Independent component analysis of 2-D electrophoresis gels

We present a novel application of independent component analysis (ICA), an exploratory data analysis technique, to two-dimensional electrophoresis (2-DE) gels, which have been used to analyze differentially expressed proteins across groups. Unlike currently used pixel-wise statistical tests, ICA is a data-driven approach that utilizes the information contained in the entire gel data. We also apply ICA on wavelet-transformed 2-DE gels to address the high dimensionality and noise problems typically found in 2-DE gels. Also, we use an analysis-of-variance (ANOVA) approach as a benchmark for comparison. Using simulated data, we show that ICA detects the group differences accurately in both the spatial and wavelet domains. We also apply these techniques to real 2-DE gels. ICA proves to be much faster than ANOVA, and unlike ANOVA it does not depend on the selection of a threshold. Application of principal component analysis reduces the dimensionality and tends to improve the performance by reducing the noise.     

Independent component analysis and its applications in signal processing for analytical chemistry

Independent component analysis (ICA) is a statistical method the goal of which is to find a linear representation of non-Gaussian data so that the components are statistically independent, or as independent as possible. In an ICA procedure, the estimated independent components (ICs) are identical to or highly correlated to the spectral profiles of the chemical components in mixtures under certain circumstances, so the latent variables obtained are chemically interpretable and useful for qualitative analysis of mixtures without prior information about the sources or reference materials, and the calculated demixing matrix is useful for simultaneous determination of polycomponents in mixtures. We review commonly used ICA algorithms and recent ICA applications in signal processing for qualitative and quantitative analysis. Furthermore, we also review the preprocessing method for ICA applications and the robustness of different ICA algorithms, and we give the empirical criterion for selection of ICA algorithms in signal processing for analytical chemistry.     

Independent component analysis (ICA) algorithms for improved spectral deconvolution of overlapped signals in 1H NMR analysis: application to foods and related products

The major challenge facing NMR spectroscopic mixture analysis is the overlapping of signals and the arising impossibility to easily recover the structures for identification of the individual components and to integrate separated signals for quantification. In this paper, various independent component analysis (ICA) algorithms [mutual information least dependent component analysis (MILCA); stochastic non‐negative ICA (SNICA); joint approximate diagonalization of eigenmatrices (JADE); and robust, accurate, direct ICA algorithm (RADICAL)] as well as deconvolution methods [simple‐to‐use‐interactive self‐modeling mixture analysis (SIMPLISMA) and multivariate curve resolution‐alternating least squares (MCR‐ALS)] are applied for simultaneous ¹H NMR spectroscopic determination of organic substances in complex mixtures. Among others, we studied constituents of the following matrices: honey, soft drinks, and liquids used in electronic cigarettes. Good quality spectral resolution of up to eight‐component mixtures was achieved (correlation coefficients between resolved and experimental spectra were not less than 0.90). In general, the relative errors in the recovered concentrations were below 12%. SIMPLISMA and MILCA algorithms were found to be preferable for NMR spectra deconvolution and showed similar performance. The proposed method was used for analysis of authentic samples. The resolved ICA concentrations match well with the results of reference gas chromatography–mass spectrometry as well as the MCR‐ALS algorithm used for comparison. ICA deconvolution considerably improves the application range of direct NMR spectroscopy for analysis of complex mixtures. Copyright © 2014 John Wiley & Sons, Ltd.     

A new approach to near-infrared spectral data analysis using independent component analysis

This paper presents a new approach to near-infrared spectral (NIR) data analysis that is based on independent component analysis (ICA). The main advantage of the new method is that it is able to separate the spectra of the constituent components from the spectra of their mixtures. The separation is a blind operation, since the constituent components of mixtures can be unknown. The ICA based method is therefore particularly useful in identifying the unknown components in a mixture as well as in estimating their concentrations. The approach is introduced by reference to case studies and compared to other techniques for NIR analysis including principal component regression (PCR), multiple linear regression (MLR), and partial least squares (PLS) as well as Fourier and wavelet transforms.     

