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 Position Details 
 
Job Title: CSIRO Undergraduate Vacation Scholarships – Health & Biosecurity 
Reference No: 2103 
Classification: CSOF1.1  
Stipend: $1462.77 per fortnight 
Location: Please refer to the List of Projects at the end of this document 
Tenure: 8 to 12 weeks from November 2015 to February 2016 
Role Purpose: The 2015/16 Vacation Scholarship Program is designed to provide students 
with the opportunity to work on real-world problems in a leading R&D 
organisation. 
Participation in the Vacation Scholarship Program has influenced previous 
scholarship holders in their choice of further study and future career options. 
Many have gone on to pursue a PhD in CSIRO or to build a successful 
research career within CSIRO, a university or industry. 
Project 
Description: 
Please refer to the list of Projects on the following pages of this document.   
If you require further information please contact the person listed as the 
contact for the project. 
How to Apply:   
Please apply for this position online at www.csiro.au/careers 
You will be required to: 
1. select your top 2 research projects in order of preference; 
2. submit a CV which includes: 
 the reasons why the research project/s you have selected are of 
interest to you; and how your previous skills/knowledge and 
experience meets the project requirements; and 
 an outline of your longer-term career aspirations and detail 
how this program will help you achieve them.  
3. upload your academic results. 
 
Referees:  Please ensure that your resume includes the name and contact 
details of your academic supervisor and at least one other referee (work or 
university). 
If you experience difficulties applying online call 1300 984 220 and someone 
will be able to assist you.  Outside business hours please email: csiro-
careers@csiro.au.  
Please do not email your application.  Applications received via this method 
may not be considered. 
About CSIRO: 
The Commonwealth Scientific and Industrial Research Organisation (CSIRO) 
is Australia’s national science agency.  At CSIRO we shape the future. We do 
this by using science to solve real issues. Our research makes a difference to 
industry, people and the planet.   
  
  
Project 
Number 
Health and Biosecurity Flagship - Vacation Scholarships Project Details 
H&B01 Project Title 
Are feral honeybees healthier? 
Project Description 
This project will involve collecting honeybees from feral nests and testing for several 
honeybee pathogen using genetic markers. Pathogen levels will be compared with those 
of local managed honeybees. 
Project Duties/Tasks 
 Identify and collect samples from feral honeybee colonies 
 Use genetic markers to test for honeybee pathogens 
Relevant Fields of Study 
 Molecular biology 
Location:  Black Mountain, ACT 
Contact:   Dr John Roberts on (02) 6246 4019 or email john.roberts@csiro.au   
H&B02 Project Title 
Disease tolerance in honeybees 
Project Description 
This project will involve exposing different genetic lines of honeybees to viruses in lab 
assays to investigate variation in disease tolerance. 
Project Duties/Tasks 
 Isolate and genetically analyse honeybee viruses 
 Conduct lab infection assays with honeybees 
Relevant Fields of Study 
 Molecular biology 
Location:  Black Mountain, ACT 
Contact:   Dr John Roberts on (02) 6246 4019 or email john.roberts@csiro.au   
H&B03 Project Title 
Mobile Application for Biosecurity Data Collection 
Project Description 
Effective biosecurity management relies on digitalised biosecurity data collection and 
management. The student is expected to develop a mobile-based application for 
biosecurity data collection. 
Project Duties/Tasks 
 Investigate existing approaches on mobile application development 
 Design mobile interface for biosecurity data collection 
 Implement the mobile application 
Relevant Fields of Study 
Strong JAVA and JaveScript programming, with experience in user interface design and/or 
some mobile application development a plus 
Location:  Sandy Bay, Tasmania 
Contact:   Dr Qing Liu and via phone on (03) 6237 5698 or email Q.Liu@csiro.au  
  
