scholarly journals Machine Learning for Large-Scale Quality Control of 3D Shape Models in Neuroimaging

2017 ◽  
Author(s):  
Dmitry Petrov ◽  
Boris A. Gutman ◽  
Shih-Hua (Julie) Yu ◽  
Theo G.M. van Erp ◽  
Jessica A. Turner ◽  
...  
Keyword(s):  
Machine Learning ◽  
Large Scale ◽  
Support Vector ◽  
Shape Features ◽  
Shape Models ◽  
Boosted Decision Trees ◽  
Human Quality ◽  
Derived Data ◽  
Deep Brain ◽  
Comparable Size

AbstractAs very large studies of complex neuroimaging phenotypes become more common, human quality assessment of MRI-derived data remains one of the last major bottlenecks. Few attempts have so far been made to address this issue with machine learning. In this work, we optimize predictive models of quality for meshes representing deep brain structure shapes. We use standard vertex-wise and global shape features computed homologously across 19 cohorts and over 7500 human-rated subjects, training kernelized Support Vector Machine and Gradient Boosted Decision Trees classifiers to detect meshes of failing quality. Our models generalize across datasets and diseases, reducing human workload by 30-70%, or equivalently hundreds of human rater hours for datasets of comparable size, with recall rates approaching inter-rater reliability.

scholarly journals QUBO formulations for training machine learning models

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.

scholarly journals Predicting ionizing radiation exposure using biochemically-inspired genomic machine learning

F1000Research ◽  
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.

scholarly journals Applying Machine Learning for Improving Performance Classification on Driving Behavior

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.

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

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.

scholarly journals Developing a Process for the Analysis of User Journeys and the Prediction of Dropout in Digital Health Interventions: Machine Learning Approach (Preprint)

2020 ◽  
Author(s):  
Vincent Bremer ◽  
Philip I Chow ◽  
Burkhardt Funk ◽  
Frances P Thorndike ◽  
Lee M Ritterband
Keyword(s):  
Machine Learning ◽  
Decision Trees ◽  
Behavioral Therapy ◽  
Digital Health ◽  
Area Under The Curve ◽  
Prediction Performance ◽  
Health Interventions ◽  
Drop Out ◽  
Support Vector ◽  
Boosted Decision Trees

BACKGROUND User dropout is a widespread concern in the delivery and evaluation of digital (ie, web and mobile apps) health interventions. Researchers have yet to fully realize the potential of the large amount of data generated by these technology-based programs. Of particular interest is the ability to predict who will drop out of an intervention. This may be possible through the analysis of user journey data—self-reported as well as system-generated data—produced by the path (or journey) an individual takes to navigate through a digital health intervention. OBJECTIVE The purpose of this study is to provide a step-by-step process for the analysis of user journey data and eventually to predict dropout in the context of digital health interventions. The process is applied to data from an internet-based intervention for insomnia as a way to illustrate its use. The completion of the program is contingent upon completing 7 sequential cores, which include an initial tutorial core. Dropout is defined as not completing the seventh core. METHODS Steps of user journey analysis, including data transformation, feature engineering, and statistical model analysis and evaluation, are presented. Dropouts were predicted based on data from 151 participants from a fully automated web-based program (Sleep Healthy Using the Internet) that delivers cognitive behavioral therapy for insomnia. Logistic regression with L1 and L2 regularization, support vector machines, and boosted decision trees were used and evaluated based on their predictive performance. Relevant features from the data are reported that predict user dropout. RESULTS Accuracy of predicting dropout (area under the curve [AUC] values) varied depending on the program core and the machine learning technique. After model evaluation, boosted decision trees achieved AUC values ranging between 0.6 and 0.9. Additional handcrafted features, including time to complete certain steps of the intervention, time to get out of bed, and days since the last interaction with the system, contributed to the prediction performance. CONCLUSIONS The results support the feasibility and potential of analyzing user journey data to predict dropout. Theory-driven handcrafted features increased the prediction performance. The ability to predict dropout at an individual level could be used to enhance decision making for researchers and clinicians as well as inform dynamic intervention regimens.

