scholarly journals KDClassifier: A urinary proteomic spectra analysis tool based on machine learning for the classification of kidney diseases

2021 ◽  
Vol 3 (3) ◽  
pp. 63-72
Author(s):  
Wanjun Zhao ◽  
Keyword(s):  
Kidney Disease ◽  
Kidney Diseases ◽  
Confusion Matrix ◽  
Gradient Boosting ◽  
Support Vector ◽  
Diagnostic Model ◽  
Analysis Tool ◽  
Data Set ◽  
Extreme Gradient Boosting

Background: We aimed to establish a novel diagnostic model for kidney diseases by combining artificial intelligence with complete mass spectrum information from urinary proteomics. Methods: We enrolled 134 patients (IgA nephropathy, membranous nephropathy, and diabetic kidney disease) and 68 healthy participants as controls, with a total of 610,102 mass spectra from their urinary proteomic profiles. The training data set (80%) was used to create a diagnostic model using XGBoost, random forest (RF), a support vector machine (SVM), and artificial neural networks (ANNs). The diagnostic accuracy was evaluated using a confusion matrix with a test dataset (20%). We also constructed receiver operating-characteristic, Lorenz, and gain curves to evaluate the diagnostic model. Results: Compared with the RF, SVM, and ANNs, the modified XGBoost model, called Kidney Disease Classifier (KDClassifier), showed the best performance. The accuracy of the XGBoost diagnostic model was 96.03%. The area under the curve of the extreme gradient boosting (XGBoost) model was 0.952 (95% confidence interval, 0.9307–0.9733). The Kolmogorov-Smirnov (KS) value of the Lorenz curve was 0.8514. The Lorenz and gain curves showed the strong robustness of the developed model. Conclusions: The KDClassifier achieved high accuracy and robustness and thus provides a potential tool for the classification of kidney diseases

scholarly journals KDClassifier: Urinary Proteomic Spectra Analysis Based on Machine Learning for Classification of Kidney Diseases

2020 ◽  
Author(s):  
Wanjun Zhao ◽  
Yong Zhang ◽  
Xinming Li ◽  
Yonghong Mao ◽  
Changwei Wu ◽  
...  
Keyword(s):  
Machine Learning ◽  
Mass Spectrum ◽  
Kidney Disease ◽  
Kidney Diseases ◽  
Training Dataset ◽  
Validation Dataset ◽  
Support Vector ◽  
Urinary Proteomics ◽  
Diagnosis Model

AbstractBackgroundBy extracting the spectrum features from urinary proteomics based on an advanced mass spectrometer and machine learning algorithms, more accurate reporting results can be achieved for disease classification. We attempted to establish a novel diagnosis model of kidney diseases by combining machine learning with an extreme gradient boosting (XGBoost) algorithm with complete mass spectrum information from the urinary proteomics.MethodsWe enrolled 134 patients (including those with IgA nephropathy, membranous nephropathy, and diabetic kidney disease) and 68 healthy participants as a control, and for training and validation of the diagnostic model, applied a total of 610,102 mass spectra from their urinary proteomics produced using high-resolution mass spectrometry. We divided the mass spectrum data into a training dataset (80%) and a validation dataset (20%). The training dataset was directly used to create a diagnosis model using XGBoost, random forest (RF), a support vector machine (SVM), and artificial neural networks (ANNs). The diagnostic accuracy was evaluated using a confusion matrix. We also constructed the receiver operating-characteristic, Lorenz, and gain curves to evaluate the diagnosis model.ResultsCompared with RF, the SVM, and ANNs, the modified XGBoost model, called a Kidney Disease Classifier (KDClassifier), showed the best performance. The accuracy of the diagnostic XGBoost model was 96.03% (CI = 95.17%-96.77%; Kapa = 0.943; McNemar’s Test, P value = 0.00027). The area under the curve of the XGBoost model was 0.952 (CI = 0.9307-0.9733). The Kolmogorov-Smirnov (KS) value of the Lorenz curve was 0.8514. The Lorenz and gain curves showed the strong robustness of the developed model.ConclusionsThis study presents the first XGBoost diagnosis model, i.e., the KDClassifier, combined with complete mass spectrum information from the urinary proteomics for distinguishing different kidney diseases. KDClassifier achieves a high accuracy and robustness, providing a potential tool for the classification of all types of kidney diseases.

