A hybrid neural network model for predicting kidney disease in hypertension patients based on electronic health records

BackgroundDisease prediction based on Electronic Health Records (EHR) has become one hot research topic in biomedical community. Existing work mainly focuses on the prediction of one target disease, and little work is proposed for multiple associated diseases prediction. Meanwhile, a piece of EHR usually contains two main information: the textual description and physical indicators. However, existing work largely adopts statistical models with discrete features from numerical physical indicators in EHR, and fails to make full use of textual description information.MethodsIn this paper, we study the problem of kidney disease prediction in hypertension patients by using neural network model. Specifically, we first model the prediction problem as a binary classification task. Then we propose a hybrid neural network which incorporates Bidirectional Long Short-Term Memory (BiLSTM) and Autoencoder networks to fully capture the information in EHR.ResultsWe construct a dataset based on a large number of raw EHR data. The dataset consists of totally 35,332 records from hypertension patients. Experimental results show that the proposed neural model achieves 89.7% accuracy for the task.ConclusionsA hybrid neural network model was presented. Based on the constructed dataset, the comparison results of different models demonstrated the effectiveness of the proposed neural model. The proposed model outperformed traditional statistical models with discrete features and neural baseline systems.

[1]  Madeleine I. G. Daepp,et al.  Diet-related chronic disease in the northeastern United States: a model-based clustering approach , 2015, International Journal of Health Geographics.

[2]  P Cullen,et al.  Implications of the human genome project for the identification of genetic risk of coronary heart disease and its prevention in children. , 2001, Nutrition, metabolism, and cardiovascular diseases : NMCD.

[3]  Yafeng Ren,et al.  Detecting the Scope of Negation and Speculation in Biomedical Texts by Using Recursive Neural Network , 2018, 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

[4]  Yue Zhang,et al.  Context-Sensitive Twitter Sentiment Classification Using Neural Network , 2016, AAAI.

[5]  Sheng-Shou Hu,et al.  China cardiovascular diseases report 2015: a summary , 2017, Journal of geriatric cardiology : JGC.

[6]  B. Brenner,et al.  Adult hypertension and kidney disease: the role of fetal programming. , 2006, Hypertension.

[7]  Gary S Collins,et al.  An independent external validation and evaluation of QRISK cardiovascular risk prediction: a prospective open cohort study , 2009, BMJ : British Medical Journal.

[8]  Donghong Ji,et al.  Long short-term memory RNN for biomedical named entity recognition , 2017, BMC Bioinformatics.

[9]  Xiangxiang Zeng,et al.  Iteratively collective prediction of disease-gene associations through the incomplete network , 2017, 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

[10]  A. Sheikh,et al.  Predicting cardiovascular risk in England and Wales: prospective derivation and validation of QRISK2 , 2008, BMJ : British Medical Journal.

[11]  D. Levy,et al.  Prediction of coronary heart disease using risk factor categories. , 1998, Circulation.

[12]  Duc-Hau Le,et al.  Ontology-based disease similarity network for disease gene prediction , 2016, Vietnam Journal of Computer Science.

[13]  Mark Walker,et al.  Combining Information from Common Type 2 Diabetes Risk Polymorphisms Improves Disease Prediction , 2006, PLoS medicine.

[14]  Bulusu Lakshmana Deekshatulu,et al.  Prediction of Heart Disease Using Random Forest and Feature Subset Selection , 2015, IBICA.

[15]  A. Folsom,et al.  Coronary heart disease risk prediction in the Atherosclerosis Risk in Communities (ARIC) study. , 2003, Journal of clinical epidemiology.

[16]  P. Greenland,et al.  Coronary artery calcium score and risk classification for coronary heart disease prediction. , 2010, JAMA.

[17]  Ming Yang,et al.  Entity recognition from clinical texts via recurrent neural network , 2017, BMC Medical Informatics and Decision Making.

[18]  Francesco Mannelli,et al.  Molecular Profiling of CD34+ Cells in Idiopathic Myelofibrosis Identifies a Set of Disease‐Associated Genes and Reveals the Clinical Significance of Wilms' Tumor Gene 1 (WT1) , 2007, Stem cells.

[19]  Jing Zheng,et al.  3-year risk prediction of Coronary Heart Disease in hypertension patients: A preliminary study , 2017, 2017 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC).

[20]  G. Assmann,et al.  Simple Scoring Scheme for Calculating the Risk of Acute Coronary Events Based on the 10-Year Follow-Up of the Prospective Cardiovascular Münster (PROCAM) Study , 2002, Circulation.

[21]  Andrew McCallum,et al.  A comparison of event models for naive bayes text classification , 1998, AAAI 1998.

[22]  Li Liao,et al.  Prediction of missing common genes for disease pairs using network based module separation on incomplete human interactome , 2017, BMC Genomics.

[23]  Sang Hong Lee,et al.  Performance of risk prediction for inflammatory bowel disease based on genotyping platform and genomic risk score method , 2017, BMC Medical Genetics.

[24]  Americanjournalofkidneydisease K/DOQI clinical practice guidelines on hypertension and antihypertensive agents in chronic kidney disease. , 2004, American journal of kidney diseases : the official journal of the National Kidney Foundation.

[25]  E. Rimm,et al.  Alternative dietary indices both strongly predict risk of chronic disease. , 2012, The Journal of nutrition.

[26]  Hongfei Lin,et al.  A protein-protein interaction extraction approach based on deep neural network , 2016, Int. J. Data Min. Bioinform..

[27]  Ting Liu,et al.  Document Modeling with Gated Recurrent Neural Network for Sentiment Classification , 2015, EMNLP.

[28]  Shan Gao,et al.  Low-level structure feature extraction for image processing via stacked sparse denoising autoencoder , 2017, Neurocomputing.

[29]  Matthew Crosby,et al.  Association for the Advancement of Artificial Intelligence , 2014 .

[30]  Clive Osmond,et al.  A developmental approach to the prevention of hypertension and kidney disease: a report from the Low Birth Weight and Nephron Number Working Group , 2017, The Lancet.

[31]  Bruce Kupelnick,et al.  K/DOQI Clinical Practice Guidelines on Hypertension and Antihypertensive Agents in Chronic Kidney Disease , 2004 .

[32]  Yue Zhang,et al.  Improving Twitter Sentiment Classification Using Topic-Enriched Multi-Prototype Word Embeddings , 2016, AAAI.

[33]  Dong-Hong Ji,et al.  Neural networks for deceptive opinion spam detection: An empirical study , 2017, Inf. Sci..

[34]  Peter M Visscher,et al.  Prediction of individual genetic risk to disease from genome-wide association studies. , 2007, Genome research.

[35]  Yoshua Bengio,et al.  Neural Machine Translation by Jointly Learning to Align and Translate , 2014, ICLR.

[36]  Chengjie Sun,et al.  LSTM-CRF for Drug-Named Entity Recognition , 2017, Entropy.

[37]  Nikhil R. Pal,et al.  Identification of a small set of plasma signalling proteins using neural network for prediction of Alzheimer's disease , 2015, Bioinform..

[38]  Han Ren,et al.  Context-augmented convolutional neural networks for twitter sarcasm detection , 2018, Neurocomputing.

[39]  B. Jaber,et al.  Prevention of radiocontrast nephropathy with N-acetylcysteine in patients with chronic kidney disease: a meta-analysis of randomized, controlled trials. , 2004, American journal of kidney diseases : the official journal of the National Kidney Foundation.

[40]  Peter L. Bartlett,et al.  Boosting Algorithms as Gradient Descent , 1999, NIPS.