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TEI of Athens eJournals

MIMIC III and its contribution to critical care prediction models

Dimitris Markopoulos, Anastasios Tsolakidis, Christos Skourlas

Abstract


Abstract:

Purpose - The present paper attempts to present the research that has been made on prediction models using deep learning methods with data retrieved from mimic III database and to identify challenges and possible areas for future research.

Methodology - A literature research was conducted for articles related to MIMIC III and prediction models related to the database published from 2016 to 2021. Also, reviews and papers related to neural networks, machine learning, data mining and implementation and usage of electronic health records (EHR) in ICU were investigated to support findings from mimic III papers.

Findings - Prediction algorithms can be very useful in ICU units. Although some algorithms, such as InSight are specialized in specific diseases, others such as XGBOOST and recurrent neural networks can be used in a broader area, presenting quite accurate results.

Originality - Usually, reviews categorize research on MIMIC database per disease or per the desired outcome, such as the prediction of length of stay and the final outcome. The current study categorizes the research based on the tools, prediction models, and algorithms used. This way, it is possible to understand better how each method performs to various conditions and desired outcomes.


Keywords


MIMIC III; neural networks; random forests; prediction models; intensive care units; big data;

References


Gonçalves, A., Portela, F., Santos, M.F., & Rua, F. “Towards of a Real-time Big Data Architecture to Intensive Care”. Procedia Computer Science. 2017, pp. 585 - 590. doi:10.1016/j.comnet.2016.12.019.

Weissman, G.E., Crane-Droesch, A., Chivers, C., Luong, T., Hanish, A., Levy, M.Z., et al. "Locally Informed Simulation to Predict Hospital Capacity Needs During the COVID-19 Pandemic". Annals of internal medicine. 07 2020, pp. 21-28. doi:10.7326/M20-1260.

Calvert J, Mao Q, Hoffman JL, Jay M, Desautels T, Mohamadlou H,Chettipally U, Das R. "Using electronic health record collected clinical variables to predict medical intensive care unit mortality". Annals of Medicine and Surgery. 2016. doi: 10.1016/j.amsu.2016.09.002.

Alistair E. W. Johnson, A Tom J. Pollard, A Roger G. Mark. "Reproducibility in critical care: a mortality prediction case study". Proceedings of the 2nd Machine Learning for Healthcare Conference. 2017, 68, pp. 361-376.

Johnson, A.E., Ghassemi, M., Nemati, S., Niehaus, K., Clifton, "Machine Learning and Decision Support in Critical Care". D., Clifford, G. 2016. Proceedings of the IEEE. pp. 444-466. doi:10.1109/JPROC.2015.2501978.

Poucke SV, Zhang Z, Schmitz M, Vukicevic M, Laenen MV, et al. "Scalable predictive analysis in critically ill patients using a visual open data analysis platform". PLOS ONE.2016,Vol.11,1.

doi: https://doi.org/10.1371/journal.pone.0145791

Ning Ding, Cuirong Guo, Changluo Li, Yang Zhou and Xiangping ChaiNing Ding, Cuirong Guo, Changluo Li, Yang Zhou and Xiangping Chai. "An Artificial Neural Networks Model for Early Predicting In-Hospital Mortality in Acute Pancreatitis in MIMIC-III". BioMed Research International. 2021, Vol. 2021. doi: https://doi.org/10.1155/2021/6638919.

Leo Anthony Celi, Sean Galvin, Guido Davidzon,Joon Lee, Daniel Scott,Roger Mark. "A Database-driven Decision Support System: Customized Mortality Prediction". Journal of Personalized Medicine. 2012, Vol. 2, pp. 138-148. doi:10.3390/jpm2040138.

Ke Lin, Yonghua Hu, Guilan Kong. "Predicting in-hospital mortality of patients with acute kidney injury in the ICU using random forest model". International Journal of Medical Informatics. 2019, Vol. 125, pp. 55-61. doi:https://doi.org/10.1016/j.ijmedinf.2019.02.002.

Bhargava K Reddy, Dursun Delen. "Predicting hospital readmission for lupus patients: An RNN-LSTM-based deep-learning methodology". Computers in Biology and Medicine. 2018, Vol. 101, pp. 199-209. doi:https://doi.org/10.1016/j.compbiomed.2018.08.029

Jagannatha, A. N., & Yu, H. "Bidirectional RNN for Medical Event Detection in Electronic Health Records". Proceedings of the conference. Association for Computational Linguistics. North American Chapter. 2016. doi: https://doi.org/10.18653/v1/n16-1056.

