Whole blood transcriptome biomarkers of unruptured intracranial aneurysm

Background The rupture of an intracranial aneurysm (IA) causes devastating subarachnoid hemorrhages, yet most IAs remain undiscovered until they rupture. Recently, we found an IA RNA expression signature of circulating neutrophils, and used transcriptome data to build predictive models for unruptured IAs. In this study, we evaluate the feasibility of using whole blood transcriptomes to predict the presence of unruptured IAs. Methods We subjected RNA from peripheral whole blood of 67 patients (34 with unruptured IA, 33 without IA) to next-generation RNA sequencing. Model genes were identified using the least absolute shrinkage and selection operator (LASSO) in a random training cohort (n = 47). These genes were used to train a Gaussian Support Vector Machine (gSVM) model to distinguish patients with IA. The model was applied to an independent testing cohort (n = 20) to evaluate performance by receiver operating characteristic (ROC) curve. Gene ontology and pathway analyses investigated the underlying biology of the model genes. Results We identified 18 genes that could distinguish IA patients in a training cohort with 85% accuracy. This SVM model also had 85% accuracy in the testing cohort, with an area under the ROC curve of 0.91. Bioinformatics reflected activation and recruitment of leukocytes, activation of macrophages, and inflammatory response, suggesting that the biomarker captures important processes in IA pathogenesis. Conclusions Circulating whole blood transcriptomes can detect the presence of unruptured IAs. Pending additional testing in larger cohorts, this could serve as a foundation to develop a simple blood-based test to facilitate screening and early detection of IAs.

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MRI-Based Radiomics for Differentiating Orbital Cavernous Hemangioma and Orbital Schwannoma

Frontiers in Medicine ◽

10.3389/fmed.2021.795038 ◽

2021 ◽

Vol 8 ◽

Author(s):

Liang Chen ◽

Ya Shen ◽

Xiao Huang ◽

Hua Li ◽

Jian Li ◽

...

Keyword(s):

Cavernous Hemangioma ◽

Training Group ◽

Superior Performance ◽

Support Vector ◽

Classification Models ◽

Validation Data ◽

Group 12 ◽

Svm Model ◽

Magnetic Resonance Imaging Mri ◽

Selection Operator

Aim: The purpose of this work was to develop and evaluate magnetic resonance imaging (MRI)-based radiomics for differentiation of orbital cavernous hemangioma (OCH) and orbital schwannoma (OSC).Methods: Fifty-eight patients (40 OCH and 18 OSC, confirmed pathohistologically) screened out from 216 consecutive patients who presented between 2015 and 2020 were divided into a training group (28 OCH and 12 OSC) and a validation group (12 OCH and 6 OSC). Radiomics features were extracted from T1-weighted imaging (T1WI) and T2-weighted imaging (T2WI). T-tests, the least absolute shrinkage and selection operator (LASSO), and principal components analysis (PCA) were used to select features for use in the classification models. A logistic regression (LR) model, support vector machine (SVM) model, decision tree (DT) model, and random forest (RF) model were constructed to differentiate OCH from OSC. The models were evaluated according to their accuracy and the area under the receiver operator characteristic (ROC) curve (AUC).Results: Six features from T1WI, five features from T2WI, and eight features from combined T1WI and T2WI were finally selected for building the classification models. The models using T2WI features showed superior performance on the validation data than those using T1WI features, especially the LR model and SVM model, which showed accuracy of 93% (85–100%) and 92%, respectively, The SVM model showed high accuracy of 93% (91–96%) on the combined feature group with an AUC of 98% (97–99%). The DT and RF models did not perform as well as the SVM model.Conclusion: Radiomics analysis using an SVM model achieved an accuracy of 93% for distinguishing OCH and OSC, which may be helpful for clinical diagnosis.

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Whole Blood Transcriptome Sequencing Reveals Gene Expression Differences between Dapulian and Landrace Piglets

BioMed Research International ◽

10.1155/2016/7907980 ◽

2016 ◽

Vol 2016 ◽

pp. 1-10

Author(s):

Jiaqing Hu ◽

Dandan Yang ◽

Wei Chen ◽

Chuanhao Li ◽

Yandong Wang ◽

...

