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Published in: European Journal of Nuclear Medicine and Molecular Imaging 13/2019

01-12-2019 | Artificial Intelligence | Original Article

Why imaging data alone is not enough: AI-based integration of imaging, omics, and clinical data

Authors: Andreas Holzinger, Benjamin Haibe-Kains, Igor Jurisica

Published in: European Journal of Nuclear Medicine and Molecular Imaging | Issue 13/2019

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Abstract

Artificial intelligence (AI) is currently regaining enormous interest due to the success of machine learning (ML), and in particular deep learning (DL). Image analysis, and thus radiomics, strongly benefits from this research. However, effectively and efficiently integrating diverse clinical, imaging, and molecular profile data is necessary to understand complex diseases, and to achieve accurate diagnosis in order to provide the best possible treatment. In addition to the need for sufficient computing resources, suitable algorithms, models, and data infrastructure, three important aspects are often neglected: (1) the need for multiple independent, sufficiently large and, above all, high-quality data sets; (2) the need for domain knowledge and ontologies; and (3) the requirement for multiple networks that provide relevant relationships among biological entities. While one will always get results out of high-dimensional data, all three aspects are essential to provide robust training and validation of ML models, to provide explainable hypotheses and results, and to achieve the necessary trust in AI and confidence for clinical applications.
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Literature
2.
go back to reference Zhang Q, Yang LT, Chen Z, Li P. A survey on deep learning for big data. Inf Fus 2018;42:146–57. Zhang Q, Yang LT, Chen Z, Li P. A survey on deep learning for big data. Inf Fus 2018;42:146–57.
3.
go back to reference Komaroff AL. The variability and inaccuracy of medical data. Proc IEEE 1979;67(9):1196–207. Komaroff AL. The variability and inaccuracy of medical data. Proc IEEE 1979;67(9):1196–207.
5.
go back to reference Holzinger A, Jurisica I. Knowledge discovery and data mining in biomedical informatics: the future is in integrative, interactive machine learning solutions. Interactive knowledge discovery and data mining in biomedical informatics: state-of-the-art and future challenges. Lecture notes in computer science LNCS 8401. In: Holzinger A and Jurisica I, editors. Springer; 2014. p. 1–18. Holzinger A, Jurisica I. Knowledge discovery and data mining in biomedical informatics: the future is in integrative, interactive machine learning solutions. Interactive knowledge discovery and data mining in biomedical informatics: state-of-the-art and future challenges. Lecture notes in computer science LNCS 8401. In: Holzinger A and Jurisica I, editors. Springer; 2014. p. 1–18.
6.
go back to reference Wang B, et al. Similarity network fusion for aggregating data types on genomic scale. Nat Methods 2014;11 (3):3377. Wang B, et al. Similarity network fusion for aggregating data types on genomic scale. Nat Methods 2014;11 (3):3377.
7.
go back to reference Holzinger A. Biomedical informatics: discovering knowledge in big data. New York: Springer; 2014. Holzinger A. Biomedical informatics: discovering knowledge in big data. New York: Springer; 2014.
8.
go back to reference Hutson M. Artificial intelligence faces reproducibility crisis. Science 2018;359(6377):725–6.PubMed Hutson M. Artificial intelligence faces reproducibility crisis. Science 2018;359(6377):725–6.PubMed
9.
go back to reference Goodman SN, Fanelli D, Ioannidis JPA. What does research reproducibility mean? Sci Transl Med 2016; 8(341):341ps12.PubMed Goodman SN, Fanelli D, Ioannidis JPA. What does research reproducibility mean? Sci Transl Med 2016; 8(341):341ps12.PubMed
10.
go back to reference Turkay C, Jeanquartier F, Holzinger A, Hauser H. On computationally-enhanced visual analysis of heterogeneous data and its application in biomedical informatics. Interactive knowledge discovery and data mining: state-of-the-art and future challenges in biomedical informatics. Lecture notes in computer science LNCS 8401. Springer; 2014. p. 117–140. Turkay C, Jeanquartier F, Holzinger A, Hauser H. On computationally-enhanced visual analysis of heterogeneous data and its application in biomedical informatics. Interactive knowledge discovery and data mining: state-of-the-art and future challenges in biomedical informatics. Lecture notes in computer science LNCS 8401. Springer; 2014. p. 117–140.
11.
go back to reference Collins FS, Varmus H. A new initiative on precision medicine. England J Med 2015;372(9):793–5. Collins FS, Varmus H. A new initiative on precision medicine. England J Med 2015;372(9):793–5.
12.
go back to reference Schiphof D, Oei EH, Hofman A, Waarsing JH, Weinans H, Bierma-Zeinstra SM. Sensitivity and associations with pain and body weight of an MRI definition of knee osteoarthritis compared with radiographic Kellgren and Lawrence criteria: a population-based study in middle-aged females. Osteoarthritis Cartilage 2014;22(3): 440–6.PubMed Schiphof D, Oei EH, Hofman A, Waarsing JH, Weinans H, Bierma-Zeinstra SM. Sensitivity and associations with pain and body weight of an MRI definition of knee osteoarthritis compared with radiographic Kellgren and Lawrence criteria: a population-based study in middle-aged females. Osteoarthritis Cartilage 2014;22(3): 440–6.PubMed
13.
go back to reference Mlecnik B, Bindea G, Kirilovsky A, Angell HK, Obenauf AC, Tosolini M, Church SE, Maby P, Vasaturo A, Angelova M, Fredriksen T, Mauger S, Waldner M, Berger A, Speicher MR, Pages F, Valge-Archer V, Galon J. The tumor microenvironment and immunoscore are critical determinants of dissemination to distant metastasis. Sci Transl Med 2016;8(327):327ra26.PubMed Mlecnik B, Bindea G, Kirilovsky A, Angell HK, Obenauf AC, Tosolini M, Church SE, Maby P, Vasaturo A, Angelova M, Fredriksen T, Mauger S, Waldner M, Berger A, Speicher MR, Pages F, Valge-Archer V, Galon J. The tumor microenvironment and immunoscore are critical determinants of dissemination to distant metastasis. Sci Transl Med 2016;8(327):327ra26.PubMed
14.
