Identification of Targeted Proteins by Jamu Formulas for Different Efficacies Using Machine Learning Approach

Background: We performed in silico prediction of the interactions between compounds of Jamu herbs and human proteins by utilizing data-intensive science and machine learning methods. Verifying the proteins that are targeted by compounds of natural herbs will be helpful to select natural herb-based drug candidates. Methods: Initially, data related to compounds, target proteins, and interactions between them were collected from open access databases. Compounds are represented by molecular fingerprints, whereas amino acid sequences are represented by numerical protein descriptors. Then, prediction models that predict the interactions between compounds and target proteins were constructed using support vector machine and random forest. Results: A random forest model constructed based on MACCS fingerprint and amino acid composition obtained the highest accuracy. We used the best model to predict target proteins for 94 important Jamu compounds and assessed the results by supporting evidence from published literature and other sources. There are 27 compounds that can be validated by professional doctors, and those compounds belong to seven efficacy groups. Conclusion: By comparing the efficacy of predicted compounds and the relations of the targeted proteins with diseases, we found that some compounds might be considered as drug candidates.

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A Novel Amino Acid Sequence-based Computational Approach to Predicting Cell-penetrating Peptides

Current Computer - Aided Drug Design ◽

10.2174/1573409914666180925100355 ◽

2019 ◽

Vol 15 (3) ◽

pp. 206-211 ◽

Cited By ~ 2

Author(s):

Jihui Tang ◽

Jie Ning ◽

Xiaoyan Liu ◽

Baoming Wu ◽

Rongfeng Hu

Keyword(s):

Machine Learning ◽

Amino Acid ◽

Amino Acid Position ◽

Cell Penetrating Peptides ◽

Support Vector ◽

Cell Penetration ◽

Drug Candidates ◽

Machine Learning Model ◽

Cell Penetrating ◽

Novel Method

Introduction: Machine Learning is a useful tool for the prediction of cell-penetration compounds as drug candidates. Materials and Methods: In this study, we developed a novel method for predicting Cell-Penetrating Peptides (CPPs) membrane penetrating capability. For this, we used orthogonal encoding to encode amino acid and each amino acid position as one variable. Then a software of IBM spss modeler and a dataset including 533 CPPs, were used for model screening. Results: The results indicated that the machine learning model of Support Vector Machine (SVM) was suitable for predicting membrane penetrating capability. For improvement, the three CPPs with the most longer lengths were used to predict CPPs. The penetration capability can be predicted with an accuracy of close to 95%. Conclusion: All the results indicated that by using amino acid position as a variable can be a perspective method for predicting CPPs membrane penetrating capability.

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Machine Learning-Based Prediction of Air Quality

Applied Sciences ◽

10.3390/app10249151 ◽

2020 ◽

Vol 10 (24) ◽

pp. 9151

Author(s):

Yun-Chia Liang ◽

Yona Maimury ◽

Angela Hsiang-Ling Chen ◽

Josue Rodolfo Cuevas Juarez

Keyword(s):

Machine Learning ◽

Air Quality ◽

Random Forest ◽

Prediction Models ◽

Superior Performance ◽

Support Vector ◽

Economic Activities ◽

Adaptive Boosting ◽

Series Of Experiments ◽

Artificial Neural Network Ann

Air, an essential natural resource, has been compromised in terms of quality by economic activities. Considerable research has been devoted to predicting instances of poor air quality, but most studies are limited by insufficient longitudinal data, making it difficult to account for seasonal and other factors. Several prediction models have been developed using an 11-year dataset collected by Taiwan’s Environmental Protection Administration (EPA). Machine learning methods, including adaptive boosting (AdaBoost), artificial neural network (ANN), random forest, stacking ensemble, and support vector machine (SVM), produce promising results for air quality index (AQI) level predictions. A series of experiments, using datasets for three different regions to obtain the best prediction performance from the stacking ensemble, AdaBoost, and random forest, found the stacking ensemble delivers consistently superior performance for R2 and RMSE, while AdaBoost provides best results for MAE.

