In silico Prediction of Inhibitory Constant of Thrombin Inhibitors Using Machine Learning

2019 ◽  
Vol 21 (9) ◽  
pp. 662-669 ◽  
Author(s):  
Junnan Zhao ◽  
Lu Zhu ◽  
Weineng Zhou ◽  
Lingfeng Yin ◽  
Yuchen Wang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Prediction Models ◽  
Regression Tree ◽  
Large Data ◽  
Thrombin Inhibitors ◽  
Coagulation Cascade ◽  
Gradient Boosting ◽  
Support Vector ◽  
Data Set ◽  
Descriptor Selection

Background: Thrombin is the central protease of the vertebrate blood coagulation cascade, which is closely related to cardiovascular diseases. The inhibitory constant Ki is the most significant property of thrombin inhibitors. Method: This study was carried out to predict Ki values of thrombin inhibitors based on a large data set by using machine learning methods. Taking advantage of finding non-intuitive regularities on high-dimensional datasets, machine learning can be used to build effective predictive models. A total of 6554 descriptors for each compound were collected and an efficient descriptor selection method was chosen to find the appropriate descriptors. Four different methods including multiple linear regression (MLR), K Nearest Neighbors (KNN), Gradient Boosting Regression Tree (GBRT) and Support Vector Machine (SVM) were implemented to build prediction models with these selected descriptors. Results: The SVM model was the best one among these methods with R2=0.84, MSE=0.55 for the training set and R2=0.83, MSE=0.56 for the test set. Several validation methods such as yrandomization test and applicability domain evaluation, were adopted to assess the robustness and generalization ability of the model. The final model shows excellent stability and predictive ability and can be employed for rapid estimation of the inhibitory constant, which is full of help for designing novel thrombin inhibitors.

Forecasting the risk at infractions: an ensemble comparison of machine learning approach

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Lei Li ◽  
Desheng Wu
Keyword(s):  
Machine Learning ◽  
Prediction Models ◽  
Short Term Memory ◽  
Model Performance ◽  
Large Data ◽  
Support Vector ◽  
Learning Approaches ◽  
Content Type ◽  
Day To Day Operations ◽  
Prediction Approach

PurposeThe infraction of securities regulations (ISRs) of listed firms in their day-to-day operations and management has become one of common problems. This paper proposed several machine learning approaches to forecast the risk at infractions of listed corporates to solve financial problems that are not effective and precise in supervision.Design/methodology/approachThe overall proposed research framework designed for forecasting the infractions (ISRs) include data collection and cleaning, feature engineering, data split, prediction approach application and model performance evaluation. We select Logistic Regression, Naïve Bayes, Random Forest, Support Vector Machines, Artificial Neural Network and Long Short-Term Memory Networks (LSTMs) as ISRs prediction models.FindingsThe research results show that prediction performance of proposed models with the prior infractions provides a significant improvement of the ISRs than those without prior, especially for large sample set. The results also indicate when judging whether a company has infractions, we should pay attention to novel artificial intelligence methods, previous infractions of the company, and large data sets.Originality/valueThe findings could be utilized to address the problems of identifying listed corporates' ISRs at hand to a certain degree. Overall, results elucidate the value of the prior infraction of securities regulations (ISRs). This shows the importance of including more data sources when constructing distress models and not only focus on building increasingly more complex models on the same data. This is also beneficial to the regulatory authorities.

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 Estimating the Optimal Dexketoprofen Pharmaceutical Formulation with Machine Learning Methods and Statistical Approaches

2021 ◽  
Vol 27 (4) ◽  
pp. 279-286
Author(s):  
Atakan Başkor ◽  
Yağmur Pirinçci Tok ◽  
Burcu Mesut ◽  
Yıldız Özsoy ◽  
Tamer Uçar
Keyword(s):  
Machine Learning ◽  
Regression Tree ◽  
Cost Effective ◽  
Pharmaceutical Formulation ◽  
Classification And Regression Tree ◽  
Gradient Boosting ◽  
Support Vector ◽  
Disintegration Time ◽  
Pharmaceutical Dosage Form ◽  
Extreme Gradient Boosting

Objectives: Orally disintegrating tablets (ODTs) can be utilized without any drinking water; this feature makes ODTs easy to use and suitable for specific groups of patients. Oral administration of drugs is the most commonly used route, and tablets constitute the most preferable pharmaceutical dosage form. However, the preparation of ODTs is costly and requires long trials, which creates obstacles for dosage trials. The aim of this study was to identify the most appropriate formulation using machine learning (ML) models of ODT dexketoprofen formulations, with the goal of providing a cost-effective and timereducing solution.Methods: This research utilized nonlinear regression models, including the k-nearest neighborhood (k-NN), support vector regression (SVR), classification and regression tree (CART), bootstrap aggregating (bagging), random forest (RF), gradient boosting machine (GBM), and extreme gradient boosting (XGBoost) methods, as well as the t-test, to predict the quantity of various components in the dexketoprofen formulation within fixed criteria.Results: All the models were developed with Python libraries. The performance of the ML models was evaluated with R2 values and the root mean square error. Hardness values of 0.99 and 2.88, friability values of 0.92 and 0.02, and disintegration time values of 0.97 and 10.09 using the GBM algorithm gave the best results.Conclusions: In this study, we developed a computational approach to estimate the optimal pharmaceutical formulation of dexketoprofen. The results were evaluated by an expert, and it was found that they complied with Food and Drug Administration criteria.