go back to reference Sanduleanu S, Woodruff HC, de Jong EEC, van Timmeren JE, Jochems A, Dubois L, Lambin P. Tracking tumor biology with radiomics: a systematic review utilizing a radiomics quality score. Radiotherapy and Oncology: Journal of the European Society for Therapeutic Radiology and Oncology 2018;127(3):349– 60. Sanduleanu S, Woodruff HC, de Jong EEC, van Timmeren JE, Jochems A, Dubois L, Lambin P. Tracking tumor biology with radiomics: a systematic review utilizing a radiomics quality score. Radiotherapy and Oncology: Journal of the European Society for Therapeutic Radiology and Oncology 2018;127(3):349– 60.
15.
go back to reference Vargas HA, Veeraraghavan H, Micco M, Nougaret S, Lakhman Y, Meier AA, Sosa R, Soslow RA, Levine DA, Weigelt B, Aghajanian C, Hricak H, Deasy J, Snyder A, Sala E. A novel representation of inter-site tumour heterogeneity from pre-treatment computed tomography textures classifies ovarian cancers by clinical outcome. Eur Radiol 2017;27(9):3991– 4001.PubMedPubMedCentral Vargas HA, Veeraraghavan H, Micco M, Nougaret S, Lakhman Y, Meier AA, Sosa R, Soslow RA, Levine DA, Weigelt B, Aghajanian C, Hricak H, Deasy J, Snyder A, Sala E. A novel representation of inter-site tumour heterogeneity from pre-treatment computed tomography textures classifies ovarian cancers by clinical outcome. Eur Radiol 2017;27(9):3991– 4001.PubMedPubMedCentral
16.
go back to reference Yin Q, Hung SC, Rathmell WK, Shen L, Wang L, Lin W, Fielding JR, Khandani AH, Woods ME, Milowsky MI, Brooks SA, Wallen EM, Shen D. Integrative radiomics expression predicts molecular subtypes of primary clear cell renal cell carcinoma. Clin Radiol 2018;73(9):782–91.PubMedPubMedCentral Yin Q, Hung SC, Rathmell WK, Shen L, Wang L, Lin W, Fielding JR, Khandani AH, Woods ME, Milowsky MI, Brooks SA, Wallen EM, Shen D. Integrative radiomics expression predicts molecular subtypes of primary clear cell renal cell carcinoma. Clin Radiol 2018;73(9):782–91.PubMedPubMedCentral
17.
go back to reference Liao Xin, Bo Cai, Tian Bin, Luo Yilin, Song Wen, Li Yinglong. 2019. Machine-learning based radiogenomics analysis of MRI features and metagenes in glioblastoma multiforme patients with different survival time. J Cell Mol Med, 4. Liao Xin, Bo Cai, Tian Bin, Luo Yilin, Song Wen, Li Yinglong. 2019. Machine-learning based radiogenomics analysis of MRI features and metagenes in glioblastoma multiforme patients with different survival time. J Cell Mol Med, 4.
18.
go back to reference Danala G, Thai T, Gunderson CC, Moxley KM, Moore K, Mannel RS, Liu H, Zheng B, Qiu Y. Applying quantitative CT image feature analysis to predict response of ovarian cancer patients to chemotherapy. Acad Radiol 2017;24(10):1233–9.PubMedPubMedCentral Danala G, Thai T, Gunderson CC, Moxley KM, Moore K, Mannel RS, Liu H, Zheng B, Qiu Y. Applying quantitative CT image feature analysis to predict response of ovarian cancer patients to chemotherapy. Acad Radiol 2017;24(10):1233–9.PubMedPubMedCentral
19.
go back to reference Cook GJR, Azad G, Owczarczyk K, Siddique M, Goh V. Challenges and promises of PET radiomics. Int J Radiat Oncol Biol Phys 2018;102(4):1083–89.PubMedPubMedCentral Cook GJR, Azad G, Owczarczyk K, Siddique M, Goh V. Challenges and promises of PET radiomics. Int J Radiat Oncol Biol Phys 2018;102(4):1083–89.PubMedPubMedCentral
20.
go back to reference Lin G, Lai CH, Yen TC. Emerging molecular imaging techniques in gynecologic oncology. PET Clin 2018;13(2):289– 99.PubMed Lin G, Lai CH, Yen TC. Emerging molecular imaging techniques in gynecologic oncology. PET Clin 2018;13(2):289– 99.PubMed
21.
go back to reference Xu Y, Hosny A, Zeleznik R, Parmar C, Coroller T, Franco I, Mak RH, Aerts HJWL. 2019. Deep learning predicts lung cancer treatment response from serial medical imaging. Clinical Cancer Research. Xu Y, Hosny A, Zeleznik R, Parmar C, Coroller T, Franco I, Mak RH, Aerts HJWL. 2019. Deep learning predicts lung cancer treatment response from serial medical imaging. Clinical Cancer Research.
