scholarly journals Detecting Rare Diseases in Electronic Health Records Using Machine Learning and Knowledge Engineering: Case Study of Acute Hepatic Porphyria

2020 ◽  
Author(s):  
Aaron Cohen ◽  
Steven Chamberlin ◽  
Thomas Deloughery ◽  
Michelle Nguyen ◽  
Steven Bedrick ◽  
...  
Keyword(s):  
Machine Learning ◽  
Rare Diseases ◽  
Knowledge Engineering ◽  
Medical Center ◽  
Academic Medical Center ◽  
Diagnostic Testing ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Data Set ◽  
Electronic Health

AbstractBackgroundWith the growing adoption of the electronic health record (EHR) worldwide over the last decade, new opportunities exist for leveraging EHR data for detection of rare diseases. Rare diseases are often not diagnosed or delayed in diagnosis by clinicians who encounter them infrequently. One such rare disease that may be amenable to EHR-based detection is acute hepatic porphyria (AHP). AHP consists of a family of rare, metabolic diseases characterized by potentially life-threatening acute attacks and, for some patients, chronic debilitating symptoms that negatively impact daily functioning and quality of life. The goal of this study was to apply machine learning and knowledge engineering to a large extract of EHR data to determine whether they could be effective in identifying patients not previously tested for AHP who should receive a proper diagnostic workup for AHP.Methods and FindingsWe used an extract of the complete EHR data of 200,000 patients from an academic medical center for up to 10 years longitudinally and enriched it with records from an additional 5,571 patients from the center containing any mention of porphyria in notes, laboratory tests, diagnosis codes, and other parts of the record. After manually reviewing all patients with the ICD-10-CM code E80.21 (Acute intermittent [hepatic] porphyria), we identified 30 patients who were positive cases for our machine learning models, with the rest of the patients used as negative cases. We parsed the record into features, which were scored by frequency of appearance and labeled by the EHR source document. We then carried out a univariate feature analysis, manually choosing features not directly tied to provider attributes or suspicion of the patient having AHP. We next trained on the full dataset, with the best cross-validation performance coming from support vector machine (SVM) algorithm using a radial basis function (RBF) kernel. The trained model was applied back to the full data set and patients were ranked by margin distance. The top 100 ranked negative cases were manually reviewed for symptom complexes similar to AHP, finding four patients where AHP diagnostic testing was likely indicated and 18 patients where AHP diagnostic testing was possibly indicated. From the top 100 ranked cases of patients with mention of porphyria in their record, we identified four patients for whom AHP diagnostic testing was possibly indicated and had not been previously performed. Based solely on the reported prevalence of AHP, we would have expected only 0.002 cases out of the 200 patients manually reviewed.ConclusionsThe application of machine learning and knowledge engineering to EHR data may facilitate the diagnosis of rare diseases such as AHP. The only manual modifications to this work were the removal of disease-specific or medical center specific features that might undermine our ability to find new cases. Further work will recommend clinical investigation to identified patients’ clinicians, evaluate more patients, assess additional feature selection and machine learning algorithms, and apply this methodology to other rare diseases.

scholarly journals Development of Machine Learning Models for Prediction of Smoking Cessation Outcome

2021 ◽  
Vol 18 (5) ◽  
pp. 2584
Author(s):  
Cheng-Chien Lai ◽  
Wei-Hsin Huang ◽  
Betty Chia-Chen Chang ◽  
Lee-Ching Hwang
Keyword(s):  
Machine Learning ◽  
Smoking Cessation ◽  
Success Rate ◽  
Prediction Models ◽  
Smoking Status ◽  
Medical Center ◽  
Machine Learning Algorithms ◽  
Classification And Regression Tree ◽  
Support Vector ◽  
Smoking Cessation Outcome

Predictors for success in smoking cessation have been studied, but a prediction model capable of providing a success rate for each patient attempting to quit smoking is still lacking. The aim of this study is to develop prediction models using machine learning algorithms to predict the outcome of smoking cessation. Data was acquired from patients underwent smoking cessation program at one medical center in Northern Taiwan. A total of 4875 enrollments fulfilled our inclusion criteria. Models with artificial neural network (ANN), support vector machine (SVM), random forest (RF), logistic regression (LoR), k-nearest neighbor (KNN), classification and regression tree (CART), and naïve Bayes (NB) were trained to predict the final smoking status of the patients in a six-month period. Sensitivity, specificity, accuracy, and area under receiver operating characteristic (ROC) curve (AUC or ROC value) were used to determine the performance of the models. We adopted the ANN model which reached a slightly better performance, with a sensitivity of 0.704, a specificity of 0.567, an accuracy of 0.640, and an ROC value of 0.660 (95% confidence interval (CI): 0.617–0.702) for prediction in smoking cessation outcome. A predictive model for smoking cessation was constructed. The model could aid in providing the predicted success rate for all smokers. It also had the potential to achieve personalized and precision medicine for treatment of smoking cessation.

