{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T14:58:01Z","timestamp":1761490681308},"reference-count":26,"publisher":"Springer Science and Business Media LLC","issue":"S18","license":[{"start":{"date-parts":[[2018,12,1]],"date-time":"2018-12-01T00:00:00Z","timestamp":1543622400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2018,12]]},"DOI":"10.1186\/s12859-018-2511-9","type":"journal-article","created":{"date-parts":[[2018,12,21]],"date-time":"2018-12-21T08:42:03Z","timestamp":1545381723000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Scalable deep text comprehension for Cancer surveillance on high-performance computing"],"prefix":"10.1186","volume":"19","author":[{"given":"John X.","family":"Qiu","sequence":"first","affiliation":[]},{"given":"Hong-Jun","family":"Yoon","sequence":"additional","affiliation":[]},{"given":"Kshitij","family":"Srivastava","sequence":"additional","affiliation":[]},{"given":"Thomas P.","family":"Watson","sequence":"additional","affiliation":[]},{"given":"J.","family":"Blair Christian","sequence":"additional","affiliation":[]},{"given":"Arvind","family":"Ramanathan","sequence":"additional","affiliation":[]},{"given":"Xiao C.","family":"Wu","sequence":"additional","affiliation":[]},{"given":"Paul A.","family":"Fearn","sequence":"additional","affiliation":[]},{"given":"Georgia D.","family":"Tourassi","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2018,12,21]]},"reference":[{"issue":"5","key":"2511_CR1","first-page":"851","volume":"18","author":"S Min","year":"2017","unstructured":"Min S, Lee B, Yoon S. Deep learning in bioinformatics. Brief Bioinform. 2017;18(5):851\u2013869.2.","journal-title":"Brief Bioinform"},{"issue":"7553","key":"2511_CR2","doi-asserted-by":"publisher","first-page":"436.3","DOI":"10.1038\/nature14539","volume":"521","author":"Y LeCun","year":"2015","unstructured":"LeCun Y, Bengio Y, Hinton G. Deep learning. Nature. 2015;521(7553):436.3.","journal-title":"Nature"},{"key":"2511_CR3","first-page":"265","volume-title":"Proceedings of the 28th International Conference on Machine Learning","author":"QV Le","year":"2011","unstructured":"Le QV, Ngiam J, Coates A, Lahiri A, Prochnow B, Ng AY. On optimization methods for deep learning. In: Proceedings of the 28th International Conference on Machine Learning; 2011. p. 265\u2013272.4."},{"issue":"3","key":"2511_CR4","doi-asserted-by":"publisher","first-page":"1080","DOI":"10.1200\/JCO.1999.17.3.1080","volume":"17","author":"TJ Smith","year":"1999","unstructured":"Smith TJ, Davidson NE, Schapira DV, Grunfeld E, Muss HB, Vogel VG III, et al. American Society of Clinical Oncology 1998 update of recommended breast cancer surveillance guidelines. J Clin Oncol. 1999;17(3):1080\u20131080.5.","journal-title":"J Clin Oncol"},{"issue":"1","key":"2511_CR5","doi-asserted-by":"publisher","first-page":"7","DOI":"10.3322\/caac.21332","volume":"66","author":"RL Siegel","year":"2016","unstructured":"Siegel RL, Miller KD, Jemal A. Cancer statistics, 2016. CA Cancer J Clin. 2016;66(1):7\u201330.6.","journal-title":"CA Cancer J Clin"},{"key":"2511_CR6","first-page":"281","volume-title":"Map-reduce for machine learning on multicore","author":"CT Chu","year":"2007","unstructured":"Chu CT, Kim SK, Lin YA, Yu Y, Bradski G, Olukotun K, et al. Map-reduce for machine learning on multicore. In: Advances in neural information processing systems; 2007. p. 281\u2013288.7."},{"issue":"9","key":"2511_CR7","doi-asserted-by":"publisher","first-page":"803","DOI":"10.1109\/TAC.1986.1104412","volume":"31","author":"J Tsitsiklis","year":"1986","unstructured":"Tsitsiklis J, Bertsekas D, Athans M. Distributed asynchronous deterministic and stochastic gradient optimization algorithms. IEEE Trans Autom Control. 1986;31(9):803\u201312.","journal-title":"IEEE Trans Autom Control"},{"key":"2511_CR8","first-page":"1223","volume-title":"Large scale distributed deep networks. In: advances in neural information processing systems","author":"J Dean","year":"2012","unstructured":"Dean J, Corrado G, Monga R, Chen K, Devin M, Mao M, et al. Large scale distributed deep networks. In: advances in neural information processing systems; 2012. p. 1223\u20131231.9."},{"issue":"2","key":"2511_CR9","first-page":"26","volume":"4","author":"T Tieleman","year":"2012","unstructured":"Tieleman T, Hinton G. Lecture 6.5-rmsprop: divide the gradient by a running average of its recent magnitude. COURSERA: Neural networks for machine learning. 2012;4(2):26\u201331.10.","journal-title":"COURSERA: Neural networks for machine learning"},{"key":"2511_CR10","first-page":"11","volume-title":"ADADELTA: an adaptive learning rate method. arXiv preprint arXiv:12125701","author":"MD Zeiler","year":"2012","unstructured":"Zeiler MD. ADADELTA: an adaptive learning rate method. arXiv preprint arXiv:12125701; 2012. p. 11."},{"key":"2511_CR11","first-page":"12","volume-title":"Adam: A method for stochastic optimization. arXiv preprint arXiv:14126980","author":"DP Kingma","year":"2014","unstructured":"Kingma DP, Ba J. Adam: A method for stochastic optimization. arXiv preprint arXiv:14126980; 2014. p. 12."