Classification of pyrolysis mass spectra by fuzzy multivariate rule induction-comparison with regression, K-nearest neighbour, neural and decision-tree methods

Application of spectroscopic techniques combined with chemometrics to the authenticity and quality attributes of rice

Rice is a staple food for two-thirds of the world's population and is grown in over a hundred countries around the world. Due to its large scale, it is vulnerable to adulteration. In addition, the quality attribute of rice is an important factor affecting the circulation and price, which is also paid more and more attention. The combination of spectroscopy and chemometrics enables rapid detection of authenticity and quality attributes in rice. This article described the application of seven spectroscopic techniques combined with chemometrics to the rice industry. For a long time, near-infrared spectroscopy and linear chemometric methods (e.g., PLSR and PLS-DA) have been widely used in the rice industry. Although some studies have achieved good accuracy, with models in many studies having greater than 90% accuracy. However, higher accuracy and stability were more likely to be obtained using multiple spectroscopic techniques, nonlinear chemometric methods, and key wavelength selection algorithms. Future research should develop larger rice databases to include more rice varieties and larger amounts of rice depending on the type of rice, and then combine various spectroscopic techniques, nonlinear chemometric methods, and key wavelength selection algorithms. This article provided a reference for a more efficient and accurate determination of rice quality and authenticity.

A feasibility research on the application of machine vision technology in appearance quality inspection of Xuesaitong dropping pills

Defect detection is a critical issue for the quality control of dropping pills, which is a special dosage form of traditional Chinese Medicine. Machine vision is a non-destructing testing technology and cost-effective with high accuracy that can be used to predict the detects of both interior and exterior of the sample by employing the camera. In this research, a machine vision system for inspecting quality of the Xuesaitong dropping pills (XDPs) that include non-spherical, abnormal sizes and colors was developed to evaluate the appearance quality of XDPs rapidly and accurately. Firstly, 270 images of XDPs containing qualified and three different types of defects were collected. Subsequently, the processing of the XDPs images were carried out. Finally, Three defecting categories classification models were developed and compared based on contour and color features. The experimental results showed that the Random Forest outperformed all the explored models and the classification accuracy for non-spherical, abnormal sizes and colors reached 98.52%, 100.00% and 100.00%, respectively. In summary, the method established in this research is scientific, reliable, fast and accurate, which has great application potential and can provide technical support for the automatic defect detection of dropping pills.

The Key Reason of False Positive Misclassification for Accurate Large-Area Mangrove Classifications

Accurate large-area mangrove classification is a challenging task due to the complexity of mangroves, such as abundant species within the mangrove category, and various appearances resulting from a large latitudinal span and varied habitats. Existing studies have improved mangrove classifications by introducing time series images, constructing new indices sensitive to mangroves, and correcting classifications by empirical constraints and visual inspections. However, false positive misclassifications are still prevalent in current classification results before corrections, and the key reason for false positive misclassification in large-area mangrove classifications is unknown. To address this knowledge gap, a hypothesis that an inadequate classification scheme (i.e., the choice of categories) is the key reason for such false positive misclassification is proposed in this paper. To validate this hypothesis, new categories considering non-mangrove vegetation near water (i.e., within one pixel from water bodies) were introduced, which is inclined to be misclassified as mangroves, into a normally-used standard classification scheme, so as to form a new scheme. In controlled conditions, two experiments were conducted. The first experiment using the same total features to derive direct mangrove classification results in China for the year 2018 on the Google Earth Engine with the standard scheme and the new scheme respectively. The second experiment used the optimal features to balance the probability of a selected feature to be effective for the scheme. A comparison shows that the inclusion of the new categories reduced the false positive pixels with a rate of 71.3% in the first experiment, and a rate of 66.3% in the second experiment. Local characteristics of false positive pixels within 1 × 1 km cells, and direct classification results in two selected subset areas were also analyzed for quantitative and qualitative validation. All the validation results from the two experiments support the finding that the hypothesis is true. The validated hypothesis can be easily applied to other studies to alleviate the prevalence of false positive misclassifications.

