Skip to main content

Artificial Intelligence in Clinical Immunology

  • Living reference work entry
  • First Online:
Artificial Intelligence in Medicine

Abstract

The field of clinical immunology is expansive and includes both clinical and laboratory science of relevance to human immune health and disease. Across the continuum of host defense, immune homeostasis/regulation, immune genetics, and laboratory immunology we are now seeing the emergence of artificial intelligence and data science approaches. These computational tools are being leveraged to analyze the inherently large datasets of relevance to clinical immunologists. Here, we outline some recent advances in clinical immunology which have been made possible or are being explored via artificial intelligence. We discuss analysis and use of electronic health record data, human cytometric data, and multiomic data after providing a brief introduction to artificial intelligence in healthcare.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Institutional subscriptions

Similar content being viewed by others

References

  1. Obermeyer Z, Lee TH. Lost in thought – the limits of the human mind and the future of medicine. N Engl J Med. 2017;377(13):1209–11. https://doi.org/10.1056/NEJMp1705348.

    Article  PubMed  PubMed Central  Google Scholar 

  2. Rajkomar A, Dean J, Kohane I. Machine learning in medicine. N Engl J Med. 2019;380(14):1347–58. https://doi.org/10.1056/NEJMra1814259.

    Article  PubMed  Google Scholar 

  3. McGlynn EA, McDonald KM, Cassel CK. Measurement is essential for improving diagnosis and reducing diagnostic error: a report from the Institute of Medicine. JAMA. 2015;314(23):2501–2. https://doi.org/10.1001/jama.2015.13453.

    Article  CAS  PubMed  Google Scholar 

  4. Schüssler-Fiorenza Rose SM, et al. A longitudinal big data approach for precision health. Nat Med. 2019;25(5):792–804. https://doi.org/10.1038/s41591-019-0414-6.

    Article  CAS  PubMed  Google Scholar 

  5. Norgeot B, Glicksberg BS, Butte AJ. A call for deep-learning healthcare. Nat Med. 2019;25(1):14–5. https://doi.org/10.1038/s41591-018-0320-3.

    Article  CAS  PubMed  Google Scholar 

  6. Rajkomar A, et al. Scalable and accurate deep learning with electronic health records. NPJ Digit Med. 2018;1:18. https://doi.org/10.1038/s41746-018-0029-1.

    Article  PubMed  PubMed Central  Google Scholar 

  7. Witten I, Frank E, Hall M, Pal C. Data mining: practical machine learning tools and techniques. Morgan Kaufmann; 2017.

    Google Scholar 

  8. Autmented intelligence in health care: report 41 of the AMA Board of Trustees. [Online]. https://static1.squarespace.com/static/58d0113a3e00bef537b02b70/t/5b6aed0a758d4610026a719c/1533734156501/AI_2018_Report_AMA.pdf

  9. Beam AL, Kohane IS. Big data and machine learning in health care. JAMA. 2018;319(13):1317–8. https://doi.org/10.1001/jama.2017.18391.

    Article  PubMed  Google Scholar 

  10. Shearer WT, Fathman CG. 30. Defining the spectrum of clinical immunology. J Allergy Clin Immunol. 2003;111(2):S766–73. https://doi.org/10.1067/mai.2003.88.

    Article  PubMed  Google Scholar 

  11. Rider NL, et al. Calculation of a primary immunodeficiency ‘risk vital sign’ via population-wide analysis of claims data to aid in clinical decision support. Front Pediatr. 2019;7:70. https://doi.org/10.3389/fped.2019.00070.

    Article  PubMed  PubMed Central  Google Scholar 

  12. Holding S, Khan S, Sewell WAC, Jolles S, Dore PC. Using calculated globulin fraction to reduce diagnostic delay in primary and secondary hypogammaglobulinaemias: results of a demonstration project. Ann Clin Biochem. 2015;52(Pt 3):319–26. https://doi.org/10.1177/0004563214545791.

    Article  CAS  PubMed  Google Scholar 

  13. Sevim Bayrak C, Itan Y. Identifying disease-causing mutations in genomes of single patients by computational approaches. Hum Genet. 2020;139(6–7):769–76. https://doi.org/10.1007/s00439-020-02179-7.