22.
go back to reference Baessler B, Weiss K, Pinto Dos Santos D. Robustness and reproducibility of radiomics in magnetic resonance imaging: a phantom study. Invest Radiol 2019;54(4):221–8.PubMed Baessler B, Weiss K, Pinto Dos Santos D. Robustness and reproducibility of radiomics in magnetic resonance imaging: a phantom study. Invest Radiol 2019;54(4):221–8.PubMed
23.
go back to reference Lau SK, Boutros PC, Pintilie M, Blackhall FH, Zhu CQ, Strumpf D, Johnston MR, Darling G, Keshavjee S, Waddell TK, Liu N, Lau D, Penn LZ, Shepherd FA, Jurisica I, Der SD, Tsao MS. Three-gene prognostic classifier for early-stage non small-cell lung cancer. J Clin Oncol 2007;25 (35):5562–9.PubMed Lau SK, Boutros PC, Pintilie M, Blackhall FH, Zhu CQ, Strumpf D, Johnston MR, Darling G, Keshavjee S, Waddell TK, Liu N, Lau D, Penn LZ, Shepherd FA, Jurisica I, Der SD, Tsao MS. Three-gene prognostic classifier for early-stage non small-cell lung cancer. J Clin Oncol 2007;25 (35):5562–9.PubMed
24.
go back to reference Shedden K, Taylor JM, Enkemann SA, Tsao MS, Yeatman TJ, Gerald WL, Eschrich S, Jurisica I, Giordano TJ, Misek DE, Chang AC, Zhu CQ, Strumpf D, Hanash S, Shepherd FA, Ding K, Seymour L, Naoki K, Pennell N, Weir B, Verhaak R, Ladd-Acosta C, Golub T, Gruidl M, Sharma A, Szoke J, Zakowski M, Rusch V, Kris M, Viale A, Motoi N, Travis W, Conley B, Seshan VE, Meyerson M, Kuick R, Dobbin KK, Lively T, Jacobson JW, Beer DG. Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study. Nat Med 2008;14(8):822–7.PubMedPubMedCentral Shedden K, Taylor JM, Enkemann SA, Tsao MS, Yeatman TJ, Gerald WL, Eschrich S, Jurisica I, Giordano TJ, Misek DE, Chang AC, Zhu CQ, Strumpf D, Hanash S, Shepherd FA, Ding K, Seymour L, Naoki K, Pennell N, Weir B, Verhaak R, Ladd-Acosta C, Golub T, Gruidl M, Sharma A, Szoke J, Zakowski M, Rusch V, Kris M, Viale A, Motoi N, Travis W, Conley B, Seshan VE, Meyerson M, Kuick R, Dobbin KK, Lively T, Jacobson JW, Beer DG. Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study. Nat Med 2008;14(8):822–7.PubMedPubMedCentral
25.
go back to reference Boutros PC, Lau SK, Pintilie M, Liu N, Shepherd FA, Der SD, Tsao MS, Penn LZ, Jurisica I. Prognostic gene signatures for non-small-cell lung cancer. Proc Natl Acad Sci USA 2009;106(8):2824–8.PubMedPubMedCentral Boutros PC, Lau SK, Pintilie M, Liu N, Shepherd FA, Der SD, Tsao MS, Penn LZ, Jurisica I. Prognostic gene signatures for non-small-cell lung cancer. Proc Natl Acad Sci USA 2009;106(8):2824–8.PubMedPubMedCentral
26.
go back to reference Beaulieu-Jones BK, Greene CS. Reproducibility of computational workflows is automated using continuous analysis. Nat Biotechnol 2017;34(4):342–6. Beaulieu-Jones BK, Greene CS. Reproducibility of computational workflows is automated using continuous analysis. Nat Biotechnol 2017;34(4):342–6.
27.
go back to reference Munafò MR, Nosek BA, Bishop VMD, Button SB, Chambers CD, du Sert N, Simonsohn U, Wagenmakers E-J, Ware JJ, Ioannidis JPA. A manifesto for reproducible science. Nat Hum Behav 2017; 1(1):s41562–016–0021. Munafò MR, Nosek BA, Bishop VMD, Button SB, Chambers CD, du Sert N, Simonsohn U, Wagenmakers E-J, Ware JJ, Ioannidis JPA. A manifesto for reproducible science. Nat Hum Behav 2017; 1(1):s41562–016–0021.
28.
go back to reference Lamb J, Crawford ED, Peck D, Modell JW, Blat IC, Wrobel MJ, Lerner J, Brunet J-P, Subramanian A, Ross KN, Reich M, Hieronymus H, Wei G, Armstrong SA, Haggarty SJ, Clemons PA, Wei R, Carr SA, Lander ES, Golub TR. The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease. Science 2006;313(5795):1929–35.PubMed Lamb J, Crawford ED, Peck D, Modell JW, Blat IC, Wrobel MJ, Lerner J, Brunet J-P, Subramanian A, Ross KN, Reich M, Hieronymus H, Wei G, Armstrong SA, Haggarty SJ, Clemons PA, Wei R, Carr SA, Lander ES, Golub TR. The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease. Science 2006;313(5795):1929–35.PubMed
29.
go back to reference Sun R, Limkin EJ, Vakalopoulou M, Dercle L, Champiat S, Han SR, Verlingue L, Brandao D, Lancia A, Ammari S, Hollebecque A, Scoazec JY, Marabelle A, Massard C, Soria JC, Robert C, Paragios N, Deutsch E, Ferte C. A radiomics approach to assess tumour-infiltrating cd8 cells and response to anti-pd-1 or anti-pd-l1 immunotherapy: an imaging biomarker, retrospective multicohort study. Lancet Oncol 2018;19(9):1180–91.PubMed Sun R, Limkin EJ, Vakalopoulou M, Dercle L, Champiat S, Han SR, Verlingue L, Brandao D, Lancia A, Ammari S, Hollebecque A, Scoazec JY, Marabelle A, Massard C, Soria JC, Robert C, Paragios N, Deutsch E, Ferte C. A radiomics approach to assess tumour-infiltrating cd8 cells and response to anti-pd-1 or anti-pd-l1 immunotherapy: an imaging biomarker, retrospective multicohort study. Lancet Oncol 2018;19(9):1180–91.PubMed
30.
