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Harnessing the power of artificial intelligence to combat infectious diseases: Progress, challenges, and future outlook

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  • Corresponding authors: zhy@ism.cams.cn (H.Z.);  wap@ism.cams.cn (A.W.)
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    1. Artificial intelligence technologies show significant promise in preventing and controlling infectious diseases.

      Advances made across all outbreak stages: pre-pandemic, early pandemic, pandemic, and periodic epidemics.

      Deep learning facilitates early detection, risk assessment, policy formulation, and vaccine development.

      Challenges arise from data quantity/quality, model complexity/interpretability, and individual privacy concerns.

      Promising directions lie in the deep integration of deep learning models with specific biological knowledge.

  • The rapid emergence and global spread of infectious diseases pose significant challenges to public health. In recent years, artificial intelligence (AI) technologies have shown great potential in enhancing our ability to prevent, detect, and control infectious disease outbreaks. However, as a growing interdisciplinarity field, a gap exists between AI scientists and infectious disease biologists, limiting the full potential of AI in this field. This review provides a comprehensive overview of the applications of AI in infectious diseases, focusing on the progress along the four stages of outbreaks: pre-pandemic, early pandemic, pandemic, and periodic epidemic stages. We discuss AI methods in early detection and risk assessment, outbreak surveillance, diagnosis and control, and understanding pathogenic mechanisms. We also propose the primary limitations, challenges, and potential solutions associated with AI tools in public health contexts while examining crucial considerations for future enhanced implementation. By harnessing the power of AI, we can develop more precise and targeted strategies to mitigate the burden of infectious diseases and improve global health.
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  • [1] Msemburi, W., Karlinsky, A., Knutson, V., et al. (2023). The WHO estimates of excess mortality associated with the COVID-19 pandemic. Nature 613: 130−137. DOI: 10.1038/s41586-022-05522-2.

    View in Article CrossRef Google Scholar Scopus

    [2] WHO. (2024). Prioritizing diseases for research and development in emergency contexts. https://www.who.int/activities/prioritizing-diseases-for-research-and-development-in-emergency-contexts.

    View in Article Google Scholar

    [3] Brownstein, J.S., Rader, B., Astley, C.M., et al. (2023). Advances in artificial intelligence for infectious-disease surveillance. N. Engl. J. Med. 388: 1597−1607. DOI: 10.1056/NEJMra2119215.

    View in Article CrossRef Google Scholar

    [4] Wong, F., de la Fuente-Nunez, C., and Collins, J.J. (2023). Leveraging artificial intelligence in the fight against infectious diseases. Science 381: 164−170. DOI: 10.1126/science.adh1114.

    View in Article CrossRef Google Scholar Scopus

    [5] Topol, E.J. (2019). High-performance medicine: The convergence of human and artificial intelligence. Nat. Med. 25: 44−56. DOI: 10.1038/s41591-018-0300-7.

    View in Article CrossRef Google Scholar

    [6] Aiello, A.E., Renson, A., and Zivich, P.N. (2020). Social media- and internet-based disease surveillance for public health. Annu. Rev. Public Health 41: 101−118. DOI: 10.1146/annurev-publhealth-040119-094402.

    View in Article CrossRef Google Scholar Scopus

    [7] Ginsberg, J., Mohebbi, M.H., Patel, R.S., et al. (2009). Detecting influenza epidemics using search engine query data. Nature 457: 1012−1014. DOI: 10.1038/nature07634.

    View in Article CrossRef Google Scholar Scopus

    [8] Lazer, D., Kennedy, R., King, G., et al. (2014). The parable of Google Flu: Traps in big data analysis. Science 343: 1203−1205. DOI: 10.1126/science.1248506.

    View in Article CrossRef Google Scholar

    [9] Kogan, N.E., Clemente, L., Liautaud, P., et al. (2021). An early warning approach to monitor COVID-19 activity with multiple digital traces in near real time. Sci. Adv. 7: eabd6989. DOI: 10.1126/sciadv.abd6989.

    View in Article CrossRef Google Scholar Scopus

    [10] Stolerman, L.M., Clemente, L., Poirier, C., et al. (2023). Using digital traces to build prospective and real-time county-level early warning systems to anticipate COVID-19 outbreaks in the United States. Sci. Adv. 9: eabq0199. DOI: 10.1126/sciadv.abq0199.

