PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins

2019 ◽  
Author(s):  
Yanju Zhang ◽  
Sha Yu ◽  
Ruopeng Xie ◽  
Jiahui Li ◽  
André Leier ◽  
...  
Keyword(s):  
Machine Learning ◽  
Secreted Proteins ◽  
Gradient Boosting ◽  
Ensemble Model ◽  
Gram Positive ◽  
Gram Positive Bacteria ◽  
Single Feature ◽  
Gradient Boosting Machine ◽  
Benchmark Datasets ◽  
Feature Based

Abstract Motivation Gram-positive bacteria have developed secretion systems to transport proteins across their cell wall, a process that plays an important role during host infection. These secretion mechanisms have also been harnessed for therapeutic purposes in many biotechnology applications. Accordingly, the identification of features that select a protein for efficient secretion from these microorganisms has become an important task. Among all the secreted proteins, ‘non-classical’ secreted proteins are difficult to identify as they lack discernable signal peptide sequences and can make use of diverse secretion pathways. Currently, several computational methods have been developed to facilitate the discovery of such non-classical secreted proteins; however, the existing methods are based on either simulated or limited experimental datasets. In addition, they often employ basic features to train the models in a simple and coarse-grained manner. The availability of more experimentally validated datasets, advanced feature engineering techniques and novel machine learning approaches creates new opportunities for the development of improved predictors of ‘non-classical’ secreted proteins from sequence data. Results In this work, we first constructed a high-quality dataset of experimentally verified ‘non-classical’ secreted proteins, which we then used to create benchmark datasets. Using these benchmark datasets, we comprehensively analyzed a wide range of features and assessed their individual performance. Subsequently, we developed a two-layer Light Gradient Boosting Machine (LightGBM) ensemble model that integrates several single feature-based models into an overall prediction framework. At this stage, LightGBM, a gradient boosting machine, was used as a machine learning approach and the necessary parameter optimization was performed by a particle swarm optimization strategy. All single feature-based LightGBM models were then integrated into a unified ensemble model to further improve the predictive performance. Consequently, the final ensemble model achieved a superior performance with an accuracy of 0.900, an F-value of 0.903, Matthew’s correlation coefficient of 0.803 and an area under the curve value of 0.963, and outperforming previous state-of-the-art predictors on the independent test. Based on our proposed optimal ensemble model, we further developed an accessible online predictor, PeNGaRoo, to serve users’ demands. We believe this online web server, together with our proposed methodology, will expedite the discovery of non-classically secreted effector proteins in Gram-positive bacteria and further inspire the development of next-generation predictors. Availability and implementation http://pengaroo.erc.monash.edu/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals An Ensemble of Random Forest Gradient Boosting Machine and Deep Learning Methods for Stock Price Prediction

2022 ◽  
Vol 15 (1) ◽  
pp. 1-19
Author(s):  
Ravinder Kumar ◽  
Lokesh Kumar Shrivastav
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Random Forest ◽  
Stock Market ◽  
Data Analytics ◽  
Gradient Boosting ◽  
Ensemble Model ◽  
Market Data ◽  
Stock Price Prediction ◽  
Gradient Boosting Machine

Stochastic time series analysis of high-frequency stock market data is a very challenging task for the analysts due to the lack availability of efficient tool and techniques for big data analytics. This has opened the door of opportunities for the developer and researcher to develop intelligent and machine learning based tools and techniques for data analytics. This paper proposed an ensemble for stock market data prediction using three most prominent machine learning based techniques. The stock market dataset with raw data size of 39364 KB with all attributes and processed data size of 11826 KB having 872435 instances. The proposed work implements an ensemble model comprises of Deep Learning, Gradient Boosting Machine (GBM) and distributed Random Forest techniques of data analytics. The performance results of the ensemble model are compared with each of the individual methods i.e. deep learning, Gradient Boosting Machine (GBM) and Random Forest. The ensemble model performs better and achieves the highest accuracy of 0.99 and lowest error (RMSE) of 0.1.

