Multimodal artificial intelligence-based pathogenomics improves survival prediction in oral squamous cell carcinoma … – Nature.com
Sung, H. et al. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 Countries. CA Cancer J. Clin. 71, 209249 (2021).
Article PubMed Google Scholar
Chen, S.-H., Hsiao, S.-Y., Chang, K.-Y. & Chang, J.-Y. New insights into oral squamous cell carcinoma: From clinical aspects to molecular tumorigenesis. Int J. Mol. Sci. 22, 2252 (2021).
Article CAS PubMed Central PubMed Google Scholar
Adrien, J., Bertolus, C., Gambotti, L., Mallet, A. & Baujat, B. Why are head and neck squamous cell carcinoma diagnosed so late? Influence of health care disparities and socio-economic factors. Oral Oncol. 50, 9097 (2014).
Article CAS PubMed Google Scholar
Gonzlez-Moles, M. ., Aguilar-Ruiz, M. & Ramos-Garca, P. Challenges in the early diagnosis of oral cancer, evidence gaps and strategies for improvement: A scoping review of systematic reviews. Cancers 14, 4967 (2022).
Article PubMed Central PubMed Google Scholar
Russo, D. et al. Development and validation of prognostic models for oral squamous cell carcinoma: A systematic review and appraisal of the literature. Cancers 13, 5755 (2021).
Article PubMed Central PubMed Google Scholar
Carreras-Torras, C. & Gay-Escoda, C. Techniques for early diagnosis of oral squamous cell carcinoma: Systematic review. Med. Oral. Patol. Oral. Cir. Bucal. 20, e305-315 (2015).
Article PubMed Central PubMed Google Scholar
Alabi, R. O. et al. Machine learning in oral squamous cell carcinoma: Current status, clinical concerns and prospects for future-A systematic review. Artif. Intell. Med. 115, 102060 (2021).
Article PubMed Google Scholar
Qiu L, Khormali A, & Liu K. Deep Biological Pathway Informed Pathology-Genomic Multimodal Survival Prediction. (2023) [cited 2023 Apr 3]; https://arxiv.org/abs/2301.02383
Vale-Silva, L. A. & Rohr, K. Long-term cancer survival prediction using multimodal deep learning. Sci. Rep. 11, 13505 (2021).
Article CAS PubMed Central ADS PubMed Google Scholar
Carrillo-Perez, F. et al. Machine-learning-based late fusion on multi-omics and multi-scale data for non-small-cell lung cancer diagnosis. JPM 12, 601 (2022).
Article PubMed Central PubMed Google Scholar
Lipkova, J. et al. Artificial intelligence for multimodal data integration in oncology. Cancer Cell. 40, 10951110 (2022).
Article CAS PubMed Central PubMed Google Scholar
Steyaert, S. et al. Multimodal deep learning to predict prognosis in adult and pediatric brain tumors. Commun. Med. 3, 44 (2023).
Article PubMed Central PubMed Google Scholar
Saravi, B. et al. Artificial intelligence-driven prediction modeling and decision making in spine surgery using hybrid machine learning models. J. Personal. Med. 12, 509 (2022).
Article Google Scholar
Zuley, M.L., Jarosz, R., Kirk, S., Lee, Y., Colen, R., & Garcia, K., et al. The Cancer Genome Atlas Head-Neck Squamous Cell Carcinoma Collection (TCGA-HNSC), The Cancer Imaging Archive, 2016 (Accessed 3 Apr 2023); https://wiki.cancerimagingarchive.net/x/VYG0
Li, X. et al. Multi-omics analysis reveals prognostic and therapeutic value of cuproptosis-related lncRNAs in oral squamous cell carcinoma. Front. Genet. 13, 984911 (2022).
Article CAS PubMed Central PubMed Google Scholar
Zou, C. et al. Identification of immune-related risk signatures for the prognostic prediction in oral squamous cell carcinoma. J. Immunol. Res. 2021, 6203759 (2021).