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

2021 ◽  
Vol 22 (16) ◽  
pp. 8958
Author(s):  
Phasit Charoenkwan ◽  
Chanin Nantasenamat ◽  
Md. Mehedi Hasan ◽  
Mohammad Ali Moni ◽  
Pietro Lio’ ◽  
...  
Keyword(s):  
Machine Learning ◽  
Large Scale ◽  
De Novo ◽  
Predictive Performance ◽  
Support Vector ◽  
Sufficient Information ◽  
Self Assessment ◽  
Accurate Identification ◽  
Bitter Peptides ◽  
Accurate Performance

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

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

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.

scholarly journals Predicting ionizing radiation exposure using biochemically-inspired genomic machine learning

F1000Research ◽  
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.

scholarly journals Bandgap prediction of two-dimensional materials using machine learning

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0255637
Author(s):  
Yu Zhang ◽  
Wenjing Xu ◽  
Guangjie Liu ◽  
Zhiyong Zhang ◽  
Jinlong Zhu ◽  
...  
Keyword(s):  
Machine Learning ◽  
Semiconductor Device ◽  
2D Materials ◽  
Support Vector ◽  
Material Structure ◽  
Two Dimensional ◽  
Promising Alternative ◽  
Two Dimensional Materials ◽  
Device Applications ◽  
Boosted Decision Trees

The bandgap of two-dimensional (2D) materials plays an important role in their applications to various devices. For instance, the gapless nature of graphene limits the use of this material to semiconductor device applications, whereas the indirect bandgap of molybdenum disulfide is suitable for electrical and photo-device applications. Therefore, predicting the bandgap rapidly and accurately for a given 2D material structure has great scientific significance in the manufacturing of semiconductor devices. Compared to the extremely high computation cost of conventional first-principles calculations, machine learning (ML) based on statistics may be a promising alternative to predicting bandgaps. Although ML algorithms have been used to predict the properties of materials, they have rarely been used to predict the properties of 2D materials. In this study, we apply four ML algorithms to predict the bandgaps of 2D materials based on the computational 2D materials database (C2DB). Gradient boosted decision trees and random forests are more effective in predicting bandgaps of 2D materials with an R2 >90% and root-mean-square error (RMSE) of ~0.24 eV and 0.27 eV, respectively. By contrast, support vector regression and multi-layer perceptron show that R2 is >70% with RMSE of ~0.41 eV and 0.43 eV, respectively. Finally, when the bandgap calculated without spin-orbit coupling (SOC) is used as a feature, the RMSEs of the four ML models decrease greatly to 0.09 eV, 0.10 eV, 0.17 eV, and 0.12 eV, respectively. The R2 of all the models is >94%. These results show that the properties of 2D materials can be rapidly obtained by ML prediction with high precision.

scholarly journals A machine learning approach to predict ethnicity using personal name and census location in Canada

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0241239
Author(s):  
Kai On Wong ◽  
Osmar R. Zaïane ◽  
Faith G. Davis ◽  
Yutaka Yasui
Keyword(s):  
Machine Learning ◽  
First Nations ◽  
Predictive Value ◽  
Large Scale ◽  
Performance Metrics ◽  
Characteristic Curve ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Learning Approach ◽  
Machine Learning Approach

Background Canada is an ethnically-diverse country, yet its lack of ethnicity information in many large databases impedes effective population research and interventions. Automated ethnicity classification using machine learning has shown potential to address this data gap but its performance in Canada is largely unknown. This study conducted a large-scale machine learning framework to predict ethnicity using a novel set of name and census location features. Methods Using census 1901, the multiclass and binary class classification machine learning pipelines were developed. The 13 ethnic categories examined were Aboriginal (First Nations, Métis, Inuit, and all-combined)), Chinese, English, French, Irish, Italian, Japanese, Russian, Scottish, and others. Machine learning algorithms included regularized logistic regression, C-support vector, and naïve Bayes classifiers. Name features consisted of the entire name string, substrings, double-metaphones, and various name-entity patterns, while location features consisted of the entire location string and substrings of province, district, and subdistrict. Predictive performance metrics included sensitivity, specificity, positive predictive value, negative predictive value, F1, Area Under the Curve for Receiver Operating Characteristic curve, and accuracy. Results The census had 4,812,958 unique individuals. For multiclass classification, the highest performance achieved was 76% F1 and 91% accuracy. For binary classifications for Chinese, French, Italian, Japanese, Russian, and others, the F1 ranged 68–95% (median 87%). The lower performance for English, Irish, and Scottish (F1 ranged 63–67%) was likely due to their shared cultural and linguistic heritage. Adding census location features to the name-based models strongly improved the prediction in Aboriginal classification (F1 increased from 50% to 84%). Conclusions The automated machine learning approach using only name and census location features can predict the ethnicity of Canadians with varying performance by specific ethnic categories.

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