Machine intelligence for radiation science: summary of the Radiation Research Society 67th annual meeting symposium

References

• Althubaiti S, Karwath A, Dallol A, Noor A, Alkhayyat SS, Alwassia R, Mineta K, Gojobori T, Beggs AD, Schofield PN, et al. 2019. Ontology-based prediction of cancer driver genes. Sci Rep. 9(1):17405.
   PubMedGoogle Scholar
• Beasley W, Thor M, McWilliam A, Green A, Mackay R, Slevin N, Olsson C, Pettersson N, Finizia C, Estilo C, et al. 2018. Image-based data mining to probe dosimetric correlates of radiation-induced trismus. Int J Radiat Oncol Biol Phys. 102(4):1330–1338.
   PubMed Web of Science ®Google Scholar
• Berrios DC, Galazka J, Grigorev K, Gebre S, Costes SV. 2021. NASA GeneLab: interfaces for the exploration of Space Omics Data. Nucleic Acids Res. 49(D1):D1515–D1522.
   PubMed Web of Science ®Google Scholar
• Birschwilks M, Gruenberger M, Adelmann C, Tapio S, Gerber G, Schofield PN, Grosche B. 2011. The european radiobiological archives: online access to data from radiobiological experiments. Radiat Res. 175(4):526–531.
   PubMed Web of Science ®Google Scholar
• Chen J, Althagafi A, Hoehndorf R. 2021. Predicting candidate genes from phenotypes, functions and anatomical site of expression. Bioinformatics. 37(6):853–860.
   PubMed Web of Science ®Google Scholar
• Clarke DJB, Wang L, Jones A, Wojciechowicz ML, Torre D, Jagodnik KM, Jenkins SL, McQuilton P, Flamholz Z, Silverstein MC, et al. 2019. FAIRshake: Toolkit to evaluate the FAIRness of research digital resources. Cell Syst. 9(5):417–421.
   PubMed Web of Science ®Google Scholar
• Clarke M, Collins R, Darby S, Davies C, Elphinstone P, Evans V, Godwin J, et al. 2005. Effects of radiotherapy and of differences in the extent of surgery for early breast cancer on local recurrence and 15-year survival: an overview of the randomised trials. The Lancet. 366(9503):2087–2106.
   PubMed Web of Science ®Google Scholar
• Cook DL, Mejino JLV, Rosse C. 2004. Evolution of a foundational model of physiology: symbolic representation for functional bioinformatics. Stud Health Technol Informat 107 (Pt 1):336–40.
   Google Scholar
• Decherchi S, Pedrini E, Mordenti M, Cavalli A, Sangiorgi L. 2021. Opportunities and challenges for machine learning in rare diseases. Front Med. 8:747612.
   Web of Science ®Google Scholar
• Griethuysen JJMv, Fedorov A, Parmar C, Hosny A, Aucoin N, Narayan V, Beets-Tan RGH, Fillion-Robin J-C, Pieper S, Aerts HJWL. 2017. Computational radiomics system to decode the radiographic phenotype. Cancer Res. 77(21):e104–7.
   Web of Science ®Google Scholar
• Harris K, Khachaturova I, Azab B, Maniatis T, Murukutla S, Chalhoub M, Hatoum H, Kilkenny T, Elsayegh D, Maroun R, et al. 2012. Small cell lung cancer doubling time and its effect on clinical presentation: a concise review. Clin Med Insights Oncol. 6:199–203.
   PubMedGoogle Scholar
• Hayamizu TF, Baldock RA, Ringwald M. 2015. Mouse anatomy ontologies: enhancements and tools for exploring and integrating biomedical data. Mamm Genome. 26(9–10):422–430.
   PubMed Web of Science ®Google Scholar
• Heemsbergen WD, Al-Mamgani A, Witte MG, van Herk M, Pos FJ, Lebesque JV. 2010. Urinary obstruction in prostate cancer patients from the Dutch Trial (68 Gy vs. 78 Gy): relationships with local dose, acute effects, and baseline characteristics. Int J Radiat Oncol Biol Physics. 78(1):19–25.
   PubMed Web of Science ®Google Scholar
• Jackson R, Matentzoglu N, Overton JA, Vita R, Balhoff JP, Buttigieg PL, Carbon S, et al. 2021. OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies. J Biolog Databases Curat. 2021:baab069.
   PubMedGoogle Scholar
• Jebsen NL, Trovik CS, Bauer HCF, Rydholm A, Monge OR, Hall KS, Alvegård T, Bruland ØS. 2008. Radiotherapy to improve local control regardless of surgical margin and malignancy grade in extremity and trunk wall soft tissue sarcoma: a Scandinavian Sarcoma Group Study. Int J Radiat Oncol Biol Phys. 71(4):1196–1203.
   PubMed Web of Science ®Google Scholar
• Kulmanov M, Smaili FZ, Gao X, Hoehndorf R. 2021. Semantic similarity and machine learning with ontologies. Brief Bioinfor. 22(4):1–18. https://doi.org/10.1093/bib/bbaa199.