scholarly journals Evaluation of Prognosis in Nasopharyngeal Cancer Using Machine Learning

2020 ◽  
Vol 19 ◽  
pp. 153303382090982
Author(s):  
Melek Akcay ◽  
Durmus Etiz ◽  
Ozer Celik ◽  
Alaattin Ozen
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Naive Bayes ◽  
Nasopharyngeal Cancer ◽  
Naïve Bayes ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Tumor Diameter ◽  
Survival Prognosis ◽  
Data Set

Background and Aim: Although the prognosis of nasopharyngeal cancer largely depends on a classification based on the tumor-lymph node metastasis staging system, patients at the same stage may have different clinical outcomes. This study aimed to evaluate the survival prognosis of nasopharyngeal cancer using machine learning. Settings and Design: Original, retrospective. Materials and Methods: A total of 72 patients with a diagnosis of nasopharyngeal cancer who received radiotherapy ± chemotherapy were included in the study. The contribution of patient, tumor, and treatment characteristics to the survival prognosis was evaluated by machine learning using the following techniques: logistic regression, artificial neural network, XGBoost, support-vector clustering, random forest, and Gaussian Naive Bayes. Results: In the analysis of the data set, correlation analysis, and binary logistic regression analyses were applied. Of the 18 independent variables, 10 were found to be effective in predicting nasopharyngeal cancer-related mortality: age, weight loss, initial neutrophil/lymphocyte ratio, initial lactate dehydrogenase, initial hemoglobin, radiotherapy duration, tumor diameter, number of concurrent chemotherapy cycles, and T and N stages. Gaussian Naive Bayes was determined as the best algorithm to evaluate the prognosis of machine learning techniques (accuracy rate: 88%, area under the curve score: 0.91, confidence interval: 0.68-1, sensitivity: 75%, specificity: 100%). Conclusion: Many factors affect prognosis in cancer, and machine learning algorithms can be used to determine which factors have a greater effect on survival prognosis, which then allows further research into these factors. In the current study, Gaussian Naive Bayes was identified as the best algorithm for the evaluation of prognosis of nasopharyngeal cancer.

scholarly journals Identification of Leukemia Subtypes from Microscopic Images Using Convolutional Neural Network

Diagnostics ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 104 ◽  
Author(s):  
Ahmed ◽  
Yigit ◽  
Isik ◽  
Alpkocak
Keyword(s):  
Machine Learning ◽  
Data Augmentation ◽  
Nearest Neighbor ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Training Data ◽  
Support Vector ◽  
K Nearest Neighbor ◽  
Data Set ◽  
Leukemia Data

Leukemia is a fatal cancer and has two main types: Acute and chronic. Each type has two more subtypes: Lymphoid and myeloid. Hence, in total, there are four subtypes of leukemia. This study proposes a new approach for diagnosis of all subtypes of leukemia from microscopic blood cell images using convolutional neural networks (CNN), which requires a large training data set. Therefore, we also investigated the effects of data augmentation for an increasing number of training samples synthetically. We used two publicly available leukemia data sources: ALL-IDB and ASH Image Bank. Next, we applied seven different image transformation techniques as data augmentation. We designed a CNN architecture capable of recognizing all subtypes of leukemia. Besides, we also explored other well-known machine learning algorithms such as naive Bayes, support vector machine, k-nearest neighbor, and decision tree. To evaluate our approach, we set up a set of experiments and used 5-fold cross-validation. The results we obtained from experiments showed that our CNN model performance has 88.25% and 81.74% accuracy, in leukemia versus healthy and multiclass classification of all subtypes, respectively. Finally, we also showed that the CNN model has a better performance than other wellknown machine learning algorithms.