Multi-Class Taxonomy of Well Integrity Anomalies Applying Inductive Learning Algorithms: Analytical Approach for Artificial-Lift Wells

2021 ◽  
Author(s):  
Mostafa Sa'eed Yakoot ◽  
Adel Mohamed Salem Ragab ◽  
Omar Mahmoud
Keyword(s):  
Decision Tree ◽  
Confusion Matrix ◽  
Learning Algorithms ◽  
Oil And Gas Industry ◽  
Classification Model ◽  
Gradient Boosting ◽  
Support Vector ◽  
Risk Category ◽  
Well Integrity ◽  
Extreme Gradient Boosting

Abstract Well integrity has become a crucial field with increased focus and being published intensively in industry researches. It is important to maintain the integrity of the individual well to ensure that wells operate as expected for their designated life (or higher) with all risks kept as low as reasonably practicable, or as specified. Machine learning (ML) and artificial intelligence (AI) models are used intensively in oil and gas industry nowadays. ML concept is based on powerful algorithms and robust database. Developing an efficient classification model for well integrity (WI) anomalies is now feasible because of having enormous number of well failures and well barrier integrity tests, and analyses in the database. Circa 9000 dataset points were collected from WI tests performed for 800 wells in Gulf of Suez, Egypt for almost 10 years. Moreover, those data have been quality-controlled and quality-assured by experienced engineers. The data contain different forms of WI failures. The contributing parameter set includes a total of 23 barrier elements. Data were structured and fed into 11 different ML algorithms to build an automated systematic tool for calculating imposed risk category of any well. Comparison analysis for the deployed models was performed to infer the best predictive model that can be relied on. 11 models include both supervised and ensemble learning algorithms such as random forest, support vector machine (SVM), decision tree and scalable boosting techniques. Out of 11 models, the results showed that extreme gradient boosting (XGB), categorical boosting (CatBoost), and decision tree are the most reliable algorithms. Moreover, novel evaluation metrics for confusion matrix of each model have been introduced to overcome the problem of existing metrics which don't consider domain knowledge during model evaluation. The innovated model will help to utilize company resources efficiently and dedicate personnel efforts to wells with the high-risk. As a result, progressive improvements on business, safety, environment, and performance of the business. This paper would be a milestone in the design and creation of the Well Integrity Database Management Program through the combination of integrity and ML.

Exploiting Rules to Enhance Machine Learning in Extracting Information From Multi-Institutional Prostate Pathology Reports

2020 ◽  
pp. 865-874
Author(s):  
Enrico Santus ◽  
Tal Schuster ◽  
Amir M. Tahmasebi ◽  
Clara Li ◽  
Adam Yala ◽  
...  
Keyword(s):  
Machine Learning ◽  
Hybrid Systems ◽  
High Performance ◽  
Feature Model ◽  
Training Data ◽  
Gradient Boosting ◽  
Support Vector ◽  
Data Set ◽  
Extreme Gradient Boosting ◽  
Pathology Reports