go back to reference Aerts HJ, Grossmann P, Tan Y, Oxnard GR, Rizvi N, Schwartz LH, Zhao B. Defining a radiomic response phenotype: a pilot study using targeted therapy in NSCLC. Sci Rep 2016;6:33860.PubMedPubMedCentral Aerts HJ, Grossmann P, Tan Y, Oxnard GR, Rizvi N, Schwartz LH, Zhao B. Defining a radiomic response phenotype: a pilot study using targeted therapy in NSCLC. Sci Rep 2016;6:33860.PubMedPubMedCentral
31.
go back to reference Tokar T, Pastrello C, Ramnarine VR, Zhu CQ, Craddock KJ, Pikor LA, Vucic EA, Vary S, Shepherd FA, Tsao MS, Lam WL, Jurisica I. Differentially expressed microRNAs in lung adenocarcinoma invert effects of copy number aberrations of prognostic genes. Oncotarget 2018;9(10):9137–55.PubMedPubMedCentral Tokar T, Pastrello C, Ramnarine VR, Zhu CQ, Craddock KJ, Pikor LA, Vucic EA, Vary S, Shepherd FA, Tsao MS, Lam WL, Jurisica I. Differentially expressed microRNAs in lung adenocarcinoma invert effects of copy number aberrations of prognostic genes. Oncotarget 2018;9(10):9137–55.PubMedPubMedCentral
32.
go back to reference Viswanath SE, Tiwari P, Lee G, Madabhushi A. Dimensionality reduction-based fusion approaches for imaging and non-imaging biomedical data: concepts, workflow, and use-cases. BMC Med Imaging 2017;17(1):2.PubMedPubMedCentral Viswanath SE, Tiwari P, Lee G, Madabhushi A. Dimensionality reduction-based fusion approaches for imaging and non-imaging biomedical data: concepts, workflow, and use-cases. BMC Med Imaging 2017;17(1):2.PubMedPubMedCentral
33.
go back to reference Ingalhalikar M, Smith A, Parker D, Satterthwaite TD, Elliott MA, Ruparel K, Hakonarson H, Gur RE, Gur RC, Verma R. Sex differences in the structural connectome of the human brain. Proc Natl Acad Sci USA 2014;111(2):823–8.PubMed Ingalhalikar M, Smith A, Parker D, Satterthwaite TD, Elliott MA, Ruparel K, Hakonarson H, Gur RE, Gur RC, Verma R. Sex differences in the structural connectome of the human brain. Proc Natl Acad Sci USA 2014;111(2):823–8.PubMed
34.
go back to reference Bigler ED. Systems biology, neuroimaging, neuropsychology, neuroconnectivity and traumatic brain injury. Front Syst Neurosci 2016;10:55.PubMedPubMedCentral Bigler ED. Systems biology, neuroimaging, neuropsychology, neuroconnectivity and traumatic brain injury. Front Syst Neurosci 2016;10:55.PubMedPubMedCentral
35.
go back to reference Cui LB, Liu L, Wang HN, Wang LX, Guo F, Xi YB, Liu TT, Li C, Tian P, Liu K, Wu WJ, Chen YH, Qin W, Yin H. Disease definition for schizophrenia by functional connectivity using radiomics strategy. Schizophrenia Bull 2018;44(5):1053–9. Cui LB, Liu L, Wang HN, Wang LX, Guo F, Xi YB, Liu TT, Li C, Tian P, Liu K, Wu WJ, Chen YH, Qin W, Yin H. Disease definition for schizophrenia by functional connectivity using radiomics strategy. Schizophrenia Bull 2018;44(5):1053–9.
36.
go back to reference Jeong H, Mason SP, Barabasi AL, Oltvai ZN. Lethality and centrality in protein networks. Nature 2001;411(6833):41–2.PubMed Jeong H, Mason SP, Barabasi AL, Oltvai ZN. Lethality and centrality in protein networks. Nature 2001;411(6833):41–2.PubMed
37.
go back to reference Przulj N, Wigle DA, Jurisica I. Functional topology in a network of protein interactions. Bioinformatics 2004;20(3):340–8.PubMed Przulj N, Wigle DA, Jurisica I. Functional topology in a network of protein interactions. Bioinformatics 2004;20(3):340–8.PubMed
38.
go back to reference Ye P, Peyser BD, Pan X, Boeke JD, Spencer FA, Bader JS. Gene function prediction from congruent synthetic lethal interactions in yeast. Molec Syst Biol 2005;1:1. Ye P, Peyser BD, Pan X, Boeke JD, Spencer FA, Bader JS. Gene function prediction from congruent synthetic lethal interactions in yeast. Molec Syst Biol 2005;1:1.
40.
go back to reference Ulitsky I, Shamir R. 2007. Identification of functional modules using network topology and high-throughput data. BMC Syst Biol, 1. Ulitsky I, Shamir R. 2007. Identification of functional modules using network topology and high-throughput data. BMC Syst Biol, 1.
41.
go back to reference Chuang HY, Lee E, Liu YT, Lee D, Ideker T. 2007. Network-based classification of breast cancer metastasis. Mol Syst Biol, 3.PubMedPubMedCentral Chuang HY, Lee E, Liu YT, Lee D, Ideker T. 2007. Network-based classification of breast cancer metastasis. Mol Syst Biol, 3.PubMedPubMedCentral
42.
go back to reference Fortney K, Kotlyar M, Jurisica I. Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging. Genome Biol 2010;11(2):R13.PubMedPubMedCentral Fortney K, Kotlyar M, Jurisica I. Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging. Genome Biol 2010;11(2):R13.PubMedPubMedCentral
43.
go back to reference Kotlyar M, Fortney K, Jurisica I. Network-based characterization of drug-regulated genes, drug targets, and toxicity. Methods 2012;57(4):499–507. Protein-Protein Interactions.PubMed Kotlyar M, Fortney K, Jurisica I. Network-based characterization of drug-regulated genes, drug targets, and toxicity. Methods 2012;57(4):499–507. Protein-Protein Interactions.PubMed
44.