Article PubMed Central PubMed Google Scholar
Macenko, M., Niethammer, M., Marron, J.S., Borland, D., Woosley, J.T., Xiaojun, G., et al. A method for normalizing histology slides for quantitative analysis. In 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2009 (IEEE, accessed 4 Apr 2023]. P. 11071110. http://ieeexplore.ieee.org/document/5193250/
Vahadane, A. et al. Structure-preserving color normalization and sparse stain separation for histological images. IEEE Trans. Med. Imaging 35, 19621971 (2016).
Article PubMed Google Scholar
Salvi, M., Acharya, U. R., Molinari, F. & Meiburger, K. M. The impact of pre- and post-image processing techniques on deep learning frameworks: A comprehensive review for digital pathology image analysis. Comput. Biol. Med. 128, 104129 (2021).
Article PubMed Google Scholar
Carpenter, A. E. et al. Cell Profiler: Image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 7, R100 (2006).
Article PubMed Central PubMed Google Scholar
Hughey, J. J. & Butte, A. J. Robust meta-analysis of gene expression using the elastic net. Nucleic Acids Res. 43, e79 (2015).
Article PubMed Central PubMed Google Scholar
Tschodu, D. et al. Re-evaluation of publicly available gene-expression databases using machine-learning yields a maximum prognostic power in breast cancer. Sci. Rep. 13, 16402 (2023).
Article CAS PubMed Central ADS PubMed Google Scholar
Kanehisa, M. & Goto, S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 2730 (2000).
Article CAS PubMed Central PubMed Google Scholar
Kanehisa, M. Toward understanding the origin and evolution of cellular organisms. Protein Sci. 28, 19471951 (2019).
Article CAS PubMed Central PubMed Google Scholar
Kanehisa, M., Furumichi, M., Sato, Y., Kawashima, M. & Ishiguro-Watanabe, M. KEGG for taxonomy-based analysis of pathways and genomes. Nucleic Acids Res. 51, D587D592 (2023).
Article CAS PubMed Google Scholar
Ye, H. et al. Metabolism-related bioinformatics analysis reveals that HPRT1 facilitates the progression of oral squamous cell carcinoma in vitro. J. Oncol. 2022, 116 (2022).
Google Scholar
Ferreira, A.-K. et al. Survival and prognostic factors in patients with oral squamous cell carcinoma. Med. Oral. Patol. Oral. Cir. Bucal. 26, e387e392 (2021).
Article PubMed Google Scholar
Asio, J., Kamulegeya, A. & Banura, C. Survival and associated factors among patients with oral squamous cell carcinoma (OSCC) in Mulago hospital, Kampala, Uganda. Cancers Head Neck. 3, 9 (2018).
Article PubMed Central PubMed Google Scholar
Girod, A., Mosseri, V., Jouffroy, T., Point, D. & Rodriguez, J. Women and squamous cell carcinomas of the oral cavity and oropharynx: Is there something new?. J. Oral Maxillof. Surg. 67, 19141920 (2009).
Article Google Scholar
Wong, K., Rostomily, R. & Wong, S. Prognostic gene discovery in glioblastoma patients using deep learning. Cancers 11, 53 (2019).
Article CAS PubMed Central PubMed Google Scholar
Hsich, E., Gorodeski, E. Z., Blackstone, E. H., Ishwaran, H. & Lauer, M. S. Identifying important risk factors for survival in patient with systolic heart failure using random survival forests. Circ. Cardiovasc. Qual. Outcomes 4, 3945 (2011).
Article PubMed Google Scholar
Ishwaran, H., Kogalur, U. B., Gorodeski, E. Z., Minn, A. J. & Lauer, M. S. High-dimensional variable selection for survival data. J. Am. Stat. Assoc. 105, 20517 (2010).
Article MathSciNet CAS Google Scholar
Ishwaran, H., Kogalur, U. B., Chen, X. & Minn, A. J. Random survival forests for high-dimensional data. Stat. Anal. Data Min. ASA Data Sci. J. 2011(4), 11532 (2011).
