Predicting Inhibitors for Multidrug Resistance Associated Protein-2 Transporter by Machine Learning Approach

2018 ◽  
Vol 21 (8) ◽  
pp. 557-566 ◽  
Author(s):  
Sahil Kharangarh ◽  
Hardeep Sandhu ◽  
Sujit Tangadpalliwar ◽  
Prabha Garg
Keyword(s):  
Machine Learning ◽  
Support Vector Machine ◽  
Multidrug Resistance ◽  
Random Forest ◽  
Predictive Models ◽  
Computational Study ◽  
Recursive Feature Elimination ◽  
Efflux Transporters ◽  
Support Vector ◽  
Efflux Transporter

Background: The efflux transporter multidrug resistance associated protein-2 belongs to ATP-binding cassette superfamily which plays an important role in multidrug resistance and drugdrug interactions. Efflux transporters are considered to be important targets for increasing the efficacy of drugs and importance of computational study of efflux transporters for predicting substrates, non-substrates, inhibitors and non-inhibitors is well documented. Previous work on predictive models for inhibitors of multidrug resistance associated Protein-2 efflux transporter showed that machine learning methods produced good results. Objective: The aim of the present work was to develop a machine learning predictive model to classify inhibitors and non-inhibitors of multidrug resistance associated protein-2 transporter using a well refined dataset. Method: In this study, the various algorithms of machine learning were used to develop the predictive models i.e. support vector machine, random forest and k-nearest neighbor. The methods like variance threshold, SelectKBest, random forest, and recursive feature elimination were used to select the features generated by PyDPI. A total of 239 molecules consisting of 124 inhibitors and 115 non-inhibitors were used for model development. Results: The best multidrug resistance associated protein-2 inhibitor model showed prediction accuracies of 0.76, 0.72 and 0.79 for training, 5-fold cross-validation and external sets, respectively. Conclusion: It was observed that support vector machine model built on features selected using recursive feature elimination method shows the best performance. The developed model can be used in the early stages of drug discovery for identifying the inhibitors of multidrug resistance associated protein-2 efflux transporter.

Identifying novel transcript biomarkers for hepatocellular carcinoma (HCC) using RNA-Seq datasets and machine learning

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Rajinder Gupta ◽  
Jos Kleinjans ◽  
Florian Caiment
Keyword(s):  
Machine Learning ◽  
Support Vector Machine ◽  
Random Forest ◽  
Machine Learning Algorithms ◽  
Recursive Feature Elimination ◽  
Support Vector ◽  
Rna Seq ◽  
Cell Models ◽  
Novel Transcript ◽  
Transcript Biomarkers

Abstract Background Hepatocellular carcinoma (HCC) is one of the leading causes of cancer death in the world owing to limitations in its prognosis. The current prognosis approaches include radiological examination and detection of serum biomarkers, however, both have limited efficiency and are ineffective in early prognosis. Due to such limitations, we propose to use RNA-Seq data for evaluating putative higher accuracy biomarkers at the transcript level that could help in early prognosis. Methods To identify such potential transcript biomarkers, RNA-Seq data for healthy liver and various HCC cell models were subjected to five different machine learning algorithms: random forest, K-nearest neighbor, Naïve Bayes, support vector machine, and neural networks. Various metrics, namely sensitivity, specificity, MCC, informedness, and AUC-ROC (except for support vector machine) were evaluated. The algorithms that produced the highest values for all metrics were chosen to extract the top features that were subjected to recursive feature elimination. Through recursive feature elimination, the least number of features were obtained to differentiate between the healthy and HCC cell models. Results From the metrics used, it is demonstrated that the efficiency of the known protein biomarkers for HCC is comparatively lower than complete transcriptomics data. Among the different machine learning algorithms, random forest and support vector machine demonstrated the best performance. Using recursive feature elimination on top features of random forest and support vector machine three transcripts were selected that had an accuracy of 0.97 and kappa of 0.93. Of the three transcripts, two were protein coding (PARP2–202 and SPON2–203) and one was a non-coding transcript (CYREN-211). Lastly, we demonstrated that these three selected transcripts outperformed randomly taken three transcripts (15,000 combinations), hence were not chance findings, and could then be an interesting candidate for new HCC biomarker development. Conclusion Using RNA-Seq data combined with machine learning approaches can aid in finding novel transcript biomarkers. The three biomarkers identified: PARP2–202, SPON2–203, and CYREN-211, presented the highest accuracy among all other transcripts in differentiating the healthy and HCC cell models. The machine learning pipeline developed in this study can be used for any RNA-Seq dataset to find novel transcript biomarkers. Code: www.github.com/rajinder4489/ML_biomarkers