},{"key":"2511_CR12","doi-asserted-by":"crossref","unstructured":"Penberthy LT, Winn DM, Scott SM. Cancer surveillance informatics. In: Oncology Informatics. Boston: Academic Press; 2016. p. 277\u2013285.13.","DOI":"10.1016\/B978-0-12-802115-6.00014-8"},{"issue":"6","key":"2511_CR13","doi-asserted-by":"publisher","first-page":"749","DOI":"10.1093\/aje\/kwt441","volume":"179","author":"DS Carrell","year":"2014","unstructured":"Carrell DS, Halgrim S, Tran DT, Buist DS, Chubak J, Chapman WW, et al. Using natural language processing to improve efficiency of manualchart abstraction in research: the case of breast cancer recurrence. Am J Epidemiol. 2014;179(6):749\u2013758.14.","journal-title":"Am J Epidemiol"},{"key":"2511_CR14","first-page":"41","volume-title":"Proceedings of the Australasian Language Technology Association Workshop","author":"Y Li","year":"2010","unstructured":"Li Y, Martinez D. Information extraction of multiple categories from pathology reports. In: Proceedings of the Australasian Language Technology Association Workshop; 2010. p. 41\u201348.15."},{"issue":"11","key":"2511_CR15","first-page":"613","volume":"18","author":"G Salton","year":"1975","unstructured":"Salton G, Wong A, Yang CS. A vector space model for automatic indexing. ACM computing surveys (CSUR). 1975 Nov;18(11):613\u201320.","journal-title":"ACM computing surveys (CSUR)"},{"key":"2511_CR16","first-page":"3111","volume-title":"Distributed representations of words and phrases and their compositionality","author":"T Mikolov","year":"2013","unstructured":"Mikolov T, Sutskever I, Chen K, Corrado GS, Dean J. Distributed representations of words and phrases and their compositionality. In: Advances in neural information processing systems; 2013. p. 3111\u20133119.17."},{"key":"2511_CR17","first-page":"18","volume-title":"Convolutional neural networks for sentence classification. arXiv preprint arXiv:14085882","author":"Y Kim","year":"2014","unstructured":"Kim Y. Convolutional neural networks for sentence classification. arXiv preprint arXiv:14085882; 2014. p. 18."},{"issue":"11","key":"2511_CR18","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1145\/1168918.1168898","volume":"41","author":"D Tarditi","year":"2006","unstructured":"Tarditi D, Puri S, Oglesby J. Accelerator: using data parallelism to program GPUs for general-purpose uses. ACM SIGPLAN Not. 2006;41(11):325\u2013335.19.","journal-title":"ACM SIGPLAN Not"},{"key":"2511_CR19","unstructured":"Fritz AG. In: International classification of diseases for oncology: ICD-O, vol. 20. Geneva: World Health Organization Press; 2000."},{"key":"2511_CR20","first-page":"21","volume-title":"A sensitivity analysis of (and practitioners\u2019 guide to) convolutional neural networks for sentence classification. arXiv preprintarXiv:151003820","author":"Y Zhang","year":"2015","unstructured":"Zhang Y, Wallace B. A sensitivity analysis of (and practitioners\u2019 guide to) convolutional neural networks for sentence classification. arXiv preprintarXiv:151003820; 2015. p. 21."},{"issue":"1","key":"2511_CR21","doi-asserted-by":"publisher","first-page":"244","DOI":"10.1109\/JBHI.2017.2700722","volume":"22","author":"JX Qiu","year":"2018","unstructured":"Qiu JX, Yoon HJ, Fearn PA, Tourassi GD. Deep learning for automated extraction of primary sites from cancer pathology reports. IEEE journal of biomedical and health informatics. 2018;22(1):244\u2013251.22.","journal-title":"IEEE journal of biomedical and health informatics"},{"key":"2511_CR22","doi-asserted-by":"crossref","unstructured":"Bottou L. Large-scale machine learning with stochastic gradient descent. In: Proceedings of COMPSTAT\u20192010. Heidelberg: Physica-Verlag; 2010. p. 177\u2013186.23.","DOI":"10.1007\/978-3-7908-2604-3_16"},{"key":"2511_CR23","unstructured":"Anderson D, Vlimant JR, Spiropulu M. An MPI-Based Python Framework for Distributed Training with Keras. arXiv preprint arXiv:171205878.2017;.24."},{"key":"2511_CR24","volume-title":"Keras. GitHub","author":"F Chollet","year":"2013","unstructured":"Chollet F, et al. Keras. GitHub. 2013. \n                    https:\/\/github.com\/fchollet\/keras\n                    \n                  ."},{"key":"2511_CR25","first-page":"265","volume-title":"Operating Systems Design and Implementation","author":"M Abadi","year":"2016","unstructured":"Abadi M, Barham P, Chen J, Chen Z, Davis A, Dean J, et al. TensorFlow: A System for Large-Scale Machine Learning. In: Operating Systems Design and Implementation, vol. vol. 16; 2016. p. 265\u2013283.26."},{"key":"2511_CR26","doi-asserted-by":"crossref","unstructured":"Piskorski J, Yangarber R. Information extraction: Past, present and future. In: Multi-source, multilingual information extraction and summarization. Berlin: Springer; 2013. p. 23\u201349.","DOI":"10.1007\/978-3-642-28569-1_2"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-018-2511-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-018-2511-9\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-018-2511-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,12,21]],"date-time":"2019-12-21T00:04:54Z","timestamp":1576886694000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-018-2511-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,12]]},"references-count":26,"journal-issue":{"issue":"S18","published-print":{"date-parts":[[2018,12]]}},"alternative-id":["2511"],"URL":"https:\/\/doi.org\/10.1186\/s12859-018-2511-9","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,12]]},"assertion":[{"value":"21 December 2018","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not Applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not Applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"488"}}