Chemometrics for Pattern Recognition

Dioxin screening in fish product by pattern recognition of biomarkers

This paper tries to explore the optimum variable selection strategy for Partial Least Squares (PLS) regression using a model dataset of cytoprotection data. The compounds of the dataset were classified using K‐means clustering technique applied on standardized descriptor matrix and ten combinations of training and test sets were generated based on the obtained clusters. For a particular training set, PLS models were developed with a number of components optimized by leave‐one‐out Q2 and then the developed models were validated (externally) using the test set compounds. For each set, PLS model was initially constructed using all descriptors (variables). The variables having least standardized values of regression coefficients were deleted and the next model was developed with a reduced set of variables. These steps were performed several times until further reduction in number of variables did not improve Q2 value. In each case, statistical parameters like predictive R2 (R2pred), squared correlation coefficient between observed and predicted values with (r2) and without ($\rm{ r_0^{\rm{2}} }$) intercept and Root Mean Square Error of Prediction (RMSEP) were calculated from the test set compounds. In case of all ten sets, Q2 values steadily increase on deletion of variables while R2pred values do not show any specific trend. In no case, the highest Q2 and highest R2pred appear in the same trial, i.e., with the same combinations of variables. This suggests that from the viewpoint of external predictability, choice of variables for PLS based on Q2 value may not be optimum. Moreover, a clear separation of r2 and r02 curves in some sets suggests that such models may not be truly predictive in spite of acceptable R2pred values. Another observation is that coefficient of determination R2 for the training set is more immune to changes on deletion of variables than the validation parameters like Q2 and R2pred. Finally, a new parameter rm2 has been suggested to indicate external predictability of QSAR models.

This article presents a multivariate method of rapidly determining chlopyrifos residue in white radish, based on near-infrared spectroscopy and partial least squares (PLS) regression. Interval PLS (iPLS) was utilized to select the optimum wave number range. The number of PLS components and the number of intervals were optimized according to root mean square error of prediction (RMSEP) and correlation coefficient (R) in prediction set. The result showed that the iPLS model was more reliable than the full model and that near-infrared spectroscopy with iPLS algorithm could be used successfully to analyze chlorpyrifos residue in white radish.

Mobile devices were used to quantify ethanol content—via colorimetry—in cachaca samples to great analytical precision. Ethanol from the spirits reacted with ceric ammonium nitrate (CAN) and nitric acid (NA) to form a red-colored complex. Images from the reaction were taken over time using a smartphone device and processed using software PhotoMetrix Pro® via partial least squares (PLS). A priori, Doehlert matrix was used for optimization of reagents concentration in the complexation reaction, with hierarchical cluster analysis (HCA) as estimation method and a flatbed scanner as measuring tool. When compared with the UV-VIS reference method, results from mobile device imaging presented a root mean square error of prediction (RMSEP) of 0.0677% (v/v). A t test showed there is no significant difference between methods (P < 0.05).

A method of rapidly determining the total polar compounds (TPCs) in frying oils using attenuated total reflectance‐Fourier transform infrared spectroscopy combined with partial least squares (PLS) regression is developed. Oils of various types and geographic origins are used to ensure that the proposed model is robust. The first derivative spectrum is selected as the spectral processing method. The interval PLS, forward interval PLS, and backward interval PLS algorithms are compared in terms of their performance. A correlation coefficient (R2) of 0.9942, a root mean square error of calibration (RMSEC) of 1.1, a root mean square error of prediction (RMSEP) of 2.30, a residual predictive deviation (RPD) of 4.1, and a limit of detection (LOD) of 1.65% are obtained by the fiPLS33 model with fewer latent variables and a lower spectral interval number. In addition, sub‐models using a single type of oil showed higher performance (R2 0.9957–0.9998, RMSEC 0.12–0.92, RMSEP 0.79–1.58, RPD 4.79–9.64, LOD 0.66–1.26%) than the general model. The TPC models developed are accurate, stable, and adaptable, and they can be used to analyze general frying oil samples quickly, regardless of the oil type, and to analyze samples of specific oil types accurately.Practical applications: The content of TPCs is an important indicator of whether the oil has been overused and whether it will be harmful during the frying process. However, traditional chemical methods are time‐consuming, and they have not been used to determine large‐sized samples. In addition, due to a lack of regional optimization, most studies on determining TPCs with FTIR give unsatisfactory model performance. A general TPC model that incorporates several oil types and regional optimization is expected to improve prediction performance. Therefore, the proposed method represents a rapid and accurate tool for measuring TPCs in edible fats and oils.

