Support vector machine-based prediction of pore-forming toxins (PFT) using distributed representation of reduced alphabets

2021 ◽  
Author(s):  
Hrushikesh Bhosale ◽  
Vigneshwar Ramakrishnan ◽  
Valadi K. Jayaraman
Keyword(s):  
Machine Learning ◽  
Amino Acids ◽  
Protein Sequence ◽  
Prediction Accuracy ◽  
Bacterial Virulence ◽  
Support Vector ◽  
Distributed Representation ◽  
Learning Framework ◽  
Hydropathy Index ◽  
Vector Machines

Bacterial virulence can be attributed to a wide variety of factors including toxins that harm the host. Pore-forming toxins are one class of toxins that confer virulence to the bacteria and are one of the promising targets for therapeutic intervention. In this work, we develop a sequence-based machine learning framework for the prediction of pore-forming toxins. For this, we have used distributed representation of the protein sequence encoded by reduced alphabet schemes based on conformational similarity and hydropathy index as input features to Support Vector Machines (SVMs). The choice of conformational similarity and hydropathy indices is based on the functional mechanism of pore-forming toxins. Our methodology achieves about 81% accuracy indicating that conformational similarity, an indicator of the flexibility of amino acids, along with hydrophobic index can capture the intrinsic features of pore-forming toxins that distinguish it from other types of transporter proteins. Increased understanding of the mechanisms of pore-forming toxins can further contribute to the use of such “mechanism-informed” features that may increase the prediction accuracy further.

scholarly journals A Method to Extract Feature Variables Contributed in Nonlinear Machine Learning Prediction

2020 ◽  
Vol 59 (01) ◽  
pp. 001-008
Author(s):  
Mayumi Suzuki ◽  
Takuma Shibahara ◽  
Yoshihiro Muragaki
Keyword(s):  
Machine Learning ◽  
Prediction Accuracy ◽  
Deep Neural Networks ◽  
Extraction Technique ◽  
Support Vector ◽  
Learning Models ◽  
Analysis Technique ◽  
Vector Machines ◽  
Backward Analysis ◽  
Machine Learning Models

Abstract Background Although advances in prediction accuracy have been made with new machine learning methods, such as support vector machines and deep neural networks, these methods make nonlinear machine learning models and thus lack the ability to explain the basis of their predictions. Improving their explanatory capabilities would increase the reliability of their predictions. Objective Our objective was to develop a factor analysis technique that enables the presentation of the feature variables used in making predictions, even in nonlinear machine learning models. Methods A factor analysis technique was consisted of two techniques: backward analysis technique and factor extraction technique. We developed a factor extraction technique extracted feature variables that was obtained from the posterior probability distribution of a machine learning model which was calculated by backward analysis technique. Results In evaluation, using gene expression data from prostate tumor patients and healthy subjects, the prediction accuracy of a model of deep neural networks was approximately 5% better than that of a model of support vector machines. Then the rate of concordance between the feature variables extracted in an earlier report using Jensen–Shannon divergence and the ones extracted in this report using backward elimination using Hilbert–Schmidt independence criteria was 40% for the top five variables, 40% for the top 10, and 49% for the top 100. Conclusion The results showed that models can be evaluated from different viewpoints by using different factor extraction techniques. In the future, we hope to use this technique to verify the characteristics of features extracted by factor extraction technique, and to perform clinical studies using the genes, we extracted in this experiment.

scholarly journals A stacking ensemble learning framework for genomic prediction

2020 ◽  
Author(s):  
Mang Liang ◽  
Tianpeng Chang ◽  
Bingxing An ◽  
Xinghai Duan ◽  
Lili Du ◽  
...  
Keyword(s):  
Machine Learning ◽  
Ensemble Learning ◽  
Genomic Prediction ◽  
Milk Fat ◽  
Prediction Accuracy ◽  
Support Vector ◽  
Fat Percentage ◽  
Prediction Ability ◽  
Learning Framework ◽  
Better Than

