iBitter-Fuse: A Novel Sequence-Based Bitter Peptide Predictor by Fusing Multi-View Features

Accurate identification of bitter peptides is of great importance for better understanding their biochemical and biophysical properties. To date, machine learning-based methods have become effective approaches for providing a good avenue for identifying potential bitter peptides from large-scale protein datasets. Although few machine learning-based predictors have been developed for identifying the bitterness of peptides, their prediction performances could be improved. In this study, we developed a new predictor (named iBitter-Fuse) for achieving more accurate identification of bitter peptides. In the proposed iBitter-Fuse, we have integrated a variety of feature encoding schemes for providing sufficient information from different aspects, namely consisting of compositional information and physicochemical properties. To enhance the predictive performance, the customized genetic algorithm utilizing self-assessment-report (GA-SAR) was employed for identifying informative features followed by inputting optimal ones into a support vector machine (SVM)-based classifier for developing the final model (iBitter-Fuse). Benchmarking experiments based on both 10-fold cross-validation and independent tests indicated that the iBitter-Fuse was able to achieve more accurate performance as compared to state-of-the-art methods. To facilitate the high-throughput identification of bitter peptides, the iBitter-Fuse web server was established and made freely available online. It is anticipated that the iBitter-Fuse will be a useful tool for aiding the discovery and de novo design of bitter peptides

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QUBO formulations for training machine learning models

Scientific Reports ◽

10.1038/s41598-021-89461-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Prasanna Date ◽

Davis Arthur ◽

Lauren Pusey-Nazzaro

Keyword(s):

Machine Learning ◽

Linear Regression ◽

Large Scale ◽

Support Vector ◽

Quantum Computers ◽

Np Hard ◽

Learning Models ◽

Moore’S Law ◽

Moore's Law ◽

Machine Learning Models

AbstractTraining machine learning models on classical computers is usually a time and compute intensive process. With Moore’s law nearing its inevitable end and an ever-increasing demand for large-scale data analysis using machine learning, we must leverage non-conventional computing paradigms like quantum computing to train machine learning models efficiently. Adiabatic quantum computers can approximately solve NP-hard problems, such as the quadratic unconstrained binary optimization (QUBO), faster than classical computers. Since many machine learning problems are also NP-hard, we believe adiabatic quantum computers might be instrumental in training machine learning models efficiently in the post Moore’s law era. In order to solve problems on adiabatic quantum computers, they must be formulated as QUBO problems, which is very challenging. In this paper, we formulate the training problems of three machine learning models—linear regression, support vector machine (SVM) and balanced k-means clustering—as QUBO problems, making them conducive to be trained on adiabatic quantum computers. We also analyze the computational complexities of our formulations and compare them to corresponding state-of-the-art classical approaches. We show that the time and space complexities of our formulations are better (in case of SVM and balanced k-means clustering) or equivalent (in case of linear regression) to their classical counterparts.

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Predicting ionizing radiation exposure using biochemically-inspired genomic machine learning

F1000Research ◽

10.12688/f1000research.14048.1 ◽

2018 ◽

Vol 7 ◽

pp. 233

Author(s):

Jonathan Z.L. Zhao ◽

Eliseos J. Mucaki ◽

Peter K. Rogan

Keyword(s):