Keyword(s):

Gene Expression ◽

Whole Blood ◽

Molecular Mechanisms ◽

Future Research ◽

Nucleotide Polymorphisms ◽

Rna Seq ◽

Single Nucleotide ◽

Neonatal Stage ◽

Pathway Analyses ◽

Blood Transcriptome

There is little genomic information regarding gene expression differences at the whole blood transcriptome level of different pig breeds at the neonatal stage. To solve this, we characterized differentially expressed genes (DEGs) in the whole blood of Dapulian (DPL) and Landrace piglets using RNA-seq (RNA-sequencing) technology. In this study, 83 DEGs were identified between the two breeds. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses identified immune response and metabolism as the most commonly enriched terms and pathways in the DEGs. Genes related to immunity and lipid metabolism were more highly expressed in the DPL piglets, while genes related to body growth were more highly expressed in the Landrace piglets. Additionally, the DPL piglets had twofold more single nucleotide polymorphisms (SNPs) and alternative splicing (AS) than the Landrace piglets. These results expand our knowledge of the genes transcribed in the piglet whole blood of two breeds and provide a basis for future research of the molecular mechanisms underlying the piglet differences.

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Septicemic Melioidosis Detection Using Support Vector Machine with Five Immune Cell Types

Disease Markers ◽

10.1155/2021/8668978 ◽

2021 ◽

Vol 2021 ◽

pp. 1-9

Author(s):

Ke Xu ◽

Fang Lian ◽

Yunfan Quan ◽

Jun Liu ◽

Li Yin ◽

...

Keyword(s):

Support Vector Machine ◽

T Cells ◽

Roc Curve ◽

Immune Cell ◽

Cell Types ◽

Curve Analysis ◽

Support Vector ◽

Roc Curve Analysis ◽

Tropical Regions ◽

Svm Model

Melioidosis, caused by Burkholderia pseudomallei (B. pseudomallei), predominantly occurs in the tropical regions. Of various types of melioidosis, septicemic melioidosis is the most lethal one with a mortality rate of 40%. Early detection of the disease is paramount for the better chances of cure. In this study, we developed a novel approach for septicemic melioidosis detection, using a machine learning technique—support vector machine (SVM). Several SVM models were built, and 19 features characterized by the corresponding immune cell types were generated by Cell type Identification Estimating Relative Subsets Of RNA Transcripts (CIBERSORT). Using these features, we trained a binomial SVM model on the training set and evaluated it on the independent testing set. Our findings indicated that this model performed well with means of sensitivity and specificity up to 0.962 and 0.979, respectively. Meanwhile, the receiver operating characteristic (ROC) curve analysis gave area under curves (AUCs) ranging from 0.952 to 1.000. Furthermore, we found that a concise SVM model, built upon a combination of CD8+ T cells, resting CD4+ memory T cells, monocytes, M2 macrophages, and activated mast cells, worked perfectly on the detection of septicemic melioidosis. Our data showed that its mean of sensitivity was up to 0.976 while that of specificity up to 0.993. In addition, the ROC curve analysis gave AUC close to 1.000. Taken together, this SVM model is a robust classification tool and may serve as a complementary diagnostic technique to septicemic melioidosis.

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The Spinning Quality Control Management Based on Decision Making by Data Mining Techniques

International Journal of Emerging Research in Management and Technology ◽

10.23956/ijermt.v7i1.25 ◽

2018 ◽

Vol 7 (1) ◽

pp. 72

Author(s):

Khalid AA Abakar ◽

Chongwen Yu

Keyword(s):

Data Mining ◽

Kernel Functions ◽

Support Vector ◽

Ann Model ◽

Data Mining Techniques ◽

Yarn Quality ◽

Yarn Properties ◽

Svm Model ◽

Rbf Kernel

This work demonstrated the possibility of using the data mining techniques such as artificial neural networks (ANN) and support vector machine (SVM) based model to predict the quality of the spinning yarn parameters. Three different kernel functions were used as SVM kernel functions which are Polynomial and Radial Basis Function (RBF) and Pearson VII Function-based Universal Kernel (PUK) and ANN model were used as data mining techniques to predict yarn properties. In this paper, it was found that the SVM model based on Person VII kernel function (PUK) have the same performance in prediction of spinning yarn quality in comparison with SVM based RBF kernel. The comparison with the ANN model showed that the two SVM models give a better prediction performance than an ANN model.

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Combination of Support Vector Machine and K-Fold cross-validation for prediction of long-term degradation of the compressive strength of marine concrete

International Journal of Computational Physics Series ◽

10.29167/a1i1p120-130 ◽

2018 ◽

Vol 1 (1) ◽

pp. 120-130 ◽

Cited By ~ 1

Author(s):

Chunxiang Qian ◽

Wence Kang ◽

Hao Ling ◽

Hua Dong ◽

Chengyao Liang ◽

...