    Article  PubMed  Google Scholar 

  14. Juhn Y, Liu H. Artificial intelligence approaches using natural language processing to advance EHR-based clinical research. J Allergy Clin Immunol. 2020;145(2):463–9. https://doi.org/10.1016/j.jaci.2019.12.897.

    Article  PubMed  Google Scholar 

  15. Chang W, Grady N. NIST big data interoperability framework: volume 1, Definitions, vol. 1. U.S. Dept. of Commerce, National Institute of Standards and Technology; 2019.

    Google Scholar 

  16. Goodfellow I, Bengio Y, Courville A. Deep learning. Cambridge, MA: MIT Press; 2016.

    Google Scholar 

  17. Alpaydin E. Introduction to machine learning. 4th ed. Cambridge, MA: MIT Press; 2020.

    Google Scholar 

  18. Ford E, Rooney P, Hurley P, Oliver S, Bremner S, Cassell J. Can the use of Bayesian analysis methods correct for incompleteness in electronic health records diagnosis data? Development of a novel method using simulated and real-life clinical data. Front Public Health. 2020;8:54. https://doi.org/10.3389/fpubh.2020.00054.

    Article  PubMed  PubMed Central  Google Scholar 

  19. Saria S, Henry KE. Too many definitions of sepsis: can machine learning leverage the electronic health record to increase accuracy and bring consensus? Crit Care Med. 2020;48(2):137–41. https://doi.org/10.1097/CCM.0000000000004144.

    Article  PubMed  Google Scholar 

  20. Dolezel D, McLeod A. Big data analytics in healthcare: investigating the diffusion of innovation. Perspect Health Inf Manag. 2019;16(Summer):1a.

    PubMed  PubMed Central  Google Scholar 

  21. Burke J. Health analytics: gaining insights to transform healthcare. Hoboken: Wiley; 2013.

    Book  Google Scholar 

  22. Topol EJ. High-performance medicine: the convergence of human and artificial intelligence. Nat Med. 2019;25(1):44–56. https://doi.org/10.1038/s41591-018-0300-7.

    Article  CAS  PubMed  Google Scholar 

  23. Sidey-Gibbons JAM, Sidey-Gibbons CJ. Machine learning in medicine: a practical introduction. BMC Med Res Methodol. 2019;19(1):64. https://doi.org/10.1186/s12874-019-0681-4.

    Article  PubMed  PubMed Central  Google Scholar 

  24. Meskó B, Görög M. A short guide for medical professionals in the era of artificial intelligence. NPJ Digit Med. 2020;3:126. https://doi.org/10.1038/s41746-020-00333-z.

    Article  PubMed  PubMed Central  Google Scholar 

  25. Esteva A, et al. A guide to deep learning in healthcare. Nat Med. 2019;25(1):24–9. https://doi.org/10.1038/s41591-018-0316-z.

    Article  CAS  PubMed  Google Scholar 

  26. Rider NL, Srinivasan R, Khoury P. Artificial intelligence and the hunt for immunological disorders. Curr Opin Allergy Clin Immunol. 2020;20(6):565–73. https://doi.org/10.1097/ACI.0000000000000691.

    Article  PubMed  PubMed Central  Google Scholar 

  27. Kohn L. To err is human: an interview with the Institute of Medicine’s Linda Kohn. Jt Comm J Qual Improv. 2000;26(4):227–34.

    CAS  PubMed  Google Scholar 

  28. Institute of Medicine (US) Roundtable on Evidence-Based Medicine. The learning healthcare system: workshop summary. Washington, DC: National Academies Press (US); 2007.

    Google Scholar 

  29. Institute of Medicine (US) and National Academy of Engineering (US) Roundtable on Value & Science-Driven Health Care. Engineering a learning healthcare system: a look at the future: workshop summary. Washington, DC: National Academies Press (US); 2011.

    Google Scholar 

  30. Rockowitz S, et al. Children’s rare disease cohorts: an integrative research and clinical genomics initiative. NPJ Genomic Med. 2020;5:29. https://doi.org/10.1038/s41525-020-0137-0.