    View in Article CrossRef Google Scholar Scopus

    [11] Jahn, K., Dreifuss, D., Topolsky, I., et al. (2022). Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC. Nat. Microbiol. 7: 1151−1160. DOI: 10.1038/s41564-022-01185-x.

    View in Article CrossRef Google Scholar Scopus

    [12] Chia, P.Y., Coleman, K.K., Tan, Y.K., et al. (2020). Detection of air and surface contamination by SARS-CoV-2 in hospital rooms of infected patients. Nat. Commun. 11: 2800. DOI: 10.1038/s41467-020-16670-2.

    View in Article CrossRef Google Scholar Scopus

    [13] Doremalen, N.V., Bushmaker, T., Morris, D.H., et al. (2020). Aerosol and surface stability of SARS-CoV-2 as compared with SARS-CoV-1. N. Engl. J. Med. 382: 1564−1567. DOI: 10.1056/NEJMc2004973.

    View in Article CrossRef Google Scholar Scopus

    [14] Karthikeyan, S., Levy, J.I., De Hoff, P., et al. (2022). Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission. Nature 609: 101−108. DOI: 10.1038/s41586-022-05049-6.

    View in Article CrossRef Google Scholar Scopus

    [15] Jones, K.E., Patel, N.G., Levy, M.A., et al. (2008). Global trends in emerging infectious diseases. Nature 451: 990−993. DOI: 10.1038/nature06536.

    View in Article CrossRef Google Scholar Scopus

    [16] Carroll, D., Daszak, P., Wolfe, N.D., et al. (2018). The global virome project. Science 359: 872−874. DOI: 10.1126/science.aap7463.

    View in Article CrossRef Google Scholar

    [17] Grange, Z.L., Goldstein, T., Johnson, C.K., et al. (2021). Ranking the risk of animal-to-human spillover for newly discovered viruses. Proc. Natl. Acad. Sci. U. S. A. 118: e2002324118. DOI: 10.1073/pnas.2002324118.

    View in Article CrossRef Google Scholar Scopus

    [18] Wardeh, M., Blagrove, M.S.C., Sharkey, K.J., et al. (2021). Divide-and-conquer: Machine-learning integrates mammalian and viral traits with network features to predict virus-mammal associations. Nat. Commun. 12: 3954. DOI: 10.1038/s41467-021-24085-w.

    View in Article CrossRef Google Scholar

    [19] Levy, J.I., Andersen, K.G., Knight, R., et al. (2023). Wastewater surveillance for public health. Science 379: 26−27. DOI: 10.1126/science.ade2503.

    View in Article CrossRef Google Scholar Scopus

    [20] Luksza, M. and Lassig, M. (2014). A predictive fitness model for influenza. Nature 507: 57−61. DOI: 10.1038/nature13087.

    View in Article CrossRef Google Scholar Scopus

    [21] Shu, Y. and McCauley, J. (2017). GISAID: Global initiative on sharing all influenza data–from vision to reality. Eurosurveillance 22: 30494. DOI: 10.2807/1560-7917.ES.2017.22.13.30494.

    View in Article CrossRef Google Scholar

    [22] Obermeyer, F., Jankowiak, M., Barkas, N., et al. (2022). Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness. Science 376 : 1327-1332. DOI: 10.1126/science.abm1208.

    View in Article Google Scholar

    [23] Maher, M.C., Bartha, I., Weaver, S., et al. (2022). Predicting the mutational drivers of future SARS-CoV-2 variants of concern. Sci. Transl. Med. 14: eabk3445. DOI: 10.1126/scitranslmed.abk3445.

    View in Article CrossRef Google Scholar Scopus

    [24] Hie, B., Zhong, E.D., Berger, B., et al. (2021). Learning the language of viral evolution and escape. Science 371: 284−288. DOI: 10.1126/science.abd7331.

    View in Article CrossRef Google Scholar Scopus

    [25] Thadani, N.N., Gurev, S., Notin, P., et al. (2023). Learning from prepandemic data to forecast viral escape. Nature 622: 818−825. DOI: 10.1038/s41586-023-06617-0.

    View in Article CrossRef Google Scholar Scopus

    [26] Brauner, J.M., Mindermann, S., Sharma, M., et al. (2021). Inferring the effectiveness of government interventions against COVID-19. Science 371: eabd9338. DOI: 10.1126/science.abd9338.