A critical review on the use of artificial neural networks in olive oil production, characterization and authentication

Artificial neural networks (ANN) are computationally based mathematical tools inspired by the fundamental cell of the nervous system, the neuron. ANN constitute a simplified artificial replica of the human brain consisting of parallel processing neural elements similar to neurons in living beings. ANN is able to store large amounts of experimental information to be used for generalization with the aid of an appropriate prediction model. ANN has proved useful for a variety of biological, medical, economic and meteorological purposes, and in agro-food science and technology. The olive oil industry has a substantial weight in Mediterranean's economy. The different steps of the olive oil production process, which include olive tree and fruit care, fruit harvest, mechanical and chemical processing, and oil packaging have been examined in depth with a view to their optimization, and so have the authenticity, sensory properties and other quality-related properties of olive oil. This paper reviews existing literature on the use of bioinformatics predictive methods based on ANN in connection with the production, processing and characterization of olive oil. It examines the state of the art in bioinformatics tools for optimizing or predicting its quality with a view to identifying potential deficiencies or aspects for improvement.

Variable selection in discriminant partial least-squares analysis

Variable selection enhances the understanding and interpretability of multivariate classification models. A new chemometric method based on the selection of the most important variables in discriminant partial least-squares (VS-DPLS) analysis is described. The suggested method is a simple extension of DPLS where a small number of elements in the weight vector w is retained for each factor. The optimal number of DPLS factors is determined by cross-validation. The new algorithm is applied to four different high-dimensional spectral data sets with excellent results. Spectral profiles from Fourier transform infrared spectroscopy and pyrolysis mass spectrometry are used. To investigate the uniqueness of the selected variables an iterative VS-DPLS procedure is performed. At each iteration, the previously found selected variables are removed to see if a new VS-DPLS classification model can be constructed using a different set of variables. In this manner, it is possible to determine regions rather than individual variables that are important for a successful classification.

Discrimination of the production season of Chinese green tea by chemical analysis in combination with supervised pattern recognition

High-performance liquid chromatography (HPLC) has been used to quantify levels of free amino acids, catechins, and caffeine in Chinese green tea. Levels of free amino acids and catechins in green tea leaves show obvious variation from spring to summer, which is useful information to identify the production season of commercial green tea. Supervised pattern recognition methods such as the K-nearest neighbor (KNN) method and Bayesian discriminant method (a type of linear discriminant analysis (LDA)) were used to discriminate between the production seasons of Chinese green tea. The optimal accuracy of the KNN method was ≤97.61 and ≤94.80% as validated by resubstitution and cross-validation tests, respectively, and that of LDA was ≤95.22 and ≤93.54%, respectively. Compared with LDA, the KNN method did not require a Gaussian distribution and was more accurate than LDA. The KNN method in combination with chemical analysis is recommended for discrimination of the production seasons of Chinese green tea.

Automated interpretation of LIBS spectra using a fuzzy logic inference engine

Automated interpretation of laser-induced breakdown spectroscopy (LIBS) data is necessary due to the plethora of spectra that can be acquired in a relatively short time. However, traditional chemometric and artificial neural network methods that have been employed are not always transparent to a skilled user. A fuzzy logic approach to data interpretation has now been adapted to LIBS spectral interpretation. Fuzzy logic inference rules were developed using methodology that includes data mining methods and operator expertise to differentiate between various copper-containing and stainless steel alloys as well as unknowns. Results using the fuzzy logic inference engine indicate a high degree of confidence in spectral assignment.