PURPOSE Literature on clinical note mining has highlighted the superiority of machine learning (ML) over hand-crafted rules. Nevertheless, most studies assume the availability of large training sets, which is rarely the case. For this reason, in the clinical setting, rules are still common. We suggest 2 methods to leverage the knowledge encoded in pre-existing rules to inform ML decisions and obtain high performance, even with scarce annotations. METHODS We collected 501 prostate pathology reports from 6 American hospitals. Reports were split into 2,711 core segments, annotated with 20 attributes describing the histology, grade, extension, and location of tumors. The data set was split by institutions to generate a cross-institutional evaluation setting. We assessed 4 systems, namely a rule-based approach, an ML model, and 2 hybrid systems integrating the previous methods: a Rule as Feature model and a Classifier Confidence model. Several ML algorithms were tested, including logistic regression (LR), support vector machine (SVM), and eXtreme gradient boosting (XGB). RESULTS When training on data from a single institution, LR lags behind the rules by 3.5% (F1 score: 92.2% v 95.7%). Hybrid models, instead, obtain competitive results, with Classifier Confidence outperforming the rules by +0.5% (96.2%). When a larger amount of data from multiple institutions is used, LR improves by +1.5% over the rules (97.2%), whereas hybrid systems obtain +2.2% for Rule as Feature (97.7%) and +2.6% for Classifier Confidence (98.3%). Replacing LR with SVM or XGB yielded similar performance gains. CONCLUSION We developed methods to use pre-existing handcrafted rules to inform ML algorithms. These hybrid systems obtain better performance than either rules or ML models alone, even when training data are limited.

scholarly journals A Comparative Analysis of Machine Learning Models for Prediction of Insurance Uptake in Kenya

2020 ◽  
Author(s):  
Nelson Yego ◽  
Juma Kasozi ◽  
Joseph Nkrunziza
Keyword(s):  
Machine Learning ◽  
Random Forest ◽  
Characteristic Curve ◽  
Confusion Matrix ◽  
Gradient Boosting ◽  
Support Vector ◽  
Sampled Data ◽  
Learning Models ◽  
Extreme Gradient Boosting ◽  
Machine Learning Models

The role of insurance in financial inclusion as well as in economic growth is immense. However, low uptake seems to impede the growth of the sector hence the need for a model that robustly predicts uptake of insurance among potential clients. In this research, we compared the performances of eight (8) machine learning models in predicting the uptake of insurance. The classifiers considered were Logistic Regression, Gaussian Naive Bayes, Support Vector Machines, K Nearest Neighbors, Decision Tree, Random Forest, Gradient Boosting Machines and Extreme Gradient boosting. The data used in the classification was from the 2016 Kenya FinAccess Household Survey. Comparison of performance was done for both upsampled and downsampled data due to data imbalance. For upsampled data, Random Forest classifier showed highest accuracy and precision compared to other classifiers but for down sampled data, gradient boosting was optimal. It is noteworthy that for both upsampled and downsampled data, tree-based classifiers were more robust than others in insurance uptake prediction. However, in spite of hyper-parameter optimization, the area under receiver operating characteristic curve remained highest for Random Forest as compared to other tree-based models. Also, the confusion matrix for Random Forest showed least false positives, and highest true positives hence could be construed as the most robust model for predicting the insurance uptake. Finally, the most important feature in predicting uptake was having a bank product hence bancassurance could be said to be a plausible channel of distribution of insurance products.

scholarly journals Meta-XGBoost for Hyperspectral Image Classification Using Extended MSER-Guided Morphological Profiles

2020 ◽  
Vol 12 (12) ◽  
pp. 1973
Author(s):  
Alim Samat ◽  
Erzhu Li ◽  
Wei Wang ◽  
Sicong Liu ◽  
Cong Lin ◽  
...  
Keyword(s):  
Random Forest ◽  
Image Classification ◽  
Classification Accuracy ◽  
Regression Tree ◽  
Superior Performance ◽  
Gradient Boosting ◽  
Support Vector ◽  
Adaptive Boosting ◽  
Extreme Gradient Boosting

