1932

Abstract

Despite the remarkable advances in cancer diagnosis, treatment, and management over the past decade, malignant tumors remain a major public health problem. Further progress in combating cancer may be enabled by personalizing the delivery of therapies according to the predicted response for each individual patient. The design of personalized therapies requires the integration of patient-specific information with an appropriate mathematical model of tumor response. A fundamental barrier to realizing this paradigm is the current lack of a rigorous yet practical mathematical theory of tumor initiation, development, invasion, and response to therapy. We begin this review with an overview of different approaches to modeling tumor growth and treatment, including mechanistic as well as data-driven models based on big data and artificial intelligence. We then present illustrative examples of mathematical models manifesting their utility and discuss the limitations of stand-alone mechanistic and data-driven models. We then discuss the potential of mechanistic models for not only predicting but also optimizing response to therapy on a patient-specific basis. We describe current efforts and future possibilities to integrate mechanistic and data-driven models. We conclude by proposing five fundamental challenges that must be addressed to fully realize personalized care for cancer patients driven by computational models.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-bioeng-081623-025834
2024-07-03
2024-07-04
Loading full text...

Full text loading...

/deliver/fulltext/bioeng/26/1/annurev-bioeng-081623-025834.html?itemId=/content/journals/10.1146/annurev-bioeng-081623-025834&mimeType=html&fmt=ahah

Literature Cited

  1. 1.
    Siegel RL, Miller KD, Wagle NS, Jemal A. 2023.. Cancer statistics, 2023. . CA Cancer J. Clin. 73:(1):1748
    [Crossref] [Google Scholar]
  2. 2.
    Yankeelov TE, Quaranta V, Evans KJ, Rericha EC. 2015.. Toward a science of tumor forecasting for clinical oncology. . Cancer Res. 75:(6):91823
    [Crossref] [Google Scholar]
  3. 3.
    Yankeelov TE, An G, Saut O, Luebeck EG, Popel AS, et al. 2016.. Multi-scale modeling in clinical oncology: opportunities and barriers to success. . Ann. Biomed. Eng. 44::262641
    [Crossref] [Google Scholar]
  4. 4.
    Bull JA, Byrne HM. 2022.. The hallmarks of mathematical oncology. . Proc. IEEE 110:(5):52340
    [Crossref] [Google Scholar]
  5. 5.
    Deisboeck TS, Wang Z, Macklin P, Cristini V. 2011.. Multiscale cancer modeling. . Annu. Rev. Biomed. Eng. 13::12755
    [Crossref] [Google Scholar]
  6. 6.
    Anderson ARA, Maini PK. 2018.. Mathematical oncology. . Bull. Math. Biol. 80:(5):94553
    [Crossref] [Google Scholar]
  7. 7.
    Rockne RC, Hawkins-Daarud A, Swanson KR, Sluka JP, Glazier JA, et al. 2019.. The 2019 mathematical oncology roadmap. . Phys. Biol. 16::041005
    [Crossref] [Google Scholar]
  8. 8.
    Kazerouni AS, Gadde M, Gardner A, Hormuth DA II, Jarrett AM, et al. 2020.. Integrating quantitative assays with biologically based mathematical modeling for predictive oncology. . iScience 23:(12):101807
    [Crossref] [Google Scholar]
  9. 9.
    Baldock A, Rockne R, Boone A, Neal M, Bridge C, et al. 2013.. From patient-specific mathematical neuro-oncology to precision medicine. . Front. Oncol. 3::62
    [Crossref] [Google Scholar]
  10. 10.
    Hormuth DA II, Farhat M, Christenson C, Curl B, Chad Quarles C, et al. 2022.. Opportunities for improving brain cancer treatment outcomes through imaging-based mathematical modeling of the delivery of radiotherapy and immunotherapy. . Adv. Drug Deliv. Rev. 187::114367
    [Crossref] [Google Scholar]
  11. 11.
    Enderling H, Alfonso JCL, Moros E, Caudell JJ, Harrison LB. 2019.. Integrating mathematical modeling into the roadmap for personalized adaptive radiation therapy. . Trends Cancer 5:(8):46774
    [Crossref] [Google Scholar]
  12. 12.
    Jarrett AM, Kazerouni AS, Wu C, Virostko J, Sorace AG, et al. 2021.. Quantitative magnetic resonance imaging and tumor forecasting of breast cancer patients in the community setting. . Nat. Protoc. 16:(11):530938
    [Crossref] [Google Scholar]
  13. 13.
    Ocaña-Tienda B, Pérez-Beteta J, Molina-García D, Asenjo B, Ortiz de Mendivil A, et al. 2022.. Growth dynamics of brain metastases differentiate radiation necrosis from recurrence. . Neuro-Oncol. Adv. 5:(1):vdac179
    [Crossref] [Google Scholar]
  14. 14.
    Shreve JT, Khanani SA, Haddad TC. 2022.. Artificial intelligence in oncology: current capabilities, future opportunities, and ethical considerations. . Am. Soc. Clin. Oncol. Educ. Book 42::84251
    [Crossref] [Google Scholar]
  15. 15.
    Baker N, Alexander F, Bremer T, Hagberg A, Kevrekidis Y, et al. 2019.. Workshop report on basic research needs for scientific machine learning: core technologies for artificial intelligence. . Tech. Rep., Off. Sci., US Dep. Energy, Washington, DC:
    [Google Scholar]
  16. 16.
    Oliveira SP, Neto PC, Fraga J, Montezuma D, Monteiro A, et al. 2021.. CAD systems for colorectal cancer from WSI are still not ready for clinical acceptance. . Sci. Rep. 11::14358
    [Crossref] [Google Scholar]
  17. 17.
    Jothi JAA, Rajam VMA. 2017.. A survey on automated cancer diagnosis from histopathology images. . Artif. Intell. Rev. 48::3182
    [Crossref] [Google Scholar]
  18. 18.