Keyword(s):

Support Vector Machine ◽

Environmental Factors ◽

Cross Validation ◽

Concrete Strength ◽

Simulation Method ◽

Support Vector ◽

Svm Model ◽

Artificial Neural Network Ann ◽

Influence Degree ◽

Fold Cross Validation

Support Vector Machine (SVM) model optimized by K-Fold cross-validation was built to predict and evaluate the degradation of concrete strength in a complicated marine environment. Meanwhile, several mathematical models, such as Artificial Neural Network (ANN) and Decision Tree (DT), were also built and compared with SVM to determine which one could make the most accurate predictions. The material factors and environmental factors that influence the results were considered. The materials factors mainly involved the original concrete strength, the amount of cement replaced by fly ash and slag. The environmental factors consisted of the concentration of Mg2+, SO42-, Cl-, temperature and exposing time. It was concluded from the prediction results that the optimized SVM model appeared to perform better than other models in predicting the concrete strength. Based on SVM model, a simulation method of variables limitation was used to determine the sensitivity of various factors and the influence degree of these factors on the degradation of concrete strength.

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MK-FSVM-SVDD: A Multiple Kernel-based Fuzzy SVM Model for Predicting DNA-binding Proteins via Support Vector Data Description

Current Bioinformatics ◽

10.2174/1574893615999200607173829 ◽

2020 ◽

Vol 15 ◽

Author(s):

Yi Zou ◽

Hongjie Wu ◽

Xiaoyi Guo ◽

Li Peng ◽

Yijie Ding ◽

...

Keyword(s):

Dna Binding ◽

Binding Proteins ◽

Detection Efficiency ◽

Dna Binding Proteins ◽

Support Vector ◽

Support Vector Data Description ◽

Vector Data ◽

Data Description ◽

Multiple Kernel ◽

Svm Model

Background: Detecting DNA-binding proetins (DBPs) based on biological and chemical methods is time consuming and expensive. Objective: In recent years, the rise of computational biology methods based on Machine Learning (ML) has greatly improved the detection efficiency of DBPs. Method: In this study, Multiple Kernel-based Fuzzy SVM Model with Support Vector Data Description (MK-FSVM-SVDD) is proposed to predict DBPs. Firstly, sex features are extracted from protein sequence. Secondly, multiple kernels are constructed via these sequence feature. Than, multiple kernels are integrated by Centered Kernel Alignment-based Multiple Kernel Learning (CKA-MKL). Next, fuzzy membership scores of training samples are calculated with Support Vector Data Description (SVDD). FSVM is trained and employed to detect new DBPs. Results: Our model is test on several benchmark datasets. Compared with other methods, MK-FSVM-SVDD achieves best Matthew's Correlation Coefficient (MCC) on PDB186 (0.7250) and PDB2272 (0.5476). Conclusion: We can conclude that MK-FSVM-SVDD is more suitable than common SVM, as the classifier for DNA-binding proteins identification.

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Contributions and limitations of using machine learning to predict noise-induced hearing loss

International Archives of Occupational and Environmental Health ◽

10.1007/s00420-020-01648-w ◽

2021 ◽

Author(s):

Feifan Chen ◽

Zuwei Cao ◽

Emad M. Grais ◽

Fei Zhao

Keyword(s):

Machine Learning ◽

Hearing Loss ◽

Roc Curve ◽

Prediction Error ◽

Noise Exposure ◽

Model Construction ◽

Support Vector ◽

Exposure Level ◽

Noise Induced Hearing Loss ◽

Current Review

Abstract Purpose Noise-induced hearing loss (NIHL) is a global issue that impacts people’s life and health. The current review aims to clarify the contributions and limitations of applying machine learning (ML) to predict NIHL by analyzing the performance of different ML techniques and the procedure of model construction. Methods The authors searched PubMed, EMBASE and Scopus on November 26, 2020. Results Eight studies were recruited in the current review following defined inclusion and exclusion criteria. Sample size in the selected studies ranged between 150 and 10,567. The most popular models were artificial neural networks (n = 4), random forests (n = 3) and support vector machines (n = 3). Features mostly correlated with NIHL and used in the models were: age (n = 6), duration of noise exposure (n = 5) and noise exposure level (n = 4). Five included studies used either split-sample validation (n = 3) or ten-fold cross-validation (n = 2). Assessment of accuracy ranged in value from 75.3% to 99% with a low prediction error/root-mean-square error in 3 studies. Only 2 studies measured discrimination risk using the receiver operating characteristic (ROC) curve and/or the area under ROC curve. Conclusion In spite of high accuracy and low prediction error of machine learning models, some improvement can be expected from larger sample sizes, multiple algorithm use, completed reports of model construction and the sufficient evaluation of calibration and discrimination risk.