Choi, Edward, Mohammad Taha Bahadori, Andy Schuetz, Walter F. Stewart, and Jimeng Sun. "Doctor ai: Predicting clinical events via recurrent neural networks". 2016. pp. 301-318.

Yu K, Zhang M, Cui T, Hauskrecht M. "Monitoring ICU Mortality Risk with A Long Short-Term Memory Recurrent Neural Network". Pacific Symposium on Biocomputing. 2020, Vol. 25, pp. 103-114.

Matthieu Scherpf, Felix Gräßer, Hagen Malberg, Sebastian Zaunseder. "Predicting sepsis with a recurrent neural network using the MIMIC III database". Computers in Biology and Medicine. 2019, 113. doi:https://doi.org/10.1016/j.compbiomed.2019.10335.

T. Gentimis, A. J. Alnaser, A. Durante, K. Cook and R. Steele, "Predicting Hospital Length of Stay using Neural Networks on MIMIC III Data". 2017. IEEE 15th Intl Conf on Dependable, Autonomic and Secure Computing, 15th Intl Conf on Pervasive Intelligence and Computing, 3rd Intl Conf on Big Data Intelligence and Computing and Cyber Science and Technology Congress (DASC/PiCom/DataCom/CyberSciTech). pp.1194-1201.doi:10.1109/DASC-PICom-DataCom-CyberSciTec.2017.191.

Davoodi R., Moradi M.H. "Mortality prediction in intensive care units (ICUs) using a deep rule-based fuzzy classifier". Journal of Biomedical Informatics. 2018, pp. 48-59.

Huang, J., Osorio, C., & Sy, L. W. "An empirical evaluation of deep learning for ICD-9 code assignment using MIMIC-III clinical notes". Computer methods and programs in biomedicine. 2019, 177, pp. 141-153.

James Mullenbach, Sarah Wiegreffe, Jon Duke, Jimeng Sun, Jacob Eisenstein. "Explainable Prediction of Medical Codes from Clinical Text". arXiv preprint arXiv:1802.05695. 2018.

Guestrin, Tianqi Chen and Carlos "XGBoost: A Scalable Tree Boosting System". New York, NY, USA : s.n., 2016. In Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD '16). Association for Computing Machinery. pp. 785-794. doi:https://doi.org/10.1145/2939672.2939785.

Li F, Xin H, Zhang J, et al. "Prediction model of in-hospital mortality in intensive care unit patients with heart failure: machine learning-based, retrospective analysis of the MIMIC-III database". BMJ Open 2021 11:e044779. doi: 10.1136/bmjopen-2020-044779.

Hou, N., Li, M., He, L. et al. "Predicting 30-days mortality for MIMIC-III patients with sepsis-3: a machine learning approach using XGboost". Journal of Translational Medicine. 2020. doi:https://doi.org/10.1186/s12967-020-02620-5.

Thais Mayumi, OshiroPedro Santoro, PerezJosé, Augusto Baranauskas, "How Many Trees in a Random Forest?" Berlin, Heidelberg : Springer, 2012. Machine Learning and Data Mining in Pattern Recognition. MLDM 2012. Lecture Notes in Computer Science. Vol. 7376, pp. 154-168. doi: https://doi.org/10.1007/978-3-642-31537-4_13.

McWilliams, Chris & Lawson, Daniel & Santos-Rodriguez, Raul & Gilchrist, Iain & Champneys, Alan & Gould, Timothy & Thomas, Mathew & Bourdeaux, Christopher. "Towards a decision support tool for intensive care discharge: machine learning algorithm development using electronic healthcare data from MIMICIII and Bristol, UK". 2019. doi: http://10.1136/bmjopen-2018-025925.

Desautels T, Calvert J, Hoffman J, Jay M, Kerem Y, Shieh L, Shimabukuro D, Chettipally U, Feldman MD, Barton C, Wales DJ, Das R. "Prediction of Sepsis in the Intensive Care Unit With Minimal Electronic Health Record Data: A Machine Learning Approach". JMIR Med Inform. 2016, Vol. 4, 3. doi: http://10.2196/medinform.5909.