    Marini N, Marchesin S, Otalora S, Wodzinski M, Caputo A, et al. 2022.. Unleashing the potential of digital pathology data by training computer-aided diagnosis models without human annotations. . npj Digit. Med. 5::102
    [Crossref] [Google Scholar]
  19. 19.
    Khened M, Kori A, Rajkumar H, Krishnamurthi G, Srinivasan B. 2021.. A generalized deep learning framework for whole-slide image segmentation and analysis. . Sci. Rep. 11::11579
    [Crossref] [Google Scholar]
  20. 20.
    Perincheri S, Levi AW, Celli R, Gershkovich P, Rimm D, et al. 2021.. An independent assessment of an artificial intelligence system for prostate cancer detection shows strong diagnostic accuracy. . Mod. Pathol. 34:(8):158895
    [Crossref] [Google Scholar]
  21. 21.
    Lewis PD, Lewis KE, Ghosal R, Bayliss S, Lloyd AJ, et al. 2010.. Evaluation of FTIR spectroscopy as a diagnostic tool for lung cancer using sputum. . BMC Cancer 10::640
    [Crossref] [Google Scholar]
  22. 22.
    Fujioka N, Morimoto Y, Arai T, Kikuchi M. 2004.. Discrimination between normal and malignant human gastric tissues by Fourier transform infrared spectroscopy. . Cancer Detect. Prev. 28:(1):3236
    [Crossref] [Google Scholar]
  23. 23.
    Lorenzo G, Hormuth DA II, Jarrett AM, Lima EA, Subramanian S, et al. 2022.. Quantitative in vivo imaging to enable tumor forecasting and treatment optimization. . In Cancer, Complexity, Computation, ed. I Balaz, A Adamatzky , pp. 5597. Berlin:: Springer
    [Google Scholar]
  24. 24.
    Hormuth DA II, Sorace AG, Virostko J, Abramson RG, Bhujwalla ZM, et al. 2019.. Translating preclinical MRI methods to clinical oncology. . J. Magn. Reson. Imaging 50:(5):137792
    [Crossref] [Google Scholar]
  25. 25.
    Jin C, Luo X, Li X, Zhou R, Zhong Y, et al. 2022.. Positron emission tomography molecular imaging–based cancer phenotyping. . Cancer 128:(14):270416
    [Crossref] [Google Scholar]
  26. 26.
    Eisenhauer EA, Therasse P, Bogaerts J, Schwartz LH, Sargent D, et al. 2009.. New response evaluation criteria in solid tumours: revised RECIST guideline (version 1.1). . Eur. J. Cancer 45:(2):22847
    [Crossref] [Google Scholar]
  27. 27.
    Wen PY, Macdonald DR, Reardon DA, Cloughesy TF, Sorensen AG, et al. 2010.. Updated response assessment criteria for high-grade gliomas: Response Assessment in Neuro-Oncology Working Group. . J. Clin. Oncol. 28:(11):196372
    [Crossref] [Google Scholar]
  28. 28.
    Padhani AR, Liu G, Mu-Koh D, Chenevert TL, Thoeny HC, et al. 2009.. Diffusion-weighted magnetic resonance imaging as a cancer biomarker: consensus and recommendations. . Neoplasia 11:(2):10225
    [Crossref] [Google Scholar]
  29. 29.
    O'Connor JPB, Tofts PS, Miles KA, Parkes LM, Thompson G, Jackson A. 2011.. Dynamic contrast-enhanced imaging techniques: CT and MRI. . Br. J. Radiol. 84:(Spec. Issue 2):S11220
    [Crossref] [Google Scholar]
  30. 30.
    Quarles CC, Bell LC, Stokes AM. 2019.. Imaging vascular and hemodynamic features of the brain using dynamic susceptibility contrast and dynamic contrast enhanced MRI. . NeuroImage 187::3255
    [Crossref] [Google Scholar]
  31. 31.
    Rajendran JG. 2004.. Hypoxia and glucose metabolism in malignant tumors: Evaluation by [18F]fluoromisonidazole and [18F]fluorodeoxyglucose positron emission tomography imaging. . Clin. Cancer Res. 10:(7):224552
    [Crossref] [Google Scholar]
  32. 32.
    Castell F, Cook GJR. 2008.. Quantitative techniques in 18FDG PET scanning in oncology. . Br. J. Cancer 98:(10):1597601
    [Crossref] [Google Scholar]
  33. 33.
    Vaupel P, Thews O, Hoeckel M. 2001.. Treatment resistance of solid tumors. . Med. Oncol. 18:(4):24359
    [Crossref] [Google Scholar]
  34. 34.
    Jolly C, Van Loo P. 2018.. Timing somatic events in the evolution of cancer. . Genome Biol. 19::95
    [Crossref] [Google Scholar]
  35. 35.
    Wu F, Fan J, He Y, Xiong A, Yu J, et al. 2021.. Single-cell profiling of tumor heterogeneity and the microenvironment in advanced non–small cell lung cancer. . Nat. Commun. 12::2540
    [Crossref] [Google Scholar]
  36. 36.
    Saadatpour A, Lai S, Guo G, Yuan GC. 2015.. Single-cell analysis in cancer genomics. . Trends Genet. 31:(10):57686
    [Crossref] [Google Scholar]
  37. 37.
    Haque A, Engel J, Teichmann SA, Lonnberg T. 2017.. A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications. . Genome Med. 9::75
    [Crossref] [Google Scholar]
  38. 38.
    Ogbeide S, Giannese F, Mincarelli L, Macaulay IC. 2022.. Into the multiverse: advances in single-cell multiomic profiling. . Trends Genet. 38:(8):83143
    [Crossref] [Google Scholar]
  39. 39.
    Howland KK, Brock A. 2023.. Cellular barcoding tracks heterogeneous clones through selective pressures and phenotypic transitions. . Trends Cancer 9:(7):591601
    [Crossref] [Google Scholar]
  40. 40.