go back to reference Hinze L, Pfirrmann M, Karim S, Degar J, McGuckin C, Vinjamur D, Sacher J, Stevenson KE, Neuberg DS, Orellana E, Stanulla M, Gregory RI, Bauer DE, Wagner FF, Stegmaier K, Gutierrez A. Synthetic lethality of Wnt pathway activation and asparaginase in drug-resistant acute leukemias. Cancer Cell 2019;35(4):664–676.e667.PubMedPubMedCentral Hinze L, Pfirrmann M, Karim S, Degar J, McGuckin C, Vinjamur D, Sacher J, Stevenson KE, Neuberg DS, Orellana E, Stanulla M, Gregory RI, Bauer DE, Wagner FF, Stegmaier K, Gutierrez A. Synthetic lethality of Wnt pathway activation and asparaginase in drug-resistant acute leukemias. Cancer Cell 2019;35(4):664–676.e667.PubMedPubMedCentral
45.
go back to reference Wong SWH, Pastrello C, Kotlyar M, Faloutsos C, Jurisica I. Sdregion: fast spotting of changing communities in biological networks. Proceedings of the ACM SIGKDD international conference on knowledge discovery and data mining. New York: ACM; 2018. p. 867–875. Wong SWH, Pastrello C, Kotlyar M, Faloutsos C, Jurisica I. Sdregion: fast spotting of changing communities in biological networks. Proceedings of the ACM SIGKDD international conference on knowledge discovery and data mining. New York: ACM; 2018. p. 867–875.
46.
go back to reference Lambin P, Rios-Velazquez E, Leijenaar R, Carvalho S, van Stiphout RG, Granton P, Zegers CM, Gillies R, Boellard R, Dekker A, Aerts HJ. Radiomics: extracting more information from medical images using advanced feature analysis. Eur J Cancer 2012;48(4):441–6.PubMedPubMedCentral Lambin P, Rios-Velazquez E, Leijenaar R, Carvalho S, van Stiphout RG, Granton P, Zegers CM, Gillies R, Boellard R, Dekker A, Aerts HJ. Radiomics: extracting more information from medical images using advanced feature analysis. Eur J Cancer 2012;48(4):441–6.PubMedPubMedCentral
47.
go back to reference Ger RB, Zhou S, Chi PM, Lee HJ, Layman RR, Jones AK, Goff DL, Fuller CD, Howell RM, Li H, Stafford RJ, Court LE, Mackin DS. Comprehensive investigation on controlling for CT imaging variabilities in radiomics studies. Sci Rep 2018;8(1):13047.PubMedPubMedCentral Ger RB, Zhou S, Chi PM, Lee HJ, Layman RR, Jones AK, Goff DL, Fuller CD, Howell RM, Li H, Stafford RJ, Court LE, Mackin DS. Comprehensive investigation on controlling for CT imaging variabilities in radiomics studies. Sci Rep 2018;8(1):13047.PubMedPubMedCentral
48.
go back to reference Jorgensen P, Nelson B, Robinson MD, Chen Y, Andrews B, Tyers M, Boone C. High-resolution genetic mapping with ordered arrays of Saccharomyces cerevisiae deletion mutants. Genetics 2002;162 (3):1091–9.PubMedPubMedCentral Jorgensen P, Nelson B, Robinson MD, Chen Y, Andrews B, Tyers M, Boone C. High-resolution genetic mapping with ordered arrays of Saccharomyces cerevisiae deletion mutants. Genetics 2002;162 (3):1091–9.PubMedPubMedCentral
49.
go back to reference Suthers PF, Zomorrodi A, Maranas CD. 2009. Genome-scale gene/reaction essentiality and synthetic lethality analysis, Vol. 5.PubMedPubMedCentral Suthers PF, Zomorrodi A, Maranas CD. 2009. Genome-scale gene/reaction essentiality and synthetic lethality analysis, Vol. 5.PubMedPubMedCentral
50.
go back to reference Chan EM, Shibue T, McFarland JM, Gaeta B, Ghandi M, Dumont N, Gonzalez A, McPartlan JS, Li T, Zhang Y, Liu JB, Lazaro J-B, Gu P, Piett CG, Apffel A, Ali SO, Deasy R, Keskula P, Ng RWS, Roberts EA, Reznichenko E, Leung L, Alimova M, Schenone M, Islam M, Maruvka YE, Liu Y, Roper J, Raghavan S, Giannakis M, Tseng Y-Y, Nagel ZD, D’Andrea A, Root DE, Boehm JS, Getz G, Chang S, Golub TR, Tsherniak A, Vazquez F, Bass AJ. Wrn helicase is a synthetic lethal target in microsatellite unstable cancers. Nature 2019;568(7753): 551–6.PubMedPubMedCentral Chan EM, Shibue T, McFarland JM, Gaeta B, Ghandi M, Dumont N, Gonzalez A, McPartlan JS, Li T, Zhang Y, Liu JB, Lazaro J-B, Gu P, Piett CG, Apffel A, Ali SO, Deasy R, Keskula P, Ng RWS, Roberts EA, Reznichenko E, Leung L, Alimova M, Schenone M, Islam M, Maruvka YE, Liu Y, Roper J, Raghavan S, Giannakis M, Tseng Y-Y, Nagel ZD, D’Andrea A, Root DE, Boehm JS, Getz G, Chang S, Golub TR, Tsherniak A, Vazquez F, Bass AJ. Wrn helicase is a synthetic lethal target in microsatellite unstable cancers. Nature 2019;568(7753): 551–6.PubMedPubMedCentral
51.
go back to reference Holzinger A, Langs G, Denk H, Zatloukal K, Mueller H. 2019. Causability and explainability of AI in medicine. Wiley Interdisciplinary Reviews, Data Mining and Knowledge Discovery. Holzinger A, Langs G, Denk H, Zatloukal K, Mueller H. 2019. Causability and explainability of AI in medicine. Wiley Interdisciplinary Reviews, Data Mining and Knowledge Discovery.