In this paper, we perform diagnostic pattern recognition on a gene-expression profile data set by using one-class classification. Unlike conventional multiclass classifiers, the one-class (OC) classifier is built on one class only. For optimal performance, it accepts samples coming from the class used for training and rejects all samples from other classes. We evaluate six OC classifiers: the Gaussian model, Parzen windows, support vector data description (with two types of kernels: inner product and Gaussian), nearest neighbor data description, K-means, and PCA on three gene-expression profile data sets, those being an SRBCT data set, a Colon data set, and a Leukemia data set. Providing there is a good splitting of training and test samples and feature selection, most OC classifiers can produce high quality results. Parzen windows and support vector data description are "over-strict" in most cases, while nearest neighbor data description is "over-loose". Other classifiers are intermediate between these two extremes. The main difficulty for the OC classifier is it is difficult to obtain an optimum decision threshold if there are a limited number of training samples.

The purpose of this study was to assess the sustainability of the system through the development of a sustainability index in beef cattle farm in coal post mining land. The study conducted in the coal mining company at Kutai regency. The method used was descriptive through case studies. The technique is done by purposive sampling based on the number of beef cattle reared in the post-mining land. Analysis of beef cattle cultivation used basis multidimensional scaling (MDS) based on the dimensions of the ecological, economic, social and cultural. Each attribute has a score. Furthermore, the score of each attribute dimensional analyzed to determine one or several points that reflect the position of the sustainability of the beef cattle farm systems. Through this MDS sustainability point position can be visualized. Sustainability index has a scale interval of 0 to 100. If the index value of more than 50 categorized sustainable and is less than 50 was not sustainable. The results of ecological dimensions index was 55.56, economic dimension index was 66.67, and sustainable index for social dimension was 72.73. If sustainability index value on the range of 50.00 – 75.00 was on the category of fair sustainable. In order to utilization of coal post mining land can be cultivated by beef cattle.

In modern hot rolling process, operating performance assessment is of great practical significance for guiding the production adjustment for operators. From the perspective of classification, operating performance assessment is a multi-class classification problem. Since support vector data description (SVDD) is a one-class classifier, conventional methods usually construct an independent SVDD model for each class, which ignores the correlation among different classes. The hyperspheres of different classes may not be isolated but overlapped. If a test sample exists in the overlapping region, how to determine which class it belongs to is a knotty problem. Moreover, conventional methods treat all samples equally, but in practice, the sample number of different classes can be imbalanced, which will affect the classification performance of SVDD. In this study, an operating performance assessment method based on weighted multi-sphere SVDD (WMSVDD) is proposed for solving the aforementioned issues. WMSVDD considers the interactions among different classes in a unified way, optimizes the hyperspheres of different classes globally, and introduces a weight coefficient to the model for eliminating the affects of uneven class sizes. Simulation results on a real hot rolling process illustrate the effectiveness of the proposed method comparing to the traditional multi-class SVDD.