    Vistain LF, Tay S. 2021.. Single-cell proteomics. . Trends Biochem. Sci. 46:(8):66172
    [Crossref] [Google Scholar]
  41. 41.
    Box GEP. 1979.. Robustness in the strategy of scientific model building. . In Robustness in Statistics, ed. RL Launer, GN Wilkinson , pp. 20136. Amsterdam:: Elsevier
    [Google Scholar]
  42. 42.
    Neyman J. 1939.. On a new class of ``contagious'' distributions, applicable in entomology and bacteriology. . Ann. Math. Stat. 10:(1):3557
    [Crossref] [Google Scholar]
  43. 43.
    Lone SN, Nisar S, Masoodi T, Singh M, Rizwan A, et al. 2022.. Liquid biopsy: a step closer to transform diagnosis, prognosis and future of cancer treatments. . Mol. Cancer 21::79
    [Crossref] [Google Scholar]
  44. 44.
    Baxi V, Edwards R, Montalto M, Saha S. 2022.. Digital pathology and artificial intelligence in translational medicine and clinical practice. . Mod. Pathol. 35:(1):2332
    [Crossref] [Google Scholar]
  45. 45.
    Vandenberghe ME, Scott ML, Scorer PW, Söderberg M, Balcerzak D, Barker C. 2017.. Relevance of deep learning to facilitate the diagnosis of HER2 status in breast cancer. . Sci. Rep. 7::45938
    [Crossref] [Google Scholar]
  46. 46.
    Raciti P, Sue J, Retamero JA, Ceballos R, Godrich R, et al. 2023.. Clinical validation of artificial intelligence–augmented pathology diagnosis demonstrates significant gains in diagnostic accuracy in prostate cancer detection. . Arch. Pathol. Lab. Med. 147:(10):117885
    [Crossref] [Google Scholar]
  47. 47.
    Menze BH, Jakab A, Bauer S, Kalpathy-Cramer J, Farahani K, et al. 2014.. The Multimodal Brain Tumor Image Segmentation benchmark (BraTS). . IEEE Trans. Med. Imaging 34:(10):19932024
    [Crossref] [Google Scholar]
  48. 48.
    Baid U, Ghodasara S, Mohan S, Bilello M, Calabrese E, et al. 2021.. The RSNA-ASNR-MICCAI BraTS 2021 benchmark on brain tumor segmentation and radiogenomic classification. . arXiv:2107.02314 [cs.CV]
  49. 49.
    Bakas S, Akbari H, Sotiras A, Bilello M, Rozycki M, et al. 2017.. Advancing The Cancer Genome Atlas glioma MRI collections with expert segmentation labels and radiomic features. . Sci. Data 4::170117
    [Crossref] [Google Scholar]
  50. 50.
    Bakas S, Akbari H, Sotiras A, Bilello M, Rozycki M, et al. 2017.. Segmentation labels for the pre-operative scans of the TCGA-GBM collection. . Tech. Rep., Cancer Imaging Arch . https://doi.org/10.7937/K9/TCIA.2017.KLXWJJ1Q
    [Google Scholar]
  51. 51.
    Ronneberger O, Fischer P, Brox T. 2015.. U-Net: convolutional networks for biomedical image segmentation. . In Medical Image Computing and Computer-Assisted Intervention—MICCAI 2015: 18th International Conference, pp. 23441. Berlin:: Springer
    [Google Scholar]
  52. 52.
    Isensee F, Jaeger PF, Kohl SA, Petersen J, Maier-Hein KH. 2021.. nnU-Net: a self-configuring method for deep learning–based biomedical image segmentation. . Nat. Methods 18:(2):20311
    [Crossref] [Google Scholar]
  53. 53.
    Wagner MW, Namdar K, Biswas A, Monah S, Khalvati F, Ertl-Wagner BB. 2021.. Radiomics, machine learning, and artificial intelligence—what the neuroradiologist needs to know. . Neuroradiology 63:(12):195767
    [Crossref] [Google Scholar]
  54. 54.
    Zhu B, Liu JZ, Cauley SF, Rosen BR, Rosen MS. 2018.. Image reconstruction by domain-transform manifold learning. . Nature 555:(7697):48792
    [Crossref] [Google Scholar]
  55. 55.
    Fu Y, Lei Y, Wang T, Curran WJ, Liu T, Yang X. 2020.. Deep learning in medical image registration: a review. . Phys. Med. Biol. 65::20TR01
    [Crossref] [Google Scholar]
  56. 56.
    Chang K, Beers AL, Bai HX, Brown JM, Ly KI, et al. 2019.. Automatic assessment of glioma burden: a deep learning algorithm for fully automated volumetric and bidimensional measurement. . Neuro-Oncology 21:(11):141222
    [Crossref] [Google Scholar]
  57. 57.
    Baid U, Rane SU, Talbar S, Gupta S, Thakur MH, et al. 2020.. Overall survival prediction in glioblastoma with radiomic features using machine learning. . Front. Comput. Neurosci. 14::61
    [Crossref] [Google Scholar]
  58. 58.
    Han W, Qin L, Bay C, Chen X, Yu KH, et al. 2020.. Deep transfer learning and radiomics feature prediction of survival of patients with high-grade gliomas. . Am. J. Neuroradiol. 41:(1):4048
    [Crossref] [Google Scholar]
  59. 59.
    Peng J, Kim DD, Patel JB, Zeng X, Huang J, et al. 2022.. Deep learning–based automatic tumor burden assessment of pediatric high-grade gliomas, medulloblastomas, and other leptomeningeal seeding tumors. . Neuro-Oncology 24:(2):28999
    [Crossref] [Google Scholar]
  60. 60.
    Chang K, Bai HX, Zhou H, Su C, Bi WL, et al. 2018.. Residual convolutional neural network for the determination of IDH status in low- and high-grade gliomas from MR imaging. . Clin. Cancer Res. 24:(5):107381
    [Crossref] [Google Scholar]
  61. 61.