scholarly journals Vehicle Price Prediction using SVM Techniques

2020 ◽  
Vol 9 (8) ◽  
pp. 398-401
Keyword(s):  
Machine Learning ◽  
Research Area ◽  
Machine Learning Algorithms ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
Data Set ◽  
Network Support ◽  
Java Application ◽  
Learning Techniques ◽  
The Individual

The prediction of price for a vehicle has been more popular in research area, and it needs predominant effort and information about the experts of this particular field. The number of different attributes is measured and also it has been considerable to predict the result in more reliable and accurate. To find the price of used vehicles a well defined model has been developed with the help of three machine learning techniques such as Artificial Neural Network, Support Vector Machine and Random Forest. These techniques were used not on the individual items but for the whole group of data items. This data group has been taken from some web portal and that same has been used for the prediction. The data must be collected using web scraper that was written in PHP programming language. Distinct machine learning algorithms of varying performances had been compared to get the best result of the given data set. The final prediction model was integrated into Java application

scholarly journals Future Prediction of Diabetics using XG Booster Classifiers

2020 ◽  
Vol 9 (3) ◽  
pp. 2128-2132
Keyword(s):  
Machine Learning ◽  
Decision Tree ◽  
Naive Bayes ◽  
Naïve Bayes ◽  
The Body ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Common Disease ◽  
Data Set ◽  
Glucose Content

Diabetes is a most common disease that occurs to most of the humans now a day. The predictions for this disease are proposed through machine learning techniques. Through this method the risk factors of this disease are identified and can be prevented from increasing. Early prediction in such disease can be controlled and save human’s life. For the early predictions of this disease we collect data set having 8 attributes diabetic of 200 patients. The patients’ sugar level in the body is tested by the features of patient’s glucose content in the body and according to the age. The main Machine learning algorithms are Support vector machine (SVM), naive bayes (NB), K nearest neighbor (KNN) and Decision Tree (DT). In the exiting the Naive Bayes the accuracy levels are 66% but in the Decision tree the accuracy levels are 70 to 71%. The accuracy levels of the patients are not proper in range. But in XG boost classifiers even after the Naïve Bayes 74 Percentage and in Decision tree the accuracy levels are 89 to 90%. In the proposed system the accuracy ranges are shown properly and this is only used mostly. A dataset of 729 patients can be stored in Mongo DB and in that 129 patients repots are taken for the prediction purpose and the remaining are used for training. The training datasets are used for the prediction purposes.

scholarly journals Rotor Unbalance Kind and Severity Identification by Current Signature Analysis with Adaptative Update to Multiclass Machine Learning Algorithms

2021 ◽  
Vol 8 (1) ◽  
pp. 28
Author(s):  
S. L. Ávila ◽  
H. M. Schaberle ◽  
S. Youssef ◽  
F. S. Pacheco ◽  
C. A. Penz
Keyword(s):  
Machine Learning ◽  
Machine Learning Algorithms ◽  
Training Data ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
Signature Analysis ◽  
Data Set ◽  
Learning Techniques ◽  
Environmental Variations ◽  
Current Signature

The health of a rotating electric machine can be evaluated by monitoring electrical and mechanical parameters. As more information is available, it easier can become the diagnosis of the machine operational condition. We built a laboratory test bench to study rotor unbalance issues according to ISO standards. Using the electric stator current harmonic analysis, this paper presents a comparison study among Support-Vector Machines, Decision Tree classifies, and One-vs-One strategy to identify rotor unbalance kind and severity problem – a nonlinear multiclass task. Moreover, we propose a methodology to update the classifier for dealing better with changes produced by environmental variations and natural machinery usage. The adaptative update means to update the training data set with an amount of recent data, saving the entire original historical data. It is relevant for engineering maintenance. Our results show that the current signature analysis is appropriate to identify the type and severity of the rotor unbalance problem. Moreover, we show that machine learning techniques can be effective for an industrial application.

scholarly journals Machine Learning Electronic Health Record Identification of Patients with Rheumatoid Arthritis: Algorithm Pipeline Development and Validation Study (Preprint)

2020 ◽  
Author(s):  
Tjardo D Maarseveen ◽  
Timo Meinderink ◽  
Marcel J T Reinders ◽  
Johannes Knitza ◽  
Tom W J Huizinga ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Machine Learning ◽  
Electronic Health Record ◽  
Support Vector ◽  
Free Text ◽  
Health Record ◽  
Electronic Health Record Data ◽  
Data Set ◽  
Record Data ◽  
Electronic Health