Systems level studies of mammalian metabolomes: the roles of mass spectrometry and nuclear magnetic resonance spectroscopy

The study of biological systems in a holistic manner (systems biology) is increasingly being viewed as a necessity to provide qualitative and quantitative descriptions of the emergent properties of the complete system. Systems biology performs studies focussed on the complex interactions of system components; emphasising the whole system rather than the individual parts. Many perturbations to mammalian systems (diet, disease, drugs) are multi-factorial and the study of small parts of the system is insufficient to understand the complete phenotypic changes induced. Metabolomics is one functional level tool being employed to investigate the complex interactions of metabolites with other metabolites (metabolism) but also the regulatory role metabolites provide through interaction with genes, transcripts and proteins (e.g. allosteric regulation). Technological developments are the driving force behind advances in scientific knowledge. Recent advances in the two analytical platforms of mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy have driven forward the discipline of metabolomics. In this critical review, an introduction to metabolites, metabolomes, metabolomics and the role of MS and NMR spectroscopy will be provided. The applications of metabolomics in mammalian systems biology for the study of the health-disease continuum, drug efficacy and toxicity and dietary effects on mammalian health will be reviewed. The current limitations and future goals of metabolomics in systems biology will also be discussed (374 references).

Classification of jet fuels by fuzzy rule-building expert systems applied to three-way data by fast gas chromatography--fast scanning quadrupole ion trap mass spectrometry

A fast method that can be used to classify unknown jet fuel types or detect possible property changes in jet fuel physical properties is of paramount interest to national defense and the airline industries. While fast gas chromatography (GC) has been used with conventional mass spectrometry (MS) to study jet fuels, fast GC was combined with fast scanning MS and used to classify jet fuels into lot numbers or origin for the first time by using fuzzy rule-building expert system (FuRES) classifiers. In the process of building classifiers, the data were pretreated with and without wavelet transformation and evaluated with respect to performance. Principal component transformation was used to compress the two-way data images prior to classification. Jet fuel samples were successfully classified with 99.8 ± 0.5% accuracy for both with and without wavelet compression. Ten bootstrapped Latin partitions were used to validate the generalized prediction accuracy. Optimized partial least squares (o-PLS) regression results were used as positively biased references for comparing the FuRES prediction results. The prediction results for the jet fuel samples obtained with these two methods were compared statistically. The projected difference resolution (PDR) method was also used to evaluate the fast GC and fast MS data. Two batches of aliquots of ten new samples were prepared and run independently 4 days apart to evaluate the robustness of the method. The only change in classification parameters was the use of polynomial retention time alignment to correct for drift that occurred during the 4-day span of the two collections. FuRES achieved perfect classifications for four models of uncompressed three-way data. This fast GC/fast MS method furnishes characteristics of high speed, accuracy, and robustness. This mode of measurement may be useful as a monitoring tool to track changes in the chemical composition of fuels that may also lead to property changes.

Study on discrimination of Roast green tea (Camellia sinensis L.) according to geographical origin by FT-NIR spectroscopy and supervised pattern recognition

Rapid discrimination of roast green tea according to geographical origin is crucial to quality control. Fourier transform near-infrared (FT-NIR) spectroscopy and supervised pattern recognition was attempted to discriminate Chinese green tea according to geographical origins (i.e. Anhui Province, Henan Province, Jiangsu Province, and Zhejiang Province) in this work. Four supervised pattern recognitions methods were used to construct the discrimination models based on principal component analysis (PCA), respectively. The number of principal components factors (PCs) and model parameters were optimized by cross-validation in the constructing model. The performances of four discrimination models were compared. Experimental results showed that the performance of SVM model is the best among four models. The optimal SVM model was achieved when 4 PCs were used, discrimination rates being all 100% in the training and prediction set. The overall results demonstrated that FT-NIR spectroscopy with supervised pattern recognition could be successfully applied to discriminate green tea according to geographical origins.

Forensic application of gas chromatography-differential mobility spectrometry with two-way classification of ignitable liquids from fire debris

With respect to the emerging role of forensic science for arson investigation, a low cost and promising onsite detection method for ignitable liquids is desirable. Gas chromatography-differential mobility spectrometry (GC-DMS) was investigated as a tool for analysis of ignitable liquids from fire debris. Headspace solid-phase microextraction (SPME) was applied as the preconcentration and sampling method. The combined information afforded by gas chromatography and differential mobility spectrometry provided unique two-way patterns for each sample of ignitable liquid. Two-way GC-DMS data were classified into one of seven ignitable liquids using a fuzzy rule-building expert system (FuRES). The performance of the classifier was validated using bootstrap Latin partitions (BLPs) and also compared to optimized partial least-squares (PLS) classifiers. Better prediction results can be obtained by using two-way GC-DMS data than only using one-way total ion chromatograms or integrated differential mobility spectra. FuRES models constructed with the neat ignitable liquids identified the spiked samples from simulated fire debris with 99.07 +/- 0.04% accuracy.

