P1923Deep and machine learning models to improve risk prediction of cardiovascular disease using data extraction from electronic health records

2019 ◽  
Vol 40 (Supplement_1) ◽  
Author(s):  
I Korsakov ◽  
A Gusev ◽  
T Kuznetsova ◽  
D Gavrilov ◽  
R Novitskiy
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Cardiovascular Disease ◽  
Logistic Regression ◽  
Deep Learning ◽  
Risk Prediction ◽  
Learning Algorithm ◽  
Learning Models ◽  
Electronic Health ◽  
Machine Learning Models

Abstract Abstract Background Advances in precision medicine will require an increasingly individualized prognostic evaluation of patients in order to provide the patient with appropriate therapy. The traditional statistical methods of predictive modeling, such as SCORE, PROCAM, and Framingham, according to the European guidelines for the prevention of cardiovascular disease, not adapted for all patients and require significant human involvement in the selection of predictive variables, transformation and imputation of variables. In ROC-analysis for prediction of significant cardiovascular disease (CVD), the areas under the curve for Framingham: 0.62–0.72, for SCORE: 0.66–0.73 and for PROCAM: 0.60–0.69. To improve it, we apply for approaches to predict a CVD event rely on conventional risk factors by machine learning and deep learning models to 10-year CVD event prediction by using longitudinal electronic health record (EHR). Methods For machine learning, we applied logistic regression (LR) and recurrent neural networks with long short-term memory (LSTM) units as a deep learning algorithm. We extract from longitudinal EHR the following features: demographic, vital signs, diagnoses (ICD-10-cm: I21-I22.9: I61-I63.9) and medication. The problem in this step, that near 80 percent of clinical information in EHR is “unstructured” and contains errors and typos. Missing data are important for the correct training process using by deep learning & machine learning algorithm. The study cohort included patients between the ages of 21 to 75 with a dynamic observation window. In total, we got 31517 individuals in the dataset, but only 3652 individuals have all features or missing features values can be easy to impute. Among these 3652 individuals, 29.4% has a CVD, mean age 49.4 years, 68,2% female. Evaluation We randomly divided the dataset into a training and a test set with an 80/20 split. The LR was implemented with Python Scikit-Learn and the LSTM model was implemented with Keras using Tensorflow as the backend. Results We applied machine learning and deep learning models using the same features as traditional risk scale and longitudinal EHR features for CVD prediction, respectively. Machine learning model (LR) achieved an AUROC of 0.74–0.76 and deep learning (LSTM) 0.75–0.76. By using features from EHR logistic regression and deep learning models improved the AUROC to 0.78–0.79. Conclusion The machine learning models outperformed a traditional clinically-used predictive model for CVD risk prediction (i.e. SCORE, PROCAM, and Framingham equations). This approach was used to create a clinical decision support system (CDSS). It uses both traditional risk scales and models based on neural networks. Especially important is the fact that the system can calculate the risks of cardiovascular disease automatically and recalculate immediately after adding new information to the EHR. The results are delivered to the user's personal account.

Train Deep Learning Models using subsurface geological images datasets

2021 ◽  
Author(s):  
Ramy Abdallah ◽  
Clare E. Bond ◽  
Robert W.H. Butler
Keyword(s):  
Artificial Intelligence ◽  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
Learning Models ◽  
Structural Interpretation ◽  
Performance Accuracy ◽  
Learning Techniques ◽  
Machine Learning Models