scholarly journals SURG-02. SURVIVAL PREDICTION AFTER NEUROSURGICAL RESECTION OF BRAIN METASTASES: A MACHINE LEARNING APPROACH

2020 ◽  
Vol 22 (Supplement_2) ◽  
pp. ii203-ii203
Author(s):  
Alexander Hulsbergen ◽  
Yu Tung Lo ◽  
Vasileios Kavouridis ◽  
John Phillips ◽  
Timothy Smith ◽  
...  
Keyword(s):  
Machine Learning ◽  
Brain Metastases ◽  
External Validation ◽  
Superior Performance ◽  
Prognostic Models ◽  
Receiver Operating Curve ◽  
Gradient Boosting ◽  
Survival Prediction ◽  
Ensemble Model ◽  
Adaptive Boosting

Abstract INTRODUCTION Survival prediction in brain metastases (BMs) remains challenging. Current prognostic models have been created and validated almost completely with data from patients receiving radiotherapy only, leaving uncertainty about surgical patients. Therefore, the aim of this study was to build and validate a model predicting 6-month survival after BM resection using different machine learning (ML) algorithms. METHODS An institutional database of 1062 patients who underwent resection for BM was split into a 80:20 training and testing set. Seven different ML algorithms were trained and assessed for performance. Moreover, an ensemble model was created incorporating random forest, adaptive boosting, gradient boosting, and logistic regression algorithms. Five-fold cross validation was used for hyperparameter tuning. Model performance was assessed using area under the receiver-operating curve (AUC) and calibration and was compared against the diagnosis-specific graded prognostic assessment (ds-GPA); the most established prognostic model in BMs. RESULTS The ensemble model showed superior performance with an AUC of 0.81 in the hold-out test set, a calibration slope of 1.14, and a calibration intercept of -0.08, outperforming the ds-GPA (AUC 0.68). Patients were stratified into high-, medium- and low-risk groups for death at 6 months; these strata strongly predicted both 6-months and longitudinal overall survival (p < 0.001). CONCLUSIONS We developed and internally validated an ensemble ML model that accurately predicts 6-month survival after neurosurgical resection for BM, outperforms the most established model in the literature, and allows for meaningful risk stratification. Future efforts should focus on external validation of our model.

scholarly journals Predicting hospitalization following psychiatric crisis care using machine learning

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Matthijs Blankers ◽  
Louk F. M. van der Post ◽  
Jack J. M. Dekker
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Prediction Models ◽  
Learning Algorithms ◽  
Nearest Neighbors ◽  
Machine Learning Algorithms ◽  
Gradient Boosting ◽  
Ensemble Model ◽  
K Nearest Neighbors ◽  
Crisis Care

Abstract Background Accurate prediction models for whether patients on the verge of a psychiatric criseis need hospitalization are lacking and machine learning methods may help improve the accuracy of psychiatric hospitalization prediction models. In this paper we evaluate the accuracy of ten machine learning algorithms, including the generalized linear model (GLM/logistic regression) to predict psychiatric hospitalization in the first 12 months after a psychiatric crisis care contact. We also evaluate an ensemble model to optimize the accuracy and we explore individual predictors of hospitalization. Methods Data from 2084 patients included in the longitudinal Amsterdam Study of Acute Psychiatry with at least one reported psychiatric crisis care contact were included. Target variable for the prediction models was whether the patient was hospitalized in the 12 months following inclusion. The predictive power of 39 variables related to patients’ socio-demographics, clinical characteristics and previous mental health care contacts was evaluated. The accuracy and area under the receiver operating characteristic curve (AUC) of the machine learning algorithms were compared and we also estimated the relative importance of each predictor variable. The best and least performing algorithms were compared with GLM/logistic regression using net reclassification improvement analysis and the five best performing algorithms were combined in an ensemble model using stacking. Results All models performed above chance level. We found Gradient Boosting to be the best performing algorithm (AUC = 0.774) and K-Nearest Neighbors to be the least performing (AUC = 0.702). The performance of GLM/logistic regression (AUC = 0.76) was slightly above average among the tested algorithms. In a Net Reclassification Improvement analysis Gradient Boosting outperformed GLM/logistic regression by 2.9% and K-Nearest Neighbors by 11.3%. GLM/logistic regression outperformed K-Nearest Neighbors by 8.7%. Nine of the top-10 most important predictor variables were related to previous mental health care use. Conclusions Gradient Boosting led to the highest predictive accuracy and AUC while GLM/logistic regression performed average among the tested algorithms. Although statistically significant, the magnitude of the differences between the machine learning algorithms was in most cases modest. The results show that a predictive accuracy similar to the best performing model can be achieved when combining multiple algorithms in an ensemble model.