Machine Learning ◽

Ionizing Radiation ◽

Radiation Exposure ◽

Large Scale ◽

Nearest Neighbor ◽

Error Rates ◽

Support Vector ◽

Dose Estimation ◽

Gene Signatures ◽

Ionizing Radiation Exposure

Background: Gene signatures derived from transcriptomic data using machine learning methods have shown promise for biodosimetry testing. These signatures may not be sufficiently robust for large scale testing, as their performance has not been adequately validated on external, independent datasets. The present study develops human and murine signatures with biochemically-inspired machine learning that are strictly validated using k-fold and traditional approaches. Methods: Gene Expression Omnibus (GEO) datasets of exposed human and murine lymphocytes were preprocessed via nearest neighbor imputation and expression of genes implicated in the literature to be responsive to radiation exposure (n=998) were then ranked by Minimum Redundancy Maximum Relevance (mRMR). Optimal signatures were derived by backward, complete, and forward sequential feature selection using Support Vector Machines (SVM), and validated using k-fold or traditional validation on independent datasets. Results: The best human signatures we derived exhibit k-fold validation accuracies of up to 98% (DDB2, PRKDC, TPP2, PTPRE, and GADD45A) when validated over 209 samples and traditional validation accuracies of up to 92% (DDB2, CD8A, TALDO1, PCNA, EIF4G2, LCN2, CDKN1A, PRKCH, ENO1, and PPM1D) when validated over 85 samples. Some human signatures are specific enough to differentiate between chemotherapy and radiotherapy. Certain multi-class murine signatures have sufficient granularity in dose estimation to inform eligibility for cytokine therapy (assuming these signatures could be translated to humans). We compiled a list of the most frequently appearing genes in the top 20 human and mouse signatures. More frequently appearing genes among an ensemble of signatures may indicate greater impact of these genes on the performance of individual signatures. Several genes in the signatures we derived are present in previously proposed signatures. Conclusions: Gene signatures for ionizing radiation exposure derived by machine learning have low error rates in externally validated, independent datasets, and exhibit high specificity and granularity for dose estimation.

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Machine learning-based feature importance approach for sensitivity analysis of steel frames

10.31224/osf.io/mvkf3 ◽

2021 ◽

Author(s):

Hyeyoung Koh ◽

Hannah Beth Blum

Keyword(s):

Machine Learning ◽

Sensitivity Analysis ◽

Feature Selection ◽

Large Scale ◽

Failure Modes ◽

Model Development ◽

Predictive Performance ◽

Computational Effort ◽

Structural Systems ◽

Feature Importance

This study presents a machine learning-based approach for sensitivity analysis to examine how parameters affect a given structural response while accounting for uncertainty. Reliability-based sensitivity analysis involves repeated evaluations of the performance function incorporating uncertainties to estimate the influence of a model parameter, which can lead to prohibitive computational costs. This challenge is exacerbated for large-scale engineering problems which often carry a large quantity of uncertain parameters. The proposed approach is based on feature selection algorithms that rank feature importance and remove redundant predictors during model development which improve model generality and training performance by focusing only on the significant features. The approach allows performing sensitivity analysis of structural systems by providing feature rankings with reduced computational effort. The proposed approach is demonstrated with two designs of a two-bay, two-story planar steel frame with different failure modes: inelastic instability of a single member and progressive yielding. The feature variables in the data are uncertainties including material yield strength, Young’s modulus, frame sway imperfection, and residual stress. The Monte Carlo sampling method is utilized to generate random realizations of the frames from published distributions of the feature parameters, and the response variable is the frame ultimate strength obtained from finite element analyses. Decision trees are trained to identify important features. Feature rankings are derived by four feature selection techniques including impurity-based, permutation, SHAP, and Spearman's correlation. Predictive performance of the model including the important features are discussed using the evaluation metric for imbalanced datasets, Matthews correlation coefficient. Finally, the results are compared with those from reliability-based sensitivity analysis on the same example frames to show the validity of the feature selection approach. As the proposed machine learning-based approach produces the same results as the reliability-based sensitivity analysis with improved computational efficiency and accuracy, it could be extended to other structural systems.

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Applying Machine Learning for Improving Performance Classification on Driving Behavior

IJITEE (International Journal of Information Technology and Electrical Engineering) ◽

10.22146/ijitee.56919 ◽

2021 ◽

Vol 4 (1) ◽

pp. 8

Author(s):

Ahmad Iwan Fadli ◽

Selo Sulistyo ◽

Sigit Wibowo

Keyword(s):

Machine Learning ◽

Traffic Accident ◽

Large Scale ◽

Detection System ◽

Difficult Problem ◽

Sensor Data ◽

Driving Safety ◽

Support Vector ◽

Classification Methods ◽

Machine Learning Classification

Traffic accident is a very difficult problem to handle on a large scale in a country. Indonesia is one of the most populated, developing countries that use vehicles for daily activities as its main transportation. It is also the country with the largest number of car users in Southeast Asia, so driving safety needs to be considered. Using machine learning classification method to determine whether a driver is driving safely or not can help reduce the risk of driving accidents. We created a detection system to classify whether the driver is driving safely or unsafely using trip sensor data, which include Gyroscope, Acceleration, and GPS. The classification methods used in this study are Random Forest (RF) classification algorithm, Support Vector Machine (SVM), and Multilayer Perceptron (MLP) by improving data preprocessing using feature extraction and oversampling methods. This study shows that RF has the best performance with 98% accuracy, 98% precision, and 97% sensitivity using the proposed preprocessing stages compared to SVM or MLP.