<p>Machine learning is being presented as a new solution for a wide range of geoscience problems. Primarily machine learning has been used for 3D seismic data processing, seismic facies analysis and well log data correlation. The rapid development in technology with open-source artificial intelligence libraries and the accessibility of affordable computer graphics processing units (GPU) makes the application of machine learning in geosciences increasingly tractable. However, the application of artificial intelligence in structural interpretation workflows of subsurface datasets is still ambiguous. This study aims to use machine learning techniques to classify images of folds and fold-thrust structures. Here we show that convolutional neural networks (CNNs) as supervised deep learning techniques provide excellent algorithms to discriminate between geological image datasets. Four different datasets of images have been used to train and test the machine learning models. These four datasets are a seismic character dataset with five classes (faults, folds, salt, flat layers and basement), folds types with three classes (buckle, chevron and conjugate), fault types with three classes (normal, reverse and thrust) and fold-thrust geometries with three classes (fault bend fold, fault propagation fold and detachment fold). These image datasets are used to investigate three machine learning models. One Feedforward linear neural network model and two convolutional neural networks models (Convolution 2d layer transforms sequential model and Residual block model (ResNet with 9, 34, and 50 layers)). Validation and testing datasets forms a critical part of testing the model’s performance accuracy. The ResNet model records the highest performance accuracy score, of the machine learning models tested. Our CNN image classification model analysis provides a framework for applying machine learning to increase structural interpretation efficiency, and shows that CNN classification models can be applied effectively to geoscience problems. The study provides a starting point to apply unsupervised machine learning approaches to sub-surface structural interpretation workflows.</p>

scholarly journals Winter Wheat Yield Prediction Using Convolutional Neural Networks from Environmental and Phenological Data

2021 ◽  
Author(s):  
Amit Kumar Srivast ◽  
Nima Safaei ◽  
Saeed Khaki ◽  
Gina Lopez ◽  
Wenzhi Zeng ◽  
...  
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Winter Wheat ◽  
Crop Yield ◽  
Wheat Yield ◽  
Yield Prediction ◽  
Learning Models ◽  
Winter Wheat Yield ◽  
Machine Learning Models

Abstract Crop yield forecasting depends on many interactive factors including crop genotype, weather, soil, and management practices. This study analyzes the performance of machine learning and deep learning methods for winter wheat yield prediction using extensive datasets of weather, soil, and crop phenology. We propose a convolutional neural network (CNN) which uses the 1-dimentional convolution operation to capture the time dependencies of environmental variables. The proposed CNN, evaluated along with other machine learning models for winter wheat yield prediction in Germany, outperformed all other models tested. To address the seasonality, weekly features were used that explicitly take soil moisture and meteorological events into account. Our results indicated that nonlinear models such as deep learning models and XGboost are more effective in finding the functional relationship between the crop yield and input data compared to linear models and deep neural networks had a higher prediction accuracy than XGboost. One of the main limitations of machine learning models is their black box property. Therefore, we moved beyond prediction and performed feature selection, as it provides key results towards explaining yield prediction (variable importance by time). As such, our study indicates which variables have the most significant effect on winter wheat yield.

scholarly journals Machine Learning Prediction of Incidence of Alzheimer’s Disease Using Large-Scale Administrative Health Data

2019 ◽  
Author(s):  
Ji Hwan Park ◽  
Han Eol Cho ◽  
Jong Hun Kim ◽  
Melanie Wall ◽  
Yaakov Stern ◽  
...  
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Risk Prediction ◽  
Clinical Features ◽  
Large Scale ◽  
Health Data ◽  
Learning Models ◽  
Administrative Health Data ◽  
History Of ◽  
Machine Learning Models

AbstractNationwide population-based cohort provides a new opportunity to build a completely automated risk prediction model based on individuals’ history of health and healthcare beyond existing risk prediction models. We tested the possibility of machine learning models to predict future incidence of Alzheimer’s disease (AD) using large-scale administrative health data. From the Korean National Health Insurance Service database between 2002 and 2010, we obtained de-identified health data in elders above 65 years (N=40,736) containing 4,894 unique clinical features including ICD-10 codes, medication codes, laboratory values, history of personal and family illness, and socio-demographics. To define incident AD two operational definitions were considered: “definite AD” with diagnostic codes and dementia medication (n=614) and “probable AD” with only diagnosis (n=2,026). We trained and validated a random forest, support vector machine, and logistic regression to predict incident AD in 1,2,3, and 4 subsequent years. For predicting future incidence of AD in balanced samples (bootstrapping), the machine learning models showed reasonable performance in 1-year prediction with AUC of 0.775 and 0.759, based on “definite AD” and “probable AD” outcomes, respectively; in 2-year, 0.730 and 0.693; in 3-year, 0.677 and 0.644; in 4-year, 0.725 and 0.683. The results were similar when the entire (unbalanced) samples were used. Important clinical features selected in logistic regression included hemoglobin level, age, and urine protein level. This study may shed a light on the utility of the data-driven machine learning model based on large-scale administrative health data in AD risk prediction, which may enable better selection of individuals at risk for AD in clinical trials or early detection in clinical settings.