To investigate the performance of extreme gradient boosting (XGBoost) in remote sensing image classification tasks, XGBoost was first introduced and comparatively investigated for the spectral-spatial classification of hyperspectral imagery using the extended maximally stable extreme-region-guided morphological profiles (EMSER_MPs) proposed in this study. To overcome the potential issues of XGBoost, meta-XGBoost was proposed as an ensemble XGBoost method with classification and regression tree (CART), dropout-introduced multiple additive regression tree (DART), elastic net regression and parallel coordinate descent-based linear regression (linear) and random forest (RaF) boosters. Moreover, to evaluate the performance of the introduced XGBoost approach with different boosters, meta-XGBoost and EMSER_MPs, well-known and widely accepted classifiers, including support vector machine (SVM), bagging, adaptive boosting (AdaBoost), multi class AdaBoost (MultiBoost), extremely randomized decision trees (ExtraTrees), RaF, classification via random forest regression (CVRFR) and ensemble of nested dichotomies with extremely randomized decision tree (END-ERDT) methods, were considered in terms of the classification accuracy and computational efficiency. The experimental results based on two benchmark hyperspectral data sets confirm the superior performance of EMSER_MPs and EMSER_MPs with mean pixel values within region (EMSER_MPsM) compared to that for morphological profiles (MPs), morphological profile with partial reconstruction (MPPR), extended MPs (EMPs), extended MPPR (EMPPR), maximally stable extreme-region-guided morphological profiles (MSER_MPs) and MSER_MPs with mean pixel values within region (MSER_MPsM) features. The proposed meta-XGBoost algorithm is capable of obtaining better results than XGBoost with the CART, DART, linear and RaF boosters, and it could be an alternative to the other considered classifiers in terms of the classification of hyperspectral images using advanced spectral-spatial features, especially from generalized classification accuracy and model training efficiency perspectives.

scholarly journals Predictive Analytics of Chronic Kidney Disease using Machine Learning Algorithm

2019 ◽  
Vol 8 (2) ◽  
pp. 940-947
Keyword(s):  
Chronic Kidney Disease ◽  
Kidney Disease ◽  
Predictive Analytics ◽  
Research Work ◽  
Classification And Regression Tree ◽  
Gradient Boosting ◽  
Support Vector ◽  
Linear Discriminant ◽  
Extreme Gradient Boosting ◽  
Data Points

According to the health statistics of India on Chronic Kidney Disease (CKD) a total of 63538 cases has been registered. Average age of men and women prone to kidney disease lies in the range of 48 to 70 years. CKD is more prevalent among male than among female. India ranks 17th position in CKD during 2015[1]. This paper focus on the predictive analytics architecture to analyse CKD dataset using feature engineering and classification algorithm. The proposed model incorporates techniques to validate the feasibility of the data points used for analysis. The main focus of this research work is to analyze the dataset of chronic kidney failure and perform the classification of CKD and Non CKD cases. The feasibility of the proposed dataset is determined through the Learning curve performance. The features which play a vital role in classification are determined using sequential forward selection algorithm. The training dataset with the selected features is fed into various classifier to determine which classifier plays a vital and accurate role in detection of CKD. The proposed dataset is classified using various Classification algorithms like Linear Regression(LR), Linear Discriminant Analysis(LDA), K-Nearest Neighbour(KNN), Classification and Regression Tree(CART), Naive Bayes(NB), Support Vector Machine(SVM), Random Forest(RF), eXtreme Gradient Boosting(XGBoost) and Ada Boost Regressor (ABR). It was found that for the given CKD dataset with 25 attributes of 11 Numeric and 14 Nominal the following classifier like LR, LDA, CART,NB,RF,XGB and ABR provides an accuracy ranging from 98% to 100% . The proposed architecture validates the dataset against the thumb rule when working with less number of data points used for classification and the classifier is validated against under fit, over fit conditions. The performance of the classifier is evaluated using accuracy and F-Score. The proposed architecture indicates that LR, RF and ABR provides a very high accuracy and F-Score

scholarly journals An Efficient Classification of Neonates Cry Using Extreme Gradient Boosting-Assisted Grouped-Support-Vector Network

2021 ◽  
Vol 2021 ◽  
pp. 1-14
Author(s):  
Chuan-Yu Chang ◽  
Sweta Bhattacharya ◽  
P. M. Durai Raj Vincent ◽  
Kuruva Lakshmanna ◽  
Kathiravan Srinivasan
Keyword(s):  
Newborn Infant ◽  
Recognition Rate ◽  
Gradient Boosting ◽  
Support Vector ◽  
Acoustic Feature ◽  
Infant Cry ◽  
Fast Recognition ◽  
Extreme Gradient Boosting ◽  
Infant Cries