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Classification models using circulating neutrophil transcripts can detect unruptured intracranial aneurysm

Journal of Translational Medicine ◽

10.1186/s12967-020-02550-2 ◽

2020 ◽

Vol 18 (1) ◽

Author(s):

Kerry E. Poppenberg ◽

Vincent M. Tutino ◽

Lu Li ◽

Muhammad Waqas ◽

Armond June ◽

...

Keyword(s):

Machine Learning ◽

Random Forest ◽

Prediction Models ◽

Model Performance ◽

Supervised Machine Learning ◽

Support Vector ◽

Learning Methods ◽

Training Cohort ◽

Network Analyses ◽

Machine Learning Methods

Abstract Background Intracranial aneurysms (IAs) are dangerous because of their potential to rupture. We previously found significant RNA expression differences in circulating neutrophils between patients with and without unruptured IAs and trained machine learning models to predict presence of IA using 40 neutrophil transcriptomes. Here, we aim to develop a predictive model for unruptured IA using neutrophil transcriptomes from a larger population and more robust machine learning methods. Methods Neutrophil RNA extracted from the blood of 134 patients (55 with IA, 79 IA-free controls) was subjected to next-generation RNA sequencing. In a randomly-selected training cohort (n = 94), the Least Absolute Shrinkage and Selection Operator (LASSO) selected transcripts, from which we constructed prediction models via 4 well-established supervised machine-learning algorithms (K-Nearest Neighbors, Random Forest, and Support Vector Machines with Gaussian and cubic kernels). We tested the models in the remaining samples (n = 40) and assessed model performance by receiver-operating-characteristic (ROC) curves. Real-time quantitative polymerase chain reaction (RT-qPCR) of 9 IA-associated genes was used to verify gene expression in a subset of 49 neutrophil RNA samples. We also examined the potential influence of demographics and comorbidities on model prediction. Results Feature selection using LASSO in the training cohort identified 37 IA-associated transcripts. Models trained using these transcripts had a maximum accuracy of 90% in the testing cohort. The testing performance across all methods had an average area under ROC curve (AUC) = 0.97, an improvement over our previous models. The Random Forest model performed best across both training and testing cohorts. RT-qPCR confirmed expression differences in 7 of 9 genes tested. Gene ontology and IPA network analyses performed on the 37 model genes reflected dysregulated inflammation, cell signaling, and apoptosis processes. In our data, demographics and comorbidities did not affect model performance. Conclusions We improved upon our previous IA prediction models based on circulating neutrophil transcriptomes by increasing sample size and by implementing LASSO and more robust machine learning methods. Future studies are needed to validate these models in larger cohorts and further investigate effect of covariates.

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rSeqTU – a machine-learning based R package for prediction of bacterial transcription units

10.1101/553057 ◽

2019 ◽

Author(s):

Sheng-Yong Niu ◽

Binqiang Liu ◽

Qin Ma ◽

Wen-Chi Chou

Keyword(s):

Machine Learning ◽

Random Forest ◽

Regulatory Networks ◽

Prediction Models ◽

R Package ◽

Transcription Unit ◽

Support Vector ◽

Rna Seq ◽

Accurate Identification ◽

Prediction Approach

AbstractA transcription unit (TU) is composed of one or multiple adjacent genes on the same strand that are co-transcribed in mostly prokaryotes. Accurate identification of TUs is a crucial first step to delineate the transcriptional regulatory networks and elucidate the dynamic regulatory mechanisms encoded in various prokaryotic genomes. Many genomic features, e.g., gene intergenic distance, and transcriptomic features including continuous and stable RNA-seq reads count signals, have been collected from a large amount of experimental data and integrated into classification techniques to computationally predict genome-wide TUs. Although some tools and web servers are able to predict TUs based on bacterial RNA-seq data and genome sequences, there is a need to have an improved machine-learning prediction approach and a better comprehensive pipeline handling QC, TU prediction, and TU visualization. To enable users to efficiently perform TU identification on their local computers or high-performance clusters and provide a more accurate prediction, we develop an R package, named rSeqTU. rSeqTU uses a random forest algorithm to select essential features describing TUs and then uses support vector machine (SVM) to build TU prediction models. rSeqTU (available at https://s18692001.github.io/rSeqTU/) has six computational functionalities including read quality control, read mapping, training set generation, random-forest-based feature selection, TU prediction, and TU visualization.