    Coudray N, Ocampo PS, Sakellaropoulos T, Narula N, Snuderl M, et al. 2018.. Classification and mutation prediction from non–small cell lung cancer histopathology images using deep learning. . Nat. Med. 24:(10):155967
    [Crossref] [Google Scholar]
  62. 62.
    Patel J, Chang K, Ahmed SR, Jang I, Kalpathy-Cramer J. 2021.. Opportunities and challenges for deep learning in brain lesions. . In Proceedings of the International MICCAI Brain Lesion Workshop, pp. 2536. Berlin:: Springer
    [Google Scholar]
  63. 63.
    Gregor K, Danihelka I, Graves A, Rezende D, Wierstra D. 2015.. DRAW: a recurrent neural network for image generation. . Proc. Mach. Learn. Res. 37::146271
    [Google Scholar]
  64. 64.
    Donahue J, Hendricks LA, Guadarrama S, Rohrbach M, Venugopalan S, et al. 2015.. Long-term recurrent convolutional networks for visual recognition and description. . In Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, pp. 262534. Piscataway, NJ:: IEEE
    [Google Scholar]
  65. 65.
    Xu Y, Hosny A, Zeleznik R, Parmar C, Coroller T, et al. 2019.. Deep learning predicts lung cancer treatment response from serial medical imaging. . Clin. Cancer Res. 25:(11):326675
    [Crossref] [Google Scholar]
  66. 66.
    Bansal N, Agarwal C, Nguyen A. 2020.. SAM: the sensitivity of attribution methods to hyperparameters. . In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, pp. 867383. Piscataway, NJ:: IEEE
    [Google Scholar]
  67. 67.
    Alcorn MA, Li Q, Gong Z, Wang C, Mai L, et al. 2019.. Strike (with) a pose: Neural networks are easily fooled by strange poses of familiar objects. . In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, pp. 484554. Piscataway, NJ:: IEEE
    [Google Scholar]
  68. 68.
    Eykholt K, Evtimov I, Fernandes E, Li B, Rahmati A, et al. 2018.. Robust physical-world attacks on deep learning visual classification. . In Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, pp. 162534. Piscataway, NJ:: IEEE
    [Google Scholar]
  69. 69.
    Linardatos P, Papastefanopoulos V, Kotsiantis S. 2020.. Explainable AI: a review of machine learning interpretability methods. . Entropy 23:(1):18
    [Crossref] [Google Scholar]
  70. 70.
    Vinuesa R, Sirmacek B. 2021.. Interpretable deep-learning models to help achieve the sustainable development goals. . Nat. Mach. Intell. 3:(11):92626
    [Crossref] [Google Scholar]
  71. 71.
    Metzcar J, Wang Y, Heiland R, Macklin P. 2019.. A review of cell-based computational modeling in cancer biology. . JCO Clin. Cancer Inform. 2:(3):113
    [Crossref] [Google Scholar]
  72. 72.
    Lima EA, Wyde RA, Sorace AG, Yankeelov TE. 2022.. Optimizing combination therapy in a murine model of HER2 breast cancer. . Comput. Methods Appl. Mech. Eng. 402::115484
    [Crossref] [Google Scholar]
  73. 73.
    Zahid MU, Mohsin N, Mohamed AS, Caudell JJ, Harrison LB, et al. 2021.. Forecasting individual patient response to radiation therapy in head and neck cancer with a dynamic carrying capacity model. . Int. J. Radiat. Oncol. Biol. Phys. 111:(3):693704
    [Crossref] [Google Scholar]
  74. 74.
    Slavkova KP, Patel SH, Cacini Z, Kazerouni AS, Gardner AL, et al. 2023.. Mathematical modelling of the dynamics of image-informed tumor habitats in a murine model of glioma. . Sci. Rep. 13::2916
    [Crossref] [Google Scholar]
  75. 75.
    Yang EY, Howard GR, Brock A, Yankeelov TE, Lorenzo G. 2022.. Mathematical characterization of population dynamics in breast cancer cells treated with doxorubicin. . Front. Mol. Biosci. 9::972146
    [Crossref] [Google Scholar]
  76. 76.
    Brady-Nicholls R, Nagy JD, Gerke TA, Zhang T, Wang AZ, et al. 2020.. Prostate-specific antigen dynamics predict individual responses to intermittent androgen deprivation. . Nat. Commun. 11::1750
    [Crossref] [Google Scholar]
  77. 77.
    Strobl MA, West J, Viossat Y, Damaghi M, Robertson-Tessi M, et al. 2021.. Turnover modulates the need for a cost of resistance in adaptive therapy. . Cancer Res. 81:(4):113547
    [Crossref] [Google Scholar]
  78. 78.
    Lorenzo G, di Muzio N, Deantoni CL, Cozzarini C, Fodor A, et al. 2022.. Patient-specific forecasting of postradiotherapy prostate-specific antigen kinetics enables early prediction of biochemical relapse. . iScience 25:(11):105430
    [Crossref] [Google Scholar]
  79. 79.
    Benzekry S, Lamont C, Beheshti A, Tracz A, Ebos JML, et al. 2014.. Classical mathematical models for description and prediction of experimental tumor growth. . PLOS Comput. Biol. 10:(8):e1003800
    [Crossref] [Google Scholar]
  80. 80.
    Yin A, Moes DJA, van Hasselt JG, Swen JJ, Guchelaar HJ. 2019.. A review of mathematical models for tumor dynamics and treatment resistance evolution of solid tumors. . CPT Pharmacometr. Syst. Pharmacol. 8:(10):72037
    [Crossref] [Google Scholar]
  81. 81.
    Wu C, Jarrett AM, Zhou Z, Elshafeey N, Adrada BE, et al. 2022.. MRI-based digital models forecast patient-specific treatment responses to neoadjuvant chemotherapy in triple-negative breast cancer. . Cancer Res. 82:(18):3394404
    [Crossref] [Google Scholar]
  82. 82.