The cry is a loud, high pitched verbal communication of infants. The very high fundamental frequency and resonance frequency characterize a neonatal infant cry having certain sudden variations. Furthermore, in a tiny duration solitary utterance, the cry signal also possesses both voiced and unvoiced features. Mostly, infants communicate with their caretakers through cries, and sometimes, it becomes difficult for the caretakers to comprehend the reason behind the newborn infant cry. As a result, this research proposes a novel work for classifying the newborn infant cries under three groups such as hunger, sleep, and discomfort. For each crying frame, twelve features get extracted through acoustic feature engineering, and the variable selection using random forests was used for selecting the highly discriminative features among the twelve time and frequency domain features. Subsequently, the extreme gradient boosting-powered grouped-support-vector network is deployed for neonate cry classification. The empirical results show that the proposed method could effectively classify the neonate cries under three different groups. The finest experimental results showed a mean accuracy of around 91% for most scenarios, and this exhibits the potential of the proposed extreme gradient boosting-powered grouped-support-vector network in neonate cry classification. Also, the proposed method has a fast recognition rate of 27 seconds in the identification of these emotional cries.

scholarly journals Prediction of Radiation Pneumonitis With Machine Learning in Stage III Lung Cancer: A Pilot Study

2021 ◽  
Vol 20 ◽  
pp. 153303382110163
Author(s):  
Melek Yakar ◽  
Durmus Etiz ◽  
Muzaffer Metintas ◽  
Guntulu Ak ◽  
Ozer Celik
Keyword(s):  
Machine Learning ◽  
Lung Cancer ◽  
Radiation Pneumonitis ◽  
Stage Iii ◽  
Gradient Boosting ◽  
Support Vector ◽  
Data Set ◽  
Volume Number ◽  
Light Gradient ◽  
Extreme Gradient Boosting

Background: Radiation pneumonitis (RP) is a dose-limiting toxicity in lung cancer radiotherapy (RT). As risk factors in the development of RP, patient and tumor characteristics, dosimetric parameters, and treatment features are intertwined, and it is not always possible to associate RP with a single parameter. This study aimed to determine the algorithm that most accurately predicted RP development with machine learning. Methods: Of the 197 cases diagnosed with stage III lung cancer and underwent RT and chemotherapy between 2014 and 2020, 193 were evaluated. The CTCAE 5.0 grading system was used for the RP evaluation. Synthetic minority oversampling technique was used to create a balanced data set. Logistic regression, artificial neural networks, eXtreme Gradient Boosting (XGB), Support Vector Machines, Random Forest, Gaussian Naive Bayes and Light Gradient Boosting Machine algorithms were used. After the correlation analysis, a permutation-based method was utilized for as a variable selection. Results: RP was seen in 51 of the 193 cases. Parameters affecting RP were determined as, total(t)V5, ipsilateral lung Dmax, contralateral lung Dmax, total lung Dmax, gross tumor volume, number of chemotherapy cycles before RT, tumor size, lymph node localization and asbestos exposure. LGBM was found to be the algorithm that best predicted RP at 85% accuracy (confidence interval: 0.73-0.96), 97% sensitivity, and 50% specificity. Conclusion: When the clinical and dosimetric parameters were evaluated together, the LGBM algorithm had the highest accuracy in predicting RP. However, in order to use this algorithm in clinical practice, it is necessary to increase data diversity and the number of patients by sharing data between centers.