Abstract Background: Machine learning (ML) is perhaps the most useful for the interpretation of large genomic datasets. However, the performance of a single machine learning method in genomic selection (GS) was unsatisfactory in existing research. To improve the genomic predictions, we constructed a stacking ensemble learning framework (SELF) integrated three machine learning methods to predict genomic estimated breeding values (GEBVs). Results: We evaluated the prediction ability of SELF by three real datasets and compared the prediction accuracy of SELF, base learners, GBLUP and BayesB. For each trait, SELF performed better than base learners, which included support vector regression (SVR), kernel ridge regression (KRR) and elastic net (ENET). The prediction accuracy of SELF had an average 7.70% improvement compared with GBLUP in three datasets. Except for the milk fat percentage (MFP) traits of the German Holstein dairy cattle dataset, SELF more robust than BayesB in the remaining traits.Conclusions: In this study, we utilized a stacking ensemble learning framework (SELF) to genomic prediction and it performed much better than GBLUP and BayesB in three real datasets with different genetic architecture. Therefore, we believed SEFL had the potential to be promoted to estimate GEBVs in other animals and plants.

scholarly journals A Stacking Ensemble Learning Framework for Genomic Prediction

2021 ◽  
Vol 12 ◽  
Author(s):  
Mang Liang ◽  
Tianpeng Chang ◽  
Bingxing An ◽  
Xinghai Duan ◽  
Lili Du ◽  
...  
Keyword(s):  
Machine Learning ◽  
Ensemble Learning ◽  
Milk Fat ◽  
Prediction Accuracy ◽  
Support Vector ◽  
Fat Percentage ◽  
Prediction Ability ◽  
Learning Framework ◽  
Best Linear Unbiased ◽  
Estimated Breeding Values

Machine learning (ML) is perhaps the most useful tool for the interpretation of large genomic datasets. However, the performance of a single machine learning method in genomic selection (GS) is currently unsatisfactory. To improve the genomic predictions, we constructed a stacking ensemble learning framework (SELF), integrating three machine learning methods, to predict genomic estimated breeding values (GEBVs). The present study evaluated the prediction ability of SELF by analyzing three real datasets, with different genetic architecture; comparing the prediction accuracy of SELF, base learners, genomic best linear unbiased prediction (GBLUP) and BayesB. For each trait, SELF performed better than base learners, which included support vector regression (SVR), kernel ridge regression (KRR) and elastic net (ENET). The prediction accuracy of SELF was, on average, 7.70% higher than GBLUP in three datasets. Except for the milk fat percentage (MFP) traits, of the German Holstein dairy cattle dataset, SELF was more robust than BayesB in all remaining traits. Therefore, we believed that SEFL has the potential to be promoted to estimate GEBVs in other animals and plants.

Identifying Cancer Targets Based on Machine Learning Methods via Chou’s 5-steps Rule and General Pseudo Components

2019 ◽  
Vol 19 (25) ◽  
pp. 2301-2317 ◽  
Author(s):  
Ruirui Liang ◽  
Jiayang Xie ◽  
Chi Zhang ◽  
Mengying Zhang ◽  
Hai Huang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Growth Rate ◽  
Big Data ◽  
Human Genome Project ◽  
Genome Project ◽  
Support Vector ◽  
Successful Implementation ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Vector Machines

In recent years, the successful implementation of human genome project has made people realize that genetic, environmental and lifestyle factors should be combined together to study cancer due to the complexity and various forms of the disease. The increasing availability and growth rate of ‘big data’ derived from various omics, opens a new window for study and therapy of cancer. In this paper, we will introduce the application of machine learning methods in handling cancer big data including the use of artificial neural networks, support vector machines, ensemble learning and naïve Bayes classifiers.

scholarly journals Predictive modeling for peri-implantitis by using machine learning techniques