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Support Vector Machines in Big Data Classification: A Systematic Literature Review

10.21203/rs.3.rs-663359/v1 ◽

2021 ◽

Author(s):

Mohammad Hassan Almaspoor ◽

Ali Safaei ◽

Afshin Salajegheh ◽

Behrouz Minaei-Bidgoli

Keyword(s):

Machine Learning ◽

Big Data ◽

Large Scale ◽

Support Vector ◽

Research Areas ◽

Large Scale Data ◽

Training Samples ◽

Big Data Classification ◽

Scale Data

Abstract Classification is one of the most important and widely used issues in machine learning, the purpose of which is to create a rule for grouping data to sets of pre-existing categories is based on a set of training sets. Employed successfully in many scientific and engineering areas, the Support Vector Machine (SVM) is among the most promising methods of classification in machine learning. With the advent of big data, many of the machine learning methods have been challenged by big data characteristics. The standard SVM has been proposed for batch learning in which all data are available at the same time. The SVM has a high time complexity, i.e., increasing the number of training samples will intensify the need for computational resources and memory. Hence, many attempts have been made at SVM compatibility with online learning conditions and use of large-scale data. This paper focuses on the analysis, identification, and classification of existing methods for SVM compatibility with online conditions and large-scale data. These methods might be employed to classify big data and propose research areas for future studies. Considering its advantages, the SVM can be among the first options for compatibility with big data and classification of big data. For this purpose, appropriate techniques should be developed for data preprocessing in order to covert data into an appropriate form for learning. The existing frameworks should also be employed for parallel and distributed processes so that SVMs can be made scalable and properly online to be able to handle big data.

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Detection of misinformation on garlic and COVID-19 in Twitter: A machine learning-based approach (Preprint)

10.2196/preprints.33056 ◽

2021 ◽

Author(s):

Myeong Gyu Kim ◽

Jae Hyun Kim ◽

Kyungim Kim

Keyword(s):

Machine Learning ◽

Social Media ◽

Latent Dirichlet Allocation ◽

Predictive Performance ◽

Machine Learning Algorithms ◽

Training Dataset ◽

Polynomial Kernel ◽

Support Vector ◽

Accurate Information ◽

Probability Number

BACKGROUND Garlic-related misinformation is prevalent whenever a virus outbreak occurs. Again, with the outbreak of coronavirus disease 2019 (COVID-19), garlic-related misinformation is spreading through social media sites, including Twitter. Machine learning-based approaches can be used to detect misinformation from vast tweets. OBJECTIVE This study aimed to develop machine learning algorithms for detecting misinformation on garlic and COVID-19 in Twitter. METHODS This study used 5,929 original tweets mentioning garlic and COVID-19. Tweets were manually labeled as misinformation, accurate information, and others. We tested the following algorithms: k-nearest neighbors; random forest; support vector machine (SVM) with linear, radial, and polynomial kernels; and neural network. Features for machine learning included user-based features (verified account, user type, number of followers, and follower rate) and text-based features (uniform resource locator, negation, sentiment score, Latent Dirichlet Allocation topic probability, number of retweets, and number of favorites). A model with the highest accuracy in the training dataset (70% of overall dataset) was tested using a test dataset (30% of overall dataset). Predictive performance was measured using overall accuracy, sensitivity, specificity, and balanced accuracy. RESULTS SVM with the polynomial kernel model showed the highest accuracy of 0.670. The model also showed a balanced accuracy of 0.757, sensitivity of 0.819, and specificity of 0.696 for misinformation. Important features in the misinformation and accurate information classes included topic 4 (common myths), topic 13 (garlic-specific myths), number of followers, topic 11 (misinformation on social media), and follower rate. Topic 3 (cooking recipes) was the most important feature in the others class. CONCLUSIONS Our SVM model showed good performance in detecting misinformation. The results of our study will help detect misinformation related to garlic and COVID-19. It could also be applied to prevent misinformation related to dietary supplements in the event of a future outbreak of a disease other than COVID-19.

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The Influence of Inhomogeneous Input Data from Different Waves on Predictive Model Development for COVID-19 ICU Patients (Preprint)

10.2196/preprints.31539 ◽

2021 ◽

Author(s):

Sebastian Johannes Fritsch ◽

Konstantin Sharafutdinov ◽

Moein Einollahzadeh Samadi ◽

Gernot Marx ◽

Andreas Schuppert ◽

...