AKI Prediction Models in ICU: A Comparative Study (Preprint)

2020 ◽  
Author(s):  
Qing Qian ◽  
Haixia Sun ◽  
Jinming Wu ◽  
Jiayang Wang ◽  
Lei Yang
Keyword(s):  
Kidney Disease ◽  
Comparative Study ◽  
Critically Ill ◽  
Critically Ill Patients ◽  
Gradient Boosting ◽  
Support Vector ◽  
Early Prediction ◽  
Icu Admission ◽  
Extreme Gradient Boosting ◽  
Mimic Iii

BACKGROUND Acute kidney injury (AKI) is highly prevalent in critically ill patients and associated with significant morbidity and mortality as well as high financial costs. Early prediction of AKI provides an opportunity to develop strategies for early diagnosis, effective prevention, and timely treatment. Machine learning models have been developed for early prediction of AKI on critically ill patients by different researchers under different scenario. OBJECTIVE This comparative study aims to assess the performances of existing models for early prediction of AKI in the Intensive Care Unit (ICU) setting. METHODS The data was collected from the MIMIC-III database for all patients above 18 years old who had valid creatinine measured for 72 hours following ICU admission. Those with existing condition of kidney disease on admission were excluded. 17 predictor variables including patient demographics and physiological indicators were selected on the basis of the Kidney Disease Improving Global Outcomes (KDIGO) and medical literatures. Six models from three different types of methods were tested including Logistic Regression (LR), Support Vector Machines (SVM), Random Forest (RF), eXtreme Gradient Boosting (XGBoost), Light Gradient Boosting Decision (LightGBM), and Convolutional Neural Network (CNN). The area under ROC curve (AUC), accuracy, precision, recall and F1 value were calculated for each model to evaluate the performance. RESULTS We extracted 17205patient ICU records from MIMIC-III dataset. LightGBM had the best performance, with all the evaluation indicators achieved the highest (with average AUC 0.905, F1 0.897, Recall 0.836, P<.001). XGBoost had the second best performance (P<.001) and LR, RF, SVM performed similarly (P=0.082, 0.158, 0.710) on AUC. CNN got the lowest score on accuracy, precision, F1 and AUC. SVM and LR had relatively low recall than others. Creatinine were found to have the most significant effect on the early prediction of AKI onset in LR, RF, SVM and LightGBM. CONCLUSIONS LightGBM demonstrated the best predictive capability in predicting AKI present at the first 72 hours of ICU admission. LightGBM and XGBoost showed great potential for clinical application owing to their high recall. This study can provide references for AI-powered clinical decision support system for early AKI prediction in ICU setting.

scholarly journals On the classification of Microsoft-Windows ransomware using hardware profile

2021 ◽  
Vol 7 ◽  
pp. e361
Author(s):  
Sana Aurangzeb ◽  
Rao Naveed Bin Rais ◽  
Muhammad Aleem ◽  
Muhammad Arshad Islam ◽  
Muhammad Azhar Iqbal
Keyword(s):  
Random Forest ◽  
Machine Learning Algorithms ◽  
Gradient Boosting ◽  
Substantial Part ◽  
Data Set ◽  
Performance Counters ◽  
Extreme Gradient Boosting ◽  
Hardware Performance Counters ◽  
Microsoft Windows

Due to the expeditious inclination of online services usage, the incidents of ransomware proliferation being reported are on the rise. Ransomware is a more hazardous threat than other malware as the victim of ransomware cannot regain access to the hijacked device until some form of compensation is paid. In the literature, several dynamic analysis techniques have been employed for the detection of malware including ransomware; however, to the best of our knowledge, hardware execution profile for ransomware analysis has not been investigated for this purpose, as of today. In this study, we show that the true execution picture obtained via a hardware execution profile is beneficial to identify the obfuscated ransomware too. We evaluate the features obtained from hardware performance counters to classify malicious applications into ransomware and non-ransomware categories using several machine learning algorithms such as Random Forest, Decision Tree, Gradient Boosting, and Extreme Gradient Boosting. The employed data set comprises 80 ransomware and 80 non-ransomware applications, which are collected using the VirusShare platform. The results revealed that extracted hardware features play a substantial part in the identification and detection of ransomware with F-measure score of 0.97 achieved by Random Forest and Extreme Gradient Boosting.

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