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tomoaki Mameno ◽  
Masahiro Wada ◽  
Kazunori Nozaki ◽  
Toshihito Takahashi ◽  
Yoshitaka Tsujioka ◽  
...  
Keyword(s):  
Machine Learning ◽  
Demographic Data ◽  
Risk Indicators ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
Machine Learning Methods ◽  
Complex Interactions ◽  
Learning Techniques ◽  
Increased Risk ◽  
Vector Machines

AbstractThe purpose of this retrospective cohort study was to create a model for predicting the onset of peri-implantitis by using machine learning methods and to clarify interactions between risk indicators. This study evaluated 254 implants, 127 with and 127 without peri-implantitis, from among 1408 implants with at least 4 years in function. Demographic data and parameters known to be risk factors for the development of peri-implantitis were analyzed with three models: logistic regression, support vector machines, and random forests (RF). As the results, RF had the highest performance in predicting the onset of peri-implantitis (AUC: 0.71, accuracy: 0.70, precision: 0.72, recall: 0.66, and f1-score: 0.69). The factor that had the most influence on prediction was implant functional time, followed by oral hygiene. In addition, PCR of more than 50% to 60%, smoking more than 3 cigarettes/day, KMW less than 2 mm, and the presence of less than two occlusal supports tended to be associated with an increased risk of peri-implantitis. Moreover, these risk indicators were not independent and had complex effects on each other. The results of this study suggest that peri-implantitis onset was predicted in 70% of cases, by RF which allows consideration of nonlinear relational data with complex interactions.

Machine Learning Approach for Predicting Lane-Change Maneuvers using the SHRP2 Naturalistic Driving Study Data

2021 ◽  
pp. 036119812110035
Author(s):  
Anik Das ◽  
Mohamed M. Ahmed
Keyword(s):  
Machine Learning ◽  
Prediction Accuracy ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Lane Change ◽  
Adaptive Boosting ◽  
Extreme Gradient Boosting ◽  
Naturalistic Driving Study ◽  
Naturalistic Driving ◽  
Change Prediction

Accurate lane-change prediction information in real time is essential to safely operate Autonomous Vehicles (AVs) on the roadways, especially at the early stage of AVs deployment, where there will be an interaction between AVs and human-driven vehicles. This study proposed reliable lane-change prediction models considering features from vehicle kinematics, machine vision, driver, and roadway geometric characteristics using the trajectory-level SHRP2 Naturalistic Driving Study and Roadway Information Database. Several machine learning algorithms were trained, validated, tested, and comparatively analyzed including, Classification And Regression Trees (CART), Random Forest (RF), eXtreme Gradient Boosting (XGBoost), Adaptive Boosting (AdaBoost), Support Vector Machine (SVM), K Nearest Neighbor (KNN), and Naïve Bayes (NB) based on six different sets of features. In each feature set, relevant features were extracted through a wrapper-based algorithm named Boruta. The results showed that the XGBoost model outperformed all other models in relation to its highest overall prediction accuracy (97%) and F1-score (95.5%) considering all features. However, the highest overall prediction accuracy of 97.3% and F1-score of 95.9% were observed in the XGBoost model based on vehicle kinematics features. Moreover, it was found that XGBoost was the only model that achieved a reliable and balanced prediction performance across all six feature sets. Furthermore, a simplified XGBoost model was developed for each feature set considering the practical implementation of the model. The proposed prediction model could help in trajectory planning for AVs and could be used to develop more reliable advanced driver assistance systems (ADAS) in a cooperative connected and automated vehicle environment.

scholarly journals Risky Driver Recognition with Class Imbalance Data and Automated Machine Learning Framework

2021 ◽  
Vol 18 (14) ◽  
pp. 7534
Author(s):  
Ke Wang ◽  
Qingwen Xue ◽  
Jian John Lu
Keyword(s):  
Machine Learning ◽  
High Risk ◽  
Loss Function ◽  
Class Imbalance ◽  
Support Vector ◽  
Trajectory Data ◽  
Recognition Model ◽  
Learning Framework ◽  
Sampling Cost ◽  
Automated Machine Learning

