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Cloud-native machine learning - Transforming bioinformatics research
CSIRO's cloud-native machine learning is transforming bioinformatics by enabling efficient data analysis and democratizing genomics through accessible platforms. Challenges include the steep learning curve for non-IT researchers, funding obstacles, and data privacy concerns. The approach promises significant advancements in disease gene discovery and healthcare improvements while emphasizing the need for scalable, cost-effective solutions.
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Cloud-native machine learning - Transforming bioinformatics research
- 1. Australia’s National ScienceAgency Cloud-native machine learning Transforming bioinformatics research
- 2. • Workflows needto be reproducible/compliant. • Data sizes are ever increasing. • Algorithms getting more complex/interdependent. #FutureOfBioinf is cloud-native Cloud-native Innovation | A/Prof Denis Bauer | @allPowerde2 |
- 3. 1. Steep learningcurve for non-IT researchers 2. Granting bodies have not fully embraced cloud expenses 3. Data privacy and protection becomes your problem Cloud is not easy Cloud-native bioinformatics | @Tbioinf @allPowerde3 |
- 4. • Impact: Diversecitations • Reach: News coverage • Influence: Global collaborators Cloud-native Innovation | A/Prof Denis Bauer | @allPowerde4 | Not easy but rewarding
- 5. CSIRO Australia’s National Science Agency Readingthe Genome Finding disease genes in billions of DNA molecules Democratize Genomics Affordable data exchange for population-scale cohorts Cloud-native Innovation Cloud-native Innovation | A/Prof Denis Bauer | @allPowerde5 |
- 6. Bioinformatics | DenisC. Bauer | @allPowerde Credit https://toolstotal.com/ • Invented WiFi, used in five billion devices globally. • Developed the vaccine for the Hendra Virus. • Developed the Total Wellbeing & Low-Carb Diets. CSIRO: We are innovators and builders Cloud-native Innovation | A/Prof Denis Bauer | @allPowerde6 |
- 7. ‘Improve health care through digitaltechnology and services.’ Cloud-native Innovation | A/Prof Denis Bauer | @allPowerde7 |
- 8. Cloud-native machine learning| A/Prof Denis Bauer | @Tbioinf @allPowerde 99% have a genetic variation that affects medical care Chanfreau-Coffinier et al. JAMA Netw Open. 2019
- 9. CSIRO Australia’s National Science Agency Readingthe Genome Finding disease genes in billions of DNA molecules Democratize Genomics Affordable data exchange for population-scale cohorts Cloud-native Innovation Cloud-native Innovation | A/Prof Denis Bauer | @allPowerde9 |
- 10. Finding the curefor ALS Credit: National Institute on Aging, National Institutes of HealthCloud-native Innovation | A/Prof Denis Bauer | @allPowerde10 | • Unprecedented scale • Groundbreaking research • Latest Technology
- 11. Finding the diseasegene(s) cases controls Gene1 Gene2 Cloud-native Innovation | A/Prof Denis Bauer | @allPowerde11 |
- 12. Complex diseases aredriven by multiple interacting genes with variable contribution cases controls Need a more sophisticated ML approach, such as Random Forest Cloud-native Innovation | A/Prof Denis Bauer | @allPowerde12 |
- 13. Finding higher orderinteractions Cloud-native bioinformatics | A/Prof Denis Bauer | @Tbioinf @allPowerde13 | Score = (5*B6*B2 – 4*B6 – 4*B2 + 1) + (7*R1*C2 – 6*R1 – 6*C2 + 1)
- 14. Machine learning on1.7 Trillion data points 80 Million features Individuals Genomic profile Disease status 22,500samples Disease genes Cloud-native Innovation | A/Prof Denis Bauer | @allPowerde14 | Transcription, medical records, population data Survival, Drug-choice, Pathogenicity Predictive markers