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Use of Hyperspectral Imaging for the Quantification of Organic Contaminants on Copper Surfaces for Electronic Applications

Sensors ◽

10.3390/s21165595 ◽

2021 ◽

Vol 21 (16) ◽

pp. 5595

Author(s):

Tim Englert ◽

Florian Gruber ◽

Jan Stiedl ◽

Simon Green ◽

Timo Jacob ◽

...

Keyword(s):

Machine Learning ◽

Random Forest ◽

Carbon Content ◽

Hyperspectral Imaging ◽

Organic Contaminants ◽

Online Monitoring ◽

Prediction Models ◽

Support Vector ◽

Large Area ◽

Fast Evaluation

To correctly assess the cleanliness of technical surfaces in a production process, corresponding online monitoring systems must provide sufficient data. A promising method for fast, large-area, and non-contact monitoring is hyperspectral imaging (HSI), which was used in this paper for the detection and quantification of organic surface contaminations. Depending on the cleaning parameter constellation, different levels of organic residues remained on the surface. Afterwards, the cleanliness was determined by the carbon content in the atom percent on the sample surfaces, characterized by XPS and AES. The HSI data and the XPS measurements were correlated, using machine learning methods, to generate a predictive model for the carbon content of the surface. The regression algorithms elastic net, random forest regression, and support vector machine regression were used. Overall, the developed method was able to quantify organic contaminations on technical surfaces. The best regression model found was a random forest model, which achieved an R2 of 0.7 and an RMSE of 7.65 At.-% C. Due to the easy-to-use measurement and the fast evaluation by machine learning, the method seems suitable for an online monitoring system. However, the results also show that further experiments are necessary to improve the quality of the prediction models.

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Machine learning in perioperative medicine: a systematic review

Journal of Anesthesia, Analgesia and Critical Care ◽

10.1186/s44158-022-00033-y ◽

2022 ◽

Vol 2 (1) ◽

Author(s):

Valentina Bellini ◽

Marina Valente ◽

Giorgia Bertorelli ◽

Barbara Pifferi ◽

Michelangelo Craca ◽

...

Keyword(s):

Machine Learning ◽

Systematic Review ◽

Health Care ◽

Random Forest ◽

Risk Stratification ◽

Prediction Models ◽

Cochrane Library ◽

Gradient Boosting ◽

Support Vector ◽

Systemic Complications

Abstract Background Risk stratification plays a central role in anesthetic evaluation. The use of Big Data and machine learning (ML) offers considerable advantages for collection and evaluation of large amounts of complex health-care data. We conducted a systematic review to understand the role of ML in the development of predictive post-surgical outcome models and risk stratification. Methods Following the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines, we selected the period of the research for studies from 1 January 2015 up to 30 March 2021. A systematic search in Scopus, CINAHL, the Cochrane Library, PubMed, and MeSH databases was performed; the strings of research included different combinations of keywords: “risk prediction,” “surgery,” “machine learning,” “intensive care unit (ICU),” and “anesthesia” “perioperative.” We identified 36 eligible studies. This study evaluates the quality of reporting of prediction models using the Transparent Reporting of a Multivariable Prediction Model for Individual Prognosis or Diagnosis (TRIPOD) checklist. Results The most considered outcomes were mortality risk, systemic complications (pulmonary, cardiovascular, acute kidney injury (AKI), etc.), ICU admission, anesthesiologic risk and prolonged length of hospital stay. Not all the study completely followed the TRIPOD checklist, but the quality was overall acceptable with 75% of studies (Rev #2, comm #minor issue) showing an adherence rate to TRIPOD more than 60%. The most frequently used algorithms were gradient boosting (n = 13), random forest (n = 10), logistic regression (LR; n = 7), artificial neural networks (ANNs; n = 6), and support vector machines (SVM; n = 6). Models with best performance were random forest and gradient boosting, with AUC > 0.90. Conclusions The application of ML in medicine appears to have a great potential. From our analysis, depending on the input features considered and on the specific prediction task, ML algorithms seem effective in outcomes prediction more accurately than validated prognostic scores and traditional statistics. Thus, our review encourages the healthcare domain and artificial intelligence (AI) developers to adopt an interdisciplinary and systemic approach to evaluate the overall impact of AI on perioperative risk assessment and on further health care settings as well.

