Spatial mutual information based hyperspectral band selection for classification.
Ontology highlight
ABSTRACT:
SUBMITTER: Amankwah A
PROVIDER: S-EPMC4396555 | biostudies-other | 2015
REPOSITORIES: biostudies-other
Similar Datasets
Project description:The accurate classification of microbes is critical in today's context for monitoring the ecological balance of a habitat. Hence, in this research work, a novel method to automate the process of identifying microorganisms has been implemented. To extract the bodies of microorganisms accurately, a generalized segmentation mechanism which consists of a combination of convolution filter (Kirsch) and a variance-based pixel clustering algorithm (Otsu) is proposed. With exhaustive corroboration, a set of twenty-five features were identified to map the characteristics and morphology for all kinds of microbes. Multiple techniques for feature selection were tested and it was found that mutual information (MI)-based models gave the best performance. Exhaustive hyperparameter tuning of multilayer layer perceptron (MLP), k-nearest neighbors (KNN), quadratic discriminant analysis (QDA), logistic regression (LR), and support vector machine (SVM) was done. It was found that SVM radial required further improvisation to attain a maximum possible level of accuracy. Comparative analysis between SVM and improvised SVM (ISVM) through a 10-fold cross validation method ultimately showed that ISVM resulted in a 2% higher performance in terms of accuracy (98.2%), precision (98.2%), recall (98.1%), and F1 score (98.1%).
| S-EPMC7927045 | biostudies-literature
Project description:We address the problem of feature selection for classifying a diverse set of chemicals using an array of metal oxide sensors. Our aim is to evaluate a filter approach to feature selection with reference to previous work, which used a wrapper approach on the same data set, and established best features and upper bounds on classification performance. We selected feature sets that exhibit the maximal mutual information with the identity of the chemicals. The selected features closely match those found to perform well in the previous study using a wrapper approach to conduct an exhaustive search of all permitted feature combinations. By comparing the classification performance of support vector machines (using features selected by mutual information) with the performance observed in the previous study, we found that while our approach does not always give the maximum possible classification performance, it always selects features that achieve classification performance approaching the optimum obtained by exhaustive search. We performed further classification using the selected feature set with some common classifiers and found that, for the selected features, Bayesian Networks gave the best performance. Finally, we compared the observed classification performances with the performance of classifiers using randomly selected features. We found that the selected features consistently outperformed randomly selected features for all tested classifiers. The mutual information filter approach is therefore a computationally efficient method for selecting near optimal features for chemical sensor arrays.
| S-EPMC3942325 | biostudies-literature
Project description:Mutual Information (MI) based feature selection methods are popular due to their ability to capture the nonlinear relationship among variables. However, existing works rarely address the error (bias) that occurs due to the use of finite samples during the estimation of MI. To the best of our knowledge, none of the existing methods address the bias issue for the high-order interaction term which is essential for better approximation of joint MI. In this paper, we first calculate the amount of bias of this term. Moreover, to select features using Electronic supplementary material The online version of this chapter (10.1007/978-3-030-47426-3_64) contains supplementary material, which is available to authorized users.
| S-EPMC7206174 | biostudies-literature
Project description:Variable (wavelength) selection is essential in the multivariate analysis of near-infrared spectra to improve model performance and provide a more straightforward interpretation. This paper proposed a new variable selection method named binning-normalized mutual information (B-NMI) based on information entropy theory. "Data binning" was applied to reduce the effects of minor measurement errors and increase the features of near-infrared spectra. "Normalized mutual information" was employed to calculate the correlation between each wavelength and the reference values. The performance of B-NMI was evaluated by two experimental datasets (ideal ternary solvent mixture dataset, fluidized bed granulation dataset) and two public datasets (gasoline octane dataset, corn protein dataset). Compared with classic methods of backward and interval PLS (BIPLS), variable importance projection (VIP), correlation coefficient (CC), uninformative variables elimination (UVE), and competitive adaptive reweighted sampling (CARS), B-NMI not only selected the most featured wavelengths from the spectra of complex real-world samples but also improved the stability and robustness of variable selection results.
| S-EPMC10419756 | biostudies-literature
Project description:UNLABELLED: BACKGROUND:Cancer therapy is a challenging research area because side effects often occur in chemo and radiation therapy. We intend to study a multi-targets and multi-components design that will provide synergistic results to improve efficiency of cancer therapy. METHODS:We have developed a general methodology, AMFES (Adaptive Multiple FEature Selection), for ranking and selecting important cancer biomarkers based on SVM (Support Vector Machine) classification. In particular, we exemplify this method by three datasets: a prostate cancer (three stages), a breast cancer (four subtypes), and another prostate cancer (normal vs. cancerous). Moreover, we have computed the target networks of these biomarkers as the signatures of the cancers with additional information (mutual information between biomarkers of the network). Then, we proposed a robust framework for synergistic therapy design approach which includes varies existing mechanisms. RESULTS:These methodologies were applied to three GEO datasets: GSE18655 (three prostate stages), GSE19536 (4 subtypes breast cancers) and GSE21036 (prostate cancer cells and normal cells) shown in. We selected 96 biomarkers for first prostate cancer dataset (three prostate stages), 72 for breast cancer (luminal A vs. luminal B), 68 for breast cancer (basal-like vs. normal-like), and 22 for another prostate cancer (cancerous vs. normal. In addition, we obtained statistically significant results of mutual information, which demonstrate that the dependencies among these biomarkers can be positive or negative. CONCLUSIONS:We proposed an efficient feature ranking and selection scheme, AMFES, to select an important subset from a large number of features for any cancer dataset. Thus, we obtained the signatures of these cancers by building their target networks. Finally, we proposed a robust framework of synergistic therapy for cancer patients. Our framework is not only supported by real GEO datasets but also aim to a multi-targets/multi-components drug design tool, which improves the traditional single target/single component analysis methods. This framework builds a computational foundation which can provide a clear classification of cancers and lead to an efficient cancer therapy.