- 15. Population-scale genomic dataanalysis requires BigData solutions Desktop compute High-performance compute cluster Apache Spark cluster Focus Small data Compute-intensive Data-intensive Node-bound Yes Yes No Parallelization 10 CPU 100+ CPU 1000+ CPU Parallelization procedure bespoke bespoke standardized Cloud-native Innovation | A/Prof Denis Bauer | @allPowerde15 |
- 16. Detecting disease genesefficiently Cloud-native bioinformatics | @Tbioinf @allPowerde16 | Analyzes 3000 individuals with 80M features in 30 minutesFaster Usedby low Accuracy high lowSpeedhigh Available on all major public cloud providers as well as on premisis Accessible
- 17. Bring analysis tothe data Cloud-native machine learning | A/Prof Denis Bauer | @Tbioinf @allPowerde CSIRO takes genome product to the world on Amazon 1 AWS review
- 18. Reproductible research withshare-able stacks Cloud-native Innovation | A/Prof Denis Bauer | @allPowerde18 |
- 19. Prioritizing variants basedon shared IBD Cloud-native bioinformatics | A/Prof Denis Bauer | @Tbioinf @allPowerde19 | Using ancestry information (identity by decent) to narrow down search area for disease genes
- 20. • TRIBES uncovers53 novel relationships up to 7th degree (great-great-great grandparent ) • Identified novel shared variant in FIG4 gene • rare variant in coding region for one SALS pair – validated by Sanger sequencing • FIG4 previously reported in familial Charcot-Marie-Tooth. Suggests low-penetrant FALS • Focus on variants in known ALS-FTD genes, that cause detrimental protein changes Expanding relationships let to novel disease variants Cloud-native bioinformatics | A/Prof Denis Bauer | @Tbioinf @allPowerde20 |
- 21. By 2030 itis estimated that 50% of the world population will have been sequenced. 20 EB Storage / year Stephens et al. BigData: Astronomical or Genomical (2015) Data acquisition of BigData disciplines in 2025 GenomicsYouTube Astronomy Twitter Frost&Sullivan Cloud-native bioinformatics | @Tbioinf @allPowerde21 |
- 22. CSIRO Australia’s National Science Agency Readingthe Genome Finding disease genes in billions of DNA molecules Democratize Genomics Affordable data exchange for population-scale cohorts Cloud-native Innovation Cloud-native Innovation | A/Prof Denis Bauer | @allPowerde22 |
- 23. • Up to$4000/month to maintain • Up to 33 hours to update as new data comes in • Up to 20 second query time Resource consumption unsustainable Cloud-native Innovation | A/Prof Denis Bauer | @allPowerde23 |
- 24. Desktop computers Cloud server (Autos-scale) Serverless Focus Fullcontrol Flexible Agility Flexibility No Overhead Scalability Cost-effective Analogy own car by madd.org ride share by blacklane.com chauffeur Recruiting instantaneous appropriately powered compute Cloud-native Innovation | A/Prof Denis Bauer | @allPowerde24 |
- 25. Re-thinking traditional architectures Cloud-nativeInnovation | A/Prof Denis Bauer | @allPowerde25 |
- 26. 5000-fold faster toupdate new data Cloud-native Innovation | A/Prof Denis Bauer | @allPowerde26 | Hosking B. et al.
- 27. 300-fold monthly costsaving Cloud-native Innovation | A/Prof Denis Bauer | @allPowerde27 | $ $ Hosking B. et al.
- 28. 17-fold faster querytime Cloud-native Innovation | A/Prof Denis Bauer | @allPowerde28 | Hosking B. et al.
- 29. Exchanging genomic datacloud-natively Cloud-native Innovation | A/Prof Denis Bauer | @allPowerde29 | Partners Serve a query in 1s and costs < $15/month to serve 100,000 WGS dataFaster & cheaper Fine grained control over data ownership and accessbetter control
- 30. 1. Steep learningcurve for non-IT researchers 2. Granting bodies have not fully embraced cloud expenses 3. Data privacy and protection becomes your problem Not “cloud-only” but “cloud-first” Cloud-native bioinformatics | @Tbioinf @allPowerde30 |
- 31. Australia’s National ScienceAgency CSIRO Health and Biosecurity Denis Bauer Denis.Bauer@csiro.au Let’s work together Visit our site: https://bioinformatics.csiro.au @allPowerde @Tbioinf