    Hormuth DA II, Al Feghali KA, Elliott AM, Yankeelov TE, Chung C. 2021.. Image-based personalization of computational models for predicting response of high-grade glioma to chemoradiation. . Sci. Rep. 11::8520
    [Crossref] [Google Scholar]
  83. 83.
    Lipková J, Angelikopoulos P, Wu S, Alberts E, Wiestler B, et al. 2019.. Personalized radiotherapy design for glioblastoma: integrating mathematical tumor models, multimodal scans, and Bayesian inference. . IEEE Trans. Med. Imaging 38:(8):187584
    [Crossref] [Google Scholar]
  84. 84.
    Corwin D, Holdsworth C, Rockne RC, Trister AD, Mrugala MM, et al. 2013.. Toward patient-specific, biologically optimized radiation therapy plans for the treatment of glioblastoma. . PLOS ONE 8:(11):e79115
    [Crossref] [Google Scholar]
  85. 85.
    Wong KCL, Summers RM, Kebebew E, Yao J. 2017.. Pancreatic tumor growth prediction with elastic-growth decomposition, image-derived motion, and FDM-FEM coupling. . IEEE Trans. Med. Imaging 36:(1):11123
    [Crossref] [Google Scholar]
  86. 86.
    Angeli S, Emblem KE, Due-Tonnessen P, Stylianopoulos T. 2018.. Towards patient-specific modeling of brain tumor growth and formation of secondary nodes guided by DTI-MRI. . NeuroImage 20::66473
    [Crossref] [Google Scholar]
  87. 87.
    Urcun S, Rohan PY, Skalli W, Nassoy P, Bordas SPA, Sciumè G. 2021.. Digital twinning of cellular capsule technology: emerging outcomes from the perspective of porous media mechanics. . PLOS ONE 16:(7):e0254512
    [Crossref] [Google Scholar]
  88. 88.
    Kremheller J, Vuong AT, Schrefler BA, Wall WA. 2019.. An approach for vascular tumor growth based on a hybrid embedded/homogenized treatment of the vasculature within a multiphase porous medium model. . Int. J. Numer. Methods Biomed. Eng. 35:(11):e3253
    [Crossref] [Google Scholar]
  89. 89.
    Lima E, Oden J, Wohlmuth B, Shahmoradi A, Hormuth DA II, et al. 2017.. Selection and validation of predictive models of radiation effects on tumor growth based on noninvasive imaging data. . Comput. Methods Appl. Mech. Eng. 327::277305
    [Crossref] [Google Scholar]
  90. 90.
    Lorenzo G, Hughes TJR, Dominguez-Frojan P, Reali A, Gomez H. 2019.. Computer simulations suggest that prostate enlargement due to benign prostatic hyperplasia mechanically impedes prostate cancer growth. . PNAS 116:(4):115261
    [Crossref] [Google Scholar]
  91. 91.
    Colli P, Gomez H, Lorenzo G, Marinoschi G, Reali A, Rocca E. 2021.. Optimal control of cytotoxic and antiangiogenic therapies on prostate cancer growth. . Math. Models Methods Appl. Sci. 31:(7):141968
    [Crossref] [Google Scholar]
  92. 92.
    Fritz M, Jha PK, Köppl T, Oden JT, Wohlmuth B. 2021.. Analysis of a new multispecies tumor growth model coupling 3D phase-fields with a 1D vascular network. . Nonlinear Anal. Real World Appl. 61::103331
    [Crossref] [Google Scholar]
  93. 93.
    Xu J, Vilanova G, Gomez H. 2020.. Phase-field model of vascular tumor growth: three-dimensional geometry of the vascular network and integration with imaging data. . Comput. Methods Appl. Mech. Eng. 359::112648
    [Crossref] [Google Scholar]
  94. 94.
    Wise S, Lowengrub J, Frieboes H, Cristini V. 2008.. Three-dimensional multispecies nonlinear tumor growth. I: Model and numerical method. . J. Theor. Biol. 253:(3):52443
    [Crossref] [Google Scholar]
  95. 95.
    Blanco B, Gomez H, Melchor J, Palma R, Soler J, Rus G. 2023.. Mechanotransduction in tumor dynamics modeling. . Phys. Life Rev. 44::279301
    [Crossref] [Google Scholar]
  96. 96.
    Stylianopoulos T, Martin JD, Snuderl M, Mpekris F, Jain SR, Jain RK. 2013.. Coevolution of solid stress and interstitial fluid pressure in tumors during progression: implications for vascular collapse. . Cancer Res. 73:(13):383341
    [Crossref] [Google Scholar]
  97. 97.
    Vavourakis V, Stylianopoulos T, Wijeratne PA. 2018.. In-silico dynamic analysis of cytotoxic drug administration to solid tumours: effect of binding affinity and vessel permeability. . PLOS Comput. Biol. 14:(10):e1006460
    [Crossref] [Google Scholar]
  98. 98.
    Lorenzo G, Heiselman JS, Liss MA, Miga MI, Gomez H, et al. 2022.. Patient-specific forecasting of prostate cancer growth during active surveillance using an imaging-informed mechanistic model. . Cancer Res. 82:(Suppl. 12):5064 ( Abstr.)
    [Crossref] [Google Scholar]
  99. 99.
    Roque T, Risser L, Kersemans V, Smart S, Allen D, et al. 2018.. A DCE-MRI driven 3-D reaction-diffusion model of solid tumor growth. . IEEE Trans. Med. Imaging 37:(3):72432
    [Crossref] [Google Scholar]
  100. 100.
    Hormuth DA II, Jarrett AM, Feng X, Yankeelov TE. 2019.. Calibrating a predictive model of tumor growth and angiogenesis with quantitative MRI. . Ann. Biomed. Eng. 47::153951
    [Crossref] [Google Scholar]
  101. 101.