Abstract 17106: Prediction of Recurrent Atherosclerotic Cardiovascular Disease Risk Using Machine Learning and Electronic Health Record Data

Circulation ◽  
2020 ◽  
Vol 142 (Suppl_3) ◽  
Author(s):  
Ashish Sarraju ◽  
Andrew Ward ◽  
Sukyung Chung ◽  
Jiang Li ◽  
David Scheinker ◽  
...  
Keyword(s):  
Machine Learning ◽  
Myocardial Infarction ◽  
Cardiovascular Disease ◽  
Risk Prediction ◽  
Health Record ◽  
Atherosclerotic Cardiovascular Disease ◽  
Learning Models ◽  
Ascvd Risk ◽  
Machine Learning Models

Introduction: Patients with atherosclerotic cardiovascular disease (ASCVD) have high risk for recurrent ASCVD events despite statin use. Pooled cohort equations (PCE) are used for ASCVD risk prediction in primary prevention but there are no validated models for recurrent risk prediction in secondary prevention. Machine learning (ML) demonstrates promise in developing novel risk prediction models using electronic health record (EHR) data. Methods: We included adults with prior ASCVD from EHR data from an outpatient Northern California system between January 1, 2009 and December 31, 2018 with at least 2 visits at least 1 year apart and 5 years of follow up. The outcome was a recurrent ASCVD event defined as the first myocardial infarction, stroke, or fatal coronary artery disease in the 5 year follow-up period. We trained ML models to predict recurrent ASCVD risk: random forests (RF), gradient boosted machines (GBM), extreme gradient boosted models (XGBoost), and logistic regression with a standard L 2 penalty (LR) and an L 1 penalty (Lasso). We evaluated performance of ML models and the PCE on a 20% held-out test cohort using the areas under the receiver operating characteristic curves (AUCs). Results: Our cohort consisted of 32,192 patients with ASCVD (Mean age 70 years, 46% women, 12% Asian and 6% Hispanic). Less than half (49%) were on guideline directed statins. XGBoost and GBM were the best performing models for recurrent ASCVD risk prediction, while the PCE performed poorly (Figure). The top 20 predictive variables for recurrent ASCVD risk included prior events (ischemic stroke, myocardial infarction), traditional risk factors (age, blood pressure, lipid levels) and socioeconomic factors (income, education). Conclusions: EHR-trained machine learning models facilitated recurrent ASCVD risk prediction in real-world secondary prevention patients. Machine learning models developed from large datasets may help bridge contemporary gaps in ASCVD risk prediction.

scholarly journals Comparison of machine and deep learning for the classification of cervical cancer based on cervicography images

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ye Rang Park ◽  
Young Jae Kim ◽  
Woong Ju ◽  
Kyehyun Nam ◽  
Soonyung Kim ◽  
...  
Keyword(s):  
Machine Learning ◽  
Cervical Cancer ◽  
Deep Learning ◽  
Learning Algorithm ◽  
Vaginal Wall ◽  
Learning Models ◽  
Operating Characteristics ◽  
Deep Learning Algorithm ◽  
Machine Learning Models

AbstractCervical cancer is the second most common cancer in women worldwide with a mortality rate of 60%. Cervical cancer begins with no overt signs and has a long latent period, making early detection through regular checkups vitally immportant. In this study, we compare the performance of two different models, machine learning and deep learning, for the purpose of identifying signs of cervical cancer using cervicography images. Using the deep learning model ResNet-50 and the machine learning models XGB, SVM, and RF, we classified 4119 Cervicography images as positive or negative for cervical cancer using square images in which the vaginal wall regions were removed. The machine learning models extracted 10 major features from a total of 300 features. All tests were validated by fivefold cross-validation and receiver operating characteristics (ROC) analysis yielded the following AUCs: ResNet-50 0.97(CI 95% 0.949–0.976), XGB 0.82(CI 95% 0.797–0.851), SVM 0.84(CI 95% 0.801–0.854), RF 0.79(CI 95% 0.804–0.856). The ResNet-50 model showed a 0.15 point improvement (p < 0.05) over the average (0.82) of the three machine learning methods. Our data suggest that the ResNet-50 deep learning algorithm could offer greater performance than current machine learning models for the purpose of identifying cervical cancer using cervicography images.

