Morphological analysis of dendrites and spines by hybridization of ridge detection with twin support vector machine.
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ABSTRACT:
SUBMITTER: Wang S
PROVIDER: S-EPMC4958009 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Advances in next-generation sequencing technologies have enabled the identification of multiple rare single nucleotide polymorphisms involved in diseases or traits. Several strategies for identifying rare variants that contribute to disease susceptibility have recently been proposed. An important feature of many of these statistical methods is the pooling or collapsing of multiple rare single nucleotide variants to achieve a reasonably high frequency and effect. However, if the pooled rare variants are associated with the trait in different directions, then the pooling may weaken the signal, thereby reducing its statistical power. In the present paper, we propose a backward support vector machine (BSVM)-based variant selection procedure to identify informative disease-associated rare variants. In the selection procedure, the rare variants are weighted and collapsed according to their positive or negative associations with the disease, which may be associated with common variants and rare variants with protective, deleterious, or neutral effects. This nonparametric variant selection procedure is able to account for confounding factors and can also be adopted in other regression frameworks. The results of a simulation study and a data example show that the proposed BSVM approach is more powerful than four other approaches under the considered scenarios, while maintaining valid type I errors.
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Project description:Background and purposeTo develop a fully automatic algorithm for the magnetic resonance imaging (MRI) identification of patients with spontaneous intracranial hypotension (SIH).Material and methodsA support vector machine (SVM) was trained with structured reports of 140 patients with clinically suspected SIH. Venous sinuses and basal cisterns were segmented on contrast-enhanced T1-weighted MPRAGE (Magnetization Prepared-Rapid Gradient Echo) sequences using a convolutional neural network (CNN). For the segmented sinuses and cisterns, 56 radiomic features were extracted, which served as input data for the SVM. The algorithm was validated with an independent cohort of 34 patients with proven cerebrospinal fluid (CSF) leaks and 27 patients who had MPRAGE scans for unrelated reasons.ResultsThe venous sinuses and the suprasellar cistern had the best discriminative power to separate SIH and non-SIH patients. On a combined score with 2 points, mean SVM score was 1.41 (±0.60) for the SIH and 0.30 (±0.53) for the non-SIH patients (p < 0.001). Area under the curve (AUC) was 0.91.ConclusionA fully automatic algorithm analyzing a single MRI sequence separates SIH and non-SIH patients with a high diagnostic accuracy. It may help to consider the need of invasive diagnostics and transfer to a SIH center.
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Project description: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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Project description:Scombroid fish poisoning caused by histamine intoxication is one of the most prevalent allergies associated with seafood consumption in the United States. Typical symptoms range from mild itching up to fatal cardiovascular collapse seen in anaphylaxis. In this paper, we demonstrate rapid, sensitive, and quantitative detection of histamine in both artificially spoiled tuna solution and real spoiled tuna samples using thin layer chromatography in tandem with surface-enhanced Raman scattering (TLC-SERS) sensing methods, enabled by machine learning analysis based on support vector regression (SVR) after feature extraction with principal component analysis (PCA). The TLC plates used herein, which were made from commercial food-grade diatomaceous earth, served simultaneously as the stationary phase to separate histamine from the blended tuna meat and as ultra-sensitive SERS substrates to enhance the detection limit. Using a simple drop cast method to dispense gold colloidal nanoparticles onto the diatomaceous earth plate, we were able to directly detect histamine concentration in artificially spoiled tuna solution down to 10 ppm. Based on the TLC-SERS spectral data of real tuna samples spoiled at room temperature for 0 to 48 hours, we used the PCA-SVR quantitative model to achieve superior predictive performance exceling traditional partial least squares regression (PLSR) method. This work proves that diatomaceous earth based TLC-SERS technique combined with machine-learning analysis is a cost-effective, reliable, and accurate approach for on-site detection and quantification of seafood allergen to enhance food safety.
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Project description:BackgroundMost malignant brain gliomas (MBGs) are associated with dismal outcomes, mainly due to their late diagnosis. Current diagnostic methods for MBGs are based on imaging and histological examination, which limits their early detection. Here, we aimed to identify reliable plasma lipid biomarkers for non-invasive diagnosis for MBGs.MethodsUntargeted lipidomic analysis was firstly performed using a discovery cohort (n=107). The data were processed by a support vector machine (SVM)-based discriminating model to retrieve a panel of candidate biomarkers. Then, a targeted quantification method was developed, and the SVM-based diagnostic model was constructed using a training cohort (n=750) and tested using a test cohort (n=225). Finally, the performance of the diagnostic model was further evaluated in an independent validation cohort (n=920) enrolled from multiple medical centers.FindingsA panel of 11 plasma lipids was identified as candidate biomarkers with an accuracy of 0.999. The diagnostic model developed achieved a high performance in distinguishing MBGs patients from normal controls with an area under the receiver-operating characteristic curve (AUC) of 0.9877 and 0.9869 in the training and test cohorts, respectively. In the validation cohort, the 11 lipid panel still achieved an accuracy of 0.9641 and an AUC of 0.9866.InterpretationThe present study demonstrates the applicability and robustness of utilizing a machine learning algorithm to analyze lipidomic data for efficient and reliable biomarker screening. The 11 lipid biomarkers show great potential for the non-invasive diagnosis of MBGs with high throughput.FundingA full list of funding bodies that contributed to this study can be found in the Acknowledgments section.