    View in Article CrossRef Google Scholar Scopus

    [27] Chang, S., Pierson, E., Koh, P.W., et al. (2021). Mobility network models of COVID-19 explain inequities and inform reopening. Nature 589: 82−87. DOI: 10.1038/s41586-020-2923-3.

    View in Article CrossRef Google Scholar Scopus

    [28] Leung, K., Wu, J.T., and Leung, G.M. (2021). Real-time tracking and prediction of COVID-19 infection using digital proxies of population mobility and mixing. Nat. Commun. 12: 1501. DOI: 10.1038/s41467-021-21776-2.

    View in Article CrossRef Google Scholar Scopus

    [29] Stockdale, J.E., Susvitasari, K., Tupper, P., et al. (2023). Genomic epidemiology offers high resolution estimates of serial intervals for COVID-19. Nat. Commun. 14: 4830. DOI: 10.1038/s41467-023-40544-y.

    View in Article CrossRef Google Scholar Scopus

    [30] Valdano, E., Colombi, D., Poletto, C., et al. (2023). Epidemic graph diagrams as analytics for epidemic control in the data-rich era. Nat. Commun. 14: 8472. DOI: 10.1038/s41467-023-43856-1.

    View in Article CrossRef Google Scholar Scopus

    [31] Cooper, B.S., Evans, S., Jafari, Y., et al. (2023). The burden and dynamics of hospital-acquired SARS-CoV-2 in England. Nature 623: 132−138. DOI: 10.1038/s41586-023-06634-z.

    View in Article CrossRef Google Scholar Scopus

    [32] Ward, T., Johnsen, A., Ng, S., et al. (2022). Forecasting SARS-CoV-2 transmission and clinical risk at small spatial scales by the application of machine learning architectures to syndromic surveillance data. Nat. Mach. Intell. 4: 814−827. DOI: 10.1038/s42256-022-00538-9.

    View in Article CrossRef Google Scholar Scopus

    [33] Nicholson, G., Lehmann, B., Padellini, T., et al. (2022). Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework. Nat. Microbiol. 7: 97−107. DOI: 10.1038/s41564-021-01029-0.

    View in Article CrossRef Google Scholar Scopus

    [34] Yang, W. and Shaman, J. (2021). Development of a model-inference system for estimating epidemiological characteristics of SARS-CoV-2 variants of concern. Nat. Commun. 12: 5573. DOI: 10.1038/s41467-021-25913-9.

    View in Article CrossRef Google Scholar Scopus

    [35] Lloyd-Smith, J.O., Schreiber, S.J., Kopp, P.E., et al. (2005). Superspreading and the effect of individual variation on disease emergence. Nature 438: 355−359. DOI: 10.1038/nature04153.

    View in Article CrossRef Google Scholar Scopus

    [36] Lemieux, J.E., Siddle, K.J., Shaw, B.M., et al. (2021). Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events. Science 371: eabe3261. DOI: 10.1126/science.abe3261.

    View in Article CrossRef Google Scholar Scopus

    [37] Lau, M.S.Y., Grenfell, B., Thomas, M., et al. (2020). Characterizing superspreading events and age-specific infectiousness of SARS-CoV-2 transmission in Georgia, USA. Proc. Natl. Acad. Sci. U. S. A. 117: 22430−22435. DOI: 10.1073/pnas.2011802117.

    View in Article CrossRef Google Scholar Scopus

    [38] Gomes, B. and Ashley, E.A. (2023). Artificial intelligence in molecular medicine. N. Engl. J. Med. 388: 2456−2465. DOI: 10.1056/NEJMra2204787.

    View in Article CrossRef Google Scholar

    [39] Sadybekov, A.V. and Katritch, V. (2023). Computational approaches streamlining drug discovery. Nature 616: 673−685. DOI: 10.1038/s41586-023-05905-z.

    View in Article CrossRef Google Scholar Scopus

    [40] Mullowney, M.W., Duncan, K.R., Elsayed, S.S., et al. (2023). Artificial intelligence for natural product drug discovery. Nat. Rev. Drug Discov. 22: 895−916. DOI: 10.1038/s41573-023-00774-7.

