the government officials of her time see it as well. The slides of the talk can be viewed here.

I can truthfully say that this interesting talk, presented by a statistician to statisticians, was thoroughly enjoyed by this non-statistician as well.

Marie-Louise Rankin
Executive Officer
Statistical Society of Australia

There are some conferences coming up soon that will be run wholly online: the 14th International Conference in Monte Carlo & Quasi-Monte Carlo Methods in Scientific Computing (MCQMC) will be held from August 9-14. StanCon will be a 24-hour event, held on August 13, for those interested in the Stan software for Bayesian computation. Also, the Bayesian Young Statisticians Meeting: Online (BAYSM:O) to be held online from November 17-18, 2020.

Our update includes some brief reviews of the book “Bayesian Probability for Babies” and the software packages JASP and Jamovi.

Ferrie, Chris (2019) "Bayesian Probability for Babies", Baby University

This book has been out for a year! I first found out about it when a graduating PhD student gave it to me as a gift. It is a children's board book, and uses cookies to explain how Bayes Theorem works, in an entertaining and intuitive way. I did a book reading at a conference, and whilst the academics didn't sit on the floor, they really enjoyed it, and more importantly, quickly got the hang of things. We can attest that this "cookie book" is well liked by at least one small child and one teenager. The author also has a YouTube video where he reads his book.

Bayesians may find a couple of beginner friendly and free statistical packages useful for teaching. Just Another Stats Package (JASP) is freely downloadable from jasp-stats.org. It provides a simple menu-based interface to simpler statistical analyses (like t-tests and ANOVA) but provides "curated" Frequentist and Bayesian outputs (for posteriors and Bayes Factors too) using a similar frontend. Then Jamovi is a relatively new R package that makes it easier to write user friendly interfaces for R functions. There are already some useful interfaces available: https://www.jamovi.org/library.html

JASP and jamovi were introduced by the same group of people, as written up here:

• Introducing jamovi
• Introducing JASP

Matt Moores & Sama Low-Choy,

On behalf of the executive committee, Bayesian Section of SSA

https://twitter.com/BayesSsa

The search is about to begin for Australia’s next constellation of Superstars of STEM.

Science & Technology Australia created #SuperstarsofSTEM in 2017. This trailblazing program builds a critical mass of high-profile women scientists, technologists, engineers and mathematicians to serve as role models to inspire young women and girls into STEM. It aims to smash society’s gender assumptions about STEM careers – and lift the public visibility of women in STEM – to make gains towards more equal media representation of women in STEM.

Over the first three years of the program, Science & Technology Australia have developed the profiles of 90 women in STEM. These women acquired advanced communication skills and exciting opportunities to use these skills in the media, on stage and speaking with Parliamentary and industry decision-makers.

Science & Technology Australia are  launching the search to find their next 60 Superstars of STEM to be part of another brilliant and diverse cohort for 2021-22. Applications open on 4 August. Apply by August 31.

STEM Jobs At Risk Without A JobKeeper Lifeline For Unis

Jobs in the science, technology, engineering and maths workforce are now at greater risk as hundreds more job losses start to be announced at universities across the country.

The peak body for the science and technology sector is asking the Australian Government to take a fresh look at the damage being inflicted by the pandemic on Australia’s research and teaching jobs.

Science & Technology Australia President Associate Professor Jeremy Brownlie said our nation’s university STEM researchers and teachers were "the lifeblood of Australia’s research system".

“The grave risk now is that we may start to lose brilliant talent from our STEM research and teaching workforce as universities face the stark choices forced by a collapse in income,” he said.

“If Australia loses this STEM talent, the danger is that we may never get them back into our research system to work on the next set of cures, breakthroughs and lifesaving treatments.”

“We ask the Government to look at the risks starting to materialise to Australia’s sovereign capability in research – and step in with a JobKeeper lifeline to university researchers and teachers.”

A Rapid Research Information Forum report in early May predicted up to 21,000 jobs could be lost at Australia’s universities over the next six months – including 7,000 in research – due to the pandemic.

It found women, early-career researchers and recent graduates are disproportionately at risk because they are more likely to be in vulnerable casual and fixed-term contract roles.

Science & Technology Australia Chief Executive Officer Misha Schubert said there was a strategic interest for the nation to safeguard our STEM research and teaching workforce through this crisis.

“Just as the Government has done in response to the devastating impact on the tourism industry, we’d ask it to look with similar compassion at the plight of the nation’s research workforce,” she said.

“If we can avert these tens of thousands of jobs being lost through the pandemic, it will put the nation further ahead in the enormous task of economic recovery.”

STA has also proposed a one-off boost to the Research Training Program which funds postgraduate research students, who make up more than half of Australia’s university research workforce.

To seek further comment, please contact STA on 02 6257 2891.