    Rockne RC, Trister AD, Jacobs J, Hawkins-Daarud AJ, Neal ML, et al. 2015.. A patient-specific computational model of hypoxia-modulated radiation resistance in glioblastoma using F-FMISO-PET. . J. R. Soc. Interface 12:(103):20141174
    [Crossref] [Google Scholar]
  102. 102.
    Hormuth DA II, Jarrett AM, Yankeelov TE. 2020.. Forecasting tumor and vasculature response dynamics to radiation therapy via image based mathematical modeling. . Radiat. Oncol. 15::114
    [Crossref] [Google Scholar]
  103. 103.
    Swanson KR, Rockne RC, Claridge J, Chaplain MA, Alvord Ellsworth CJ, Anderson AR. 2011.. Quantifying the role of angiogenesis in malignant progression of gliomas: in silico modeling integrates imaging and histology. . Cancer Res. 71:(24):736675
    [Crossref] [Google Scholar]
  104. 104.
    Gholami A, Mang A, Biros G. 2016.. An inverse problem formulation for parameter estimation of a reaction–diffusion model of low grade gliomas. . J. Math. Biol. 72::40933
    [Crossref] [Google Scholar]
  105. 105.
    Wu C, Hormuth DA II, Lorenzo G, Jarrett AM, Pineda F, et al. 2022.. Towards patient-specific optimization of neoadjuvant treatment protocols for breast cancer based on image-guided fluid dynamics. . IEEE Trans. Biomed. Eng. 69:(11):333444
    [Crossref] [Google Scholar]
  106. 106.
    Judenhofer MS, Cherry SR. 2013.. Applications for preclinical PET/MRI. . Semin. Nucl. Med. 43:(1):1929
    [Crossref] [Google Scholar]
  107. 107.
    Mascheroni P, Savvopoulos S, Alfonso JCL, Meyer-Hermann M, Hatzikirou H. 2021.. Improving personalized tumor growth predictions using a Bayesian combination of mechanistic modeling and machine learning. . Commun. Med. 1::19
    [Crossref] [Google Scholar]
  108. 108.
    Alber M, Buganza Tepole A, Cannon WR, De S, Dura-Bernal S, et al. 2019.. Integrating machine learning and multiscale modeling—perspectives, challenges, and opportunities in the biological, biomedical, and behavioral sciences. . npj Digit. Med. 2::115
    [Crossref] [Google Scholar]
  109. 109.
    Viguerie A, Grave M, Barros GF, Lorenzo G, Reali A, Coutinho ALGA. 2022.. Data-driven simulation of Fisher–Kolmogorov tumor growth models using dynamic mode decomposition. . J. Biomech. Eng. 144::121001
    [Crossref] [Google Scholar]
  110. 110.
    Nardini JT, Lagergren JH, Hawkins-Daarud A, Curtin L, Morris B, et al. 2020.. Learning equations from biological data with limited time samples. . Bull. Math. Biol. 82::119
    [Crossref] [Google Scholar]
  111. 111.
    Brummer AB, Xella A, Woodall R, Adhikarla V, Cho H, et al. 2023.. Data driven model discovery and interpretation for CAR T-cell killing using sparse identification and latent variables. . Front. Immunol. 14::1115536
    [Crossref] [Google Scholar]
  112. 112.
    Lenhart S, Workman JT. 2007.. Optimal Control Applied to Biological Models. Philadelphia: Chapman & Hall/CRC:
    [Crossref] [Google Scholar]
  113. 113.
    Schättler H, Ledzewicz U. 2016.. Optimal Control for Mathematical Models of Cancer Therapies. New York:: Springer
    [Google Scholar]
  114. 114.
    Benzekry S, Hahnfeldt P. 2013.. Maximum tolerated dose versus metronomic scheduling in the treatment of metastatic cancers. . J. Theor. Biol. 335::23544
    [Crossref] [Google Scholar]
  115. 115.
    Irurzun-Arana I, Janda A, Ardanza-Trevijano S, Trocóniz IF. 2018.. Optimal dynamic control approach in a multi-objective therapeutic scenario: application to drug delivery in the treatment of prostate cancer. . PLOS Comput. Biol. 14:(4):e1006087
    [Crossref] [Google Scholar]
  116. 116.
    Bodzioch M, Bajger P, Foryś U. 2021.. Angiogenesis and chemotherapy resistance: optimizing chemotherapy scheduling using mathematical modeling. . J. Cancer Res. Clin. Oncol. 147:(8):228199
    [Crossref] [Google Scholar]
  117. 117.
    Jarrett AM, Faghihi D, Hormuth DA II, Lima EABF, Virostko J, et al. 2020.. Optimal control theory for personalized therapeutic regimens in oncology: background, history, challenges, and opportunities. . J. Clin. Med. 9:(5):1314
    [Crossref] [Google Scholar]
  118. 118.
    Chua CYX, Ho J, Demaria S, Ferrari M, Grattoni A. 2020.. Emerging technologies for local cancer treatment. . Adv. Ther. 3:(9):2000027
    [Crossref] [Google Scholar]
  119. 119.
    Desrosiers A, Derbali RM, Hassine S, Berdugo J, Long V, et al. 2022.. Programmable self-regulated molecular buffers for precise sustained drug delivery. . Nat. Commun. 13::6504
    [Crossref] [Google Scholar]
  120. 120.
    Iyengar R, Zhao S, Chung SW, Mager DE, Gallo JM. 2012.. Merging systems biology with pharmacodynamics. . Sci. Transl. Med. 4::126ps7
    [Crossref] [Google Scholar]
  121. 121.
    Shi J, Kantoff PW, Wooster R, Farokhzad OC. 2017.. Cancer nanomedicine: progress, challenges and opportunities. . Nat. Rev. Cancer 17::2037
    [Crossref] [Google Scholar]
  122. 122.
    Niederer SA, Sacks MS, Girolami M, Willcox K. 2021.. Scaling digital twins from the artisanal to the industrial. . Nat. Comput. Sci. 1::31320
    [Crossref] [Google Scholar]
  123. 123.