Article MathSciNet Google Scholar
Katzman, J. L. et al. Deepsurv: personalized treatment recommender system using a cox proportional hazards deep neural network. BMC Med. Res. Methol. 18, 187202 (2018).
Google Scholar
Sargent, D. J. Comparison of artificial neural networks with other statistical approaches. Cancer 91, 16361642 (2001).
Article CAS PubMed Google Scholar
Xiang, A., Lapuerta, P., Ryutov, A., Buckley, J. & Azen, S. Comparison of the performance of neural network methods and Cox regression for censored survival data. Comput. Stat. Data Anal. 34, 24357 (2000).
Article Google Scholar
Nie, Z., Zhao, P., Shang, Y. & Sun, B. Nomograms to predict the prognosis in locally advanced oral squamous cell carcinoma after curative resection. BMC Cancer 21, 372 (2021).
Article PubMed Central PubMed Google Scholar
Nojavanasghari, B., Gopinath, D., Koushik, J., Baltruaitis, T., & Morency, L. P. Deep multimodal fusion for persuasiveness prediction. In Proceedings of the 18th ACM International Conference on Multimodal Interaction. 284288 (2016).
Kampman, O., Barezi, E. J., Bertero, D., & Fung, P. Investigating audio, video, and text fusion methods for end-to-end automatic personality prediction. In Proceedings of the 56th Annual Meeting of the Association for Computational Linguistics vol. 2.606611 (2018).
Wang, Z., Li, R., Wang, M. & Li, A. Gpdbn: Deep bilinear network integrating both genomic data and pathological images for breast cancer prognosis prediction. Bioinformatics 27, 29632970 (2021).
Article Google Scholar
Subramanian, V., Syeda-Mahmood, T., & Do, M. N. Multimodal fusion using sparse cca for breast cancer survival prediction. In Proceedings of IEEE 18th International Symposium on Biomedical Imaging (ISBI).14291432 (2021).
Mai, S., Hu, H., & Xing, S. Modality to modality translation: An adversarial representation learning and graph fusion network for multimodal fusion. In Proceedings of the AAAI Conference on Artificial Intelligence 164172 (2020).
Mobadersany, P. et al. Predicting cancer outcomes from histology and genomics. Predicting cancer outcomes from histology and genomics using convolutional networks. Proc. Natl. Acad. Sci. 115, 29702979 (2018).
Article ADS Google Scholar
Wang, C. et al. A cancer survival prediction method based on graph convolutional network. IEEE Trans. Nanobiosci. 19, 117126 (2020).
Article Google Scholar
Zadeh, A., Chen, M., Poria, S., Cambria, E., & Morency, L. P Tensor fusion network for multimodal sentiment analysis. In Proceedings of the 2017 Conference on Empirical Methods in Natural Language Processing, 11031114 (2017).
Chen, R. J. et al. Pathomic fusion: An integrated framework for fusing histopathology and genomic features for cancer diagnosis and prognosis. IEEE Trans. Med. Imaging 41, 757770 (2022).
Article PubMed Central PubMed Google Scholar
Kim, J. H., On, K. W., Lim, W., Kim, J., Ha, J. W., & Zhang, B. T. Hadamard product for low-rank bilinear pooling. In Proceedings of International Conference on Learning Representations, 114 (2017)
Liu, Z., Shen, Y., Lakshminarasimhan, V. B., Liang, P. P., Zadeh, A., & Morency, L. P. Efficient low-rank multimodal fusion with modality-specific factors. In Proceedings of the 56th Annual Meeting of the Association for Computational Linguistics. 22472256 (2021)
Li, R., Wu, X., Li, A. & Wang, M. Hfbsurv: Hierarchical multimodal fusion with factorized bilinear models for cancer survival prediction. Bioinformatics 38, 25872594 (2022).
Article CAS PubMed Central PubMed Google Scholar
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Multimodal artificial intelligence-based pathogenomics improves survival prediction in oral squamous cell carcinoma ... - Nature.com