scholarly journals Machine learning models to identify low adherence to influenza vaccination among Korean adults with cardiovascular disease

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Moojung Kim ◽  
Young Jae Kim ◽  
Sung Jin Park ◽  
Kwang Gi Kim ◽  
Pyung Chun Oh ◽  
...  
Keyword(s):  
Machine Learning ◽  
Cardiovascular Disease ◽  
Influenza Vaccination ◽  
Machine Learning Techniques ◽  
Gradient Boosting ◽  
Support Vector ◽  
Age Group ◽  
Learning Models ◽  
Extreme Gradient Boosting ◽  
Machine Learning Models

Abstract Background Annual influenza vaccination is an important public health measure to prevent influenza infections and is strongly recommended for cardiovascular disease (CVD) patients, especially in the current coronavirus disease 2019 (COVID-19) pandemic. The aim of this study is to develop a machine learning model to identify Korean adult CVD patients with low adherence to influenza vaccination Methods Adults with CVD (n = 815) from a nationally representative dataset of the Fifth Korea National Health and Nutrition Examination Survey (KNHANES V) were analyzed. Among these adults, 500 (61.4%) had answered "yes" to whether they had received seasonal influenza vaccinations in the past 12 months. The classification process was performed using the logistic regression (LR), random forest (RF), support vector machine (SVM), and extreme gradient boosting (XGB) machine learning techniques. Because the Ministry of Health and Welfare in Korea offers free influenza immunization for the elderly, separate models were developed for the < 65 and ≥ 65 age groups. Results The accuracy of machine learning models using 16 variables as predictors of low influenza vaccination adherence was compared; for the ≥ 65 age group, XGB (84.7%) and RF (84.7%) have the best accuracies, followed by LR (82.7%) and SVM (77.6%). For the < 65 age group, SVM has the best accuracy (68.4%), followed by RF (64.9%), LR (63.2%), and XGB (61.4%). Conclusions The machine leaning models show comparable performance in classifying adult CVD patients with low adherence to influenza vaccination.

414 Deep Neural Networks: A Survey Tool for Obstructive Sleep Apnea Prediction

SLEEP ◽  
2021 ◽  
Vol 44 (Supplement_2) ◽  
pp. A164-A164
Author(s):  
Pahnwat Taweesedt ◽  
JungYoon Kim ◽  
Jaehyun Park ◽  
Jangwoon Park ◽  
Munish Sharma ◽  
...  
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Obstructive Sleep Apnea ◽  
Sleep Apnea ◽  
Deep Neural Networks ◽  
Support Vector ◽  
Learning Models ◽  
Obstructive Sleep ◽  
Screening Questionnaires ◽  
Machine Learning Models

Abstract Introduction Obstructive sleep apnea (OSA) is a common sleep-related breathing disorder with an estimation of one billion people. Full-night polysomnography is considered the gold standard for OSA diagnosis. However, it is time-consuming, expensive and is not readily available in many parts of the world. Many screening questionnaires and scores have been proposed for OSA prediction with high sensitivity and low specificity. The present study is intended to develop models with various machine learning techniques to predict the severity of OSA by incorporating features from multiple questionnaires. Methods Subjects who underwent full-night polysomnography in Torr sleep center, Texas and completed 5 OSA screening questionnaires/scores were included. OSA was diagnosed by using Apnea-Hypopnea Index ≥ 5. We trained five different machine learning models including Deep Neural Networks with the scaled principal component analysis (DNN-PCA), Random Forest (RF), Adaptive Boosting classifier (ABC), and K-Nearest Neighbors classifier (KNC) and Support Vector Machine Classifier (SVMC). Training:Testing subject ratio of 65:35 was used. All features including demographic data, body measurement, snoring and sleepiness history were obtained from 5 OSA screening questionnaires/scores (STOP-BANG questionnaires, Berlin questionnaires, NoSAS score, NAMES score and No-Apnea score). Performance parametrics were used to compare between machine learning models. Results Of 180 subjects, 51.5 % of subjects were male with mean (SD) age of 53.6 (15.1). One hundred and nineteen subjects were diagnosed with OSA. Area Under the Receiver Operating Characteristic Curve (AUROC) of DNN-PCA, RF, ABC, KNC, SVMC, STOP-BANG questionnaire, Berlin questionnaire, NoSAS score, NAMES score, and No-Apnea score were 0.85, 0.68, 0.52, 0.74, 0.75, 0.61, 0.63, 0,61, 0.58 and 0,58 respectively. DNN-PCA showed the highest AUROC with sensitivity of 0.79, specificity of 0.67, positive-predictivity of 0.93, F1 score of 0.86, and accuracy of 0.77. Conclusion Our result showed that DNN-PCA outperforms OSA screening questionnaires, scores and other machine learning models. Support (if any):