Multimode process monitoring based on Bayesian method

Multimode process monitoring has recently attracted much attention both in academy and industry. Conventional methods assume that either the process data are Gaussian in each operation mode, or some process knowledge should be incorporated, thus making the methods supervised. In this paper, a new unsupervised method is developed for multimode process monitoring, which is based on Bayesian inference and two‐step independent component analysis–principal component analysis (ICA–PCA) feature extraction strategy. ICA–PCA is first introduced for feature extraction and dimension reduction. By transferring the traditional monitoring statistic to fault probability in each operation mode, monitoring results in different operation modes can be easily combined by the Bayesian inference. Another contribution of the present paper is the development of a new fault identification method. Through analyses of the posterior probability and the joint probability for the monitored data sample, the correct operation mode or fault scenario can be identified. Three case studies are demonstrated to evaluate the feasibility and efficiency of the proposed method. Copyright © 2009 John Wiley & Sons, Ltd.     

A new regression method based on independent component analysis

Based on independent component analysis (ICA), a new regression method, independent component regression (ICR), was developed to build the model of NIR spectra and the routine components of plant samples. It is found that ICR and principal component regression (PCR) are completely equivalent when they are applied in quantitative prediction. However, independent components (ICs) can give more chemical explanation than principal components (PCs) because independence is a high-order statistic that is a much stronger condition than orthogonality. Three ICs are obtained by ICA from the NIR spectra of plant samples; it is found that they are strongly correlated to the NIR spectra of water, hydrocarbons and organonitrogen compounds, respectively. Therefore, ICA may be a promising tool to retrieve both quantitative and qualitative information from complex chemical data sets.     

Determination of rice type by 1H NMR spectroscopy in combination with different chemometric tools

A 400‐MHz ¹H nuclear magnetic resonance (NMR) spectroscopy and multivariate data analysis were used in the context of food surveillance to discriminate 46 authentic rice samples according to type. It was found that the optimal sample preparation consists of preparing aqueous rice extracts at pH 1.9. For the first time, the chemometric method independent component analysis (ICA) was applied to differentiate clusters of rice from the same type (Basmati, non‐Basmati long‐grain rice, and round‐grain rice) and, to a certain extent, their geographical origin. ICA was found to be superior to classical principal component analysis (PCA) regarding the verification of rice authenticity. The chemical shifts of the principal saccharides and acetic acid were found to be mostly responsible for the observed clustering. Among classification methods (linear discriminant analysis, factorial discriminant analysis, partial least squares discriminant analysis (PLS‐DA), soft independent modeling of class analogy, and ICA), PLS‐DA and ICA gave the best values of specificity (0.96 for both methods) and sensitivity (0.94 for PLS‐DA and 1.0 for ICA). Hence, NMR spectroscopy combined with chemometrics could be used as a screening method in the official control of rice samples. Copyright © 2013 John Wiley & Sons, Ltd.     

Independent component analysis yields chemically interpretable latent variables in multivariate regression

This work shows that independent component analysis (ICA) can be used to obtain statistically independent and, therefore, chemically interpretable latent variables (LVs) in multivariate regression. Two novel algorithms based on ICA are introduced and compared with two classical methods on simulated data: principal component regression and partial least-squares regression. All methods compared yield accurate predictions, but only those based on ICA yield LVs that are chemically interpretable. Practical limitations of ICA-based regression with respect to the underlying assumptions, sample size, and measurement noise are discussed and illustrated by means of simulations.     

Detection of explosives on the surface of banknotes by Raman hyperspectral imaging and independent component analysis

The aim of this study was to develop a methodology using Raman hyperspectral imaging and chemometric methods for identification of pre- and post-blast explosive residues on banknote surfaces. The explosives studied were of military, commercial and propellant uses. After the acquisition of the hyperspectral imaging, independent component analysis (ICA) was applied to extract the pure spectra and the distribution of the corresponding image constituents. The performance of the methodology was evaluated by the explained variance and the lack of fit of the models, by comparing the ICA recovered spectra with the reference spectra using correlation coefficients and by the presence of rotational ambiguity in the ICA solutions. The methodology was applied to forensic samples to solve an automated teller machine explosion case. Independent component analysis proved to be a suitable method of resolving curves, achieving equivalent performance with the multivariate curve resolution with alternating least squares (MCR-ALS) method. At low concentrations, MCR-ALS presents some limitations, as it did not provide the correct solution. The detection limit of the methodology presented in this study was 50 μg cm⁻².     