Bootstrap classification and point-based feature selection from age-staged mouse cerebellum tissues of matrix assisted laser desorption/ionization mass spectra using a fuzzy rule-building expert system

A bootstrap method for point-based detection of candidate biomarker peaks has been developed from pattern classifiers. Point-based detection methods are advantageous in comparison to peak-based methods. Peak determination and selection are problematic when spectral peaks are not baseline resolved or on a varying baseline. The benefit of point-based detection is that peaks can be globally determined from the characteristic features of the entire data set (i.e., subsets of candidate points) as opposed to the traditional method of selecting peaks from individual spectra and then combining the peak list into a data set. The point-based method is demonstrated to be more effective and efficient using a synthetic data set when compared to using Mahalanobis distance for feature selection. In addition, probabilities that characterize the uniqueness of the peaks are determined. This method was applied for detecting peaks that characterize age-specific patterns of protein expression of developing and adult mouse cerebella from matrix assisted laser desorption/ionization (MALDI) mass spectrometry (MS) data. The mice comprised three age groups: 42 adults, 19 14-day-old pups, and 16 7-day-old pups. Three sequential spectra were obtained from each tissue section to yield 126, 57 and 48 spectra for adult, 14-day-old pup, and 7-day-old pup spectra, respectively. Each spectrum comprised 71,879 mass measurements in a range of 3.5-50 kDa. A previous study revealed that 846 unique peaks were detected that were consistent for 50% of the mice in each age group (C. Laurent, D.F. Levinson, S.A. Schwartz, P.B. Harrington, S.P. Markey, R.M. Caprioli, P. Levitt, Direct profiling of the cerebellum by MALDI MS: a methodological study in postnatal and adult mouse, J. Neurosci. Res. 81 (2005) 613-621.). A fuzzy rule-building expert system (FuRES) was applied to investigate the correlation of age with features in the MS data. FuRES detected two outlier pup-14 spectra. Prediction was evaluated using 100 bootstrap samples of 2 Latin-partitions (i.e., 50:50 split between training and prediction set) of the mice. The spectra without the outliers yielded classification rates of 99.1+/-0.1%, 90.1+/-0.8%, and 97.0+/-0.6% for adults, 14-day-old pups, and 7-day-old pups, respectively. At a 95% level of significance, 100 bootstrap samples disclosed 35 adult and 21 pup distinguishing peaks for separating adults from pups; and 8 14-day-old and 15 7-day-old predictive peaks for separating 14-day-old pup from 7-day-old pup spectra. A compressed matrix comprising 40,393 points that were outside the 95% confidence intervals of one of the two FuRES discriminants was evaluated and the classification improved significantly for all classes. When peaks that satisfied a quality criterion were integrated, the 55 integrated peak areas furnished significantly improved classification for all classes: the selected peak areas furnished classification rates of 100%, 97.3+/-0.6%, and 97.4+/-0.3% for adult, 14-day-old pups, and 7-day-old pups using 100 bootstrap Latin partitions evaluations with the predictions averaged. When the bootstrap size was increased to 1000 samples, the results were not significantly affected. The FuRES predictions were consistent with those obtained by discriminant partial least squares (DPLS) classifications.

Classification of soil samples according to geographic origin using gamma-ray spectrometry and pattern recognition methods

Multivariate data analysis methods were used to recognize and classify soils of unknown geographic origin. A total of 103 soil samples were differentiated into classes, according to regions in Serbia and Montenegro from which they were collected. Their radionuclide (226Ra, 238U, 235U, 40K, 134Cs, 137Cs, 232Th and 7Be) activities detected by gamma-ray spectrometry were then used as the inputs in different pattern recognition methods. For the classification of soil samples using eight selected radionuclides, the prediction ability of linear discriminant analysis (LDA), k-nearest neighbours (kNN), soft independent modelling of class analogy (SIMCA) and artificial neural network (ANN) were 82.8%, 88.6%, 60.0% and 92.1%, respectively.