BACKGROUND Financial codes are often used to extract diagnoses from electronic health records. This approach is prone to false positives. Alternatively, queries are constructed, but these are highly center and language specific. A tantalizing alternative is the automatic identification of patients by employing machine learning on format-free text entries. OBJECTIVE The aim of this study was to develop an easily implementable workflow that builds a machine learning algorithm capable of accurately identifying patients with rheumatoid arthritis from format-free text fields in electronic health records. METHODS Two electronic health record data sets were employed: Leiden (n=3000) and Erlangen (n=4771). Using a portion of the Leiden data (n=2000), we compared 6 different machine learning methods and a naïve word-matching algorithm using 10-fold cross-validation. Performances were compared using the area under the receiver operating characteristic curve (AUROC) and the area under the precision recall curve (AUPRC), and F1 score was used as the primary criterion for selecting the best method to build a classifying algorithm. We selected the optimal threshold of positive predictive value for case identification based on the output of the best method in the training data. This validation workflow was subsequently applied to a portion of the Erlangen data (n=4293). For testing, the best performing methods were applied to remaining data (Leiden n=1000; Erlangen n=478) for an unbiased evaluation. RESULTS For the Leiden data set, the word-matching algorithm demonstrated mixed performance (AUROC 0.90; AUPRC 0.33; F1 score 0.55), and 4 methods significantly outperformed word-matching, with support vector machines performing best (AUROC 0.98; AUPRC 0.88; F1 score 0.83). Applying this support vector machine classifier to the test data resulted in a similarly high performance (F1 score 0.81; positive predictive value [PPV] 0.94), and with this method, we could identify 2873 patients with rheumatoid arthritis in less than 7 seconds out of the complete collection of 23,300 patients in the Leiden electronic health record system. For the Erlangen data set, gradient boosting performed best (AUROC 0.94; AUPRC 0.85; F1 score 0.82) in the training set, and applied to the test data, resulted once again in good results (F1 score 0.67; PPV 0.97). CONCLUSIONS We demonstrate that machine learning methods can extract the records of patients with rheumatoid arthritis from electronic health record data with high precision, allowing research on very large populations for limited costs. Our approach is language and center independent and could be applied to any type of diagnosis. We have developed our pipeline into a universally applicable and easy-to-implement workflow to equip centers with their own high-performing algorithm. This allows the creation of observational studies of unprecedented size covering different countries for low cost from already available data in electronic health record systems.

A Novel Ensemble Stacking Classification of Genetic Variations Using Machine Learning Algorithms

2021 ◽  
Author(s):  
Jahnavi Yeturu ◽  
Poongothai Elango ◽  
S. P. Raja ◽  
P. Nagendra Kumar
Keyword(s):  
Machine Learning ◽  
Heart Diseases ◽  
Learning Algorithms ◽  
Genetic Mutation ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Genetic Mutations ◽  
Validation Data ◽  
Data Set

Genetics is the clinical review of congenital mutation, where the principal advantage of analyzing genetic mutation of humans is the exploration, analysis, interpretation and description of the genetic transmitted and inherited effect of several diseases such as cancer, diabetes and heart diseases. Cancer is the most troublesome and disordered affliction as the proportion of cancer sufferers is growing massively. Identification and discrimination of the mutations that impart to the enlargement of tumor from the unbiased mutations is difficult, as majority tumors of cancer are able to exercise genetic mutations. The genetic mutations are systematized and categorized to sort the cancer by way of medical observations and considering clinical studies. At the present time, genetic mutations are being annotated and these interpretations are being accomplished either manually or using the existing primary algorithms. Evaluation and classification of each and every individual genetic mutation was basically predicated on evidence from documented content built on medical literature. Consequently, as a means to build genetic mutations, basically, depending on the clinical evidences persists a challenging task. There exist various algorithms such as one hot encoding technique is used to derive features from genes and their variations, TF-IDF is used to extract features from the clinical text data. In order to increase the accuracy of the classification, machine learning algorithms such as support vector machine, logistic regression, Naive Bayes, etc., are experimented. A stacking model classifier has been developed to increase the accuracy. The proposed stacking model classifier has obtained the log loss 0.8436 and 0.8572 for cross-validation data set and test data set, respectively. By the experimentation, it has been proved that the proposed stacking model classifier outperforms the existing algorithms in terms of log loss. Basically, minimum log loss refers to the efficient model. Here the log loss has been reduced to less than 1 by using the proposed stacking model classifier. The performance of these algorithms can be gauged on the basis of the various measures like multi-class log loss.