    View in Article CrossRef Google Scholar Scopus

    [41] Pandey, M., Fernandez, M., Gentile, F., et al. (2022). The transformational role of GPU computing and deep learning in drug discovery. Nat. Mach. Intell. 4: 211−221. DOI: 10.1038/s42256-022-00463-x.

    View in Article CrossRef Google Scholar Scopus

    [42] Turbe, V., Herbst, C., Mngomezulu, T., et al. (2021). Deep learning of HIV field-based rapid tests. Nat. Med. 27: 1165−1170. DOI: 10.1038/s41591-021-01384-9.

    View in Article CrossRef Google Scholar Scopus

    [43] Huang, S.C., Chaudhari, A.S., Langlotz, C.P., et al. (2022). Developing medical imaging AI for emerging infectious diseases. Nat. Commun. 13: 7060. DOI: 10.1038/s41467-022-34234-4.

    View in Article CrossRef Google Scholar Scopus

    [44] Rajpurkar, P. and Lungren, M.P. (2023). The current and future state of AI interpretation of medical images. N. Engl. J. Med. 388: 1981−1990. DOI: 10.1056/NEJMra2301725.

    View in Article CrossRef Google Scholar

    [45] Jin, C., Chen, W., Cao, Y., et al. (2020). Development and evaluation of an artificial intelligence system for COVID-19 diagnosis. Nat. Commun. 11: 5088. DOI: 10.1038/s41467-020-18685-1.

    View in Article CrossRef Google Scholar Scopus

    [46] Mei, X., Lee, H.-C., Diao, K.-y., et al. (2020). Artificial intelligence–enabled rapid diagnosis of patients with COVID-19. Nat. Med. 26: 1224−1228. DOI: 10.1038/s41591-020-0931-3.

    View in Article CrossRef Google Scholar Scopus

    [47] Dvijotham, K.D., Winkens, J., Barsbey, M., et al. (2023). Enhancing the reliability and accuracy of AI-enabled diagnosis via complementarity-driven deferral to clinicians. Nat. Med. 29: 1814−1820. DOI: 10.1038/s41591-023-02437-x.

    View in Article CrossRef Google Scholar Scopus

    [48] Roberts, M., Driggs, D., Thorpe, M., et al. (2021). Common pitfalls and recommendations for using machine learning to detect and prognosticate for COVID-19 using chest radiographs and CT scans. Nat. Mach. Intell. 3: 199−217. DOI: 10.1038/s42256-021-00307-0.

    View in Article CrossRef Google Scholar Scopus

    [49] Bai, X., Wang, H., Ma, L., et al. (2021). Advancing COVID-19 diagnosis with privacy-preserving collaboration in artificial intelligence. Nat. Mach. Intell. 3: 1081−1089. DOI: 10.1038/s42256-021-00421-z.

    View in Article CrossRef Google Scholar Scopus

    [50] Ktena, I., Wiles, O., Albuquerque, I., et al. (2024). Generative models improve fairness of medical classifiers under distribution shifts. Nat. Med. 30: 1166−1173. DOI: 10.1038/s41591-024-02838-6.

    View in Article CrossRef Google Scholar Scopus

    [51] Liang, W., Yao, J., Chen, A., et al. (2020). Early triage of critically ill COVID-19 patients using deep learning. Nat. Commun. 11: 3543. DOI: 10.1038/s41467-020-17280-8.

    View in Article CrossRef Google Scholar Scopus

    [52] Hoertel, N., Blachier, M., Blanco, C., et al. (2020). A stochastic agent-based model of the SARS-CoV-2 epidemic in France. Nat. Med. 26: 1417−1421. DOI: 10.1038/s41591-020-1001-6.

    View in Article CrossRef Google Scholar Scopus

    [53] Schwab, P., Mehrjou, A., Parbhoo, S., et al. (2021). Real-time prediction of COVID-19 related mortality using electronic health records. Nat. Commun. 12: 1058. DOI: 10.1038/s41467-020-20816-7.

    View in Article CrossRef Google Scholar Scopus

    [54] Gao, J., Heintz, J., Mack, C., et al. (2023). Evidence-driven spatiotemporal COVID-19 hospitalization prediction with Ising dynamics. Nat. Commun. 14: 3093. DOI: 10.1038/s41467-023-38756-3.

    View in Article CrossRef Google Scholar Scopus

    [55] Tomasev, N., Harris, N., Baur, S., et al. (2021). Use of deep learning to develop continuous-risk models for adverse event prediction from electronic health records. Nat. Protoc. 16: 2765−2787. DOI: 10.1038/s41596-021-00513-5.