Classification study of solvation free energies of organic molecules using machine learning techniques

RSC Advances ◽  
2014 ◽  
Vol 4 (106) ◽  
pp. 61624-61630 ◽  
Author(s):  
N. S. Hari Narayana Moorthy ◽  
Silvia A. Martins ◽  
Sergio F. Sousa ◽  
Maria J. Ramos ◽  
Pedro A. Fernandes
Keyword(s):  
Machine Learning ◽  
Support Vector Machine ◽  
Random Forest ◽  
Organic Molecules ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
Classification Models ◽  
Free Energies ◽  
Learning Techniques ◽  
Solvation Free Energies

Classification models to predict the solvation free energies of organic molecules were developed using decision tree, random forest and support vector machine approaches and with MACCS fingerprints, MOE and PaDEL descriptors.

scholarly journals Execution Assessment of Machine Learning Algorithms for Spam Profile Detection on Instagram

2021 ◽  
Vol 10 (3) ◽  
pp. 1889-1894
Keyword(s):  
Machine Learning ◽  
Support Vector Machine ◽  
Random Forest ◽  
Nearest Neighbor ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Learning Tools ◽  
Learning Models ◽  
K Nearest Neighbor

Witheverypassingsecondsocialnetworkcommunityisgrowingrapidly,becauseofthat,attackershaveshownkeeninterestinthesekindsofplatformsandwanttodistributemischievouscontentsontheseplatforms.Withthefocus on introducing new set of characteristics and features forcounteractivemeasures,agreatdealofstudieshasresearchedthe possibility of lessening the malicious activities on social medianetworks. This research was to highlight features for identifyingspammers on Instagram and additional features were presentedto improve the performance of different machine learning algorithms. Performance of different machine learning algorithmsnamely, Multilayer Perceptron (MLP), Random Forest (RF), K-Nearest Neighbor (KNN) and Support Vector Machine (SVM)were evaluated on machine learning tools named, RapidMinerand WEKA. The results from this research tells us that RandomForest (RF) outperformed all other selected machine learningalgorithmsonbothselectedmachinelearningtools.OverallRandom Forest (RF) provided best results on RapidMiner. Theseresultsareusefulfortheresearcherswhoarekeentobuildmachine learning models to find out the spamming activities onsocialnetworkcommunities.

scholarly journals Application of Natural Language Processing with Supervised Machine Learning Techniques to Predict the Overall Drugs Performance

2020 ◽  
Vol 11 (40) ◽  
pp. 8-23
Author(s):  
Pius MARTHIN ◽  
Duygu İÇEN
Keyword(s):  
Machine Learning ◽  
Support Vector Machine ◽  
Random Forest ◽  
Semantic Analysis ◽  
Classification Tree ◽  
Supervised Machine Learning ◽  
Training Dataset ◽  
Support Vector ◽  
Learning Models ◽  
Machine Learning Models

Online product reviews have become a valuable source of information which facilitate customer decision with respect to a particular product. With the wealthy information regarding user's satisfaction and experiences about a particular drug, pharmaceutical companies make the use of online drug reviews to improve the quality of their products. Machine learning has enabled scientists to train more efficient models which facilitate decision making in various fields. In this manuscript we applied a drug review dataset used by (Gräβer, Kallumadi, Malberg,& Zaunseder, 2018), available freely from machine learning repository website of the University of California Irvine (UCI) to identify best machine learning model which provide a better prediction of the overall drug performance with respect to users' reviews. Apart from several manipulations done to improve model accuracy, all necessary procedures required for text analysis were followed including text cleaning and transformation of texts to numeric format for easy training machine learning models. Prior to modeling, we obtained overall sentiment scores for the reviews. Customer's reviews were summarized and visualized using a bar plot and word cloud to explore the most frequent terms. Due to scalability issues, we were able to use only the sample of the dataset. We randomly sampled 15000 observations from the 161297 training dataset and 10000 observations were randomly sampled from the 53766 testing dataset. Several machine learning models were trained using 10 folds cross-validation performed under stratified random sampling. The trained models include Classification and Regression Trees (CART), classification tree by C5.0, logistic regression (GLM), Multivariate Adaptive Regression Spline (MARS), Support vector machine (SVM) with both radial and linear kernels and a classification tree using random forest (Random Forest). Model selection was done through a comparison of accuracies and computational efficiency. Support vector machine (SVM) with linear kernel was significantly best with an accuracy of 83% compared to the rest. Using only a small portion of the dataset, we managed to attain reasonable accuracy in our models by applying the TF-IDF transformation and Latent Semantic Analysis (LSA) technique to our TDM.