52.
go back to reference Krittanawong C, Zhang HJ, Wang Z, Aydar M, Kitai T. Artificial intelligence in precision cardiovascular medicine. J Am Coll Cardiol 2017;69(21):2657–64.PubMed Krittanawong C, Zhang HJ, Wang Z, Aydar M, Kitai T. Artificial intelligence in precision cardiovascular medicine. J Am Coll Cardiol 2017;69(21):2657–64.PubMed
53.
go back to reference Hamet P, Tremblay J. Artificial intelligence in medicine. Metabolism 2017;69:S36–40. Hamet P, Tremblay J. Artificial intelligence in medicine. Metabolism 2017;69:S36–40.
54.
go back to reference Robertson S, Azizpour H, Smith K, Hartman J. Digital image analysis in breast pathology—from image processing techniques to artificial intelligence. Transl Res 2018;194:19–35.PubMed Robertson S, Azizpour H, Smith K, Hartman J. Digital image analysis in breast pathology—from image processing techniques to artificial intelligence. Transl Res 2018;194:19–35.PubMed
55.
go back to reference Topol EJ. High-performance medicine: the convergence of human and artificial intelligence. Nat Med 2019;25 (1):44–56.PubMed Topol EJ. High-performance medicine: the convergence of human and artificial intelligence. Nat Med 2019;25 (1):44–56.PubMed
56.
go back to reference Hosny A, Parmar C, Quackenbush J, Schwartz LH, Aerts H. Artificial intelligence in radiology. Nat Rev Cancer 2018;18(8):500–510.PubMedPubMedCentral Hosny A, Parmar C, Quackenbush J, Schwartz LH, Aerts H. Artificial intelligence in radiology. Nat Rev Cancer 2018;18(8):500–510.PubMedPubMedCentral
57.
go back to reference Kang J, Rancati T, Lee S, Oh J, Kerns SL, Scott JG, Schwartz R, Kim S, Rosenstein BS. Machine learning and radiogenomics: lessons learned and future directions. Frontiers Oncol 2018;8:228. Kang J, Rancati T, Lee S, Oh J, Kerns SL, Scott JG, Schwartz R, Kim S, Rosenstein BS. Machine learning and radiogenomics: lessons learned and future directions. Frontiers Oncol 2018;8:228.
58.
go back to reference Sun R, Limkin E, Vakalopoulou M, Dercle L, Champiat S, Han S, Verlingue L, Brandao D, Lancia A, Ammari S, Hollebecque A, Scoazec J-Y, Marabelle A, Massard C, Soria J-C, Robert C, Paragios N, Deutsch E, Ferté C. A radiomics approach to assess tumour-infiltrating CD8 cells and response to anti-PD-1 or anti-PD-L1 immunotherapy: an imaging biomarker, retrospective multicohort study. Lancet Oncol 2018;19(9):1180–91.PubMed Sun R, Limkin E, Vakalopoulou M, Dercle L, Champiat S, Han S, Verlingue L, Brandao D, Lancia A, Ammari S, Hollebecque A, Scoazec J-Y, Marabelle A, Massard C, Soria J-C, Robert C, Paragios N, Deutsch E, Ferté C. A radiomics approach to assess tumour-infiltrating CD8 cells and response to anti-PD-1 or anti-PD-L1 immunotherapy: an imaging biomarker, retrospective multicohort study. Lancet Oncol 2018;19(9):1180–91.PubMed
59.
go back to reference Iorio F, Knijnenburg TA, Vis DJ, Bignell GR, Menden MP, Schubert M, Aben N, Gonçalves E, Barthorpe S, Lightfoot H, Cokelaer T, Greninger P, van Dyk E, Chang H, de Silva H, Heyn H, Deng X, Egan RK, Liu Q, Mironenko T, Mitropoulos X, Richardson L, Wang J, Zhang T, Moran S, Sayols S, Soleimani M, Tamborero D, López-Bigas N, Ross-Macdonald P, Esteller M, Gray NS, Haber DA, Stratton MR, Benes CH, Wessels LFA, Saez-Rodriguez J, McDermott U, Garnett MJ. A landscape of pharmacogenomic interactions in cancer. Cell 2016;166(3):740–54.PubMedPubMedCentral Iorio F, Knijnenburg TA, Vis DJ, Bignell GR, Menden MP, Schubert M, Aben N, Gonçalves E, Barthorpe S, Lightfoot H, Cokelaer T, Greninger P, van Dyk E, Chang H, de Silva H, Heyn H, Deng X, Egan RK, Liu Q, Mironenko T, Mitropoulos X, Richardson L, Wang J, Zhang T, Moran S, Sayols S, Soleimani M, Tamborero D, López-Bigas N, Ross-Macdonald P, Esteller M, Gray NS, Haber DA, Stratton MR, Benes CH, Wessels LFA, Saez-Rodriguez J, McDermott U, Garnett MJ. A landscape of pharmacogenomic interactions in cancer. Cell 2016;166(3):740–54.PubMedPubMedCentral
60.
go back to reference Seashore-Ludlow B, Rees MG, Cheah JH, Cokol M, Price EV, Coletti ME, Jones V, Bodycombe NE, Soule CK, Gould J, Alexander B, Li A, Montgomery P, Wawer MJ, Kuru N, Kotz JD, Hon S-YC, Munoz B, Liefeld T, Dancik V, Bittker JA, Palmer M, Bradner JE, Shamji AF, Clemons PA, Schreiber SL. Harnessing connectivity in a large-scale small-molecule sensitivity dataset. Cancer Discovery. Seashore-Ludlow B, Rees MG, Cheah JH, Cokol M, Price EV, Coletti ME, Jones V, Bodycombe NE, Soule CK, Gould J, Alexander B, Li A, Montgomery P, Wawer MJ, Kuru N, Kotz JD, Hon S-YC, Munoz B, Liefeld T, Dancik V, Bittker JA, Palmer M, Bradner JE, Shamji AF, Clemons PA, Schreiber SL. Harnessing connectivity in a large-scale small-molecule sensitivity dataset. Cancer Discovery.
