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Biobanks and Biobank-Based Artificial Intelligence (AI) Implementation Through an International Lens

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Artificial Intelligence and Machine Learning for Digital Pathology

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 12090))

Abstract

Artificial Intelligence (AI) is gradually changing medical practice. With recent progress in digitized data acquisition, machine learning and computing infrastructure, AI applications are expanding into areas that were previously thought to be the exclusive domain of human experts. One such area is biobanking, which forms a natural extension for AI-driven activities, both because biobanking is a foundational activity for downstream precision medical research, as well as because biobanking can increasingly accommodate high-throughput sample-, image- and data-handling operational models. The increasing AI-driven appetite for higher volumes of data and images often necessitates the cross-border collaboration of biobanks; likely to develop to one of the major forces dictating the international biobanking collaboration in the near future. However there are significant challenges ahead at the same time: firstly key practical issues surrounding the implementation of AI into existing research and clinical workflows, including data standardization, data sharing and interoperability across multiple platforms. Secondly governance concerns such as privacy, transparency of algorithms, data interpretation and how the latter might impact patient safety. Here a high-level summary of these opportunities and challenges will be presented from the perspective of AI driving more and stronger international collaborations in biobanking.

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References

  1. Burnham, C.A., Dunne Jr., W.M., Greub, G., Novak, S.M., Patel, R.: Automation in the clinical microbiology laboratory. Clin. Chem. 59(12), 1696–1702 (2013)

    Article  Google Scholar 

  2. Bourbeau, P.P., Ledeboer, N.A.: Automation in clinical microbiology. J. Clin. Microbiol. 51(6), 1658–1665 (2013)

    Article  Google Scholar 

  3. Beam, A.L., Kohane, I.S.: Translating artificial intelligence into clinical care. JAMA 316(22), 2368–2369 (2016)

    Article  Google Scholar 

  4. Parodi, B.: Biobanks: a definition. In: Mascalzoni, D. (ed.) Ethics, Law and Governance of Biobanking. The International Library of Ethics, Law and Technology, vol. 14, pp. 15–19. Springer, Dordrecht (2015). https://doi.org/10.1007/978-94-017-9573-9_2

    Chapter  Google Scholar 

  5. Roses, A.D.: Pharmacogenetics and the practice of medicine. Nature 405, 857–865 (2000)

    Article  Google Scholar 

  6. Dakappa, P.H., Prasad, K., Rao, S.B., Bolumbu, G., Bhat, G.K., Mahabala, C.: Classification of infectious and noninfectious diseases using artificial neural networks from 24-hour continuous tympanic temperature data of patients with undifferentiated fever. Crit. Rev. Biomed. Eng. 46(2), 173–183 (2018)

    Article  Google Scholar 

  7. Tou, H., Yao, L., Wei, Z., Zhuang, X., Zhang, B.: Automatic infection detection based on electronic medical records. BMC Bioinf. 19(Suppl 5), 117 (2018)

    Article  Google Scholar 

  8. Nault, V., Pepin, J., Beaudoin, M., Perron, J., Moutquin, J.M., Valiquette, L.: Sustained impact of a computer-assisted antimicrobial stewardship intervention on antimicrobial use and length of stay. J. Antimicrob. Chemother. 72(3), 933–940 (2017)

    Google Scholar 

  9. Wong, Z.S.Y., Zhou, J., Zhang, Q.: Artificial intelligence for infectious disease big data analytics. Infect. Dis. Health 24(1), 44–48 (2019)

    Article  Google Scholar 

  10. Van den Wijngaert, S., et al.: Bigger and better? Representativeness of the influenza a surveillance using one consolidated clinical microbiology laboratory data set as compared to the Belgian sentinel network of laboratories. Front. Public Health 7, 150 (2019)

    Article  Google Scholar 

  11. Poplin, R., Varadarajan, A., Blumer, K., Liu, Y., McConnell, M., Corrado, G., et al.: Predicting cardiovascular risk factors from retinal fundus photographs using deep learning. Nat. Biomed. Eng. 2, 158–164 (2018)

    Article  Google Scholar 

  12. Niehous, K., et al.: Early stage colorectal cancer detection using artificial intelligence and whole-genome sequencing of cell-free DNA in a retrospective cohort of 1,040 patients. Am. J. Gastroenterol. 113, S169 (2018)

    Article  Google Scholar 

  13. Sammani, A., Jansen, M., Linschoten, M., et al.: UNRAVEL: big data analytics research data platform to improve care of patients with cardiomyopathies using routine electronic health records and standardised biobanking. Neth Heart J. 27(9), 426–434 (2019)

    Article  Google Scholar 

  14. Holzinger, A., Roecker, C., Ziefle, M.: Smart Health. Springer, Switzerland (2015). https://doi.org/10.1007/978-3-319-16226-3

    Book  Google Scholar 

  15. Thompson, R., et al.: RD-connect: an integrated platform connecting databases, registries, biobanks and clinical bioinformatics for rare disease research. J. Gen. Int. Med. 29, S780–7 (2014)

    Article  Google Scholar 

  16. Vande Loock, K., Van der Stock, E., Debucquoy, A., et al.: The Belgian virtual tumorbank: a tool for translational cancer research. Front. Med. 6, 120 (2019)

    Article  Google Scholar 

  17. NIH Human Microbiome Portfolio Analysis Team: A review of 10 years of human microbiome research activities at the US National Institutes of Health, Fiscal Years 2007–2016. Microbiome. 7(1), 31 (2019)

    Google Scholar 

  18. Mendy, M., Caboux, E., Sylla, B.S., Dillner, J., Chinquee, J., Wild, C.: Infrastructure and facilities for human biobanking in low- and middle-income countries: a situation analysis. Pathobiology 81, 252–260 (2014)