Keyword(s):

Machine Learning ◽

Convex Hull ◽

Prediction Models ◽

Model Development ◽

Predictive Performance ◽

Support Vector ◽

Good Prediction ◽

The Impact ◽

Second Wave ◽

Over Time

BACKGROUND During the course of the COVID-19 pandemic, a variety of machine learning models were developed to predict different aspects of the disease, such as long-term causes, organ dysfunction or ICU mortality. The number of training datasets used has increased significantly over time. However, these data now come from different waves of the pandemic, not always addressing the same therapeutic approaches over time as well as changing outcomes between two waves. The impact of these changes on model development has not yet been studied. OBJECTIVE The aim of the investigation was to examine the predictive performance of several models trained with data from one wave predicting the second wave´s data and the impact of a pooling of these data sets. Finally, a method for comparison of different datasets for heterogeneity is introduced. METHODS We used two datasets from wave one and two to develop several predictive models for mortality of the patients. Four classification algorithms were used: logistic regression (LR), support vector machine (SVM), random forest classifier (RF) and AdaBoost classifier (ADA). We also performed a mutual prediction on the data of that wave which was not used for training. Then, we compared the performance of models when a pooled dataset from two waves was used. The populations from the different waves were checked for heterogeneity using a convex hull analysis. RESULTS 63 patients from wave one (03-06/2020) and 54 from wave two (08/2020-01/2021) were evaluated. For both waves separately, we found models reaching sufficient accuracies up to 0.79 AUROC (95%-CI 0.76-0.81) for SVM on the first wave and up 0.88 AUROC (95%-CI 0.86-0.89) for RF on the second wave. After the pooling of the data, the AUROC decreased relevantly. In the mutual prediction, models trained on second wave´s data showed, when applied on first wave´s data, a good prediction for non-survivors but an insufficient classification for survivors. The opposite situation (training: first wave, test: second wave) revealed the inverse behaviour with models correctly classifying survivors and incorrectly predicting non-survivors. The convex hull analysis for the first and second wave populations showed a more inhomogeneous distribution of underlying data when compared to randomly selected sets of patients of the same size. CONCLUSIONS Our work demonstrates that a larger dataset is not a universal solution to all machine learning problems in clinical settings. Rather, it shows that inhomogeneous data used to develop models can lead to serious problems. With the convex hull analysis, we offer a solution for this problem. The outcome of such an analysis can raise concerns if the pooling of different datasets would cause inhomogeneous patterns preventing a better predictive performance.

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Identification of DNA-binding proteins via Hypergraph based Laplacian Support Vector Machine

Current Bioinformatics ◽

10.2174/1574893616666210806091922 ◽

2021 ◽

Vol 16 ◽

Author(s):

Yuqing Qian ◽

Hao Meng ◽

Weizhong Lu ◽

Zhijun Liao ◽

Yijie Ding ◽

...

Keyword(s):

Machine Learning ◽

Dna Binding ◽

Large Scale ◽

Binding Proteins ◽

Predictive Accuracy ◽

Dna Binding Proteins ◽

Research Field ◽

Support Vector ◽

Data Sets ◽

Independent Test

Background: The identification of DNA binding proteins (DBP) is an important research field. Experiment-based methods are time-consuming and labor-intensive for detecting DBP. Objective: To solve the problem of large-scale DBP identification, some machine learning methods are proposed. However, these methods have insufficient predictive accuracy. Our aim is to develop a sequence-based machine learning model to predict DBP. Methods: In our study, we extract six types of features (including NMBAC, GE, MCD, PSSM-AB, PSSM-DWT, and PsePSSM) from protein sequences. We use Multiple Kernel Learning based on Hilbert-Schmidt Independence Criterion (MKL-HSIC) to estimate the optimal kernel. Then, we construct a hypergraph model to describe the relationship between labeled and unlabeled samples. Finally, Laplacian Support Vector Machines (LapSVM) is employed to train the predictive model. Our method is tested on PDB186, PDB1075, PDB2272 and PDB14189 data sets. Result: Compared with other methods, our model achieves best results on benchmark data sets. Conclusion: The accuracy of 87.1% and 74.2% are achieved on PDB186 (Independent test of PDB1075) and PDB2272 (Independent test of PDB14189), respectively.