scholarly journals Data Analytics for Monitoring the Satisfactory Parameters of Airline Passengers using Machine Learning Algorithms in Python

2020 ◽  
Vol 9 (3) ◽  
pp. 1231-1235
Keyword(s):  
Machine Learning ◽  
Data Analytics ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Gradient Boosting ◽  
Complex Information ◽  
Huge Data ◽  
Gradient Boosting Machine ◽  
Airline Passengers ◽  
Effective Representation

An effective representation by machine learning algorithms is to obtain the results especially in Big Data, there are numerous applications can produce outcome, whereas a Random Forest Algorithm (RF) Gradient Boosting Machine (GBM), Decision tree (DT) in Python will able to give the higher accuracy in regard with classifying various parameters of Airliner Passengers satisfactory levels. The complex information of airline passengers has provided huge data for interpretation through different parameters of satisfaction that contains large information in quantity wise. An algorithm has to support in classifying these data’s with accuracies. As a result some of the methods may provide less precision and there is an opportunity of information cancellation and furthermore information missing utilizing conventional techniques. Subsequently RF and GBM used to conquer the unpredictability and exactness about the information provided. The aim of this study is to identify an Algorithm which is suitable for classifying the satisfactory level of airline passengers with data analytics using python by knowing the output. The optimization and Implementation of independent variables by training and testing for accuracy in python platform determined the variation between the each parameters and also recognized RF and GBM as a better algorithm in comparison with other classifying algorithms.

Development of a Diabetes Melitus Detection and Prediction Model Using Light Gradient Boosting Machine and K-Nearest Neighbour

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
B. A Omodunbi
Keyword(s):  
Diabetes Mellitus ◽  
Machine Learning ◽  
Hybrid Model ◽  
Learning Model ◽  
Experimental Result ◽  
Gradient Boosting ◽  
Light Gradient ◽  
Machine Learning Model ◽  
Gradient Boosting Machine ◽  
Receiver Operating

Diabetes mellitus is a health disorder that occurs when the blood sugar level becomes extremely high due to body resistance in producing the required amount of insulin. The aliment happens to be among the major causes of death in Nigeria and the world at large. This study was carried out to detect diabetes mellitus by developing a hybrid model that comprises of two machine learning model namely Light Gradient Boosting Machine (LGBM) and K-Nearest Neighbor (KNN). This research is aimed at developing a machine learning model for detecting the occurrence of diabetes in patients. The performance metrics employed in evaluating the finding for this study are Receiver Operating Characteristics (ROC) Curve, Five-fold Cross-validation, precision, and accuracy score. The proposed system had an accuracy of 91% and the area under the Receiver Operating Characteristic Curve was 93%. The experimental result shows that the prediction accuracy of the hybrid model is better than traditional machine learning

scholarly journals Prediction of Acute Kidney Injury after Liver Transplantation: Machine Learning Approaches vs. Logistic Regression Model

2018 ◽  
Vol 7 (11) ◽  
pp. 428 ◽  
Author(s):  
Hyung-Chul Lee ◽  
Soo Yoon ◽  
Seong-Mi Yang ◽  
Won Kim ◽  
Ho-Geol Ryu ◽  
...  
Keyword(s):  
Machine Learning ◽  
Liver Transplantation ◽  
Acute Kidney Injury ◽  
Logistic Regression ◽  
Regression Analysis ◽  
Logistic Regression Analysis ◽  
Kidney Injury ◽  
Gradient Boosting ◽  
Learning Approaches ◽  
Gradient Boosting Machine