ANOVA–principal component analysis and ANOVA–simultaneous component analysis: a comparison

ANOVA–simultaneous component analysis (ASCA) is a recently developed tool to analyze multivariate data. In this paper, we enhance the explorative capability of ASCA by introducing a projection of the observations on the principal component subspace to visualize the variation among the measurements. We compare the significance of experimental effects for ASCA and ANOVA–principal component analysis (PCA), a similar tool to explore multivariate data, by using permutation tests. Furthermore, we quantify the quality of the loadings estimate obtained with ASCA and compare this with the loadings estimate obtained with ANOVA–PCA. Copyright © 2011 John Wiley & Sons, Ltd.     

A novel approach for dimension reduction of microarray

This paper proposes a new hybrid search technique for feature (gene) selection (FS) using Independent component analysis (ICA) and Artificial Bee Colony (ABC) called ICA + ABC, to select informative genes based on a Naïve Bayes (NB) algorithm. An important trait of this technique is the optimization of ICA feature vector using ABC. ICA + ABC is a hybrid search algorithm that combines the benefits of extraction approach, to reduce the size of data and wrapper approach, to optimize the reduced feature vectors. This hybrid search technique is facilitated by evaluating the performance of ICA + ABC on six standard gene expression datasets of classification. Extensive experiments were conducted to compare the performance of ICA + ABC with the results obtained from recently published Minimum Redundancy Maximum Relevance (mRMR) +ABC algorithm for NB classifier. Also to check the performance that how ICA + ABC works as feature selection with NB classifier, compared the combination of ICA with popular filter techniques and with other similar bio inspired algorithm such as Genetic Algorithm (GA) and Particle Swarm Optimization (PSO). The result shows that ICA + ABC has a significant ability to generate small subsets of genes from the ICA feature vector, that significantly improve the classification accuracy of NB classifier compared to other previously suggested methods.     

Standardless multicomponent qNMR analysis of compounds with overlapped resonances based on the combination of ICA and PULCON

A fast and reliable nuclear magnetic resonance (NMR) method for quantitative analysis of targeted compounds with overlapped signals in complex mixtures has been established. The method is based on the combination of chemometric treatment for spectra deconvolution and the PULCON principle (pulse length based concentration determination) for quantification. Independent component analysis (ICA) (mutual information least dependent component analysis (MILCA) algorithm) was applied for spectra deconvolution in up to six component mixtures with known composition. The resolved matrices (independent components, ICs and ICA scores) were used for identification of analytes, calculating their relative concentrations and absolute integral intensity of selected resonances. The absolute analyte concentrations in multicomponent mixtures and authentic samples were then calculated using the PULCON principle. Instead of conventional application of absolute integral intensity in case of undisturbed signals, the multiplication of resolved IC absolute integral and its relative concentration in the mixture for each component was used. Correction factors that are required for quantification and are unique for each analyte were also estimated. The proposed method was applied for analysis of up to five components in lemon and orange juice samples with recoveries between 90% and 111%. The total duration of analysis is approximately 45 min including measurements, spectra decomposition and quantification. The results demonstrated that the proposed method is a promising tool for rapid simultaneous quantification of up to six components in case of spectral overlap and the absence of reference materials. Copyright © 2015 John Wiley & Sons, Ltd.     

Application of neural networks with novel independent component analysis methodologies for the simultaneous determination of cadmium,copper, and lead using an ISE array

The paper introduces a novel chemometric strategy based on independent component analysis (ICA) coupled with a back‐propagation neural network. In this approach, one of the most popular ICA methods, the fast fixed‐point algorithm for ICA (fastICA), was implemented by the genetic algorithm (geneticICA) to avoid the local maxima problem commonly observed with fastICA. As a case study, an ion‐selective electrode (ISE) array, consisting of three working electrodes and one reference electrode, was used for the simultaneous determination of three heavy metals (cadmium, copper, and lead) in aqueous solutions, which are normally prone to severe interferences. The robustness and appropriateness of the approach were assessed using the average mean of relative error (MRE) of triplicated external validation. After configuration and optimization, the average MRE for Cu was <5%. For the determination of Cd and Pb, whose ISEs normally cannot tolerate Cu ions even at the microgram per liter levels, the MREs were 8%. This article demonstrated that this approach can be applied to the detection of heavy metal contamination in industrial wastewater with prediction accuracies comparable with other popular quantitative chemometric neural network methods. Copyright © 2014 John Wiley & Sons, Ltd.     