61.
go back to reference Haverty PM, Lin E, Tan J, Yu Y, Lam B, Lianoglou S, Neve RM, Martin S, Settleman J, Yauch RL, Bourgon R. Reproducible pharmacogenomic profiling of cancer cell line panels. Nature 2016; 533(7603):333–7.PubMed Haverty PM, Lin E, Tan J, Yu Y, Lam B, Lianoglou S, Neve RM, Martin S, Settleman J, Yauch RL, Bourgon R. Reproducible pharmacogenomic profiling of cancer cell line panels. Nature 2016; 533(7603):333–7.PubMed
62.
go back to reference Gao H, Korn JM, Ferretti S, Monahan JE, Wang Y, Singh M, Zhang C, Schnell C, Yang G, Zhang Y, Balbin AO, Barbe S, Cai H, Casey F, Chatterjee S, Chiang DY, Chuai S, Cogan SM, Collins SD, Dammassa E, Ebel N, Embry M, Green J, Kauffmann A, Kowal C, Leary RJ, Lehar J, Liang Y, Loo Alice, Lorenzana E III, Robert E, McLaughlin ME, Merkin J, Meyer R, Naylor TL, Patawaran M, Reddy A, Röelli C, Ruddy DA, Salangsang F, Santacroce F, Singh AP, Tang Y, Tinetto W, Tobler S, Velazquez R, Venkatesan K, Arx F, Wang H, Wang Z, Wiesmann M, Wyss D, Xu F, Bitter H, Atadja P, Lees E, Hofmann F, Li E, Keen N, Cozens R, Jensen M, Pryer NK, Williams JA, Sellers WR. High-throughput screening using patient-derived tumor xenografts to predict clinical trial drug response. Nat Med 2015;21(11):1318–25.PubMed Gao H, Korn JM, Ferretti S, Monahan JE, Wang Y, Singh M, Zhang C, Schnell C, Yang G, Zhang Y, Balbin AO, Barbe S, Cai H, Casey F, Chatterjee S, Chiang DY, Chuai S, Cogan SM, Collins SD, Dammassa E, Ebel N, Embry M, Green J, Kauffmann A, Kowal C, Leary RJ, Lehar J, Liang Y, Loo Alice, Lorenzana E III, Robert E, McLaughlin ME, Merkin J, Meyer R, Naylor TL, Patawaran M, Reddy A, Röelli C, Ruddy DA, Salangsang F, Santacroce F, Singh AP, Tang Y, Tinetto W, Tobler S, Velazquez R, Venkatesan K, Arx F, Wang H, Wang Z, Wiesmann M, Wyss D, Xu F, Bitter H, Atadja P, Lees E, Hofmann F, Li E, Keen N, Cozens R, Jensen M, Pryer NK, Williams JA, Sellers WR. High-throughput screening using patient-derived tumor xenografts to predict clinical trial drug response. Nat Med 2015;21(11):1318–25.PubMed
63.
go back to reference LeCun Y, Bengio Y, Hinton G. Deep learning. Nature 2015;521(7553):436.PubMed LeCun Y, Bengio Y, Hinton G. Deep learning. Nature 2015;521(7553):436.PubMed
64.
go back to reference Chartrand G, Cheng PM, Vorontsov E, Drozdzal M, Turcotte S, Pal CJ, Kadoury S, An T. Deep learning A primer for radiologists. Radiographics Rev Publ Radiological Soc North Am Inc 2017;37(7): 2113–31. Chartrand G, Cheng PM, Vorontsov E, Drozdzal M, Turcotte S, Pal CJ, Kadoury S, An T. Deep learning A primer for radiologists. Radiographics Rev Publ Radiological Soc North Am Inc 2017;37(7): 2113–31.
65.
go back to reference Sharp G, Fritscher KD, Pekar V, Peroni M, Shusharina N, Veeraraghavan H, Yang J. Vision 20/20: perspectives on automated image segmentation for radiotherapy. Med Phys 2014;41(5):050902.PubMedPubMedCentral Sharp G, Fritscher KD, Pekar V, Peroni M, Shusharina N, Veeraraghavan H, Yang J. Vision 20/20: perspectives on automated image segmentation for radiotherapy. Med Phys 2014;41(5):050902.PubMedPubMedCentral
66.
go back to reference Cardenas CE, Yang J, Anderson BM, Court LE, Brock KB. Advances in auto-segmentation. Semin Radiat Oncol 2019;29(3):185–97. Adaptive Radiotherapy and Automation.PubMed Cardenas CE, Yang J, Anderson BM, Court LE, Brock KB. Advances in auto-segmentation. Semin Radiat Oncol 2019;29(3):185–97. Adaptive Radiotherapy and Automation.PubMed
67.
go back to reference Kreimeyer K, Foster M, Pandey A, Arya N, Halford G, Jones SF, Forshee R, Walderhaug M, Botsis T. 2017. Natural language processing systems for capturing and standardizing unstructured clinical information: a systematic review. J Biomed Inform, 73. Kreimeyer K, Foster M, Pandey A, Arya N, Halford G, Jones SF, Forshee R, Walderhaug M, Botsis T. 2017. Natural language processing systems for capturing and standardizing unstructured clinical information: a systematic review. J Biomed Inform, 73.
68.
go back to reference Asim M, Wasim M, Khan M, Mahmood W, Abbasi H. 2018. A survey of ontology learning techniques and applications. Database, 2018. Asim M, Wasim M, Khan M, Mahmood W, Abbasi H. 2018. A survey of ontology learning techniques and applications. Database, 2018.