| S-EPMC3524788 | biostudies-literature
Project description:Covariance-based discovery of polymorphisms under co-selective pressure or epistasis has received considerable recent attention in population genomics. Both statistical modeling of the population level covariation of alleles across the chromosome and model-free testing of dependencies between pairs of polymorphisms have been shown to successfully uncover patterns of selection in bacterial populations. Here we introduce a model-free method, SpydrPick, whose computational efficiency enables analysis at the scale of pan-genomes of many bacteria. SpydrPick incorporates an efficient correction for population structure, which adjusts for the phylogenetic signal in the data without requiring an explicit phylogenetic tree. We also introduce a new type of visualization of the results similar to the Manhattan plots used in genome-wide association studies, which enables rapid exploration of the identified signals of co-evolution. Simulations demonstrate the usefulness of our method and give some insight to when this type of analysis is most likely to be successful. Application of the method to large population genomic datasets of two major human pathogens, Streptococcus pneumoniae and Neisseria meningitidis, revealed both previously identified and novel putative targets of co-selection related to virulence and antibiotic resistance, highlighting the potential of this approach to drive molecular discoveries, even in the absence of phenotypic data.
| S-EPMC6765119 | biostudies-literature
Project description:BackgroundEpileptic seizures are characterized by aberrant synchronization. We hypothesized that higher synchronization across the seizure onset zone (SOZ) channels during a temporal lobe seizure contributes to impaired consciousness.New methodAll symmetric bivariate synchronization measures were extended to multivariate measure by a principal component analysis (PCA) based technique. A novel nonparametric method has been proposed to test the statistical significance between increased synchronization across the seizure onset zone (SOZ) channels and reduced consciousness.ResultsIncreased synchronization in the gamma band towards seizure termination significantly contributes to impaired consciousness (p < 0.1). Synchronization reaches its peak in the extratemporal region (frontal lobe) ahead of the temporal region (p < 0.05). Synchronization is prominent in beta and gamma bands by most methods and it is more in the second half of seizure duration than in the first (p < 0.05).ConclusionsMutual information is the only synchronization measure out of the six that we studied, whose increase can be associated with the loss of consciousness in a statistically significant way.
| S-EPMC7773881 | biostudies-literature
Project description:Information theoretic-based similarity measures, in particular mutual information, are widely used for intermodal/intersubject 3-D brain image registration. However, conventional mutual information does not consider spatial dependency between adjacent voxels in images, thus reducing its efficacy as a similarity measure in image registration. This paper first presents a review of the existing attempts to incorporate spatial dependency into the computation of mutual information (MI). Then, a recently introduced spatially dependent similarity measure, named spatial MI, is extended to 3-D brain image registration. This extension also eliminates its artifact for translational misregistration. Finally, the effectiveness of the proposed 3-D spatial MI as a similarity measure is compared with three existing MI measures by applying controlled levels of noise degradation to 3-D simulated brain images.
| S-EPMC4025931 | biostudies-other
Project description:As the big data science develops, efficient methods are demanded for various data analysis. Granger causality provides the prime model for quantifying causal interactions. However, this theoretic model does not meet the requirement for real-world data analysis, because real-world time series are diverse whose models are usually unknown. Therefore, model-free measures such as information transfer measures are strongly desired. Here, we propose the multi-scale extension of conditional mutual information measures using MORLET wavelet, which are named the WM and WPM. The proposed measures are computational efficient and interpret information transfer by multi-scales. We use both synthetic data and real-world examples to demonstrate the efficiency of the new methods. The results of the new methods are robust and reliable. Via the simulation studies, we found the new methods outperform the wavelet extension of transfer entropy (WTE) in both computational efficiency and accuracy. The features and properties of the proposed measures are also discussed.
| S-EPMC6283631 | biostudies-literature
Project description:The purposes are to solve the isomorphism encountered while processing hyperspectral remote sensing data and improve the accuracy of hyperspectral remote sensing data in extracting and classifying lithological information. Taking rocks as the research object, Backpropagation Neural Network (BPNN) is introduced. After the hyperspectral image data are normalized, the lithological spectrum and spatial information are the feature extraction targets to construct a deep learning-based lithological information extraction model. The performance of the model is analyzed using specific instance data. Results demonstrate that the overall accuracy and the Kappa coefficient of the lithological information extraction and classification model based on deep learning were 90.58% and 0.8676, respectively. This model can precisely distinguish the properties of rock masses and provide better performance compared with the state of other analysis models. After introducing deep learning, the recognition accuracy and the Kappa coefficient of the proposed BPNN model increased by 8.5% and 0.12, respectively, compared with the traditional BPNN. The proposed extraction and classification model can provide some research values and practical significances for the hyperspectral rock and mineral classification.
| S-EPMC8516202 | biostudies-literature