scholarly journals Machine Learning-Based Malicious X.509 Certificates’ Detection

2021 ◽  
Vol 11 (5) ◽  
pp. 2164
Author(s):  
Jiaxin Li ◽  
Zhaoxin Zhang ◽  
Changyong Guo
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Ensemble Learning ◽  
Traffic Analysis ◽  
Learning Models ◽  
Detection Model ◽  
Analysis Tools ◽  
Average Accuracy ◽  
Machine Learning Models

X.509 certificates play an important role in encrypting the transmission of data on both sides under HTTPS. With the popularization of X.509 certificates, more and more criminals leverage certificates to prevent their communications from being exposed by malicious traffic analysis tools. Phishing sites and malware are good examples. Those X.509 certificates found in phishing sites or malware are called malicious X.509 certificates. This paper applies different machine learning models, including classical machine learning models, ensemble learning models, and deep learning models, to distinguish between malicious certificates and benign certificates with Verification for Extraction (VFE). The VFE is a system we design and implement for obtaining plentiful characteristics of certificates. The result shows that ensemble learning models are the most stable and efficient models with an average accuracy of 95.9%, which outperforms many previous works. In addition, we obtain an SVM-based detection model with an accuracy of 98.2%, which is the highest accuracy. The outcome indicates the VFE is capable of capturing essential and crucial characteristics of malicious X.509 certificates.

scholarly journals High performance logistic regression for privacy-preserving genome analysis

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Martine De Cock ◽  
Rafael Dowsley ◽  
Anderson C. A. Nascimento ◽  
Davis Railsback ◽  
Jianwei Shen ◽  
...  
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Genome Analysis ◽  
Local Area Network ◽  
Local Area ◽  
Activation Function ◽  
Area Network ◽  
Learning Models ◽  
Data Set ◽  
Machine Learning Models

Abstract Background In biomedical applications, valuable data is often split between owners who cannot openly share the data because of privacy regulations and concerns. Training machine learning models on the joint data without violating privacy is a major technology challenge that can be addressed by combining techniques from machine learning and cryptography. When collaboratively training machine learning models with the cryptographic technique named secure multi-party computation, the price paid for keeping the data of the owners private is an increase in computational cost and runtime. A careful choice of machine learning techniques, algorithmic and implementation optimizations are a necessity to enable practical secure machine learning over distributed data sets. Such optimizations can be tailored to the kind of data and Machine Learning problem at hand. Methods Our setup involves secure two-party computation protocols, along with a trusted initializer that distributes correlated randomness to the two computing parties. We use a gradient descent based algorithm for training a logistic regression like model with a clipped ReLu activation function, and we break down the algorithm into corresponding cryptographic protocols. Our main contributions are a new protocol for computing the activation function that requires neither secure comparison protocols nor Yao’s garbled circuits, and a series of cryptographic engineering optimizations to improve the performance. Results For our largest gene expression data set, we train a model that requires over 7 billion secure multiplications; the training completes in about 26.90 s in a local area network. The implementation in this work is a further optimized version of the implementation with which we won first place in Track 4 of the iDASH 2019 secure genome analysis competition. Conclusions In this paper, we present a secure logistic regression training protocol and its implementation, with a new subprotocol to securely compute the activation function. To the best of our knowledge, we present the fastest existing secure multi-party computation implementation for training logistic regression models on high dimensional genome data distributed across a local area network.

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