H&B04 Project Title 
Evaluation of plant pests and pathogens impact using internet and social media metrics 
Project Description 
This project will attempt to assess whether different measures of electronic interactions 
can be related to actual impacts where there is data, with the aim of using them as 
predictors where there is no data.  For example, is the nuber of web pages found on a 
search under the scientific name of an organism sufficient or is the common name better?  
Are the terms “pest” or “damage” necessary as well? Is a crop name required? Is the 
number of twitter threads better? 
Project Duties/Tasks 
 Critically research background of using electronic statistics to assess social 
phenomena (Daniel Watts) and produce summary of methods and supporting 
evidence 
 Research availability and reliability of data on economics of pests and pathogens 
on official lists (supplied), consult experts for ground truthing 
 Continue research and produce summary 
 Decide electronic media search sources and search strategies (what to search, 
what terms and what metrics (eg pages, hits, traffic, threads etc) and commence 
data collection 
 Data collection; produce summary 
 Analyse relationships between different measures of impact 
 Write report; presentation of report and feedback 
Relevant Fields of Study 
Biology/ecology, however other disciplines considered. 
Location:  Black Mountain, Canberra 
Contact:   Dean Paini on (02) 6246 4178 or email Dean.Paini@csiro.au 
H&B05 Project Title 
The Digital Doctor: predict adverse drug reactions from a patient’s genome 
Project Description 
Drugs that are usually safe can cause severe adverse reactions in patients with a particular 
genotype.  This project aims to validate genomic markers for drug toxicity in whole 
genome sequencing data from the 1000 genomes project.  The analysis will contribute to 
a journal publication detailing the application of pharmacogenomics markers in Australian 
clinical practice. 
Project Duties/Tasks 
 Compare genotype information of pharmacogenomics markers with the LD-
derived exonic surrogate markers as well as imputed genotypes 
 Summarize and visualize comparison results 
 Contribute towards manuscript 
Relevant Fields of Study 
 Bioinformatics 
 Information Technology 
 Biostatistics 
 Computational Biology 
Location:  North Ryde, Sydney NSW 
Contact:   Denis Bauer on (02) 9325 3174 or denis.bauer@csiro.au 
  
H&B06 Project Title 
Tele-Medicine based clinical decision support system for sight threatening eye disease 
Project Description 
In this project, we will be developing image analysis and machine learning algorithms for 
early detection of eye disease such as diabetic related eye disease.  The algorithms 
developed and properly validated will be integrated into an electronic health record 
system or a telemedicine system for use in the field in hospitals to screen for sight 
threatening eye diseases. 
Project Duties/Tasks 
 Develop image processing algorithms and machine learning techniques for 
detection of retinal pathologies (e.g. bright lesions) related to diabetic retinopathy 
and other retinal diseases 
 Validation of algorithms based on a large retinal image data set 
 Build an end-user program which could be integrated into our Remote-l 
telemedicine system 
Relevant Fields of Study 
 Signal processing 
 Image processing 
 Biomedical engineering 
 Software engineering 
Location:  Perth, WA 
Contact:   Dr Di Xiao on (08) 9333 6147 or Di.Xiao@csiro.au 
H&B07 Project Title 
Mobile Health for diabetes 
Project Description 
In this project we intend to review and summarise users’ feedback on mobile apps for 
diabetes.  The aim of this research is to identify the most important features and 
functions of mobile health apps from consumer’. 
Project Duties/Tasks 
 To search for diabetes related mobile apps (for iOS, android, or both) and select 
the best ones 
 To extract and summarise user’s feedback on the selected apps 
 To qualitatively research the findings using content analysis and thematic mapping 
techniques 
Relevant Fields of Study 
 Marketing 
 Management 
 Public Health 
 Psychology 
 Medicine (prior experience with qualitative research is an advantage) 
Location:  Herston, Brisbane, Qld  
Contact:   Farhad Fatehi on (07) 3253 3617 or farhad.fatehi@csiro.au 
 