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Correlation between the structure and skin permeability of compounds

Scientific Reports ◽

10.1038/s41598-021-89587-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Ruolan Zeng ◽

Jiyong Deng ◽

Limin Dang ◽

Xinliang Yu

Keyword(s):

Large Data ◽

Qsar Model ◽

Coefficient Of Determination ◽

Support Vector ◽

Skin Permeability ◽

Data Set ◽

Test Set ◽

Svm Algorithm ◽

Svm Model ◽

Toxicity Relationship

AbstractA three-descriptor quantitative structure–activity/toxicity relationship (QSAR/QSTR) model was developed for the skin permeability of a sufficiently large data set consisting of 274 compounds, by applying support vector machine (SVM) together with genetic algorithm. The optimal SVM model possesses the coefficient of determination R2 of 0.946 and root mean square (rms) error of 0.253 for the training set of 139 compounds; and a R2 of 0.872 and rms of 0.302 for the test set of 135 compounds. Compared with other models reported in the literature, our SVM model shows better statistical performance in a model that deals with more samples in the test set. Therefore, applying a SVM algorithm to develop a nonlinear QSAR model for skin permeability was achieved.

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New Multi-View Classification Method with Uncertain Data

ACM Transactions on Knowledge Discovery from Data ◽

10.1145/3458282 ◽

2021 ◽

Vol 16 (1) ◽

pp. 1-23

Author(s):

Bo Liu ◽

Haowen Zhong ◽

Yanshan Xiao

Keyword(s):

Learning Strategy ◽

State Of The Art ◽

Uncertain Data ◽

Real Life ◽

Support Vector ◽

Classification Methods ◽

Complementary Information ◽

Novel Approach ◽

Svm Model ◽

Iterative Framework

Multi-view classification aims at designing a multi-view learning strategy to train a classifier from multi-view data, which are easily collected in practice. Most of the existing works focus on multi-view classification by assuming the multi-view data are collected with precise information. However, we always collect the uncertain multi-view data due to the collection process is corrupted with noise in real-life application. In this case, this article proposes a novel approach, called uncertain multi-view learning with support vector machine (UMV-SVM) to cope with the problem of multi-view learning with uncertain data. The method first enforces the agreement among all the views to seek complementary information of multi-view data and takes the uncertainty of the multi-view data into consideration by modeling reachability area of the noise. Then it proposes an iterative framework to solve the proposed UMV-SVM model such that we can obtain the multi-view classifier for prediction. Extensive experiments on real-life datasets have shown that the proposed UMV-SVM can achieve a better performance for uncertain multi-view classification in comparison to the state-of-the-art multi-view classification methods.

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Three-Dimensional Site Characterization Model of Bangalore Using Support Vector Machine

ISRN Soil Science ◽

10.5402/2012/346439 ◽

2012 ◽

Vol 2012 ◽

pp. 1-10

Author(s):

Pijush Samui

Keyword(s):

Support Vector Machine ◽

Three Dimensional ◽

Site Characterization ◽

Standard Penetration Test ◽

Support Vector ◽

Characterization Model ◽

Svm Model ◽

Input Variables ◽

Learning Machine ◽

A Site

The main objective of site characterization is the prediction of in situ soil properties at any half-space point at a site based on limited tests. In this study, the Support Vector Machine (SVM) has been used to develop a three dimensional site characterization model for Bangalore, India based on large amount of Standard Penetration Test. SVM is a novel type of learning machine based on statistical learning theory, uses regression technique by introducing ε-insensitive loss function. The database consists of 766 boreholes, with more than 2700 field SPT values () spread over 220 sq km area of Bangalore. The model is applied for corrected () values. The three input variables (, , and , where , , and are the coordinates of the Bangalore) were used for the SVM model. The output of SVM was the data. The results presented in this paper clearly highlight that the SVM is a robust tool for site characterization. In this study, a sensitivity analysis of SVM parameters (σ, , and ε) has been also presented.

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