Preface. Acknowledgments. 1 Introduction. 1.1 The nature of paleontological data. 1.2 Advantages and pitfalls of paleontological data analysis. 1.3 Software. 2 Basic statistical methods. 2.1 Introduction. 2.2 Statistical distributions. 2.3 Shapiro-Wilk test for normal distribution. 2.4 F test for equality of variances. 2.5 Student's t test and Welch test for equality of means. 2.6 Mann-Whitney U test for equality of medians. 2.7 Kolmogorov-Smirnov test for equality of distributions. 2.8 Permutation and resampling. 2.9 One-way ANOVA. 2.10 Kruskal-Wallis test. 2.11 Linear correlation. 2.12 Non-parametric tests for correlation. 2.13 Linear regression. 2.14 Reduced major axis regression. 2.15 Nonlinear curve fitting. 2.16 Chi-square test. 3 Introduction to multivariate data analysis. 3.1 Approaches to multivariate data analysis. 3.2 Multivariate distributions. 3.3 Parametric multivariate tests. 3.4 Non-parametric multivariate tests. 3.5 Hierarchical cluster analysis. 3.5 K-means cluster analysis. 4 Morphometrics. 4.1 Introduction. 4.2 The allometric equation. 4.3 Principal components analysis (PCA). 4.4 Multivariate allometry. 4.5 Discriminant analysis for two groups. 4.6 Canonical variate analysis (CVA). 4.7 MANOVA. 4.8 Fourier shape analysis. 4.9 Elliptic Fourier analysis. 4.10 Eigenshape analysis. 4.11 Landmarks and size measures. 4.12 Procrustean fitting. 4.13 PCA of landmark data. 4.14 Thin-plate spline deformations. 4.15 Principal and partial warps. 4.16 Relative warps. 4.17 Regression of partial warp scores. 4.18 Disparity measures. 4.19 Point distribution statistics. 4.20 Directional statistics. Case study: The ontogeny of a Silurian trilobite. 5 Phylogenetic analysis. 5.1 Introduction. 5.2 Characters. 5.3 Parsimony analysis. 5.4 Character state reconstruction. 5.5 Evaluation of characters and tree topologies. 5.6 Consensus trees. 5.7 Consistency index. 5.8 Retention index. 5.9 Bootstrapping. 5.10 Bremer support. 5.11 Stratigraphical congruency indices. 5.12 Phylogenetic analysis with Maximum Likelihood. Case study: The systematics of heterosporous ferns. 6 Paleobiogeography and paleoecology. 6.1 Introduction. 6.2 Diversity indices. 6.3 Taxonomic distinctness. 6.4 Comparison of diversity indices. 6.5 Abundance models. 6.6 Rarefaction. 6.7 Diversity curves. 6.8 Size-frequency and survivorship curves. 6.9 Association similarity indices for presence/absence data. 6.10 Association similarity indices for abundance data. 6.11 ANOSIM and NPMANOVA. 6.12 Correspondence analysis. 6.13 Principal Coordinates analysis (PCO). 6.14 Non-metric Multidimensional Scaling (NMDS). 6.15 Seriation. Case study: Ashgill brachiopod paleocommunities from East China. 7 Time series analysis. 7.1 Introduction. 7.2 Spectral analysis. 7.3 Autocorrelation. 7.4 Cross-correlation. 7.5 Wavelet analysis. 7.6 Smoothing and filtering. 7.7 Runs test. Case study: Sepkoski's generic diversity curve for the Phanerozoic. 8 Quantitative biostratigraphy. 8.1 Introduction. 8.2 Parametric confidence intervals on stratigraphic ranges. 8.3 Non-parametric confidence intervals on stratigraphic ranges. 8.4 Graphic correlation. 8.5 Constrained optimisation. 8.6 Ranking and scaling. 8.7 Unitary Associations. 8.8 Biostratigraphy by ordination. 8.9 What is the best method for quantitative biostratigraphy?. Appendix A: Plotting techniques. Appendix B: Mathematical concepts and notation. References. Index

Quaternary surface water temperature estimations: New diatom transfer functions for the Southern Ocean