  
H&B08 Project Title 
Identification of biomarkers associated with early identification of Alzheimer’s Disease 
Project Description 
In an effort to identify biomarkers for the early detection of Alzheimer’s Disease, the 
current project aims to investigate over 1000 protein markers from both Australia and 
overseas.  Once the most informative biomarkers have been identified, graphical network 
analyses will be compared with Gene Ontology (G.O.) pathway information to assess their 
functional significance. 
Project Duties/Tasks 
 Conduct feature selection analyses of biological data related to Alzheimer’s 
Disease 
 Conduct graphical network analyses and compare results with G.O. pathways 
available online 
 Contribute towards manuscript with results identified 
Relevant Fields of Study 
 Biostatistics 
 Mathematics 
 Computational Biology 
 Statistical Genetics 
Location:  Herston, Brisbane, Qld  
Contact:   James Doecke on (07) 3253 3697 or james.doecke@csiro.au 
H&B09 Project Title 
Enhance and optimize the performance of automatic diabetic retinopathy grading 
algorithm in our tele-medicine software 
Project Description 
This project will involve improving our image processing routines that analyse retinal 
images.  The student will work on optimizing the algorthyms within our tele-medicine 
system to reduce the time it takes in processing the images and providing initial grading to 
our clinical users. 
Project Duties/Tasks 
 Investigate the use of various computer science techniques in the existing 
software, including parallel processing and multi-threading (e.g. using 
boost/openMP) 
 Utilising GPU for faster image processing (e.g. using CUDA libraries) 
 Work with our tele-medicine platform (Remote-l) to integrate the new grading 
algorithm 
 Re-write existing C++ code in Python 
 Time permitting we will also investigate the use of cloud computing platforms such 
as Google’s or Amazon to investigate potential to move the grading to a cloud 
based system 
Relevant Fields of Study 
 Signal processing 
 Image processing 
 Biomedical engineering 
 Software engineering 
Location:  Floreat, WA  
Contact:   Janardhan Vignarajan on (08) 9333 6132 or janardhan.vignarajan@csiro.au 
  
H&B10 
Project Title 
Early identification of need for surgery for Crohn’s Disease 
Project Description 
Investigate the magnetic resonance enterology (MRE) biomarkers from participants with 
Crohn’s disease to identify markers of inflammation that associated with surgery.  Using a 
combination of clinical phenotype information with the MRE data, the project aims to 
identify those individuals that are at risk of needing surgery so that early intervention 
maybe provides as an alternative. 
Project Duties/Tasks 
 Identify those MRE biomarkers that are associated with inflammation leading to 
surgery 
 In addition to the MRE markers, find associated clinical phenotype markers that are 
also predictive of surgery 
 Write a report from work conducted that will be used to contribute to a journal 
publication 
Relevant Fields of Study 
 Biostatistics 
 Mathematics 
 Medical science 
 Medical imaging 
Location:  Herston, Brisbane, Qld   
Contact:   Jason Dowling on (07) 3253 3634 or jason.dowling@csiro.au 
 
H&B11 
Project Title 
CSIRO Health Diet Score 
Project Description 
The CSIRO Healthy Diet Score allows Australians to measure the quality of their eating 
habits using a simple online assessment tool. This project will see the development of the 
next generation tool for the CSIRO healthy diet score. The project will produce a mobile 
app that will use of smart phone features to gather information and will provide users 
with recommendations for products that will help them to improve their health. 
Project Duties/Tasks 
 Work with domain experts to develop requirements including novel food recall 
techniques 
 Develop mobile prototype (iOS/Android/HTML5) 
 Conduct user testing 
Relevant Fields of Study 
 Computer science 
 Computer engineering 
Location:  Marsfield, NSW  
Contact:   Jill Freyne on 02 9372 4453 or email jill.freyne@csiro.au 
 
  
H&B12 
Project Title 
Health indicator for grocery shopping 
Project Description 
This project will develop a persuasive tool to help shoppers understand their grocery 
shopping. The tool will combine purchase data with nutrition information to raise 
awareness of the food choices. The candidate would work with technical, behavioural 
science and nutrition experts to design and develop the tool. 
Project Duties/Tasks 
 Work with domain experts to develop requirements 
 Develop mobile or web prototype 
 Conduct user testing 
Relevant Fields of Study 
 Computer science 
 Computer engineering 
Location:  Marsfield, NSW  
Contact:   Shlomo Berkovsky on 02 9372 4235 or email shlomo.berkovsky@csiro.au 
 