    Article  Google Scholar 

  31. Zhao J, et al. Learning from longitudinal data in electronic health record and genetic data to improve cardiovascular event prediction. Sci Rep. 2019;9(1):717. https://doi.org/10.1038/s41598-018-36745-x.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Kuo T-T, Gabriel RA, Cidambi KR, Ohno-Machado L. EXpectation propagation LOgistic REgRession on permissioned blockCHAIN (ExplorerChain): decentralized online healthcare/genomics predictive model learning. J Am Med Inform Assoc JAMIA. 2020;27(5):747–56. https://doi.org/10.1093/jamia/ocaa023.

    Article  PubMed  Google Scholar 

  33. Marafino BJ, Dudley RA, Shah NH, Chen JH. Accurate and interpretable intensive care risk adjustment for fused clinical data with generalized additive models. AMIA Jt Summits Transl Sci Proc. 2018;2017:166–75.

    PubMed  Google Scholar 

  34. Agarwal V, Han L, Madan I, Saluja S, Shidham A, Shah NH. Predicting hospital visits from geo-tagged internet search logs. AMIA Jt Summits Transl Sci Proc. 2016;2016:15–24.

    PubMed  PubMed Central  Google Scholar 

  35. Agarwal V, Smuck M, Tomkins-Lane C, Shah NH. Inferring physical function from wearable activity monitors: analysis of free-living activity data from patients with knee osteoarthritis. JMIR MHealth UHealth. 2018;6(12):e11315. https://doi.org/10.2196/11315.

    Article  PubMed  PubMed Central  Google Scholar 

  36. Datta S, Posada J, Olson G, Wencheng L, O’Reilly C, Deepa B. A new paradigm for accelerating clinical data science at Stanford. arXiv. 2020. [Online]. https://arxiv.org/abs/2003.10534

  37. Ta CN, Dumontier M, Hripcsak G, Tatonetti NP, Weng C. Columbia Open Health Data, clinical concept prevalence and co-occurrence from electronic health records. Sci Data. 2018;5:180273. https://doi.org/10.1038/sdata.2018.273.

    Article  PubMed  PubMed Central  Google Scholar 

  38. Gombar S, Callahan A, Califf R, Harrington R, Shah NH. It is time to learn from patients like mine. NPJ Digit Med. 2019;2:16. https://doi.org/10.1038/s41746-019-0091-3.

    Article  PubMed  PubMed Central  Google Scholar 

  39. Froelicher D, Misbach M, Troncoso-Pastoriza JR, Raisaro JL, Hubaux J-P. MedCo2: privacy-preserving cohort exploration and analysis. Stud Health Technol Inform. 2020;270:317–21. https://doi.org/10.3233/SHTI200174.

    Article  PubMed  Google Scholar 

  40. Berliner Senderey A, et al. It’s how you say it: Systematic A/B testing of digital messaging cut hospital no-show rates. PLoS One. 2020;15(6):e0234817. https://doi.org/10.1371/journal.pone.0234817.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Schuler A, Callahan A, Jung K, Shah NH. Performing an informatics consult: methods and challenges. J Am Coll Radiol JACR. 2018;15(3 Pt B):563–8. https://doi.org/10.1016/j.jacr.2017.12.023.

    Article  PubMed  Google Scholar 

  42. Angus DC. Randomized clinical trials of artificial intelligence. JAMA. 2020;323(11):1043–5. https://doi.org/10.1001/jama.2020.1039.

    Article  PubMed  Google Scholar 

  43. Schinkel M, Paranjape K, Nannan Panday RS, Skyttberg N, Nanayakkara PWB. Clinical applications of artificial intelligence in sepsis: a narrative review. Comput Biol Med. 2019;115:103488. https://doi.org/10.1016/j.compbiomed.2019.103488.

    Article  CAS  PubMed  Google Scholar 

  44. Yarmohammadi H, Estrella L, Doucette J, Cunningham-Rundles C. Recognizing primary immune deficiency in clinical practice. Clin Vaccine Immunol CVI. 2006;13(3):329–32. https://doi.org/10.1128/CVI.13.3.329-332.2006.