Identifying constituents in commercial gasoline using Fourier transform-infrared spectroscopy and independent component analysis

A new method is proposed that enables the identification of five refinery fractions present in commercial gasoline mixtures using infrared spectroscopic analysis. The data analysis and interpretation was carried out based on independent component analysis (ICA) and spectral similarity techniques. The FT-IR spectra of the gasoline constituents were determined using the ICA method, exclusively based on the spectra of their mixtures as a blind separation procedure, i.e. assuming unknown the spectra of the constituents. The identity of the constituents was subsequently determined using similarity measures commonly employed in spectra library searches against the spectra of the constituent components. The high correlation scores that were obtained in the identification of the constituents indicates that the developed method can be employed as a rapid and effective tool in quality control, fingerprinting or forensic applications, where gasoline constituents are suspected.     

Uncommon multivariate statistical methods for environmental studies: A review

In this paper we describe the characteristics and the applications of the multivariate methods for spectroscopic and chromatographic techniques independent component analysis (ICA) and two-dimensional correlation spectroscopy (2DCOS) focused to their use in environmental studies. In our opinion, these methods are important because they allow to characterize environmental samples with different aims and scopes from those generally obtained by means of more common multivariate methods such as principal component analysis (PCA) and partial least squares (PLS). The new insights of these methods in recent environmental studies are reviewed and debated.     

WE-ASCA: The Weighted-Effect ASCA for Analyzing Unbalanced Multifactorial Designs—A Raman Spectra-Based Example

Analyses of multifactorial experimental designs are used as an explorative technique describing hypothesized multifactorial effects based on their variation. The procedure of analyzing multifactorial designs is well established for univariate data, and it is known as analysis of variance (ANOVA) tests, whereas only a few methods have been developed for multivariate data. In this work, we present the weighted-effect ASCA, named WE-ASCA, as an enhanced version of ANOVA-simultaneous component analysis (ASCA) to deal with multivariate data in unbalanced multifactorial designs. The core of our work is to use general linear models (GLMs) in decomposing the response matrix into a design matrix and a parameter matrix, while the main improvement in WE-ASCA is to implement the weighted-effect (WE) coding in the design matrix. This WE-coding introduces a unique solution to solve GLMs and satisfies a constrain in which the sum of all level effects of a categorical variable equal to zero. To assess the WE-ASCA performance, two applications were demonstrated using a biomedical Raman spectral data set consisting of mice colorectal tissue. The results revealed that WE-ASCA is ideally suitable for analyzing unbalanced designs. Furthermore, if WE-ASCA is applied as a preprocessing tool, the classification performance and its reproducibility can significantly improve.     

Estimation of source infrared spectra profiles of acetylspiramycin active components from troches using kernel independent component analysis

Kernel independent component analysis (KICA), a kind of independent component analysis (ICA) algorithms based on kernel, was preliminarily investigated for blind source separation (BSS) of source spectra profiles from troches. The robustness of different ICA algorithms (KICA, FastICA and Infomax) was first checked by using them in the retrieval of source infrared (IR), ultraviolet (UV) and mass spectra (MS) from synthetic mixtures. It was found that KICA is the most robust method for retrieval of source spectra profiles. KICA algorithm is subsequently adopted in the analysis of diffuse reflection IR of acetylspiramycin (ASPM) troches. It is observed that KICA is able to isolate the theoretically predicted spectral features corresponding to the ASPM active components, excipients and other minor components as different independent (spectral) component. A troche can be authenticated and semi-quantified using the estimated ICs. KICA is an useful method for estimation of source spectral features of molecules with different geometry and stoichiometry, while features belonging to very similar molecules remain grouped.     

Independent component analysis as a pretreatment method for parallel factor analysis to eliminate artefacts from multiway data

Parallel factor analysis (PARAFAC) has successfully been used in many applications for the analysis of excitation-emission fluorescence data. However, some measurement “artefacts”, such as Rayleigh or Raman scattering, can pose a problem for the extraction of the PARAFAC components and their interpretation. Replacing the spectral zones corresponding to these signals by missing values in the data is not necessarily a method of choice in the cases where informative signals lie in the same wavelength regions. In this article, independent component analysis (ICA) is used on the unfolded cubic array, and the independent components related to the Rayleigh and Raman scattering are identified and removed prior to the reconstruction of the excitation-emission fluorescence data cube. PARAFAC is then applied on these data reconstructed after selective artefact removal, and satisfactory models can be obtained. This procedure, although particularly useful for 3D fluorescence data, may be applied to other types of data as well.