H&B13 
Project Title 
Foetal Brain Development – 3D MRI reconstruction and analysis 
Project Description 
Fast Magnetic Resonance Imaging (MRI) sequences enables acquiring stacks of 2D images 
of the foetus in-utero. However, because of the constant foetal motion, random 
displacement occurs in-between images, and reconstructing an accurate 3D volume for 
quantitative evaluation is challenging. Novel super-resolution techniques combine N 
stacks of low resolution MRIs and remove the effect of random displacements to produce 
a motion free high-resolution 3D reconstruction. This project will involve building a 
reliable 3D foetal imaging workflow that is useful for our clinical partners. 
Project Duties/Tasks 
 Building a reliable 3D foetal imaging reconstruction workflow using recent open 
source and in-house software tools (C++ or Bash or Python) 
 Adapting, optimizing or writing new software modules to adapt the reconstruction 
method to the images provided by our clinical partners (C++ and/or CUDA) 
 Analyse the accuracy of the proposed solution 
Relevant Fields of Study 
 Medical physics 
 Computer science 
 Software engineering 
 Biomedical engineering 
 
Location:  Herston, Brisbane, Qld  
Contact:   Jurgen Fripp on (07) 3253 3660 or email jurgen.fripp@csiro.au 
 
  
H&B14 Project Title 
Neuroimaging Analysis and Executive Functions 
Project Description 
This project will examine the relationship between behavioural presentations of three 
syndromes characterized by executive dysfunction (disinhibited, apathetic and 
dysexecutive) and functional neuroimaging measures using the resting state FDG-PET 
amongst older adults. The vacation scholar will learn about the analysis of the 
neuroimaging data, and the administration, scoring and interpretation of 
neuropsychological tests. 
Project Duties/Tasks 
 Data collection and involvement in the neuropsychological tests 
 Developing the current statistical analysis platform in R/python/C++ 
 Analysing the correlation between neuroimaging and psychometric data 
 Documentation, preparation of scientific/technical report, or an conference 
abstract 
Relevant Fields of Study 
 Computer science 
 Electrical engineering 
 Mathematics 
 Statistics 
 Psychology 
 Neuroscience 
Location:  Hollywood Private Hospital (Offsite, WA)  
Contact:   Kaikai Shen (08) 6298 6313 or email Kaikai.Shen@csiro.au 
H&B15 Project Title 
Neuroimaging Analysis at Ultra High Fields 
Project Description 
This project will involve developing software and analysis techniques to segment the brain 
and calculate the thickness of the cortex from very high resolution MR data acquired at 
the University of Queensland on their new 7T MRI scanner.  In addition, the project will 
extract myelin and T2* surface maps of the brain. 
Project Duties/Tasks 
 Customize and extend MilxView’s C++ neuroimaging software to accurately 
segment and calculate cortical thickness from very high resolution MR data. 
 Support anatomist in performing manual analysis and validation of software.  
 Write technical report on results. 
Relevant Fields of Study 
 Computer science 
 Electrical engineering 
 Mathematics 
Location:  Herston, Brisbane, Qld  
Contact:   Kaikai Shen (08) 6298 6313 or email Kaikai.Shen@csiro.au 
  
H&B16 Project Title 
SunLite: promoting the awareness of UV exposure using wearable technologies 
Project Description 
Understanding the impact of ultraviolet (UV) exposure on the healthy body can help 
people to decrease the risks of sunburn and skin cancer. This project focuses on the use of 
wearable technologies for the design of persuasive interventions to make people aware of 
their UV exposure and provide them with tailored protection guidelines. 
Project Duties/Tasks 
 Study and evaluate commercial wearable UV ray monitoring devices (API, logging, 
communication, battery life, etc) 
 Develop an application for recording UV exposure using the selected wearable 
technology and collecting essential user data 
 Design and implement several graphical visualisation (charts, diagrams, etc) of the 
UV exposure user data 
 Implement tailored persuasive interventions (alerts, text messages, etc) for 
increasing user awareness of their UV exposure levels.   
Relevant Fields of Study 
 Computer science 
 Information technology 
 Human computer interaction 
Location:  Marsfield, NSW  
Contact:    Shlomo Berkovsky: (02) 9372 4253 or shlomo.berkovsky@csiro.au 
                    Sazzad Hussain:      (02) 9372 4177 or sazzad.hussain@csiro.au 
H&B17 Project Title 
Beating the state-of-the-art in medical concept recognition using Deep Learning 
Project Description 
Health data repositories often contain valuable information stored in free text which is 
unstructured and ambiguous. This project will investigate if Deep Learning, a new trend in 
Artificial Intelligence that uses neural networks that are several layers deep, can be used 
to improve the performance of current state-of-the-art Natural Language Processing 
techniques that are used to identify medical concepts in free text. 
Project Duties/Tasks 
The project will be divided into five phases: 
 Understanding the state of the art (2 weeks): The student will look at key papers 
that explain the state of the art in concept identification from medical text. 
 Preparing the evaluation framework (3 weeks): It is important to have a 
framework in place to quickly evaluate new methods on a wide range of test 
collections. In this task the student will help with the design and implementation 
of a testing framework that uses several test corpora. 
 Replicating state-of-the-art results (1 week): Using the evaluation framework, the 
student will replicate some of the well-known concept identification techniques. 
 Designing a Deep Learning approach for the concept identification task (5 weeks): 
This is the core task of the project. The student will design and implement a deep 
learning approach to concept identification in medical text. 
 