    Article  CAS  PubMed  Google Scholar 

  45. Ferrante G, Licari A, Fasola S, Marseglia GL, La Grutta S. Artificial intelligence in the diagnosis of pediatric allergic diseases. Pediatr Allergy Immunol. 2020;32:405. https://doi.org/10.1111/pai.13419.

    Article  PubMed  Google Scholar 

  46. Bayesian artificial intelligence – 2nd Edition – Kevin B. Korb – Ann. https://www.routledge.com/Bayesian-Artificial-Intelligence/Korb-Nicholson/p/book/9781439815915. Accessed 06 Feb 2021.

  47. Rider NL, et al. PI Prob: a risk prediction and clinical guidance system for evaluating patients with recurrent infections. PLoS One. 2021;16:e0237285.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. McLachlan S, Dube K, Hitman GA, Fenton NE, Kyrimi E. Bayesian networks in healthcare: distribution by medical condition. Artif Intell Med. 2020;107:101912. https://doi.org/10.1016/j.artmed.2020.101912.

    Article  PubMed  Google Scholar 

  49. Richesson RL, Sun J, Pathak J, Kho AN, Denny JC. Clinical phenotyping in selected national networks: demonstrating the need for high-throughput, portable, and computational methods. Artif Intell Med. 2016;71:57–61. https://doi.org/10.1016/j.artmed.2016.05.005.

    Article  PubMed  PubMed Central  Google Scholar 

  50. Tangye SG, et al. Human inborn errors of immunity: 2019 update on the classification from the International Union of Immunological Societies Expert Committee. J Clin Immunol. 2020;40(1):24–64. https://doi.org/10.1007/s10875-019-00737-x.

    Article  PubMed  PubMed Central  Google Scholar 

  51. Keerthikumar S, et al. Prediction of candidate primary immunodeficiency disease genes using a support vector machine learning approach. DNA Res. 2009;16(6):345–51. https://doi.org/10.1093/dnares/dsp019.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Martorell-Marugán J, et al. Deep learning in omics data analysis and precision medicine. In: Husi H, editor. Computational biology. Brisbane: Codon Publications; 2019.

    Google Scholar 

  53. Robinson PN, Haendel MA. Ontologies, knowledge representation, and machine learning for translational research: recent contributions. Yearb Med Inform. 2020;29(1):159–62. https://doi.org/10.1055/s-0040-1701991.

    Article  PubMed  PubMed Central  Google Scholar 

  54. Resnick ES, Bhatt P, Sidi P, Cunningham-Rundles C. Examining the use of ICD-9 diagnosis codes for primary immune deficiency diseases in New York State. J Clin Immunol. 2013;33(1):40–8. https://doi.org/10.1007/s10875-012-9773-1.

    Article  CAS  PubMed  Google Scholar 

  55. Köhler S, et al. Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Res. 2019;47(D1):D1018–27. https://doi.org/10.1093/nar/gky1105.

    Article  CAS  PubMed  Google Scholar 

  56. Köhler S. Improved ontology-based similarity calculations using a study-wise annotation model. Database. 2018;2018:bay026. https://doi.org/10.1093/database/bay026.

    Article  PubMed Central  Google Scholar 

  57. Son JH, et al. Deep phenotyping on electronic health records facilitates genetic diagnosis by clinical exomes. Am J Hum Genet. 2018;103(1):58–73. https://doi.org/10.1016/j.ajhg.2018.05.010.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Tracy JM, Özkanca Y, Atkins DC, Hosseini Ghomi R. Investigating voice as a biomarker: deep phenotyping methods for early detection of Parkinson’s disease. J Biomed Inform. 2020;104:103362. https://doi.org/10.1016/j.jbi.2019.103362.

    Article  PubMed  Google Scholar 

  59. Sharma H, et al. Developing a portable natural language processing based phenotyping system. BMC Med Inform Decis Mak. 2019;19(Suppl 3):78. https://doi.org/10.1186/s12911-019-0786-z.

    Article  PubMed  PubMed Central  Google Scholar 

  60. All of Us Research Program Investigators, et al. The ‘All of Us’ Research Program. N Engl J Med. 2019;381(7):668–76. https://doi.org/10.1056/NEJMsr1809937.