This email was sent to eo@statsoc.org.au
Science & Technology Australia, 3/8 Phipps Close, Deakin, Australian Capital Territory 2600, Australia

The heartbreaking scale of this pandemic’s toll on jobs continues. Yesterday’s Australian Bureau of Statistics figures revealed almost one million Australians are now out of work. And the nation’s official unemployment rate is now at a two-decade high – reaching 7.4 per cent in June – despite the creation of more than 210,000 jobs in June. 
 
In a media release this morning, STA has warned jobs in the science, technology, engineering and maths workforce are now at greater risk as hundreds more job losses start to be announced at universities across the country. We have asked the Australian Government to take a fresh look at the damage being inflicted by the pandemic on our research workforce and consider again a JobKeeper lifeline for universities and a one-off boost to the Research Training Program to help keep postgraduate research students employed.

We also continue to engage closely with the proposed changes to higher education funding. The two groups of Vice-Chancellors working with Government on the industry linkages fund and research funding both met for the first time this week. STA will continue to draw the views of our membership into consultation processes.  

STA’s Board also met this week. It was heartening to see our clusters report on work by many member societies to deepen Indigenous partnerships, and promote Indigenous STEM knowledge. Work towards STA’s inaugural Reconciliation Action Plan is also well advanced. Our draft RAP has now been lodged with Reconciliation Australia for feedback. We thank our RAP working group which includes the leadership of STA’s Indigenous member associations – Quandamooka First Nations man Professor Chris Matthews of the Aboriginal and Torres Strait Islander Mathematics Alliance and Kamilaroi man and Deadly Science founder Corey Tutt – for their leadership and expertise in this important work.
 
Our thanks to each of you for your membership renewals in recent weeks. Our members are the lifeblood of STA and we are here to support you through these challenging times.
 
Until next time, 

Misha Schubert 
CEO, Science & Technology Australia 

NEW REPORTS AND POLICY CHANGES OF INTEREST TO STA MEMBERS 

• The long-awaited Australian & New Zealand Standard Research Classifications review has been released;
• Education Minister Dan Tehan announced two working groups on sustainable research funding and an Industry Linkages Fund;
• The Department of Prime Minister & Cabinet released a research report into Vocational Education and Training;
• The Public Policy Forum has released a report on science disinformation in the time of the pandemic; 
• The UK has released its research & development roadmap; 
• TEQSA released a good practice note on preventing and responding to sexual assault and harassment in higher education settings;
• The Australian National Audit Office reported Referrals, Assessments and Approvals of Controlled Actions under the Environment Protection and Biodiversity Conservation Act 1999;
• A University of Sydney study found almost 45% of PhD students are considering leaving their PhD for financial reasons;
• The Australian Education Union has released its survey into the state of the VET/TAFE sector; and 
• The Bushfire and Natural Hazards CRC has released its 2020-21 bushfire season outlook.

Further information: Peter Derbyshire, STA Policy Manager - peter.derbyshire@sta.org.au

Dear SSA Canberra et al.,

Please (also) forward to those who you think may be interested in the below.

SSA Canberra is inviting young statisticians who are planning to attend a conference/workshop/short course in a field related to statistics or data science to apply for financial support in the form of a "SSA Canberra registration grant".

What does the grant support?
SSA Canberra will award an amount up to $200 AUD per successful application. The amount to be awarded will depend on the registration costs of the event the applicant is attending. Note the conference/workshop does not necessarily have to be held in the ACT (since most events are currently online anyway!), nor does it have to be an SSA event.

Who can apply?
Applicants must be:

• A current student in, or within five years of last conferred degree from, the ACT or in a regional area of NSW outside Newcastle-Sydney-Wollongong;
• A member of the SSA Canberra branch at the time of registration; membership is only $20 for full time students, so it is worth joining just to apply for the grant!

If you have questions regarding eligibility or anything else, please contact the SSA Canberra council at ssacanberra@gmail.com

How do I apply?
Prepare the following documents and a submit a single PDF form containing:

1. If attending a conference, evidence of your submitted abstract for a poster/talk to that conference. If attending a workshop/short course, evidence of your confirmed registration to that event;
2. A brief resume of up to three pages;
3. A letter up to one A4 page describing the anticipated benefits to you that will result from attending the event, and declaring any other financial support being offered to you to attend.

Please send these via email to ssacanberra@gmail.com 

When do I have to apply by?
We are accepting applications on an ongoing basis until 31 December 2020, or until the budget we have allocated for the rego grant runs out. So it is first-in-first-served, subject of course to a proposal being successful!

A maximum of one successful grant will be awarded per person.

Outcome and show me the money!
Successful applications will be notified by email in due course. Afterwards, SSA Canberra will then look to reimburse registration fees after receiving the receipts.

If I am successful, who do I have to do?
1) If presenting at a conference, please acknowledge the financial support of SSA Canberra.
2) Contribute a short piece about their experience of attending the conference/workshop/short course etc...to the SSA newsletter, to be sent to ssacanberra@gmail.com.