Mao, Qingqing, Melissa Jay, Jana L. Hoffman, Jacob Calvert, Christopher Barton, David Shimabukuro, Lisa Shieh et al. "Multicentre validation of a sepsis prediction algorithm using only vital sign data in the emergency department, general ward and ICU". BMJ open 8. 2018. doi:http://dx.doi.org/10.1136/bmjopen-2017-017833.

Jacob S. Calvert, Daniel A. Price, Uli K. Chettipally, Christopher W. Barton, Mitchell D. Feldman, Jana L. Hoffman, Melissa Jay, Ritankar Das. "A computational approach to early sepsis detection. Computers in Biology and Medicine". 2016, 74, pp. 69-73. doi: https://doi.org/10.1016/j.compbiomed.2016.05.003.

Jacob Calvert, Qingqing Mao, Angela J. Rogers, Christopher Barton, Melissa Jay, Thomas Desautels, Hamid Mohamadlou, Jasmine Jan, Ritankar Das. "A computational approach to mortality prediction of alcohol use disorder inpatients". Computers in Biology and Medicine. 2016, 75, pp. 74-79. doi: https://doi.org/10.1016/j.compbiomed.2016.05.015.

A. Budrionis, M. Miara, P. Miara, S. Wilk and J. G. Bellika. "Benchmarking PySyft Federated Learning Framework on MIMIC-III Dataset". IEEE Access. 2021, Vol. 9, pp. 116869-116878. doi: 10.1109/ACCESS.2021.3105929.

Zhu Yibing, Zhang Jin, Wang Guowei, Yao Renqi, Ren Chao, Chen Ge et al. "Machine Learning Prediction Models for Mechanically Ventilated Patients: Analyses of the MIMIC-III Database". Frontiers in Medicine. 2021, p. 955. doi: http://10.3389/fmed.2021.662340.

Sanjay Purushotham, Chuizheng Meng, Zhengping Che, Yan Liu. "Benchmark of Deep Learning Models on Large Healthcare MIMIC Datasets". Journal of Biomedical Informatics. 2018, Vol. 83, pp. 112-134. doi: https://doi.org/10.1016/j.jbi.2018.04.007.

Shirly Wang, Matthew B. A. McDermott,Geeticka Chauhan,Marzyeh Ghassemi,Michael C. Hughes,Tristan Naumann. "MIMIC-Extract: A Data Extraction, Preprocessing, and Representation Pipeline for MIMIC-III". Proceedings of the ACM Conference on Health, Inference, and Learning, Association for Computing Machinery. 2020, pp. 222-235.

Zhale Nowroozilarki, Arash Pakbin,James Royalty,Donald K.K. Lee,Bobak J. Mortazavi. "Real-time Mortality Prediction Using MIMIC-IV ICU Data Via Boosted Nonparametric Hazard". doi: https://10.1109/BHI50953.2021.9508537.

Gao Q, Wang D, Sun P, Luan X, Wang W. Sentiment Analysis "Based on the Nursing Notes on In-Hospital 28-Day Mortality of Sepsis Patients Utilizing the MIMIC-III Database". Comput Math Methods Med. 2021 Oct 13;2021:3440778. 2021, p. doi: 10.1155/2021/3440778.

Syed, Mahanaz & Syed, Shorabuddin & Sexton, Kevin & Syeda, Hafsa & Garza, Maryam & Zozus et al. "Informatics Application of Machine Learning in Intensive Care Unit (ICU) Settings Using MIMIC Dataset: Systematic Review". Informatics. 2021, Vol. 8, 16. doi: https://doi.org/10.3390/informatics8010016.

Tang F., Ishwaran H. "Random forest missing data algorithms". Stat Anal Data Min: The ASA Data Sci Journal. 2017, Vol. 10, pp. 363– 377. doi: https://doi.org/10.1002/sam.11348

Alexander Meyer, Dina Zverinski, Boris Pfahringer, Jörg Kempfert, Titus Kuehne et al. Machine learning for real-time prediction of complications in critical care: a retrospective study. The Lancet Respiratory Medicine. 2018, Vol. 6, 12, pp. 905-91 .


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DOI: 10.26265/jiim.v6i2.4495

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