High-throughput classification of yeast mutants for functional genomics using metabolic footprinting

Many technologies have been developed to help explain the function of genes discovered by systematic genome sequencing. At present, transcriptome and proteome studies dominate large-scale functional analysis strategies. Yet the metabolome, because it is 'downstream', should show greater effects of genetic or physiological changes and thus should be much closer to the phenotype of the organism. We earlier presented a functional analysis strategy that used metabolic fingerprinting to reveal the phenotype of silent mutations of yeast genes. However, this is difficult to scale up for high-throughput screening. Here we present an alternative that has the required throughput (2 min per sample). This 'metabolic footprinting' approach recognizes the significance of 'overflow metabolism' in appropriate media. Measuring intracellular metabolites is time-consuming and subject to technical difficulties caused by the rapid turnover of intracellular metabolites and the need to quench metabolism and separate metabolites from the extracellular space. We therefore focused instead on direct, noninvasive, mass spectrometric monitoring of extracellular metabolites in spent culture medium. Metabolic footprinting can distinguish between different physiological states of wild-type yeast and between yeast single-gene deletion mutants even from related areas of metabolism. By using appropriate clustering and machine learning techniques, the latter based on genetic programming, we show that metabolic footprinting is an effective method to classify 'unknown' mutants by genetic defect.

Chemometric detection of thermally degraded samples in the analysis of drugs of abuse with gas chromatography-Fourier-transform infrared spectroscopy

We present a chemometric procedure for the identification of the reference standard chromatographic peak in cases where the GC-FTIR analysis of commercial standards results in the appearance of more than one peak in the GC chromatogram. The procedure has been designed for phenethylamines, which represent the class with the largest number of individual molecules on the illicit drug market, and which are abused for their stimulant and/or hallucinogenic effects. The similarity between their vapor-phase FTIR spectra was modeled using principal component analysis (PCA), and class identity was assigned on the basis of soft independent modeling of class analogy (SIMCA). Additional peaks could be assigned to impurities in the standards, but most often they were artifacts formed during the GC-FTIR analysis of thermolabile or chemically unstable compounds. The latter case is illustrated by the identification of the reference standard chromatographic peak and FTIR spectrum of the potent psychotropic amphetamine derivative N-methyl-1-(3,4-methylenedioxyphenyl)-2-butanamine (MBDB), and by the elucidation of the chemical changes that occur in the molecule of MBDB due to thermal degradation.

Rapid and quantitative detection of the microbial spoilage of meat by fourier transform infrared spectroscopy and machine learning

Fourier transform infrared (FT-IR) spectroscopy is a rapid, noninvasive technique with considerable potential for application in the food and related industries. We show here that this technique can be used directly on the surface of food to produce biochemically interpretable "fingerprints." Spoilage in meat is the result of decomposition and the formation of metabolites caused by the growth and enzymatic activity of microorganisms. FT-IR was exploited to measure biochemical changes within the meat substrate, enhancing and accelerating the detection of microbial spoilage. Chicken breasts were purchased from a national retailer, comminuted for 10 s, and left to spoil at room temperature for 24 h. Every hour, FT-IR measurements were taken directly from the meat surface using attenuated total reflectance, and the total viable counts were obtained by classical plating methods. Quantitative interpretation of FT-IR spectra was possible using partial least-squares regression and allowed accurate estimates of bacterial loads to be calculated directly from the meat surface in 60 s. Genetic programming was used to derive rules showing that at levels of 10(7) bacteria.g(-1) the main biochemical indicator of spoilage was the onset of proteolysis. Thus, using FT-IR we were able to acquire a metabolic snapshot and quantify, noninvasively, the microbial loads of food samples accurately and rapidly in 60 s, directly from the sample surface. We believe this approach will aid in the Hazard Analysis Critical Control Point process for the assessment of the microbiological safety of food at the production, processing, manufacturing, packaging, and storage levels.