69.
go back to reference Deshpande PR, Rajan S, Sudeepthi LB, Abdul CN. Patient-reported outcomes: a new era in clinical research. Perspectives Clin Res 2011;2(4):137–44. Deshpande PR, Rajan S, Sudeepthi LB, Abdul CN. Patient-reported outcomes: a new era in clinical research. Perspectives Clin Res 2011;2(4):137–44.
70.
go back to reference Loh E. Medicine and the rise of the robots: a qualitative review of recent advances of artificial intelligence in health. BMJ Leader 2018;2(2):59–63. Loh E. Medicine and the rise of the robots: a qualitative review of recent advances of artificial intelligence in health. BMJ Leader 2018;2(2):59–63.
71.
go back to reference Dias D, Cunha J. Wearable health Devices—Vital sign monitoring, systems and technologies. Sensors 2018; 18(8):2414.PubMedCentral Dias D, Cunha J. Wearable health Devices—Vital sign monitoring, systems and technologies. Sensors 2018; 18(8):2414.PubMedCentral
72.
go back to reference Guyon I, Bennett K, Cawley G, Escalante HJ, Escalera S, Ho TK, Macia N, Ray B, Saeed M, Statnikov A. Design of the 2015 ChaLearn AutoML Challenge. 2015 International joint conference on neural networks (IJCNN). IEEE; 2015. p. 1–8. Guyon I, Bennett K, Cawley G, Escalante HJ, Escalera S, Ho TK, Macia N, Ray B, Saeed M, Statnikov A. Design of the 2015 ChaLearn AutoML Challenge. 2015 International joint conference on neural networks (IJCNN). IEEE; 2015. p. 1–8.
73.
go back to reference Silver D, Huang A, Maddison CJ, Guez A, Sifre L, van den Driessche G, Schrittwieser J, Antonoglou I, Panneershelvam V, Lanctot M, Dieleman S, Grewe D, Nham J, Kalchbrenner N, Sutskever I, Lillicrap T, Leach M, Kavukcuoglu K, Graepel T, Hassabis D. Mastering the game of go with deep neural networks and tree search. Nature 2016;529(7587):484–9.PubMed Silver D, Huang A, Maddison CJ, Guez A, Sifre L, van den Driessche G, Schrittwieser J, Antonoglou I, Panneershelvam V, Lanctot M, Dieleman S, Grewe D, Nham J, Kalchbrenner N, Sutskever I, Lillicrap T, Leach M, Kavukcuoglu K, Graepel T, Hassabis D. Mastering the game of go with deep neural networks and tree search. Nature 2016;529(7587):484–9.PubMed
74.
go back to reference Stickel C, Ebner M, Steinbach-Nordmann S, Searle G, Holzinger A. Emotion detection: application of the valence arousal space for rapid biological usability testing to enhance universal access. Universal access in human–computer interaction. Addressing diversity, lecture notes in computer science, LNCS 5614. In: Stephanidis C, editors. Springer; 2009. p. 615–24. Stickel C, Ebner M, Steinbach-Nordmann S, Searle G, Holzinger A. Emotion detection: application of the valence arousal space for rapid biological usability testing to enhance universal access. Universal access in human–computer interaction. Addressing diversity, lecture notes in computer science, LNCS 5614. In: Stephanidis C, editors. Springer; 2009. p. 615–24.
75.
go back to reference Esteva A, Kuprel B, Novoa RA, Ko J, Swetter SM, Blau HM, Thrun S. Dermatologist-level classification of skin cancer with deep neural networks. Nature 2017;542(7639):115–8.PubMedPubMedCentral Esteva A, Kuprel B, Novoa RA, Ko J, Swetter SM, Blau HM, Thrun S. Dermatologist-level classification of skin cancer with deep neural networks. Nature 2017;542(7639):115–8.PubMedPubMedCentral
76.
go back to reference Holzinger A. Interactive machine learning for health informatics: when do we need the human-in-the-loop? Brain Inform 2016;3(2):119–31.PubMedPubMedCentral Holzinger A. Interactive machine learning for health informatics: when do we need the human-in-the-loop? Brain Inform 2016;3(2):119–31.PubMedPubMedCentral
77.
go back to reference Holzinger A, Stocker C, Ofner B, Prohaska G, Brabenetz A, Hofmann-Wellenhof R. Combining HCI, natural language processing, and knowledge discovery - potential of IBM content analytics as an assistive technology in the biomedical domain. Springer lecture notes in computer science LNCS 7947. Springer; 2013. Holzinger A, Stocker C, Ofner B, Prohaska G, Brabenetz A, Hofmann-Wellenhof R. Combining HCI, natural language processing, and knowledge discovery - potential of IBM content analytics as an assistive technology in the biomedical domain. Springer lecture notes in computer science LNCS 7947. Springer; 2013.
78.
go back to reference Holzinger A, Plass M, Holzinger K, Crisan GC, Pintea C-M, Palade V. Towards interactive machine learning (IML): applying ant colony algorithms to solve the traveling salesman problem with the human-in-the-loop approach. Springer lecture notes in computer science LNCS 9817. Springer; 2016. p. 81–95. Holzinger A, Plass M, Holzinger K, Crisan GC, Pintea C-M, Palade V. Towards interactive machine learning (IML): applying ant colony algorithms to solve the traveling salesman problem with the human-in-the-loop approach. Springer lecture notes in computer science LNCS 9817. Springer; 2016. p. 81–95.
Metadata
Title
Why imaging data alone is not enough: AI-based integration of imaging, omics, and clinical data
Authors
Andreas Holzinger
Benjamin Haibe-Kains
Igor Jurisica
Publication date
01-12-2019
Publisher
Springer Berlin Heidelberg
Published in
European Journal of Nuclear Medicine and Molecular Imaging / Issue 13/2019
Print ISSN: 1619-7070
Electronic ISSN: 1619-7089
DOI
https://doi.org/10.1007/s00259-019-04382-9

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