    View in Article CrossRef Google Scholar Scopus

    [56] Gao, Y., Cai, G.Y., Fang, W., et al. (2020). Machine learning based early warning system enables accurate mortality risk prediction for COVID-19. Nat. Commun. 11: 5033. DOI: 10.1038/s41467-020-18684-2.

    View in Article CrossRef Google Scholar Scopus

    [57] Dayan, I., Roth, H.R., Zhong, A., et al. (2021). Federated learning for predicting clinical outcomes in patients with COVID-19. Nat. Med. 27: 1735−1743. DOI: 10.1038/s41591-021-01506-3.

    View in Article CrossRef Google Scholar Scopus

    [58] Lassau, N., Ammari, S., Chouzenoux, E., et al. (2021). Integrating deep learning CT-scan model, biological and clinical variables to predict severity of COVID-19 patients. Nat. Commun. 12: 634. DOI: 10.1038/s41467-020-20657-4.

    View in Article CrossRef Google Scholar Scopus

    [59] Yan, L., Zhang, H.-T., Goncalves, J., et al. (2020). An interpretable mortality prediction model for COVID-19 patients. Nat. Mach. Intell. 2: 283−288. DOI: 10.1038/s42256-020-0180-7.

    View in Article CrossRef Google Scholar Scopus

    [60] Devaux, Y., Zhang, L., Lumley, A.I., et al. (2024). Development of a long noncoding RNA-based machine learning model to predict COVID-19 in-hospital mortality. Nat. Commun. 15: 4259. DOI: 10.1038/s41467-024-47557-1.

    View in Article CrossRef Google Scholar Scopus

    [61] Lauritsen, S.M., Kristensen, M., Olsen, M.V., et al. (2020). Explainable artificial intelligence model to predict acute critical illness from electronic health records. Nat. Commun. 11: 3852. DOI: 10.1038/s41467-020-17431-x.

    View in Article CrossRef Google Scholar Scopus

    [62] Thompson, E.J., Williams, D.M., Walker, A.J., et al. (2022). Long COVID burden and risk factors in 10 UK longitudinal studies and electronic health records. Nat. Commun. 13: 3528. DOI: 10.1038/s41467-022-30836-0.

    View in Article CrossRef Google Scholar Scopus

    [63] Zang, C., Zhang, Y., Xu, J., et al. (2023). Data-driven analysis to understand long COVID using electronic health records from the RECOVER initiative. Nat. Commun. 14: 1948. DOI: 10.1038/s41467-023-37653-z.

    View in Article CrossRef Google Scholar Scopus

    [64] Zhang, H., Zang, C., Xu, Z., et al. (2023). Data-driven identification of post-acute SARS-CoV-2 infection subphenotypes. Nat. Med. 29: 226−235. DOI: 10.1038/s41591-022-02116-3.

    View in Article CrossRef Google Scholar Scopus

    [65] Ferretti, L., Wymant, C., Kendall, M., et al. (2020). Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing. Science 368: eabb6936. DOI: 10.1126/science.abb6936.

    View in Article CrossRef Google Scholar Scopus

    [66] Kucharski, A.J., Klepac, P., Conlan, A.J.K., et al. (2020). Effectiveness of isolation, testing, contact tracing, and physical distancing on reducing transmission of SARS-CoV-2 in different settings: A mathematical modelling study. Lancet Infect. Dis. 20: 1151−1160. DOI: 10.1016/S1473-3099(20)30457-6.

    View in Article CrossRef Google Scholar

    [67] Kendall, M., Tsallis, D., Wymant, C., et al. (2023). Epidemiological impacts of the NHS COVID-19 app in England and Wales throughout its first year. Nat. Commun. 14: 858. DOI: 10.1038/s41467-023-36495-z.

    View in Article CrossRef Google Scholar Scopus

    [68] Wymant, C., Ferretti, L., Tsallis, D., et al. (2021). The epidemiological impact of the NHS COVID-19 app. Nature 594: 408−412. DOI: 10.1038/s41586-021-03606-z.

    View in Article CrossRef Google Scholar Scopus

    [69] Ferretti, L., Wymant, C., Petrie, J., et al. (2024). Digital measurement of SARS-CoV-2 transmission risk from 7 million contacts. Nature 626: 145−150. DOI: 10.1038/s41586-023-06952-2.