Validation using sensitivity and target transform factor analyses of neural network models for classifying bacteria from mass spectra

Temperature constrained cascade correlation networks (TCCCNs) are computational neural networks that configure their own architecture, train rapidly, and give reproducible prediction results. TCCCN classification models were built using the Latin-partition method for five classes of pathogenic bacteria. Neural networks are problematic in that the relationships among the inputs (i.e., mass spectra) and the outputs (i.e., the bacterial identities) are not apparent. In this study, neural network models were constructed that successfully classified the targeted bacteria and the classification model was validated using sensitivity and target transformation factor analysis (TTFA). Without validation of the classification model, it is impossible to ascertain whether the bacteria are classified by peaks in the mass spectrum that have no causal relationships with the bacteria, but instead randomly correlate with the bacterial classes. Multiple single output network models did not offer any benefits when compared to single network models that had multiple outputs. A multiple output TCCCN model achieved classification accuracies of 96 +/- 2% and exhibited improved performance over multiple single output TCCCN models. Chemical ionization mass spectra were obtained from in situ thermal hydrolysis methylation of freeze-dried bacteria. Mass spectral peaks that pertain to the neural network classification model of the pathogenic bacterial classes were obtained by sensitivity analysis. A significant number of mass spectral peaks that had high sensitivity corresponded to known biomarkers, which is the first time that the significant peaks used by a neural network model to classify mass spectra have been divulged. Furthermore, TTFA furnishes a useful visual target as to which peaks in the mass spectrum correlate with the bacterial identities.

Recognition of environmental and genetic effects on barley phenolic fingerprints by neural networks

Through computational analysis of high-performance liquid chromatography (HPLC) traces we find correlations between secondary metabolites and growth conditions of six varieties of barley. Using artificial neural networks, it was possible to classify chromatograms for which the varieties were fertilized by nitrogen and treated by fungicide. For each variety of barley we could also differentiate it from the others. Surprisingly, all these classification tasks could be solved successfully by a simple network with no hidden units. When adding to the methodology pruning of the network weights, we were able to reduce the set of peaks in the chromatograms and obtain a necessary subset from which the growth conditions and differentiation may be decided. In some instances, more complex networks with hidden units could lead to a further reduction of the number of peaks used. In most cases, far more than half of the peaks are redundant. We find that it requires fewer information-rich peaks to perform the variety differentiation tasks than to recognize any of the growth conditions. Analysis of the network weights reveals correlations between weighted combinations of peaks.

Efficient improvement of silage additives by using genetic algorithms

The enormous variety of substances which may be added to forage in order to manipulate and improve the ensilage process presents an empirical, combinatorial optimization problem of great complexity. To investigate the utility of genetic algorithms for designing effective silage additive combinations, a series of small-scale proof of principle silage experiments were performed with fresh ryegrass. Having established that significant biochemical changes occur over an ensilage period as short as 2 days, we performed a series of experiments in which we used 50 silage additive combinations (prepared by using eight bacterial and other additives, each of which was added at six different levels, including zero [i.e. , no additive]). The decrease in pH, the increase in lactate concentration, and the free amino acid concentration were measured after 2 days and used to calculate a "fitness" value that indicated the quality of the silage (compared to a control silage made without additives). This analysis also included a "cost" element to account for different total additive levels. In the initial experiment additive levels were selected randomly, but subsequently a genetic algorithm program was used to suggest new additive combinations based on the fitness values determined in the preceding experiments. The result was very efficient selection for silages in which large decreases in pH and high levels of lactate occurred along with low levels of free amino acids. During the series of five experiments, each of which comprised 50 treatments, there was a steady increase in the amount of lactate that accumulated; the best treatment combination was that used in the last experiment, which produced 4.6 times more lactate than the untreated silage. The additive combinations that were found to yield the highest fitness values in the final (fifth) experiment were assessed to determine a range of biochemical and microbiological quality parameters during full-term silage fermentation. We found that these combinations compared favorably both with uninoculated silage and with a commercial silage additive. The evolutionary computing methods described here are a convenient and efficient approach for designing silage additives.