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Predicting Nigerian Stock Returns using Technical Analysis and Machine Learning

European Journal of Electrical Engineering and Computer Science ◽

10.24018/ejece.2019.3.2.65 ◽

2019 ◽

Vol 3 (2) ◽

Author(s):

D. O. Oyewola ◽

Emmanuel Gbenga Gbenga Dada ◽

Omole Ezekiel Olaoluwa ◽

K.A. Al-Mustapha

Keyword(s):

Machine Learning ◽

Random Forest ◽

Stock Returns ◽

Stock Price ◽

Prediction Models ◽

Technical Analysis ◽

Classification Problem ◽

Support Vector ◽

Stock Market Returns ◽

Stock Price Prediction

Models of stock price prediction have customarily utilized technical indicators alone to produce trading signals. In this paper, we construct trading techniques by applying machine-learning methods to technical analysis indicators and stock market returns data. The resulting prediction models can be utilized as an artificial trader used to trade on any given stock trade. Here the issue of stock trading decision prediction is enunciated as a classification problem with two class values representing the buy and sell signals. The stacking technique utilized in this paper is to assist trader with applying the proposed algorithms in their trading using random forest which was staked with different algorithms which incorporates Logistic Regression (LR), Random Forest (RF), Support Vector Machine (SVM) and Neural Network (NN). The experimental results indicated that Top Layer of Random Forest (TRF) produced the best performance among all the algorithms compared. This is an indication that it is a promising strategy for forecasting Nigerian stock returns.

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Classification Models using Circulating Neutrophil Transcripts Can Detect Unruptured Intracranial Aneurysm

10.21203/rs.3.rs-17161/v2 ◽

2020 ◽

Author(s):

Kerry E Poppenberg ◽

Vincent M Tutino ◽

Lu Li ◽

Muhammad Waqas ◽

Armond June ◽

...

Keyword(s):

Machine Learning ◽

Random Forest ◽

Prediction Models ◽

Model Performance ◽

Supervised Machine Learning ◽

Support Vector ◽

Learning Methods ◽

Training Cohort ◽

Network Analyses ◽

Machine Learning Methods

Abstract Background: Intracranial aneurysms (IAs) are dangerous because of their potential to rupture. We previously found significant RNA expression differences in circulating neutrophils between patients with and without unruptured IAs and trained machine learning models to predict presence of IA using 40 neutrophil transcriptomes. Here, we aim to develop a predictive model for unruptured IA using neutrophil transcriptomes from a larger population and more robust machine learning methods. Methods: Neutrophil RNA extracted from the blood of 134 patients (55 with IA, 79 IA-free controls) was subjected to next-generation RNA sequencing. In a randomly-selected training cohort (n=94), the Least Absolute Shrinkage and Selection Operator (LASSO) selected transcripts, from which we constructed prediction models via 4 well-established supervised machine-learning algorithms (K-Nearest Neighbors, Random Forest, and Support Vector Machines with Gaussian and cubic kernels). We tested the models in the remaining samples (n=40) and assessed model performance by receiver-operating-characteristic (ROC) curves. Real-time quantitative polymerase chain reaction (RT-qPCR) of 9 IA-associated genes was used to verify gene expression in a subset of 49 neutrophil RNA samples. We also examined the potential influence of demographics and comorbidities on model prediction. Results: Feature selection using LASSO in the training cohort identified 37 IA-associated transcripts. Models trained using these transcripts had a maximum accuracy of 90% in the testing cohort. The testing performance across all methods had an average area under ROC curve (AUC)=0.97, an improvement over our previous models. The Random Forest model performed best across both training and testing cohorts. RT-qPCR confirmed expression differences in 7 of 9 genes tested. Gene ontology and IPA network analyses performed on the 37 model genes reflected dysregulated inflammation, cell signaling, and apoptosis processes. In our data, demographics and comorbidities did not affect model performance. Conclusions: We improved upon our previous IA prediction models based on circulating neutrophil transcriptomes by increasing sample size and by implementing LASSO and more robust machine learning methods. Future studies are needed to validate these models in larger cohorts and further investigate effect of covariates.