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Machine Learning Readmission Risk Modeling: A Pediatric Case Study

BioMed Research International ◽

10.1155/2019/8532892 ◽

2019 ◽

Vol 2019 ◽

pp. 1-9 ◽

Cited By ~ 3

Author(s):

Patricio Wolff ◽

Manuel Graña ◽

Sebastián A. Ríos ◽

Maria Begoña Yarza

Keyword(s):

Machine Learning ◽

Multilayer Perceptron ◽

Naive Bayes ◽

Class Imbalance ◽

Predictive Performance ◽

Naïve Bayes ◽

Distribution Model ◽

Training Dataset ◽

Support Vector ◽

Pediatric Hospital

Background. Hospital readmission prediction in pediatric hospitals has received little attention. Studies have focused on the readmission frequency analysis stratified by disease and demographic/geographic characteristics but there are no predictive modeling approaches, which may be useful to identify preventable readmissions that constitute a major portion of the cost attributed to readmissions.Objective. To assess the all-cause readmission predictive performance achieved by machine learning techniques in the emergency department of a pediatric hospital in Santiago, Chile.Materials. An all-cause admissions dataset has been collected along six consecutive years in a pediatric hospital in Santiago, Chile. The variables collected are the same used for the determination of the child’s treatment administrative cost.Methods. Retrospective predictive analysis of 30-day readmission was formulated as a binary classification problem. We report classification results achieved with various model building approaches after data curation and preprocessing for correction of class imbalance. We compute repeated cross-validation (RCV) with decreasing number of folders to assess performance and sensitivity to effect of imbalance in the test set and training set size.Results. Increase in recall due to SMOTE class imbalance correction is large and statistically significant. The Naive Bayes (NB) approach achieves the best AUC (0.65); however the shallow multilayer perceptron has the best PPV and f-score (5.6 and 10.2, resp.). The NB and support vector machines (SVM) give comparable results if we consider AUC, PPV, and f-score ranking for all RCV experiments. High recall of deep multilayer perceptron is due to high false positive ratio. There is no detectable effect of the number of folds in the RCV on the predictive performance of the algorithms.Conclusions. We recommend the use of Naive Bayes (NB) with Gaussian distribution model as the most robust modeling approach for pediatric readmission prediction, achieving the best results across all training dataset sizes. The results show that the approach could be applied to detect preventable readmissions.

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Mapping of the Canopy Openings in Mixed Beech–Fir Forest at Sentinel-2 Subpixel Level Using UAV and Machine Learning Approach

Remote Sensing ◽

10.3390/rs12233925 ◽

2020 ◽

Vol 12 (23) ◽

pp. 3925

Author(s):

Ivan Pilaš ◽

Mateo Gašparović ◽

Alan Novkinić ◽

Damir Klobučar

Keyword(s):

Machine Learning ◽

Forest Canopy ◽

Vegetation Index ◽

Predictive Performance ◽

Spatial Extent ◽

Gradient Boosting ◽

Support Vector ◽

Stochastic Gradient Boosting ◽

Extreme Gradient Boosting ◽

Sentinel 2

The presented study demonstrates a bi-sensor approach suitable for rapid and precise up-to-date mapping of forest canopy gaps for the larger spatial extent. The approach makes use of Unmanned Aerial Vehicle (UAV) red, green and blue (RGB) images on smaller areas for highly precise forest canopy mask creation. Sentinel-2 was used as a scaling platform for transferring information from the UAV to a wider spatial extent. Various approaches to an improvement in the predictive performance were examined: (I) the highest R2 of the single satellite index was 0.57, (II) the highest R2 using multiple features obtained from the single-date, S-2 image was 0.624, and (III) the highest R2 on the multitemporal set of S-2 images was 0.697. Satellite indices such as Atmospherically Resistant Vegetation Index (ARVI), Infrared Percentage Vegetation Index (IPVI), Normalized Difference Index (NDI45), Pigment-Specific Simple Ratio Index (PSSRa), Modified Chlorophyll Absorption Ratio Index (MCARI), Color Index (CI), Redness Index (RI), and Normalized Difference Turbidity Index (NDTI) were the dominant predictors in most of the Machine Learning (ML) algorithms. The more complex ML algorithms such as the Support Vector Machines (SVM), Random Forest (RF), Stochastic Gradient Boosting (GBM), Extreme Gradient Boosting (XGBoost), and Catboost that provided the best performance on the training set exhibited weaker generalization capabilities. Therefore, a simpler and more robust Elastic Net (ENET) algorithm was chosen for the final map creation.

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