  
 Evaluating the Deep Learning approach (1 week): Using the evaluation framework, 
the student will compare the performance of the deep learning solution against 
other state-of-the-art techniques. 
Relevant Fields of Study 
Computer Science, Information Technology and related disciplines. 
Skills/Knowledge required:  
 Java, algorithm development, machine learning; and  
at least one of following desirable skills/knowledge:  
 Natural language processing, neural networks, deep learning 
Location:  Herston, Brisbane, Qld  
Contact:   Alejandro Metke on (07) 3253 3645 or email alejandro.metke@csiro.au 
H&B18 Project Title 
Automated Classification of Queries to a Medical Search Engine 
Project Description 
Our team is developing a search engine specifically designed for medical/clinical data.  
Specifically, this student project will look at applying machine learning methods to better 
categorise clinical search queries into different types (diseases, treatments, test, etc.) and 
then utilise these categories to improve search results. 
Project Duties/Tasks 
 Collate a dataset of clinical queries and their categories 
 Develop statistical machine learning classifiers (e.g., Support Vector Machines) to 
classify data of clinical queries 
 Evaluate the effectiveness of the classifiers 
 Integrate the classifier within an existing clinical search engine 
Relevant Fields of Study 
Computer science / software engineering / I.T.   The project involves following skills: 
 Good programming skills (preferable in Java, Python or C++) 
 Knowledge of algorithms, data structures 
 Natural language processing 
 Some statistics experience 
 
Location:  Herston, Brisbane Qld  
Contact:   Dr Bevan Koopman on (07) 3253 3635 or bevan.koopman@csiro.au 
H&B19 Project Title 
A Scenario Specific Medical Search Engine 
Project Description 
Our team is developing a search engine specifically designed for medical/clinical data.  
Specifically, this student project will adapt search results according different clinical 
scenarios – diseases, treatments, tests, etc. 
Project Duties/Tasks 
 Setup the a search engine and index a collection of medical records 
 Divide the medical records according to mentions of different scenarios – diseases, 
treatments, tests, etc. 
  
 Adapt the search engine ranking mechanism to favour specific scenarios 
 Evaluate the effectiveness of different scenario specific rankings. 
Relevant Fields of Study 
Computer science / software engineering / I.T.   The project involves following skills: 
 Good programming skills (preferable in Java, Python or C++) 
 Knowledge of algorithms, data structures 
 Natural language processing 
 Some statistics experience 
Location:  Herston, Brisbane Qld  
Contact:   Dr Bevan Koopman on (07) 3253 3635 or bevan.koopman@csiro.au 
H&B20 Project Title 
Visualising Medical Search Engine Results 
Project Description 
Our team is developing a search engine specifically designed for medical/clinical data.  
Specifically, this student project will extract different clinical scenarios – diseases, 
treatments, tests, etc. – from search engine results and present those in a visual, 
interactive search results UI. 
Project Duties/Tasks 
 Setup the ElasticSearch search engine and index a collection of medical records 
 Divide the medical records according to mentions of different scenarios – diseases, 
treatments, tests, etc. – and index these separately 
 Extend the basic search engine results to include interactive plots and 
visualisations providing summaries of the different clinical scenarios 
Relevant Fields of Study 
Computer science / software engineering / I.T.   The project involves following skills: 
 Good programming skills (preferable in Java, Python or C++) 
 Front-end web UI skills  
 Web services, including REST, JSON, etc. 
Location:  Herston, Brisbane Qld  
Contact:   Dr Bevan Koopman on (07) 3253 3635 or bevan.koopman@csiro.au