   Web of Science ®Google Scholar
• McWilliam A, Kennedy J, Hodgson C, Osorio EV, Faivre-Finn C, van Herk M. 2017. Radiation dose to heart base linked with poorer survival in lung cancer patients. Eur J Cancer. 85:106–113.
   PubMed Web of Science ®Google Scholar
• Mukherjee P, Zhou M, Lee E, Schicht A, Balagurunathan Y, Napel S, Gillies R, Wong S, Thieme A, Leung A, et al. 2020. A shallow convolutional neural network predicts prognosis of lung cancer patients in multi-institutional CT-image data. Nat Mach Intell. 2(5):274–282.
   PubMedGoogle Scholar
• Palma G, Monti S, D'Avino V, Conson M, Liuzzi R, Pressello MC, Donato V, Deasy JO, Quarantelli M, Pacelli R, et al. 2016. A voxel-based approach to explore local dose differences associated with radiation-induced lung damage. Int J Radiat Oncol Biol Phys. 96(1):127–133.
   PubMed Web of Science ®Google Scholar
• Robinson PN, Haendel MA. 2020. Ontologies, knowledge representation, and machine learning for translational research: recent contributions. Yearb Med Inform. 29(1):159–162.
   PubMedGoogle Scholar
• Schofield PN, Kulka U, Tapio S, Grosche B. 2019. Big data in radiation biology and epidemiology; an overview of the historical and contemporary landscape of data and biomaterial archives. Int J Radiat Biol. 95(7):861–878.
   PubMed Web of Science ®Google Scholar
• Schofield PN, Sundberg JP, Sundberg BA, McKerlie C, Gkoutos GV. 2013. The mouse pathology ontology, MPATH; structure and applications. J Biomed Sem. 4(1):18.
   PubMedGoogle Scholar
• Shah RP, Selby HM, Mukherjee P, Verma S, Xie P, Xu Q, Das M, Malik S, Gevaert O, Sandy N. 2021. Machine learning radiomics model for early identification of small-cell lung cancer on computed tomography scans. JCO Clin Cancer Inform. 5:746–757.
   PubMed Web of Science ®Google Scholar
• Smaili FZ, Gao X, Hoehndorf R. 2020. Formal axioms in biomedical ontologies improve analysis and interpretation of associated data. Bioinformatics. 36(7):2229–2236.
   PubMed Web of Science ®Google Scholar
• Suh E, Stratton KL, Leisenring WM, Nathan PC, Ford JS, Freyer DR, McNeer JL, Stock W, Stovall M, Krull KR, et al. 2020. Late mortality and chronic health conditions in long-term survivors of early-adolescent and young adult cancers: a retrospective cohort analysis from the childhood cancer survivor study. Lancet Oncol. 21(3):421–435.
   PubMed Web of Science ®Google Scholar
• Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F. 2021. Global Cancer Statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 Countries. CA Cancer J Clin. 71(3):209–249.
   PubMed Web of Science ®Google Scholar
• The Gene Ontology Consortium. 2021. The gene ontology resource: enriching a gold mine. Nucleic Acids Res. 49(D1):D325–34.
   PubMed Web of Science ®Google Scholar
• Torre LA, Siegel RL, Ward EM, Jemal A. 2016. Global cancer incidence and mortality rates and trends – an UpdateGlobal cancer rates and trends – an update. Cancer Epidemiol Biomarkers Prevent. 25(1):16–27.
   PubMed Web of Science ®Google Scholar
• Veiga C, Lim P, Anaya VM, Chandy E, Ahmad R, D’Souza D, Gaze M, Moinuddin S, Gains J. 2021. Atlas construction and spatial normalisation to facilitate radiation-induced late effects research in childhood cancer. Phys Med Biol. 66(10):105005.
   Web of Science ®Google Scholar
• Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten J-W, da Silva Santos LB, Bourne PE, et al. 2016. The FAIR guiding principles for scientific data management and stewardship. Sci Data. 3(1):160018.
   PubMed Web of Science ®Google Scholar
• Wilkinson MD, Dumontier M, Sansone S-A, da S, Santos LOB, Prieto M, McQuilton P, Gautier J, Murphy D, Crosas M, et al. 2018. Evaluating FAIR-compliance through an objective, automated, community-governed framework. bioRxiv.418376.
   Google Scholar
• Wilson LJ, Bryce-Atkinson A, Green A, Li Y, Merchant TE, van Herk M, Vasquez Osorio E, Faught AM, Aznar MC. 2022. Image-based data mining applies to data collected from children. Phys Med. 99:31–43.
   PubMed Web of Science ®Google Scholar
• Zwanenburg A, Vallières M, Abdalah MA, Aerts HJWL, Andrearczyk V, Apte A, Ashrafinia S, Bakas S, Beukinga RJ, Boellaard R, et al. 2020. The image biomarker standardization initiative: standardized quantitative radiomics for high-throughput image-based phenotyping. Radiology. 295(2):328–338.
   PubMed Web of Science ®Google Scholar