    Wu C, Lorenzo G, Hormuth DA II, Lima EABF, Slavkova KP, et al. 2022.. Integrating mechanism-based modeling with biomedical imaging to build practical digital twins for clinical oncology. . Biophys. Rev. 3::021304
    [Crossref] [Google Scholar]
  124. 124.
    Rasheed A, San O, Kvamsdal T. 2020.. Digital twin: values, challenges and enablers from a modeling perspective. . IEEE Access 8::219802012
    [Crossref] [Google Scholar]
  125. 125.
    Tao F, Zhang H, Liu A, Nee AYC. 2019.. Digital twin in industry: state-of-the-art. . IEEE Trans. Ind. Inform. 15:(4):240515
    [Crossref] [Google Scholar]
  126. 126.
    Kapteyn MG, Pretorius JV, Willcox KE. 2021.. A probabilistic graphical model foundation for enabling predictive digital twins at scale. . Nat. Comput. Sci. 1:(5):33747
    [Crossref] [Google Scholar]
  127. 127.
    Malone HR, Syed ON, Downes MS, D'Ambrosio AL, Quest DO, Kaiser MG. 2010.. Simulation in neurosurgery: a review of computer-based simulation environments and their surgical applications. . Neurosurgery 67:(4):110516
    [Crossref] [Google Scholar]
  128. 128.
    Brunet JN, Mendizabal A, Petit A, Golse N, Vibert E, Cotin S. 2019.. Physics-based deep neural network for augmented reality during liver surgery. . In Medical Image Computing and Computer Assisted Intervention—MICCAI 2019: 22nd International Conference, pp. 13745. Cham, Switz:.: Springer
    [Google Scholar]
  129. 129.
    Corral-Acero J, Margara F, Marciniak M, Rodero C, Loncaric F, et al. 2020.. The `digital twin' to enable the vision of precision cardiology. . Eur. Heart J. 41:(48):455664
    [Crossref] [Google Scholar]
  130. 130.
    Woodall RT, Hormuth DA II, Wu C, Abdelmalik MR, Phillips WT, et al. 2021.. Patient specific, imaging-informed modeling of rhenium-186 nanoliposome delivery via convection-enhanced delivery in glioblastoma multiforme. . Biomed. Phys. Eng. Express 7::045012
    [Crossref] [Google Scholar]
  131. 131.
    Wembacher-Schroeder E, Kerstein N, Bander ED, Pandit-Taskar N, Thomson R, Souweidane MM. 2021.. Evaluation of a patient-specific algorithm for predicting distribution for convection-enhanced drug delivery into the brainstem of patients with diffuse intrinsic pontine glioma. . J. Neurosurg. Pediatr. 28:(1):3442
    [Crossref] [Google Scholar]
  132. 132.
    Shamanna P, Saboo B, Damodharan S, Mohammed J, Mohamed M, et al. 2020.. Reducing HbA1c in type 2 diabetes using digital twin technology-enabled precision nutrition: a retrospective analysis. . Diabetes Ther. 11::270314
    [Crossref] [Google Scholar]
  133. 133.
    Lal RA, Ekhlaspour L, Hood K, Buckingham B. 2019.. Realizing a closed-loop (artificial pancreas) system for the treatment of type 1 diabetes. . Endocr. Rev. 40:(6):152146
    [Crossref] [Google Scholar]
  134. 134.
    Hernandez-Boussard T, Macklin P, Greenspan EJ, Gryshuk AL, Stahlberg E, et al. 2021.. Digital twins for predictive oncology will be a paradigm shift for precision cancer care. . Nat. Med. 27:(12):206566
    [Crossref] [Google Scholar]
  135. 135.
    Hadjicharalambous M, Ioannou E, Aristokleous N, Gazeli K, Anastassiou C, Vavourakis V. 2022.. Combined anti-angiogenic and cytotoxic treatment of a solid tumour: in silico investigation of a xenograft animal model's digital twin. . J. Theor. Biol. 553::111246
    [Crossref] [Google Scholar]
  136. 136.
    Benzekry S. 2020.. Artificial intelligence and mechanistic modeling for clinical decision making in oncology. . Clin. Pharmacol. Ther. 108:(3):47186
    [Crossref] [Google Scholar]
  137. 137.
    Sobester A, Forrester A, Keane A. 2008.. Engineering Design via Surrogate Modelling: A Practical Guide. New York:: Wiley
    [Google Scholar]
  138. 138.
    Garcez AD, Lamb LC. 2023.. Neurosymbolic AI: the 3rd wave. . Artif. Intell. Rev. 56::1238406
    [Crossref] [Google Scholar]
  139. 139.
    Khan S, Naseer M, Hayat M, Zamir SW, Khan FS, Shah M. 2022.. Transformers in vision: a survey. . ACM Comput. Surv. 54:(Suppl. 10):200
    [Google Scholar]
  140. 140.
    Tay Y, Dehghani M, Bahri D, Metzler D. 2022.. Efficient transformers: a survey. . ACM Comput. Surv. 55:(6):109
    [Google Scholar]
  141. 141.
    Raissi M, Perdikaris P, Karniadakis GE. 2019.. Physics-informed neural networks: a deep learning framework for solving forward and inverse problems involving nonlinear partial differential equations. . J. Comput. Phys. 378::686707
    [Crossref] [Google Scholar]
  142. 142.
    Kuenzi BM, Park J, Fong SH, Sanchez KS, Lee J, et al. 2020.. Predicting drug response and synergy using a deep learning model of human cancer cells. . Cancer Cell 38:(5):67284
    [Crossref] [Google Scholar]
  143. 143.
    Lagergren JH, Nardini JT, Baker RE, Simpson MJ, Flores KB. 2020.. Biologically-informed neural networks guide mechanistic modeling from sparse experimental data. . PLOS Comput. Biol. 16:(12):e1008462
    [Crossref] [Google Scholar]
  144. 144.