scholarly journals The use of machine learning in rare diseases: a scoping review

2020 ◽  
Vol 15 (1) ◽  
Author(s):  
Julia Schaefer ◽  
Moritz Lehne ◽  
Josef Schepers ◽  
Fabian Prasser ◽  
Sylvia Thun
Keyword(s):  
Machine Learning ◽  
Rare Disease ◽  
Rare Diseases ◽  
Scoping Review ◽  
Input Data ◽  
Skin Diseases ◽  
Demographic Data ◽  
Support Vector ◽  
Research Activity ◽  
Data Set

Abstract Background Emerging machine learning technologies are beginning to transform medicine and healthcare and could also improve the diagnosis and treatment of rare diseases. Currently, there are no systematic reviews that investigate, from a general perspective, how machine learning is used in a rare disease context. This scoping review aims to address this gap and explores the use of machine learning in rare diseases, investigating, for example, in which rare diseases machine learning is applied, which types of algorithms and input data are used or which medical applications (e.g., diagnosis, prognosis or treatment) are studied. Methods Using a complex search string including generic search terms and 381 individual disease names, studies from the past 10 years (2010–2019) that applied machine learning in a rare disease context were identified on PubMed. To systematically map the research activity, eligible studies were categorized along different dimensions (e.g., rare disease group, type of algorithm, input data), and the number of studies within these categories was analyzed. Results Two hundred eleven studies from 32 countries investigating 74 different rare diseases were identified. Diseases with a higher prevalence appeared more often in the studies than diseases with a lower prevalence. Moreover, some rare disease groups were investigated more frequently than to be expected (e.g., rare neurologic diseases and rare systemic or rheumatologic diseases), others less frequently (e.g., rare inborn errors of metabolism and rare skin diseases). Ensemble methods (36.0%), support vector machines (32.2%) and artificial neural networks (31.8%) were the algorithms most commonly applied in the studies. Only a small proportion of studies evaluated their algorithms on an external data set (11.8%) or against a human expert (2.4%). As input data, images (32.2%), demographic data (27.0%) and “omics” data (26.5%) were used most frequently. Most studies used machine learning for diagnosis (40.8%) or prognosis (38.4%) whereas studies aiming to improve treatment were relatively scarce (4.7%). Patient numbers in the studies were small, typically ranging from 20 to 99 (35.5%). Conclusion Our review provides an overview of the use of machine learning in rare diseases. Mapping the current research activity, it can guide future work and help to facilitate the successful application of machine learning in rare diseases.

scholarly journals Waste Management System Fraud Detection Using Machine Learning Algorithms to Minimize Penalties Avoidance and Redemption Abuse

Recycling ◽  
2021 ◽  
Vol 6 (4) ◽  
pp. 65
Author(s):  
Ali Hewiagh ◽  
Kannan Ramakrishnan ◽  
Timothy Tzen Vun Yap ◽  
Ching Seong Tan
Keyword(s):  
Machine Learning ◽  
Random Forest ◽  
Waste Management ◽  
Management System ◽  
Learning Algorithms ◽  
Fraud Detection ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Data Set ◽  
Waste Management System

Online frauds have pernicious impacts on different system domains, including waste management systems. Fraudsters illegally obtain rewards for their recycling activities or avoid penalties for those who are required to recycle their own waste. Although some approaches have been introduced to prevent such fraudulent activities, the fraudsters continuously seek new ways to commit illegal actions. Machine learning technology has shown significant and impressive results in identifying new online fraud patterns in different system domains such as e-commerce, insurance, and banking. The purpose of this paper, therefore, is to analyze a waste management system and develop a machine learning model to detect fraud in the system. The intended system allows consumers, individuals, and organizations to track, monitor, and update their performance in their recycling activities. The data set provided by a waste management organization is used for the analysis and the model training. This data set contains transactions of users’ recycling activities and behaviors. Three machine learning algorithms, random forest, support vector machine, and multi-layer perceptron are used in the experiments and the best detection model is selected based on the model’s performance. Results show that each of these algorithms can be used for fraud detection in waste managements with high accuracy. The random forest algorithm produces the optimal model with an accuracy of 96.33%, F1-score of 95.20%, and ROC of 98.92%.

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