    Article  Google Scholar 

  61. Optimizing strategies for clinical decision support. National Academy of Medicine. https://nam.edu/optimizing-strategies-clinical-decision-support/. Accessed 24 Jan 2021.

  62. Reinventing clinical decision support: data analytics, artificial intelligence, and diagnostic reasoning. Routledge & CRC Press. https://www.routledge.com/Reinventing-Clinical-Decision-Support-Data-Analytics-Artificial-Intelligence/Cerrato-Halamka/p/book/9780367186234. Accessed 24 Jan 2021.

  63. Clinical Decision Support | HealthIT.gov. https://www.healthit.gov/topic/safety/clinical-decision-support. Accessed 24 Jan 2021.

  64. Wang T, Liu G, Lin H. A machine learning approach to predict intravenous immunoglobulin resistance in Kawasaki disease patients: a study based on a Southeast China population. PloS One. 2020;15(8):e0237321. https://doi.org/10.1371/journal.pone.0237321.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Zhang Y, et al. High-throughput phenotyping with electronic medical record data using a common semi-supervised approach (PheCAP). Nat Protoc. 2019;14(12):3426–44. https://doi.org/10.1038/s41596-019-0227-6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Cai T, et al. EXTraction of EMR numerical data: an efficient and generalizable tool to EXTEND clinical research. BMC Med Inform Decis Mak. 2019;19(1):226. https://doi.org/10.1186/s12911-019-0970-1.

    Article  PubMed  PubMed Central  Google Scholar 

  67. Jorge A, et al. Identifying lupus patients in electronic health records: development and validation of machine learning algorithms and application of rule-based algorithms. Semin Arthritis Rheum. 2019;49(1):84–90. https://doi.org/10.1016/j.semarthrit.2019.01.002.

    Article  PubMed  PubMed Central  Google Scholar 

  68. Zhao SS, et al. Incorporating natural language processing to improve classification of axial spondyloarthritis using electronic health records. Rheumatology Oxf Engl. 2020;59(5):1059–65. https://doi.org/10.1093/rheumatology/kez375.

    Article  Google Scholar 

  69. Falissard B, et al. Qualitative assessment of adult patients’ perception of atopic dermatitis using natural language processing analysis in a cross-sectional study. Dermatol Ther. 2020;10(2):297–305. https://doi.org/10.1007/s13555-020-00356-0.

    Article  Google Scholar 

  70. Banerji A, et al. Natural language processing combined with ICD-9-CM codes as a novel method to study the epidemiology of allergic drug reactions. J Allergy Clin Immunol Pract. 2020;8(3):1032–38.e1. https://doi.org/10.1016/j.jaip.2019.12.007.

    Article  PubMed  Google Scholar 

  71. Seol HY, et al. Expert artificial intelligence-based natural language processing characterises childhood asthma. BMJ Open Respir Res. 2020;7(1):e000524. https://doi.org/10.1136/bmjresp-2019-000524.

    Article  PubMed  PubMed Central  Google Scholar 

  72. Wi C-I, et al. Natural language processing for asthma ascertainment in different practice settings. J Allergy Clin Immunol Pract. 2018;6(1):126–31. https://doi.org/10.1016/j.jaip.2017.04.041.

    Article  PubMed  Google Scholar 

  73. Wu ST, Juhn YJ, Sohn S, Liu H. Patient-level temporal aggregation for text-based asthma status ascertainment. J Am Med Inform Assoc JAMIA. 2014;21(5):876–84. https://doi.org/10.1136/amiajnl-2013-002463.

    Article  PubMed  Google Scholar 

  74. Sohn S, et al. Ascertainment of asthma prognosis using natural language processing from electronic medical records. J Allergy Clin Immunol. 2018;141(6):2292–94.e3. https://doi.org/10.1016/j.jaci.2017.12.1003.

    Article  PubMed  PubMed Central  Google Scholar 

  75. Sauer BC, et al. Performance of a natural language processing (NLP) tool to extract pulmonary function test (PFT) reports from structured and semistructured veteran affairs (VA) data. EGEMS Wash DC. 2016;4(1):1217. https://doi.org/10.13063/2327-9214.1217.