    View in Article CrossRef Google Scholar Scopus

    [70] Kretzschmar, M.E., Rozhnova, G., Bootsma, M.C.J., et al. (2020). Impact of delays on effectiveness of contact tracing strategies for COVID-19: A modelling study. Lancet Public Health 5: e452−e459. DOI: 10.1016/S2468-2667(20)30157-2.

    View in Article CrossRef Google Scholar

    [71] Colizza, V., Grill, E., Mikolajczyk, R., et al. (2021). Time to evaluate COVID-19 contact-tracing apps. Nat. Med. 27: 361−362. DOI: 10.1038/s41591-021-01236-6.

    View in Article CrossRef Google Scholar Scopus

    [72] Pandit, J.A., Radin, J.M., Quer, G., et al. (2022). Smartphone apps in the COVID-19 pandemic. Nat. Biotechnol. 40: 1013−1022. DOI: 10.1038/s41587-022-01350-x.

    View in Article CrossRef Google Scholar Scopus

    [73] Flaxman, S., Mishra, S., Gandy, A., et al. (2020). Estimating the effects of non-pharmaceutical interventions on COVID-19 in Europe. Nature 584: 257−261. DOI: 10.1038/s41586-020-2405-7.

    View in Article CrossRef Google Scholar Scopus

    [74] Kraemer, M.U.G., Yang, C.-H., Gutierrez, B., et al. (2020). The effect of human mobility and control measures on the COVID-19 epidemic in China. Science 368: 493−497. DOI: 10.1126/science.abb4218.

    View in Article CrossRef Google Scholar Scopus

    [75] Candido, D.S., Claro, I.M., de Jesus, J.G., et al. (2020). Evolution and epidemic spread of SARS-CoV-2 in Brazil. Science 369: 1255−1260. DOI: 10.1126/science.abd2161.

    View in Article CrossRef Google Scholar Scopus

    [76] Haug, N., Geyrhofer, L., Londei, A., et al. (2020). Ranking the effectiveness of worldwide COVID-19 government interventions. Nat. Hum. Behav. 4: 1303−1312. DOI: 10.1038/s41562-020-01009-0.

    View in Article CrossRef Google Scholar Scopus

    [77] Ge, Y., Wu, X., Zhang, W., et al. (2023). Effects of public-health measures for zeroing out different SARS-CoV-2 variants. Nat. Commun. 14: 5270. DOI: 10.1038/s41467-023-40940-4.

    View in Article CrossRef Google Scholar Scopus

    [78] Li, Y., Campbell, H., Kulkarni, D., et al. (2021). The temporal association of introducing and lifting non-pharmaceutical interventions with the time-varying reproduction number (R) of SARS-CoV-2: A modelling study across 131 countries. Lancet Infect. Dis. 21: 193−202. DOI: 10.1016/S1473-3099(20)30785-4.

    View in Article CrossRef Google Scholar

    [79] Zhang, H., Zhang, L., Lin, A., et al. (2023). Algorithm for optimized mRNA design improves stability and immunogenicity. Nature 621: 396−403. DOI: 10.1038/s41586-023-06127-z.

    View in Article CrossRef Google Scholar Scopus

    [80] Abramson, J., Adler, J., Dunger, J., et al. (2024). Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630: 493−500. DOI: 10.1038/s41586-024-07487-w.

    View in Article CrossRef Google Scholar Scopus

    [81] Lutz, I.D., Wang, S., Norn, C., et al. (2023). Top-down design of protein architectures with reinforcement learning. Science 380: 266−273. DOI: 10.1126/science.adf6591.

    View in Article CrossRef Google Scholar Scopus

    [82] Loomba, S., de Figueiredo, A., Piatek, S.J., et al. (2021). Measuring the impact of COVID-19 vaccine misinformation on vaccination intent in the UK and USA. Nat. Hum. Behav. 5: 337−348. DOI: 10.1038/s41562-021-01056-1.

    View in Article CrossRef Google Scholar Scopus

    [83] Band, G., Le, Q.S., Clarke, G.M., et al. (2019). Insights into malaria susceptibility using genome-wide data on 17,000 individuals from Africa, Asia and Oceania. Nat. Commun. 10: 5732. DOI: 10.1038/s41467-019-13480-z.