scholarly journals Detecting Real-Time Fall of Elderly People Using Machine Learning

2021 ◽  
Vol 9 (12) ◽  
pp. 1913-1918
Author(s):  
Prathima P
Keyword(s):  
Machine Learning ◽  
Support Vector Machine ◽  
Random Forest ◽  
Elderly People ◽  
Fall Detection ◽  
Machine Learning Algorithms ◽  
Supervised Machine Learning ◽  
Support Vector ◽  
False Alarms ◽  
Severe Injuries

Abstract: Fall is a significant national health issue for the elderly people, generally resulting in severe injuries when the person lies down on the floor over an extended period without any aid after experiencing a great fall. Thus, elders need to be cared very attentively. A supervised-machine learning based fall detection approach with accelerometer, gyroscope is devised. The system can detect falls by grouping different actions as fall or non-fall events and the care taker is alerted immediately as soon as the person falls. The public dataset SisFall with efficient class of features is used to identify fall. The Random Forest (RF) and Support Vector Machine (SVM) machine learning algorithms are employed to detect falls with lesser false alarms. The SVM algorithm obtain a highest accuracy of 99.23% than RF algorithm. Keywords: Fall detection, Machine learning, Supervised classification, Sisfall, Activities of daily living, Wearable sensors, Random Forest, Support Vector Machine

scholarly journals Aspect Category Classification dengan Pendekatan Machine Learning Menggunakan Dataset Bahasa Indonesia

2021 ◽  
Vol 10 (3) ◽  
pp. 229-235
Author(s):  
Syaifulloh Amien Pandega Perdana ◽  
Teguh Bharata Aji ◽  
Ridi Ferdiana
Keyword(s):  
Machine Learning ◽  
Support Vector Machine ◽  
Random Forest ◽  
Sentiment Analysis ◽  
Support Vector ◽  
Term Weighting ◽  
Inverse Document Frequency ◽  
Term Frequency ◽  
Document Frequency ◽  
Bahasa Indonesia

Ulasan pelanggan merupakan opini terhadap kualitas barang atau jasa yang dirasakan konsumen. Ulasan pelanggan mengandung informasi yang berguna bagi konsumen maupun penyedia barang atau jasa. Ketersediaan ulasan pelanggan dalam jumlah besar pada website membutuhkan suatu framework untuk mengekstraksi sentimen secara otomatis. Sebuah ulasan pelanggan sering kali mengandung banyak aspek sehingga Aspect Based Sentiment Analysis (ABSA) harus digunakan untuk mengetahui polaritas masing-masing aspek. Salah satu tugas penting dalam ABSA adalah Aspect Category Detection. Metode machine learning untuk Aspect Category Detection sudah banyak dilakukan pada domain berbahasa Inggris, tetapi pada domain bahasa Indonesia masih sedikit. Makalah ini membandingkan kinerja tiga algoritme machine learning, yaitu Naïve Bayes (NB), Support Vector Machine (SVM), dan Random Forest (RF) pada ulasan pelanggan berbahasa Indonesia menggunakan Term Frequency–Inverse Document Frequency (TF-IDF) sebagai term weighting. Hasil menunjukkan bahwa RF memiliki kinerja paling unggul dibandingkan NB dan SVM pada tiga domain yang berbeda, yaitu restoran, hotel, dan e-commerce, dengan nilai f1-score untuk masing-masing domain adalah 84.3%, 85.7%, dan 89,3%.

scholarly journals Predição de sinistros agrícolas: uma abordagem comparativa utilizando aprendizagem de máquina

2020 ◽  
Vol 24 (4) ◽  
pp. 533-554
Author(s):  
Arthur Lula Mota ◽  
Daniel Lima Miquelluti ◽  
Vitor Augusto Ozaki
Keyword(s):  
Machine Learning ◽  
Support Vector Machine ◽  
Random Forest ◽  
Support Vector ◽  
Nearest Neighbours

O seguro agrícola tem ganho maior atenção no Brasil desde o início da década passada, com a implementação do Programa de Subvenção ao Prêmio do Seguro Rural. O presente estudo testou o desempenho de algoritmos de Machine Learning para as seguradoras anteciparem a ocorrência de sinistro, elaborando previsões por meio de dados de apólices e bases de dados climáticas entre os anos de 2006 e 2017. Foram testados os algoritmos Random Forest, Support Vector Machine e k-Nearest Neighbours. O segundo mostrou melhor performance preditiva de sinistros. No entanto, todos os métodos apresentaram baixa capacidade preditiva para a ocorrência de sinistros.