    Article  Google Scholar 

  19. Simeon-Dubach, D., Henderson, M.K.: Sustainability in Biobanking. Biopreserv. Biobank. 12(5), 287–288 (2014)

    Article  Google Scholar 

  20. Hulsen, T., et al.: From big data to precision medicine. Front. Med. 6, 34 (2019)

    Article  Google Scholar 

  21. Doucet, M., Yuille, M., Georghiou, L., Dagher, G.: Biobank sustainability: current status and future prospects. J. Bioreposit. Sci. Appl. Med. 5, 1–7 (2017)

    Article  Google Scholar 

  22. Caulfield, T., Burningham, S., Joly, Y., et al.: A review of the key issues associated with the commercialization of biobanks. J. Law Biosci. 1(1), 94–110 (2014)

    Article  Google Scholar 

  23. Kinkorová, J., Topolčan, O.: Biobanks in horizon 2020: sustainability and attractive perspectives. EPMA J. 9, 345 (2018)

    Article  Google Scholar 

  24. Simeon-Dubach, D., Kozlakidis, Z.: New standards and updated best practices will give modern biobanking a boost in professionalism. Biopreserv. Biobank. 16(1), 1–2 (2018)

    Article  Google Scholar 

  25. Gliklich, R.E., Dreyer, N.A.: Registries for evaluating patient outcomes: a user’s guide. 3rd edition Editor: Michelle B Leavy. Agency for Healthcare Research and Quality (U.S.), Rockville, MD (2014)

    Google Scholar 

  26. Cadigan, R.J., Juengst, E., Davis, A., Henderson, G.: Underutilization of specimens in biobanks: an ethical as well as a practical concern? Genet. Med. 16(10), 738–740 (2014)

    Article  Google Scholar 

  27. Catchpoole, D.R.: Biohoarding: treasures not seen, stories not told. J. Health Serv. Res. Policy 21(2), 140–142 (2016)

    Article  Google Scholar 

  28. Kozlakidis, Z.: Biobanking with big data: a need for developing “big data metrics”. Biopreserv. Biobank. 14(5), 450–451 (2016)

    Article  Google Scholar 

  29. Char, D.S., Shah, N.H., Magnus, D.: Implementing machine learning in health care—addressing ethical challenges. N. Engl. J. Med. 378, 981–983 (2018)

    Article  Google Scholar 

  30. Paul, S., Gade, A., Mallipeddi, S.: The state of cloud-based biospecimen and biobank data management tools. Biopreserv. Biobank. 15(2), 169–172 (2017)

    Article  Google Scholar 

  31. Barchi, F., Little, M.T.: National ethics guidance in Sub-Saharan Africa on the collection and use of human biological specimens: a systematic review. BMC Med. Ethics 16, 64 (2016)

    Article  Google Scholar 

  32. Ledeboer, N.A., Dallas, S.D.: The automated clinical microbiology laboratory: fact or fantasy? J. Clin. Microbiol. 52(9), 3140–3146 (2014)

    Article  Google Scholar 

  33. Krittanawong, C., Zhang, H., Wang, Z., Aydar, M., Kitai, T.: Big data, artificial intelligence, and cardiovascular precision medicine. J. Am. Coll. Cardiol. 69(21), 2657–2664 (2017)

    Article  Google Scholar 

  34. Caulfield, T., Borry, P., Gottweis, H.: Industry involvement in publicly funded biobanks. Nat. Rev. Genet. 15, 220 (2014)

    Article  Google Scholar 

  35. Hämäläinen, I., Törnwall, O., Simell, B., Zatloukal, K., Perola, M., van Ommen, G.-J.B.: Role of academic biobanks in public–private partnerships in the european biobanking and biomolecular resources research infrastructure community. Biopreserv. Biobank. 17(1), 46–51 (2019)

    Article  Google Scholar 

  36. Hofman, P., Bréchot, C., Zatloukal, K.: Public-private relationship in biobanking: a still underestimated key component of open innovation. Virchows Arch. 464(1), 3–9 (2014)

    Article  Google Scholar 

  37. Hashimoto, D.A., Rosman, G., Rus, D., Meireles, O.R.: Artificial intelligence in surgery: promises and perils. Ann. Surg. 268, 70–76 (2018)

    Article  Google Scholar 

  38. Garattini, C., Raffle, J., Aisyah, D.N., Sartain, F., Kozlakidis, Z.: Big data analytics, infectious diseases and associated ethical impacts. Philos. Technol. 32(1), 69–85 (2019)

    Article  Google Scholar 

  39. Patrzyk, P.M., Link, D., Marewski, J.N.: Human-like machines: transparency and comprehensibility. Behav. Brain Sci. 40, e276 (2017)

    Article  Google Scholar 

  40. Holzinger, A., Langs, G., Denk, H., Zatloukal, K., Mueller, H.: Causability and explainabilty of artificial intelligence in medicine. WIREs Data Min. Knowl. Discov. 9, e1312 (2019)

    Google Scholar 

  41. Sussillo, D., Barak, O.: Opening the black box: low-dimensional dynamics in high-dimensional recurrent neural networks. Neural Comput. 25, 626–649 (2013)

    Article  MathSciNet  Google Scholar 

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Kozlakidis, Z. (2020). Biobanks and Biobank-Based Artificial Intelligence (AI) Implementation Through an International Lens. In: Holzinger, A., Goebel, R., Mengel, M., Müller, H. (eds) Artificial Intelligence and Machine Learning for Digital Pathology. Lecture Notes in Computer Science(), vol 12090. Springer, Cham. https://doi.org/10.1007/978-3-030-50402-1_12

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  • DOI: https://doi.org/10.1007/978-3-030-50402-1_12

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