| S-EPMC9189781 | biostudies-literature
Project description:Accumulation of head impacts may contribute to acute and long-term brain trauma. Wearable sensors can measure impact exposure, yet current sensors do not have validated impact detection methods for accurate exposure monitoring. Here we demonstrate a head impact detection method that can be implemented on a wearable sensor for detecting field football head impacts. Our method incorporates a support vector machine classifier that uses biomechanical features from the time domain and frequency domain, as well as model predictions of head-neck motions. The classifier was trained and validated using instrumented mouthguard data from collegiate football games and practices, with ground truth data labels established from video review. We found that low frequency power spectral density and wavelet transform features (10~30 Hz) were the best performing features. From forward feature selection, fewer than ten features optimized classifier performance, achieving 87.2% sensitivity and 93.2% precision in cross-validation on the collegiate dataset (n = 387), and over 90% sensitivity and precision on an independent youth dataset (n = 32). Accurate head impact detection is essential for studying and monitoring head impact exposure on the field, and the approach in the current paper may help to improve impact detection performance on wearable sensors.
| S-EPMC5762632 | biostudies-literature
Project description:MotivationBreast cancer is a type of cancer that develops in breast tissues, and, after skin cancer, it is the most commonly diagnosed cancer in women in the United States. Given that an early diagnosis is imperative to prevent breast cancer progression, many machine learning models have been developed in recent years to automate the histopathological classification of the different types of carcinomas. However, many of them are not scalable to large-scale datasets.ResultsIn this study, we propose the novel Primal-Dual Multi-Instance Support Vector Machine to determine which tissue segments in an image exhibit an indication of an abnormality. We derive an efficient optimization algorithm for the proposed objective by bypassing the quadratic programming and least-squares problems, which are commonly employed to optimize Support Vector Machine models. The proposed method is computationally efficient, thereby it is scalable to large-scale datasets. We applied our method to the public BreaKHis dataset and achieved promising prediction performance and scalability for histopathological classification.Availability and implementationSoftware is publicly available at: https://1drv.ms/u/s!AiFpD21bgf2wgRLbQq08ixD0SgRD?e=OpqEmY.Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC9235475 | biostudies-literature
Project description:BackgroundProviding a noninvasive, rapid, and cost-effective approach to diagnose of myocardial infarction (MI) is essential in the early stages of electrocardiogram (ECG) signaling. In this article, we proposed the new optimization method for support vector machine (SVM) classifier to MI classification.MethodsAfter preprocessing ECG signal and noise removal, three features such as Q-wave integral, T-wave integral, and QRS-complex integral have been extracted in this study. After that, different statistical tests have evaluated the matrix of these features. To more accurately detect and classify the MI disease, optimizing the SVM classification parameters using the grasshopper optimization algorithm (GOA) was first used in this study (that called SVM-GOA).ResultsAfter applying the GOA on the SVM classifier for all three kernels, the final results of MI detection for sensitivity, specificity, and accuracy were 100% ± 0%, 100% ± 0%, and 100% ± 0%, respectively. The final results of different MI types' classification after applying the GOA on SVM for polynomial kernel were obtained 100% ± 0%, 97.37% ± 0%, and 94.2% ± 0.2% for sensitivity and specificity and accuracy, respectively. However, the results of both linear and RBF kernels that were used for the SVM classifier method have also shown a significant increase after using GOA.ConclusionThis article's results show the highly desirable effect of applying a GOA to optimize different kernel parameters used in the SVM classifier for accurate detection and classification of MI. The proposed algorithm's final results show that the proposed system has a relatively higher performance than other previous studies.
| S-EPMC8382032 | biostudies-literature
Project description:We combined local photolysis of caged compounds with fluorescence imaging to visualize molecular diffusion within dendrites of cerebellar Purkinje cells. Diffusion of a volume marker, fluorescein dextran, within spiny dendrites was remarkably slow in comparison to its diffusion in smooth dendrites. Computer simulations indicate that this retardation is due to a transient trapping of molecules within dendritic spines, yielding anomalous diffusion. We considered the influence of spine trapping on the diffusion of calcium ions (Ca(2+)) and inositol-1,4,5-triphospate (IP(3)), two synaptic second messengers. Diffusion of IP(3) was strongly influenced by the presence of dendritic spines, while Ca(2+) was removed so rapidly that it could not diffuse far enough to be trapped. We conclude that an important function of dendritic spines may be to trap chemical signals and thereby create slowed anomalous diffusion within dendrites.
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Project description:BackgroundSynthesizing and characterizing aptamers with high affinity and specificity have been extensively carried out for analytical and biomedical applications. Few publications can be found that describe structure-activity relationships (SARs) of candidate aptamer sequences.MethodologyThis paper reports pattern recognition with support vector machine (SVM) classification techniques for the identification of streptavidin-binding aptamers as "low" or "high" affinity aptamers. The SVM parameters C and ? were optimized using genetic algorithms. Four descriptors, the topological descriptor PW4 (path/walk 4--Randic shape index), the connectivity index X3A (average connectivity index chi-3), the topological charge index JGI2 (mean topological charge index of order 2), and the free energy E of the secondary structure, were used to describe the structures of candidate aptamer sequences from SELEX selection (Schütze et al. (2011) PLoS ONE (12):e29604).ConclusionsThe predicted fractions of winning streptavidin-binding aptamers for ten rounds of SELEX conform to the aptamer evolutionary principles of SELEX-based screening. The feasibility of applying pattern recognition based on SVM and genetic algorithms for streptavidin-binding aptamers has been demonstrated.
| S-EPMC4057401 | biostudies-literature