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Data driven research and
leadership - future prospects
Arho Virkki, PhD
Head of Auria Clinical Informatics at Turku University Hospital
Adjunct Professor in Medical Mathematics at Turku University
1) Data Services for Scientific Research,
2) Research-as-a-Service (RaaS),
3) Data Commensuration and Quality Assurance,
4) Clinical Decision Support and
5) Information Security
Year Data Sets
2014 9
2015 24
2016 114
2017 126
2018 287
2019 129
Table. Research
data sets extracted
since 2019-06-97
Auria Clinical Informatics at Turku University Hospital
Data-Driven Research and Innovation
Numeric and categorical data can be used for
1) Statistical analysis
2) Computing risk factors
3) Estimating population-level risks
4) …
Data-Driven Research and Innovation
Or, for visualising
1) Time series or
2) Patient care paths
Series example: The subtle increase in laboratory measurements
between 2005 – 2018
Path example: Thousands of sleep apnea patients are treated
annually at Turku University Hospital. The diagram shows a snapshot
of the treatment path between first diagnosis, referral, visit and
getting a mouthpiece.
Data-Driven Research and Innovation
Example:
Automated pattern detection with machine learning to speed up clinical
diagnoses.
Motivation: If the patient can be diagnosed and treated < 10 minutes after
arrival in the ICU, the probability of surviving increases significantly.
Dataset for Machine Learning (58 057 slices)
First Machine Learning Results
More Pattern Detection (2D pathological images)
Example:
Automated pattern
detection with
machine learning to
improve the
accuracy of 2D
image classification
Crowdsourcing Research
Example 1 (right):
Junction Hackathon
2017, Health Tech
Challenge, Espoo,
Finland with
anonymized data.
Example 2 (next slides):
Invite-only Hackathon
for all public biobanks in
Finland with real
(pseydonymized) data
Example 2: #biopankkihack
Hotel Kämp, Helsinki, May 16-17, 2018
#biopankkihack
Hotel Kämp, Helsinki, May 16-17, 2018
#biopankkihack
Hotel Kämp, Helsinki, May 16-17, 2018
Data Lake is a component of Data Platform.
It is used as staging area between
operational systems and dedicated analysis
platforms, or directly as an in-house
computing platform.
Findata offers secure data sandboxes with
real-life data for scientific research. We take
care of security – and offer full freedom for
innovative research.
Scientific
Research
and
Innovation
Secure
Data
Sandboxes
Data Lake
Electronic Health
Records
Secure Sandboxes for Data
Liberty with 100% Open Source Tools and Algorithms
https://github.com/auriadih
Contact:
Auria Clinical Informatics
Turku University Hospital
atp@tyks.fi
http://auria.fi/en
http://aci.vsshp.fi

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Virkki presentation VTT SmartHealth Ecosystem Event 12.6.2019

  • 1. Data driven research and leadership - future prospects Arho Virkki, PhD Head of Auria Clinical Informatics at Turku University Hospital Adjunct Professor in Medical Mathematics at Turku University
  • 2. 1) Data Services for Scientific Research, 2) Research-as-a-Service (RaaS), 3) Data Commensuration and Quality Assurance, 4) Clinical Decision Support and 5) Information Security Year Data Sets 2014 9 2015 24 2016 114 2017 126 2018 287 2019 129 Table. Research data sets extracted since 2019-06-97 Auria Clinical Informatics at Turku University Hospital
  • 3. Data-Driven Research and Innovation Numeric and categorical data can be used for 1) Statistical analysis 2) Computing risk factors 3) Estimating population-level risks 4) …
  • 4. Data-Driven Research and Innovation Or, for visualising 1) Time series or 2) Patient care paths Series example: The subtle increase in laboratory measurements between 2005 – 2018 Path example: Thousands of sleep apnea patients are treated annually at Turku University Hospital. The diagram shows a snapshot of the treatment path between first diagnosis, referral, visit and getting a mouthpiece.
  • 5. Data-Driven Research and Innovation Example: Automated pattern detection with machine learning to speed up clinical diagnoses. Motivation: If the patient can be diagnosed and treated < 10 minutes after arrival in the ICU, the probability of surviving increases significantly.
  • 6. Dataset for Machine Learning (58 057 slices)
  • 8. More Pattern Detection (2D pathological images) Example: Automated pattern detection with machine learning to improve the accuracy of 2D image classification
  • 9. Crowdsourcing Research Example 1 (right): Junction Hackathon 2017, Health Tech Challenge, Espoo, Finland with anonymized data. Example 2 (next slides): Invite-only Hackathon for all public biobanks in Finland with real (pseydonymized) data
  • 10. Example 2: #biopankkihack Hotel Kämp, Helsinki, May 16-17, 2018
  • 13. Data Lake is a component of Data Platform. It is used as staging area between operational systems and dedicated analysis platforms, or directly as an in-house computing platform. Findata offers secure data sandboxes with real-life data for scientific research. We take care of security – and offer full freedom for innovative research. Scientific Research and Innovation Secure Data Sandboxes Data Lake Electronic Health Records Secure Sandboxes for Data
  • 14. Liberty with 100% Open Source Tools and Algorithms https://github.com/auriadih
  • 15. Contact: Auria Clinical Informatics Turku University Hospital atp@tyks.fi http://auria.fi/en http://aci.vsshp.fi