scholarly journals Machine Learning Approach to Reduce Alert Fatigue Using a Disease Medication–Related Clinical Decision Support System: Model Development and Validation (Preprint)

2020 ◽  
Author(s):  
Tahmina Nasrin Poly ◽  
Md.Mohaimenul Islam ◽  
Muhammad Solihuddin Muhtar ◽  
Hsuan-Chia Yang ◽  
Phung Anh (Alex) Nguyen ◽  
...  
Keyword(s):  
Machine Learning ◽  
Decision Support ◽  
Clinical Decision Support ◽  
Prediction Models ◽  
Clinical Decision ◽  
Gradient Boosting ◽  
Support Vector ◽  
Learning Models ◽  
Alert Fatigue ◽  
Machine Learning Models

BACKGROUND Computerized physician order entry (CPOE) systems are incorporated into clinical decision support systems (CDSSs) to reduce medication errors and improve patient safety. Automatic alerts generated from CDSSs can directly assist physicians in making useful clinical decisions and can help shape prescribing behavior. Multiple studies reported that approximately 90%-96% of alerts are overridden by physicians, which raises questions about the effectiveness of CDSSs. There is intense interest in developing sophisticated methods to combat alert fatigue, but there is no consensus on the optimal approaches so far. OBJECTIVE Our objective was to develop machine learning prediction models to predict physicians’ responses in order to reduce alert fatigue from disease medication–related CDSSs. METHODS We collected data from a disease medication–related CDSS from a university teaching hospital in Taiwan. We considered prescriptions that triggered alerts in the CDSS between August 2018 and May 2019. Machine learning models, such as artificial neural network (ANN), random forest (RF), naïve Bayes (NB), gradient boosting (GB), and support vector machine (SVM), were used to develop prediction models. The data were randomly split into training (80%) and testing (20%) datasets. RESULTS A total of 6453 prescriptions were used in our model. The ANN machine learning prediction model demonstrated excellent discrimination (area under the receiver operating characteristic curve [AUROC] 0.94; accuracy 0.85), whereas the RF, NB, GB, and SVM models had AUROCs of 0.93, 0.91, 0.91, and 0.80, respectively. The sensitivity and specificity of the ANN model were 0.87 and 0.83, respectively. CONCLUSIONS In this study, ANN showed substantially better performance in predicting individual physician responses to an alert from a disease medication–related CDSS, as compared to the other models. To our knowledge, this is the first study to use machine learning models to predict physician responses to alerts; furthermore, it can help to develop sophisticated CDSSs in real-world clinical settings.

scholarly journals Machine Learning-Based Three-Month Outcome Prediction in Acute Ischemic Stroke: A Single Cerebrovascular-Specialty Hospital Study in South Korea

Diagnostics ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1909
Author(s):  
Dougho Park ◽  
Eunhwan Jeong ◽  
Haejong Kim ◽  
Hae Wook Pyun ◽  
Haemin Kim ◽  
...  
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Ischemic Stroke ◽  
Acute Ischemic Stroke ◽  
Functional Outcome ◽  
Outcome Prediction ◽  
Prediction Models ◽  
Gradient Boosting ◽  
Support Vector ◽  
Extreme Gradient Boosting

Background: Functional outcomes after acute ischemic stroke are of great concern to patients and their families, as well as physicians and surgeons who make the clinical decisions. We developed machine learning (ML)-based functional outcome prediction models in acute ischemic stroke. Methods: This retrospective study used a prospective cohort database. A total of 1066 patients with acute ischemic stroke between January 2019 and March 2021 were included. Variables such as demographic factors, stroke-related factors, laboratory findings, and comorbidities were utilized at the time of admission. Five ML algorithms were applied to predict a favorable functional outcome (modified Rankin Scale 0 or 1) at 3 months after stroke onset. Results: Regularized logistic regression showed the best performance with an area under the receiver operating characteristic curve (AUC) of 0.86. Support vector machines represented the second-highest AUC of 0.85 with the highest F1-score of 0.86, and finally, all ML models applied achieved an AUC > 0.8. The National Institute of Health Stroke Scale at admission and age were consistently the top two important variables for generalized logistic regression, random forest, and extreme gradient boosting models. Conclusions: ML-based functional outcome prediction models for acute ischemic stroke were validated and proven to be readily applicable and useful.