    Article  PubMed  PubMed Central  Google Scholar 

  76. Sohn S, et al. Clinical documentation variations and NLP system portability: a case study in asthma birth cohorts across institutions. J Am Med Inform Assoc JAMIA. 2018;25(3):353–9. https://doi.org/10.1093/jamia/ocx138.

    Article  PubMed  Google Scholar 

  77. Banerjee A, et al. Use of machine learning and artificial intelligence to predict SARS-CoV-2 infection from full blood counts in a population. Int Immunopharmacol. 2020;86:106705. https://doi.org/10.1016/j.intimp.2020.106705.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Cady NC, et al. Multiplexed detection and quantification of human antibody response to COVID-19 infection using a plasmon enhanced biosensor platform. Biosens Bioelectron. 2021;171:112679. https://doi.org/10.1016/j.bios.2020.112679.

    Article  CAS  PubMed  Google Scholar 

  79. Shrock E, et al. Viral epitope profiling of COVID-19 patients reveals cross-reactivity and correlates of severity. Science. 2020;370(6520):eabd4250. https://doi.org/10.1126/science.abd4250.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Malik YS, et al. How artificial intelligence may help the Covid-19 pandemic: pitfalls and lessons for the future. Rev Med Virol. 2020;e2205. https://doi.org/10.1002/rmv.2205.

  81. Cahill G, Kutac C, Rider NL. Visualizing and assessing US county-level COVID19 vulnerability. Am J Infect Control. 2020;49:678. https://doi.org/10.1016/j.ajic.2020.12.009.

    Article  PubMed  PubMed Central  Google Scholar 

  82. Li M, et al. Identifying novel factors associated with COVID-19 transmission and fatality using the machine learning approach. Sci Total Environ. 2020;764:142810. https://doi.org/10.1016/j.scitotenv.2020.142810.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Albahri OS, et al. Helping doctors hasten COVID-19 treatment: towards a rescue framework for the transfusion of best convalescent plasma to the most critical patients based on biological requirements via ml and novel MCDM methods. Comput Methods Prog Biomed. 2020;196:105617. https://doi.org/10.1016/j.cmpb.2020.105617.

    Article  CAS  Google Scholar 

  84. Mirabelli C, et al. Morphological cell profiling of SARS-CoV-2 infection identifies drug repurposing candidates for COVID-19. BioRxiv Prepr Serv Biol. 2020. https://doi.org/10.1101/2020.05.27.117184.

  85. Zhang H, et al. A novel virtual screening procedure identifies pralatrexate as inhibitor of SARS-CoV-2 RdRp and it reduces viral replication in vitro. PLoS Comput Biol. 2020;16(12):e1008489. https://doi.org/10.1371/journal.pcbi.1008489.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Black S, Bloom DE, Kaslow DC, Pecetta S, Rappuoli R. Transforming vaccine development. Semin Immunol. 2020;50:101413. https://doi.org/10.1016/j.smim.2020.101413.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Ong E, Wong MU, Huffman A, He Y. COVID-19 coronavirus vaccine design using reverse vaccinology and machine learning. Front Immunol. 2020;11:1581. https://doi.org/10.3389/fimmu.2020.01581.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Fortino V, et al. Machine-learning-driven biomarker discovery for the discrimination between allergic and irritant contact dermatitis. Proc Natl Acad Sci U S A. 2020;117(52):33474–85. https://doi.org/10.1073/pnas.2009192117.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Lombard C, et al. Clinical parameters vs cytokine profiles as predictive markers of IgE-mediated allergy in young children. PloS One. 2015;10(7):e0132753. https://doi.org/10.1371/journal.pone.0132753.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Ghosh D, Bernstein JA, Khurana Hershey GK, Rothenberg ME, Mersha TB. Leveraging multilayered ‘omics’ data for atopic dermatitis: a road map to precision medicine. Front Immunol. 2018;9:2727. https://doi.org/10.3389/fimmu.2018.02727.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Fu S, Zarrinpar A. Recent advances in precision medicine for individualized immunosuppression. Curr Opin Organ Transplant. 2020;25(4):420–5. https://doi.org/10.1097/MOT.0000000000000771.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Adom D, Rowan C, Adeniyan T, Yang J, Paczesny S. Biomarkers for allogeneic HCT outcomes. Front Immunol. 2020;11:673. https://doi.org/10.3389/fimmu.2020.00673.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Partanen J, et al. Review of genetic variation as a predictive biomarker for chronic graft-versus-host-disease after allogeneic stem cell transplantation. Front Immunol. 2020;11:575492. https://doi.org/10.3389/fimmu.2020.575492.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Gandelman JS, et al. Machine learning reveals chronic graft-versus-host disease phenotypes and stratifies survival after stem cell transplant for hematologic malignancies. Haematologica. 2019;104(1):189–96. https://doi.org/10.3324/haematol.2018.193441.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. de Oliveira Lima E, et al. Metabolomics and machine learning approaches combined in pursuit for more accurate paracoccidioidomycosis diagnoses. mSystems. 2020;5(3):e00258-20. https://doi.org/10.1128/mSystems.00258-20.