    Siegel RL, Miller KD, Jemal A. 2017.. Cancer statistics, 2017. . CA Cancer J. Clin. 67:(1):730
    [Crossref] [Google Scholar]
  145. 145.
    Badve S, Dabbs DJ, Schnitt SJ, Baehner FL, Decker T, et al. 2011.. Basal-like and triple-negative breast cancers: a critical review with an emphasis on the implications for pathologists and oncologists. . Mod. Pathol. 24:(2):15767
    [Crossref] [Google Scholar]
  146. 146.
    Wendt MK, Schiemann WP. 2009.. Therapeutic targeting of the focal adhesion complex prevents oncogenic TGF-β signaling and metastasis. . Breast Cancer Res. 11:(5):R68
    [Crossref] [Google Scholar]
  147. 147.
    Hapach LA, Carey SP, Schwager SC, Taufalele PV, Wang W, et al. 2021.. Phenotypic heterogeneity and metastasis of breast cancer cells. . Cancer Res. 81:(13):364963
    [Crossref] [Google Scholar]
  148. 148.
    Jun BH, Guo T, Libring S, Chanda MK, Paez JS, et al. 2020.. Fibronectin-expressing mesenchymal tumor cells promote breast cancer metastasis. . Cancers 12:(9):2553
    [Crossref] [Google Scholar]
  149. 149.
    Shinde A, Libring S, Alpsoy A, Abdullah A, Schaber JA, et al. 2018.. Autocrine fibronectin inhibits breast cancer metastasis. . Mol. Cancer Res. 16:(10):157989
    [Crossref] [Google Scholar]
  150. 150.
    Welch DR, Hurst DR. 2019.. Defining the hallmarks of metastasis. . Cancer Res. 79:(12):301127
    [Crossref] [Google Scholar]
  151. 151.
    Venis SM, Moon HR, Yang Y, Utturkar SM, Konieczny SF, Han B. 2021.. Engineering of a functional pancreatic acinus with reprogrammed cancer cells by induced PTF1a expression. . Lab Chip 21:(19):367585
    [Crossref] [Google Scholar]
  152. 152.
    Virumbrales-Muñoz M, Ayuso JM, Loken JR, Denecke KM, Rehman S, et al. 2022.. Microphysiological model of renal cell carcinoma to inform anti-angiogenic therapy. . Biomaterials 283::121454
    [Crossref] [Google Scholar]
  153. 153.
    Enriquez A, Libring S, Field TC, Jimenez J, Lee T, et al. 2021.. High-throughput magnetic actuation platform for evaluating the effect of mechanical force on 3D tumor microenvironment. . Adv. Funct. Mater. 31:(1):2005021
    [Crossref] [Google Scholar]
  154. 154.
    Jordahl S, Solorio L, Neale DB, McDermott S, Jordahl JH, et al. 2019.. Engineered fibrillar fibronectin networks as three-dimensional tissue scaffolds. . Adv. Mater. 31:(46):e1904580
    [Crossref] [Google Scholar]
  155. 155.
    Lugo-Cintrón KM, Gong MM, Ayuso JM, Tomko LA, Beebe DJ, et al. 2020.. Breast fibroblasts and ECM components modulate breast cancer cell migration through the secretion of MMPs in a 3D microfluidic co-culture model. . Cancers 12:(5):1173
    [Crossref] [Google Scholar]
  156. 156.
    Shinde A, Paez JS, Libring S, Hopkins K, Solorio L, Wendt MK. 2020.. Transglutaminase-2 facilitates extracellular vesicle–mediated establishment of the metastatic niche. . Oncogenesis 9:(2):16
    [Crossref] [Google Scholar]
  157. 157.
    Provenzano PP, Eliceiri KW, Campbell JM, Inman DR, White JG, Keely PJ. 2006.. Collagen reorganization at the tumor-stromal interface facilitates local invasion. . BMC Med. 4::38
    [Crossref] [Google Scholar]
  158. 158.
    Benner P, Gugercin S, Willcox K. 2015.. A survey of projection-based model reduction methods for parametric dynamical systems. . SIAM Rev. 57:(4):483531
    [Crossref] [Google Scholar]
  159. 159.
    Jaffray DA. 2012.. Image-guided radiotherapy: from current concept to future perspectives. . Nat. Rev. Clin. Oncol. 9:(12):68899
    [Crossref] [Google Scholar]
  160. 160.
    Ahmed SR, Befano B, Lemay A, Egemen D, Rodriguez AC, et al. 2022.. Reproducible and clinically translatable deep neural networks for cervical screening. . medRxiv 2022.12.17.22282984. https://doi.org/10.1101/2022.12.17.22282984
  161. 161.
    Ahmed SR, Lemay A, Hoebel KV, Kalpathy-Cramer J. 2023.. Reproducible and clinically translatable deep neural networks for cervical screening. . Sci. Rep. 13::21772
    [Crossref] [Google Scholar]
  162. 162.
    Lemay A, Hoebel K, Bridge CP, Befano B, De Sanjosé S, et al. 2022.. Improving the repeatability of deep learning models with Monte Carlo dropout. . npj Digit. Med. 5::174
    [Crossref] [Google Scholar]
  163. 163.
    Cohen J. 1960.. A coefficient of agreement for nominal scales. . Educ. Psychol. Meas. 20:(1):3746
    [Crossref] [Google Scholar]
  164. 164.
    Gichoya JW, Banerjee I, Bhimireddy AR, Burns JL, Celi LA, et al. 2022.. AI recognition of patient race in medical imaging: a modelling study. . Lancet Digit. Health 4:(6):e40614
    [Crossref] [Google Scholar]
  165. 165.
    Obermeyer Z, Powers B, Vogeli C, Mullainathan S. 2019.. Dissecting racial bias in an algorithm used to manage the health of populations. . Science 366:(6464):44753
    [Crossref] [Google Scholar]
/content/journals/10.1146/annurev-bioeng-081623-025834
Loading
/content/journals/10.1146/annurev-bioeng-081623-025834
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error