scholarly journals Comparison of machine learning algorithms applied to symptoms to determine infectious causes of death in children: national survey of 18,000 verbal autopsies in the Million Death Study in India

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Susan Idicula-Thomas ◽  
Ulka Gawde ◽  
Prabhat Jha
Keyword(s):  
Machine Learning ◽  
Verbal Autopsy ◽  
Causes Of Death ◽  
Prediction Models ◽  
Machine Learning Algorithms ◽  
Classification And Regression Tree ◽  
Gradient Boosting ◽  
Support Vector ◽  
Diarrhoeal Diseases

Abstract Background Machine learning (ML) algorithms have been successfully employed for prediction of outcomes in clinical research. In this study, we have explored the application of ML-based algorithms to predict cause of death (CoD) from verbal autopsy records available through the Million Death Study (MDS). Methods From MDS, 18826 unique childhood deaths at ages 1–59 months during the time period 2004–13 were selected for generating the prediction models of which over 70% of deaths were caused by six infectious diseases (pneumonia, diarrhoeal diseases, malaria, fever of unknown origin, meningitis/encephalitis, and measles). Six popular ML-based algorithms such as support vector machine, gradient boosting modeling, C5.0, artificial neural network, k-nearest neighbor, classification and regression tree were used for building the CoD prediction models. Results SVM algorithm was the best performer with a prediction accuracy of over 0.8. The highest accuracy was found for diarrhoeal diseases (accuracy = 0.97) and the lowest was for meningitis/encephalitis (accuracy = 0.80). The top signs/symptoms for classification of these CoDs were also extracted for each of the diseases. A combination of signs/symptoms presented by the deceased individual can effectively lead to the CoD diagnosis. Conclusions Overall, this study affirms that verbal autopsy tools are efficient in CoD diagnosis and that automated classification parameters captured through ML could be added to verbal autopsies to improve classification of causes of death.

scholarly journals HOW MACHINE LEARNING METHOD PERFORMANCE FOR IMBALANCED DATA

TEKNOKOM ◽  
2021 ◽  
Vol 4 (2) ◽  
pp. 48-52
Author(s):  
Pardomuan Robinson Sihombing
Keyword(s):  
Machine Learning ◽  
Regression Tree ◽  
Imbalanced Data ◽  
Large Data ◽  
Original Data ◽  
Classification And Regression Tree ◽  
Support Vector ◽  
Method Performance ◽  
Survey Statistics ◽  
Working Status

This study will examine the application of several classification methods to machine learning models by taking into account the case of imbalanced data. The research was conducted on a case study of classification modeling for working status in Banten Province in 2020. The data used comes from the National Labor Force Survey, Statistics Indonesia. The machine learning methods used are Classification and Regression Tree (CART), Naïve Bayes, Random Forest, Rotation Forest, Support Vector Machine (SVM), Neural Network Analysis, One Rule (OneR), and Boosting. Classification modeling using resample techniques in cases of imbalanced data and large data sets is proven to improve classification accuracy, especially for minority classes, which can be seen from the sensitivity and specificity values that are more balanced than the original data (without treatment). Furthermore, the eight classification models tested shows that the Boost model provides the best performance based on the highest sensitivity, specificity, G-mean, and kappa coefficient values. The most important/most influential variables in the classification of working status are marital status, education, and age.

scholarly journals Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework

2018 ◽  
Vol 20 (6) ◽  
pp. 2185-2199 ◽  
Author(s):  
Yanju Zhang ◽  
Ruopeng Xie ◽  
Jiawei Wang ◽  
André Leier ◽  
Tatiana T Marquez-Lago ◽  
...  
Keyword(s):  
Machine Learning ◽  
Computational Methods ◽  
Prediction Models ◽  
Gradient Boosting ◽  
Support Vector ◽  
Post Translational Modification ◽  
K Nearest Neighbor ◽  
Ensemble Models ◽  
Light Gradient ◽  
Optimal Ensemble