    Article  Google Scholar 

  96. Proietti C, et al. Immune signature against Plasmodium falciparum antigens predicts clinical immunity in distinct malaria endemic communities. Mol Cell Proteomics MCP. 2020;19(1):101–13. https://doi.org/10.1074/mcp.RA118.001256.

    Article  CAS  PubMed  Google Scholar 

  97. Dieterle MG, et al. Systemic inflammatory mediators are effective biomarkers for predicting adverse outcomes in Clostridioides difficile infection. mBio. 2020;11(3):e00180-20. https://doi.org/10.1128/mBio.00180-20.

    Article  PubMed  PubMed Central  Google Scholar 

  98. Tap J, et al. Identification of an intestinal microbiota signature associated with severity of irritable Bowel syndrome. Gastroenterology. 2017;152(1):111–23.e8. https://doi.org/10.1053/j.gastro.2016.09.049.

    Article  PubMed  Google Scholar 

  99. Douglas GM, et al. Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn’s disease. Microbiome. 2018;6(1):13. https://doi.org/10.1186/s40168-018-0398-3.

    Article  PubMed  PubMed Central  Google Scholar 

  100. Doherty MK, et al. Fecal microbiota signatures are associated with response to Ustekinumab therapy among Crohn’s disease patients. mBio. 2018;9(2). https://doi.org/10.1128/mBio.02120-17.

  101. Kitsios GD, et al. Respiratory microbiome profiling for etiologic diagnosis of pneumonia in mechanically ventilated patients. Front Microbiol. 2018;9:1413. https://doi.org/10.3389/fmicb.2018.01413.

    Article  PubMed  PubMed Central  Google Scholar 

  102. Nearing JT, et al. Infectious complications are associated with alterations in the gut microbiome in pediatric patients with acute lymphoblastic leukemia. Front Cell Infect Microbiol. 2019;9:28. https://doi.org/10.3389/fcimb.2019.00028.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Zhao CY, et al. Microbiome data enhances predictive models of lung function in people with cystic fibrosis. J Infect Dis. 2020. https://doi.org/10.1093/infdis/jiaa655.

  104. Artacho A, et al. The pre-treatment gut microbiome is associated with lack of response to methotrexate in new onset rheumatoid arthritis. Arthritis Rheumatol. Hoboken NJ. 2020. https://doi.org/10.1002/art.41622.

  105. Lejeune S, et al. Childhood asthma heterogeneity at the era of precision medicine: modulating the immune response or the microbiota for the management of asthma attack. Biochem Pharmacol. 2020;179:114046. https://doi.org/10.1016/j.bcp.2020.114046.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Haran JP, et al. Alzheimer’s disease microbiome is associated with dysregulation of the anti-inflammatory P-glycoprotein pathway. mBio. 2019;10(3). https://doi.org/10.1128/mBio.00632-19.