Acute kidney injury (AKI) after liver transplantation has been reported to be associated with increased mortality. Recently, machine learning approaches were reported to have better predictive ability than the classic statistical analysis. We compared the performance of machine learning approaches with that of logistic regression analysis to predict AKI after liver transplantation. We reviewed 1211 patients and preoperative and intraoperative anesthesia and surgery-related variables were obtained. The primary outcome was postoperative AKI defined by acute kidney injury network criteria. The following machine learning techniques were used: decision tree, random forest, gradient boosting machine, support vector machine, naïve Bayes, multilayer perceptron, and deep belief networks. These techniques were compared with logistic regression analysis regarding the area under the receiver-operating characteristic curve (AUROC). AKI developed in 365 patients (30.1%). The performance in terms of AUROC was best in gradient boosting machine among all analyses to predict AKI of all stages (0.90, 95% confidence interval [CI] 0.86–0.93) or stage 2 or 3 AKI. The AUROC of logistic regression analysis was 0.61 (95% CI 0.56–0.66). Decision tree and random forest techniques showed moderate performance (AUROC 0.86 and 0.85, respectively). The AUROC of support the vector machine, naïve Bayes, neural network, and deep belief network was smaller than that of the other models. In our comparison of seven machine learning approaches with logistic regression analysis, the gradient boosting machine showed the best performance with the highest AUROC. An internet-based risk estimator was developed based on our model of gradient boosting. However, prospective studies are required to validate our results.

scholarly journals Supervised Machine-learning Predictive Analytics for Prediction of Postinduction Hypotension

2018 ◽  
Vol 129 (4) ◽  
pp. 675-688 ◽  
Author(s):  
Samir Kendale ◽  
Prathamesh Kulkarni ◽  
Andrew D. Rosenberg ◽  
Jing Wang
Keyword(s):  
Machine Learning ◽  
Receiver Operating Characteristic Curve ◽  
Operating Characteristic ◽  
Predictive Analytics ◽  
Characteristic Curve ◽  
Supervised Machine Learning ◽  
Gradient Boosting ◽  
Machine Learning Methods ◽  
Gradient Boosting Machine ◽  
Operating Characteristic Curve

AbstractEditor’s PerspectiveWhat We Already Know about This TopicWhat This Article Tells Us That Is NewBackgroundHypotension is a risk factor for adverse perioperative outcomes. Machine-learning methods allow large amounts of data for development of robust predictive analytics. The authors hypothesized that machine-learning methods can provide prediction for the risk of postinduction hypotension.MethodsData was extracted from the electronic health record of a single quaternary care center from November 2015 to May 2016 for patients over age 12 that underwent general anesthesia, without procedure exclusions. Multiple supervised machine-learning classification techniques were attempted, with postinduction hypotension (mean arterial pressure less than 55 mmHg within 10 min of induction by any measurement) as primary outcome, and preoperative medications, medical comorbidities, induction medications, and intraoperative vital signs as features. Discrimination was assessed using cross-validated area under the receiver operating characteristic curve. The best performing model was tuned and final performance assessed using split-set validation.ResultsOut of 13,323 cases, 1,185 (8.9%) experienced postinduction hypotension. Area under the receiver operating characteristic curve using logistic regression was 0.71 (95% CI, 0.70 to 0.72), support vector machines was 0.63 (95% CI, 0.58 to 0.60), naive Bayes was 0.69 (95% CI, 0.67 to 0.69), k-nearest neighbor was 0.64 (95% CI, 0.63 to 0.65), linear discriminant analysis was 0.72 (95% CI, 0.71 to 0.73), random forest was 0.74 (95% CI, 0.73 to 0.75), neural nets 0.71 (95% CI, 0.69 to 0.71), and gradient boosting machine 0.76 (95% CI, 0.75 to 0.77). Test set area for the gradient boosting machine was 0.74 (95% CI, 0.72 to 0.77).ConclusionsThe success of this technique in predicting postinduction hypotension demonstrates feasibility of machine-learning models for predictive analytics in the field of anesthesiology, with performance dependent on model selection and appropriate tuning.

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