AbstractAs a newly discovered post-translational modification (PTM), lysine malonylation (Kmal) regulates a myriad of cellular processes from prokaryotes to eukaryotes and has important implications in human diseases. Despite its functional significance, computational methods to accurately identify malonylation sites are still lacking and urgently needed. In particular, there is currently no comprehensive analysis and assessment of different features and machine learning (ML) methods that are required for constructing the necessary prediction models. Here, we review, analyze and compare 11 different feature encoding methods, with the goal of extracting key patterns and characteristics from residue sequences of Kmal sites. We identify optimized feature sets, with which four commonly used ML methods (random forest, support vector machines, K-nearest neighbor and logistic regression) and one recently proposed [Light Gradient Boosting Machine (LightGBM)] are trained on data from three species, namely, Escherichia coli, Mus musculus and Homo sapiens, and compared using randomized 10-fold cross-validation tests. We show that integration of the single method-based models through ensemble learning further improves the prediction performance and model robustness on the independent test. When compared to the existing state-of-the-art predictor, MaloPred, the optimal ensemble models were more accurate for all three species (AUC: 0.930, 0.923 and 0.944 for E. coli, M. musculus and H. sapiens, respectively). Using the ensemble models, we developed an accessible online predictor, kmal-sp, available at http://kmalsp.erc.monash.edu/. We hope that this comprehensive survey and the proposed strategy for building more accurate models can serve as a useful guide for inspiring future developments of computational methods for PTM site prediction, expedite the discovery of new malonylation and other PTM types and facilitate hypothesis-driven experimental validation of novel malonylated substrates and malonylation sites.

scholarly journals Machine Learning Approach to Reduce Alert Fatigue Using a Disease Medication–Related Clinical Decision Support System: Model Development and Validation

10.2196/19489 ◽  
2020 ◽  
Vol 8 (11) ◽  
pp. e19489
Author(s):  
Tahmina Nasrin Poly ◽  
Md.Mohaimenul Islam ◽  
Muhammad Solihuddin Muhtar ◽  
Hsuan-Chia Yang ◽  
Phung Anh (Alex) Nguyen ◽  
...  
Keyword(s):  
Machine Learning ◽  
Decision Support ◽  
Clinical Decision Support ◽  
Prediction Models ◽  
Clinical Decision ◽  
Gradient Boosting ◽  
Support Vector ◽  
Learning Models ◽  
Alert Fatigue ◽  
Machine Learning Models

Background Computerized physician order entry (CPOE) systems are incorporated into clinical decision support systems (CDSSs) to reduce medication errors and improve patient safety. Automatic alerts generated from CDSSs can directly assist physicians in making useful clinical decisions and can help shape prescribing behavior. Multiple studies reported that approximately 90%-96% of alerts are overridden by physicians, which raises questions about the effectiveness of CDSSs. There is intense interest in developing sophisticated methods to combat alert fatigue, but there is no consensus on the optimal approaches so far. Objective Our objective was to develop machine learning prediction models to predict physicians’ responses in order to reduce alert fatigue from disease medication–related CDSSs. Methods We collected data from a disease medication–related CDSS from a university teaching hospital in Taiwan. We considered prescriptions that triggered alerts in the CDSS between August 2018 and May 2019. Machine learning models, such as artificial neural network (ANN), random forest (RF), naïve Bayes (NB), gradient boosting (GB), and support vector machine (SVM), were used to develop prediction models. The data were randomly split into training (80%) and testing (20%) datasets. Results A total of 6453 prescriptions were used in our model. The ANN machine learning prediction model demonstrated excellent discrimination (area under the receiver operating characteristic curve [AUROC] 0.94; accuracy 0.85), whereas the RF, NB, GB, and SVM models had AUROCs of 0.93, 0.91, 0.91, and 0.80, respectively. The sensitivity and specificity of the ANN model were 0.87 and 0.83, respectively. Conclusions In this study, ANN showed substantially better performance in predicting individual physician responses to an alert from a disease medication–related CDSS, as compared to the other models. To our knowledge, this is the first study to use machine learning models to predict physician responses to alerts; furthermore, it can help to develop sophisticated CDSSs in real-world clinical settings.

scholarly journals Global Warming Prediction in India using Machine Learning

2019 ◽  
Vol 9 (1) ◽  
pp. 4061-4065
Keyword(s):  
Machine Learning ◽  
Global Warming ◽  
Linear Regression ◽  
Greenhouse Gases ◽  
Learning Algorithm ◽  
Regression Tree ◽  
Global Temperature ◽  
Support Vector ◽  
Data Set ◽  
Average Annual Temperature

Long term global warming prediction can be of major importance in various sectors like climate related studies, agricultural, energy, medical and many more. This paper evaluates the performance of several Machine Learning algorithm (Linear Regression, Multi-Regression tree, Support Vector Regression (SVR), lasso) in problem of annual global warming prediction, from previous measured values over India. The first challenge dwells on creating a reliable, efficient statistical reliable data model on large data set and accurately capture relationship between average annual temperature and potential factors such as concentration of carbon dioxide, methane, nitrous oxide. The data is predicted and forecasted by linear regression because it is obtaining the highest accuracy for greenhouse gases and temperature among all the technologies which can be used. It was also found that CO2 is the plays the role of major contributor temperature change, followed by CH4, then by N20. After seeing the analysed and predicted data of the greenhouse gases and temperature, the global warming can be reduced comparatively within few years. The reduction of global temperature can help the whole world because not only human but also different animals are suffering from the global temperature.

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