    View in Article CrossRef Google Scholar Scopus

    [84] Sveinbjornsson, G., Gudbjartsson, D.F., Halldorsson, B.V., et al. (2016). HLA class II sequence variants influence tuberculosis risk in populations of European ancestry. Nat. Genet. 48: 318−322. DOI: 10.1038/ng.3498.

    View in Article CrossRef Google Scholar Scopus

    [85] Zheng, R., Li, Z., He, F., et al. (2018). Genome-wide association study identifies two risk loci for tuberculosis in Han Chinese. Nat. Commun. 9: 4072. DOI: 10.1038/s41467-018-06539-w.

    View in Article CrossRef Google Scholar Scopus

    [86] The International HIV Controllers Study. (2010). The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science 330: 1551−1557. DOI: 10.1126/science.1195271.

    View in Article CrossRef Google Scholar Scopus

    [87] Niemi, M.E.K., Karjalainen, J., Liao, R.G., et al. (2021). Mapping the human genetic architecture of COVID-19. Nature 600: 472−477. DOI: 10.1038/s41586-021-03767-x.

    View in Article CrossRef Google Scholar Scopus

    [88] Horowitz, J.E., Kosmicki, J.A., Damask, A., et al. (2022). Genome-wide analysis provides genetic evidence that ACE2 influences COVID-19 risk and yields risk scores associated with severe disease. Nat. Genet. 54: 382−392. DOI: 10.1038/s41588-021-01006-7.

    View in Article CrossRef Google Scholar Scopus

    [89] Zhang, Q., Bastard, P., Liu, Z., et al. (2020). Inborn errors of type I IFN immunity in patients with life-threatening COVID-19. Science 370: eabd4570. DOI: 10.1126/science.abd4570.

    View in Article CrossRef Google Scholar Scopus

    [90] Ge, T., Chen, C.Y., Ni, Y., et al. (2019). Polygenic prediction via Bayesian regression and continuous shrinkage priors. Nat. Commun. 10: 1776. DOI: 10.1038/s41467-019-09718-5.

    View in Article CrossRef Google Scholar Scopus

    [91] Fiziev, P.P., McRae, J., Ulirsch, J.C., et al. (2023). Rare penetrant mutations confer severe risk of common diseases. Science 380: eabo1131. DOI: 10.1126/science.abo1131.

    View in Article CrossRef Google Scholar Scopus

    [92] Frazer, J., Notin, P., Dias, M., et al. (2021). Disease variant prediction with deep generative models of evolutionary data. Nature 599: 91−95. DOI: 10.1038/s41586-021-04043-8.

    View in Article CrossRef Google Scholar Scopus

    [93] Zanini, F., Robinson, M.L., Croote, D., et al. (2018). Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue. Proc. Natl. Acad. Sci. U. S. A. 115: E12363−E12369. DOI: 10.1073/pnas.1813819115.

    View in Article CrossRef Google Scholar Scopus

    [94] Kotliar, D., Lin, A.E., Logue, J., et al. (2020). Single-cell profiling of ebola virus disease in vivo reveals viral and host dynamics. Cell 183: 1383−1401. DOI: 10.1016/j.cell.2020.10.002.

    View in Article CrossRef Google Scholar

    [95] Bost, P., Giladi, A., Liu, Y., et al. (2020). Host-viral infection maps reveal signatures of severe COVID-19 patients. Cell 181: 1475−1488. DOI: 10.1016/j.cell.2020.05.006.

    View in Article CrossRef Google Scholar

    [96] Aquino, Y., Bisiaux, A., Li, Z., et al. (2023). Dissecting human population variation in single-cell responses to SARS-CoV-2. Nature 621: 120−128. DOI: 10.1038/s41586-023-06422-9.

    View in Article CrossRef Google Scholar Scopus

    [97] Ren, X., Wen, W., Fan, X., et al. (2021). COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas. Cell 184: 1895−1913. DOI: 10.1016/j.cell.2021.01.053.

    View in Article CrossRef Google Scholar Scopus

    [98] Stephenson, E., Reynolds, G., Botting, R.A., et al. (2021). Single-cell multi-omics analysis of the immune response in COVID-19. Nat. Med. 27: 904−916. DOI: 10.1038/s41591-021-01329-2.