scholarly journals Performance Comparison of Oil Spill and Ship Classification from X-Band Dual- and Single-Polarized SAR Image Using Support Vector Machine, Random Forest, and Deep Neural Network

2021 ◽  
Vol 13 (16) ◽  
pp. 3203
Author(s):  
Won-Kyung Baek ◽  
Hyung-Sup Jung
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Support Vector Machine ◽  
Random Forest ◽  
Performance Improvement ◽  
Oil Spill ◽  
Deep Neural Network ◽  
Support Vector ◽  
Sar Image ◽  
X Band

It is well known that the polarization characteristics in X-band synthetic aperture radar (SAR) image analysis can provide us with additional information for marine target classification and detection. Normally, dual-and single-polarized SAR images are acquired by SAR satellites, and then we must determine how accurate the marine mapping performance from dual-polarized (pol) images is versus the marine mapping performance from the single-pol images in a given machine learning model. The purpose of this study is to compare the performance of single- and dual-pol SAR image classification achieved by the support vector machine (SVM), random forest (RF), and deep neural network (DNN) models. The test image is a TerraSAR-X dual-pol image acquired from the 2007 Kerch Strait oil spill event. For this, 824,026 pixels and 1,648,051 pixels were extracted from the image for the training and test, respectively, and sea, ship, oil, and land objects were classified from the image by using the three machine learning methods. The mean f1-scores of the SVM, RF, and DNN models resulting from the single-pol image were approximately 0.822, 0.882, and 0.889, respectively, and those from the dual-pol image were about 0.852, 0.908, and 0.898, respectively. The performance improvement achieved by dual-pol was about 3.6%, 2.9%, and 1% in SVM, RF, and DNN, respectively. The DNN model had the best performance (0.889) in the single-pol test while the RF model was best (0.908) in the dual-pol test. The performance improvement was approximately 2.1% and not noticeable. If the condition that dual-pol images have two-times lower spatial resolution versus single-pol images in the azimuth direction is considered, a small improvement may not be valuable. Therefore, the results show that the performance improvement by X-band dual-pol image may be not remarkable when classifying the sea, ships, oil spills, and sea and land surfaces.

scholarly journals Machine learning model for predicting the optimal depth of tracheal tube insertion in pediatric patients: A retrospective cohort study

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0257069
Author(s):  
Jae-Geum Shim ◽  
Kyoung-Ho Ryu ◽  
Sung Hyun Lee ◽  
Eun-Ah Cho ◽  
Sungho Lee ◽  
...  
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Artificial Neural Network ◽  
Support Vector Machine ◽  
Random Forest ◽  
Tracheal Tube ◽  
Pediatric Patients ◽  
Support Vector ◽  
Learning Models ◽  
Machine Learning Models

Objective To construct a prediction model for optimal tracheal tube depth in pediatric patients using machine learning. Methods Pediatric patients aged <7 years who received post-operative ventilation after undergoing surgery between January 2015 and December 2018 were investigated in this retrospective study. The optimal location of the tracheal tube was defined as the median of the distance between the upper margin of the first thoracic(T1) vertebral body and the lower margin of the third thoracic(T3) vertebral body. We applied four machine learning models: random forest, elastic net, support vector machine, and artificial neural network and compared their prediction accuracy to three formula-based methods, which were based on age, height, and tracheal tube internal diameter(ID). Results For each method, the percentage with optimal tracheal tube depth predictions in the test set was calculated as follows: 79.0 (95% confidence interval [CI], 73.5 to 83.6) for random forest, 77.4 (95% CI, 71.8 to 82.2; P = 0.719) for elastic net, 77.0 (95% CI, 71.4 to 81.8; P = 0.486) for support vector machine, 76.6 (95% CI, 71.0 to 81.5; P = 1.0) for artificial neural network, 66.9 (95% CI, 60.9 to 72.5; P < 0.001) for the age-based formula, 58.5 (95% CI, 52.3 to 64.4; P< 0.001) for the tube ID-based formula, and 44.4 (95% CI, 38.3 to 50.6; P < 0.001) for the height-based formula. Conclusions In this study, the machine learning models predicted the optimal tracheal tube tip location for pediatric patients more accurately than the formula-based methods. Machine learning models using biometric variables may help clinicians make decisions regarding optimal tracheal tube depth in pediatric patients.

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