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Machine learning predictivity applied to consumer creditworthiness

Future Business Journal ◽

10.1186/s43093-020-00041-w ◽

2020 ◽

Vol 6 (1) ◽

Author(s):

Maisa Cardoso Aniceto ◽

Flavio Barboza ◽

Herbert Kimura

Keyword(s):

Machine Learning ◽

Support Vector Machine ◽

Random Forest ◽

Credit Risk ◽

Performance Metrics ◽

Prediction Models ◽

Machine Learning Techniques ◽

Support Vector ◽

Learning Techniques ◽

Default Prediction

AbstractCredit risk evaluation has a relevant role to financial institutions, since lending may result in real and immediate losses. In particular, default prediction is one of the most challenging activities for managing credit risk. This study analyzes the adequacy of borrower’s classification models using a Brazilian bank’s loan database, and exploring machine learning techniques. We develop Support Vector Machine, Decision Trees, Bagging, AdaBoost and Random Forest models, and compare their predictive accuracy with a benchmark based on a Logistic Regression model. Comparisons are analyzed based on usual classification performance metrics. Our results show that Random Forest and Adaboost perform better when compared to other models. Moreover, Support Vector Machine models show poor performance using both linear and nonlinear kernels. Our findings suggest that there are value creating opportunities for banks to improve default prediction models by exploring machine learning techniques.

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Applications of Machine Learning for the Classification of Porcine Reproductive and Respiratory Syndrome Virus Sublineages Using Amino Acid Scores of ORF5 Gene

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.683134 ◽

2021 ◽

Vol 8 ◽

Author(s):

Jeonghoon Kim ◽

Kyuyoung Lee ◽

Ruwini Rupasinghe ◽

Shahbaz Rezaei ◽

Beatriz Martínez-López ◽

...

Keyword(s):

Machine Learning ◽

Phylogenetic Analysis ◽

Amino Acid ◽

Random Forest ◽

Real Time ◽

Classification Model ◽

Support Vector ◽

Operating Characteristics ◽

Orf5 Gene

Porcine reproductive and respiratory syndrome is an infectious disease of pigs caused by PRRS virus (PRRSV). A modified live-attenuated vaccine has been widely used to control the spread of PRRSV and the classification of field strains is a key for a successful control and prevention. Restriction fragment length polymorphism targeting the Open reading frame 5 (ORF5) genes is widely used to classify PRRSV strains but showed unstable accuracy. Phylogenetic analysis is a powerful tool for PRRSV classification with consistent accuracy but it demands large computational power as the number of sequences gets increased. Our study aimed to apply four machine learning (ML) algorithms, random forest, k-nearest neighbor, support vector machine and multilayer perceptron, to classify field PRRSV strains into four clades using amino acid scores based on ORF5 gene sequence. Our study used amino acid sequences of ORF5 gene in 1931 field PRRSV strains collected in the US from 2012 to 2020. Phylogenetic analysis was used to labels field PRRSV strains into one of four clades: Lineage 5 or three clades in Linage 1. We measured accuracy and time consumption of classification using four ML approaches by different size of gene sequences. We found that all four ML algorithms classify a large number of field strains in a very short time (<2.5 s) with very high accuracy (>0.99 Area under curve of the Receiver of operating characteristics curve). Furthermore, the random forest approach detects a total of 4 key amino acid positions for the classification of field PRRSV strains into four clades. Our finding will provide an insightful idea to develop a rapid and accurate classification model using genetic information, which also enables us to handle large genome datasets in real time or semi-real time for data-driven decision-making and more timely surveillance.

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