    View in Article CrossRef Google Scholar Scopus

    [99] Wang, J., Ma, A., Chang, Y., et al. (2021). scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses. Nat. Commun. 12: 1882. DOI: 10.1038/s41467-021-22197-x.

    View in Article CrossRef Google Scholar Scopus

    [100] Amodio, M., van Dijk, D., Srinivasan, K., et al. (2019). Exploring single-cell data with deep multitasking neural networks. Nat. Methods 16: 1139−1145. DOI: 10.1038/s41592-019-0576-7.

    View in Article CrossRef Google Scholar Scopus

    [101] Xiong, L., Tian, K., Li, Y., et al. (2022). Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space. Nat. Commun. 13: 6118. DOI: 10.1038/s41467-022-33758-z.

    View in Article CrossRef Google Scholar Scopus

    [102] Zhao, Y., Cai, H., Zhang, Z., et al. (2021). Learning interpretable cellular and gene signature embeddings from single-cell transcriptomic data. Nat. Commun. 12: 5261. DOI: 10.1038/s41467-021-25534-2.

    View in Article CrossRef Google Scholar Scopus

    [103] Moller, A.F. and Madsen, J.G.S. (2023). JOINTLY: Interpretable joint clustering of single-cell transcriptomes. Nat. Commun. 14: 8473. DOI: 10.1038/s41467-023-44279-8.

    View in Article CrossRef Google Scholar

    [104] Boby, M.L., Fearon, D., Ferla, M., et al. (2023). Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors. Science 382: eabo7201. DOI. DOI: 10.1126/science.abo7201.

    View in Article CrossRef Google Scholar Scopus

    [105] Singhal, K., Azizi, S., Tu, T., et al. (2023). Large language models encode clinical knowledge. Nature 620: 172−180. DOI: 10.1038/s41586-023-06291-2.

    View in Article CrossRef Google Scholar Scopus

    [106] Van Veen, D., Van Uden, C., Blankemeier, L., et al. (2024). Adapted large language models can outperform medical experts in clinical text summarization. Nat. Med. 30: 1134−1142. DOI: 10.1038/s41591-024-02855-5.

    View in Article CrossRef Google Scholar Scopus

    [107] Han, T., Adams, L.C., Bressem, K.K., et al. (2024). Comparative analysis of multimodal large language model performance on clinical vignette questions. JAMA 331: 1320−1321. DOI: 10.1001/jama.2023.27861.

    View in Article CrossRef Google Scholar

    [108] Pais, C., Liu, J., Voigt, R., et al. (2024). Large language models for preventing medication direction errors in online pharmacies. Nat. Med. 30: 1574−1582. DOI: 10.1038/s41591-024-02933-8.

    View in Article CrossRef Google Scholar Scopus

    [109] Tayebi Arasteh, S., Han, T., Lotfinia, M., et al. (2024). Large language models streamline automated machine learning for clinical studies. Nat. Commun. 15: 1603. DOI: 10.1038/s41467-024-45879-8.

    View in Article CrossRef Google Scholar Scopus

    [110] Lu, M.Y., Chen, B., Williamson, D.F.K., et al. (2024). A multimodal generative AI copilot for human pathology. Nature. DOI: 10.1038/s41586-024-07618-3.

    View in Article Google Scholar

    [111] Boiko, D.A., MacKnight, R., Kline, B., et al. (2023). Autonomous chemical research with large language models. Nature 624: 570−578. DOI: 10.1038/s41586-023-06792-0.

    View in Article CrossRef Google Scholar Scopus

    [112] Cui, H., Wang, C., Maan, H., et al. (2024). scGPT: Toward building a foundation model for single-cell multi-omics using generative AI. Nat. Methods DOI: 10.1038/s41592-024-02201-0.

    View in Article Google Scholar

  • Cite this article:

    Zhou H., Li Y., Li J., et al., (2024). Harnessing the power of artificial intelligence to combat infectious diseases: Progress, challenges, and future outlook. The Innovation Medicine 2(4): 100091. https://doi.org/10.59717/j.xinn-med.2024.100091
    Zhou H., Li Y., Li J., et al., (2024). Harnessing the power of artificial intelligence to combat infectious diseases: Progress, challenges, and future outlook. The Innovation Medicine 2(4): 100091. https://doi.org/10.59717/j.xinn-med.2024.100091

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