Identifying high-risk drivers before an accident happens is necessary for traffic accident control and prevention. Due to the class-imbalance nature of driving data, high-risk samples as the minority class are usually ill-treated by standard classification algorithms. Instead of applying preset sampling or cost-sensitive learning, this paper proposes a novel automated machine learning framework that simultaneously and automatically searches for the optimal sampling, cost-sensitive loss function, and probability calibration to handle class-imbalance problem in recognition of risky drivers. The hyperparameters that control sampling ratio and class weight, along with other hyperparameters, are optimized by Bayesian optimization. To demonstrate the performance of the proposed automated learning framework, we establish a risky driver recognition model as a case study, using video-extracted vehicle trajectory data of 2427 private cars on a German highway. Based on rear-end collision risk evaluation, only 4.29% of all drivers are labeled as risky drivers. The inputs of the recognition model are the discrete Fourier transform coefficients of target vehicle’s longitudinal speed, lateral speed, and the gap between the target vehicle and its preceding vehicle. Among 12 sampling methods, 2 cost-sensitive loss functions, and 2 probability calibration methods, the result of automated machine learning is consistent with manual searching but much more computation-efficient. We find that the combination of Support Vector Machine-based Synthetic Minority Oversampling TEchnique (SVMSMOTE) sampling, cost-sensitive cross-entropy loss function, and isotonic regression can significantly improve the recognition ability and reduce the error of predicted probability.

NIMG-46. SYSTEMATIC LITERATURE REVIEW OF ARTIFICIAL INTELLIGENCE ALGORITHMS USING PRE-THERAPY MR IMAGING FOR GLIOMA MOLECULAR SUBTYPE CLASSIFICATION

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi139-vi139
Author(s):  
Jan Lost ◽  
Tej Verma ◽  
Niklas Tillmanns ◽  
W R Brim ◽  
Harry Subramanian ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Machine Learning ◽  
Deep Learning ◽  
Literature Review ◽  
Prediction Accuracy ◽  
Molecular Subtypes ◽  
Molecular Subtype ◽  
Tumor Resection ◽  
Support Vector ◽  
Hospital Data

Abstract PURPOSE Identifying molecular subtypes in gliomas has prognostic and therapeutic value, traditionally after invasive neurosurgical tumor resection or biopsy. Recent advances using artificial intelligence (AI) show promise in using pre-therapy imaging for predicting molecular subtype. We performed a systematic review of recent literature on AI methods used to predict molecular subtypes of gliomas. METHODS Literature review conforming to PRSIMA guidelines was performed for publications prior to February 2021 using 4 databases: Ovid Embase, Ovid MEDLINE, Cochrane trials (CENTRAL), and Web of Science core-collection. Keywords included: artificial intelligence, machine learning, deep learning, radiomics, magnetic resonance imaging, glioma, and glioblastoma. Non-machine learning and non-human studies were excluded. Screening was performed using Covidence software. Bias analysis was done using TRIPOD guidelines. RESULTS 11,727 abstracts were retrieved. After applying initial screening exclusion criteria, 1,135 full text reviews were performed, with 82 papers remaining for data extraction. 57% used retrospective single center hospital data, 31.6% used TCIA and BRATS, and 11.4% analyzed multicenter hospital data. An average of 146 patients (range 34-462 patients) were included. Algorithms predicting IDH status comprised 51.8% of studies, MGMT 18.1%, and 1p19q 6.0%. Machine learning methods were used in 71.4%, deep learning in 27.4%, and 1.2% directly compared both methods. The most common algorithm for machine learning were support vector machine (43.3%), and for deep learning convolutional neural network (68.4%). Mean prediction accuracy was 76.6%. CONCLUSION Machine learning is the predominant method for image-based prediction of glioma molecular subtypes. Major limitations include limited datasets (60.2% with under 150 patients) and thus limited generalizability of findings. We recommend using larger annotated datasets for AI network training and testing in order to create more robust AI algorithms, which will provide better prediction accuracy to real world clinical datasets and provide tools that can be translated to clinical practice.

Sign in / Sign up

Export Citation Format

Share Document