  107. McKinnon KM. Flow cytometry: an overview. Curr Protoc Immunol. 2018;120:5.1.1–11. https://doi.org/10.1002/cpim.40.

    Article  Google Scholar 

  108. Kay AW, Strauss-Albee DM, Blish CA. Application of mass cytometry (CyTOF) for functional and phenotypic analysis of natural killer cells. Methods Mol Biol Clifton NJ. 2016;1441:13–26. https://doi.org/10.1007/978-1-4939-3684-7_2.

    Article  CAS  Google Scholar 

  109. Culos A, et al. Integration of mechanistic immunological knowledge into a machine learning pipeline improves predictions. Nat Mach Intell. 2020;2(10):619–28. https://doi.org/10.1038/s42256-020-00232-8.

    Article  PubMed  PubMed Central  Google Scholar 

  110. Hu Z, Tang A, Singh J, Bhattacharya S, Butte AJ. A robust and interpretable end-to-end deep learning model for cytometry data. Proc Natl Acad Sci U S A. 2020;117(35):21373–80. https://doi.org/10.1073/pnas.2003026117.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Castelvecchi D. Can we open the black box of AI? Nature. 2016;538(7623):20–3. https://doi.org/10.1038/538020a.

    Article  CAS  PubMed  Google Scholar 

  112. IBM’s Watson recommended ‘unsafe and incorrect’ cancer treatments, STAT report finds. https://www.beckershospitalreview.com/artificial-intelligence/ibm-s-watson-recommended-unsafe-and-incorrect-cancer-treatments-stat-report-finds.html. Accessed 24 Jan 2021.

  113. Gianfrancesco MA, Tamang S, Yazdany J, Schmajuk G. Potential biases in machine learning algorithms using electronic health record data. JAMA Intern Med. 2018;178(11):1544–7. https://doi.org/10.1001/jamainternmed.2018.3763.

    Article  PubMed  PubMed Central  Google Scholar 

  114. Stringhini S, et al. Socioeconomic status and the 25 × 25 risk factors as determinants of premature mortality: a multicohort study and meta-analysis of 1·7 million men and women. Lancet Lond Engl. 2017;389(10075):1229–37. https://doi.org/10.1016/S0140-6736(16)32380-7.

    Article  Google Scholar 

  115. Arpey NC, Gaglioti AH, Rosenbaum ME. How socioeconomic status affects patient perceptions of health care: a qualitative study. J Prim Care Community Health. 2017;8(3):169–75. https://doi.org/10.1177/2150131917697439.

    Article  PubMed  PubMed Central  Google Scholar 

  116. Esteva A, et al. Dermatologist-level classification of skin cancer with deep neural networks. Nature. 2017;542(7639):115–8. https://doi.org/10.1038/nature21056.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. Chinn IK, Orange JS. A 2020 update on the use of genetic testing for patients with primary immunodeficiency. Expert Rev Clin Immunol. 2020;16(9):897–909. https://doi.org/10.1080/1744666X.2020.1814145.

    Article  CAS  PubMed  Google Scholar 

  118. Stray-Pedersen A, et al. Primary immunodeficiency diseases: genomic approaches delineate heterogeneous Mendelian disorders. J Allergy Clin Immunol. 2017;139(1):232–45. https://doi.org/10.1016/j.jaci.2016.05.042.

    Article  PubMed  Google Scholar 

  119. Norgeot B, et al. Minimum information about clinical artificial intelligence modeling: the MI-CLAIM checklist. Nat Med. 2020;26(9):1320–4. https://doi.org/10.1038/s41591-020-1041-y.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Nicholas L. Rider .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Nature Switzerland AG

About this entry

Check for updates. Verify currency and authenticity via CrossMark

Cite this entry

Chin, A., Rider, N.L. (2021). Artificial Intelligence in Clinical Immunology. In: Lidströmer, N., Ashrafian, H. (eds) Artificial Intelligence in Medicine. Springer, Cham. https://doi.org/10.1007/978-3-030-58080-3_83-1

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-58080-3_83-1

  • Received:

  • Accepted:

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-58080-3

  • Online ISBN: 978-3-030-58080-3

  • eBook Packages: Springer Reference MedicineReference Module Medicine

Publish with us

Policies and ethics