The bioactive compounds Acetyl-11-keto-β-boswellic acid (AKBA) and 11-keto-β-boswellic acid (KBA), found in the resin of the Boswellia tree, exhibit anti-inflammatory properties, rendering Boswellia resin an intriguing natural medicinal products. However, the content of boswellic acids varies across different Boswellia species and proper knowledge of its species-dependent nature, as well as alternatives to the resource- and time-intensive HPLC analysis, are lacking. Here we present a comprehensive investigation into the boswellic acid content of seven Boswellia species from ten countries and introduce a novel and non-destructive Near-Infrared spectroscopy method for predicting boswellic acid concentrations in solid resin samples. The HPLC-UV reference analysis revealed AKBA concentrations of up to 7.27 % (w/w) with KBA concentrations reaching up to 1.28 % (w/w). Principal Component Analysis of the HPLC and NIR spectroscopy data unveiled species-specific variations, facilitating differentiation based on boswellic acid content, characteristic chromatograms and NIR spectra. Using the HPLC-UV quantification as reference, we developed a Partial Least Squares regression model based on NIR spectra of the resin samples. This model demonstrated highly satisfactory predictive capabilities for AKBA content, achieving a root mean square error of prediction of 0.74 % (w/w) and an R2val of 0.79 in independent test set validation. Although the model was less effective for predicting KBA content, it still offered valuable estimates. The spectroscopic method introduced in this study provides a cost-effective and solvent-free approach for predicting boswellic acid content, demonstrating the potential for application in non-laboratory settings through the use of miniaturized NIR spectrometers. Consequently, this method aligns well with the principles of green chemistry and addresses the growing demand for alternative analytical techniques.

Melon (Cucumis melo L.) is a high-value agricultural commodity known worldwide for its sweet taste and crisp flesh texture, which are important factors for quality and consumer acceptance. Unfortunately, quality testing and determining the optimal harvest time for achieving desired melon characteristics are traditionally performed through destructive methods. The aim of this study was to explore the potential of acoustic and ultrasonic tests for predicting the physicochemical properties of Honey Globe melons (Cucumis melo L. var. inodorus). A total of 100 melon samples were used in this study. For the nondestructive ultrasonic testing, attenuation values served as its variable, whereas in acoustic testing, variables included frequency, magnitude, short-term energy, and zero-moment. Fruit’s flesh firmness and total soluble solids (TSS) as physicochemical quality properties were determined using destructive tests. The calibration phase involved 80 melon samples, employing a K-Fold Cross Validation approach with ten folds, done on Partial Least Square Regression (PLS) modeling. Another 20 melon samples were used for blind testing. Reliability evaluation was done on key metrics, consisting of R2 values, RMSEC (Root Mean Square Error of Calibration), RMSECV (Root Mean Square Error of Cross-Validation), RMSEP (Root Mean Square Error of Prediction), and RPD (Ratio of Performance to Deviation). Analysis results on these metrics collectively support the conclusion that both ultrasonic and acoustic methods exhibit their potential to predict the firmness properties of melon fruits. The best evaluation result that has been conducted for the ultrasonic test uses attenuation, age, and density as predictors to predict fruit firmness, with R2 = 0.763 and RPD = 2.945, while the acoustic test achieved the best result with magnitude used as a predictor to predict fruit firmness with R2 = 0.718 and RPD = 2.230. However, evaluation metrics on the prediction of total soluble solids for both nondestructive tests were still not good enough for application with low R2 and RPD value.

ABSTRACTGastrodia elata is a traditional Chinese medicine with medicinal and edible values. In this paper, two kinds of datasets were acquired: partial spectra (artificially obtained peak segment spectra) and full spectra (4000–400 cm−1). Competitive adaptive reweighted sampling algorithm (CARS) and successive projection algorithm (SPA) were utilized to extract the characteristic variables of the two datasets, and Partial Least Squares Discriminant Analysis (PLS‐DA) models, Support Vector Machines (SVM) models, Random Forests (RF) models, and Residual convolutional neural networks (ResNet) were established. It was found that among the PLS‐DA models whole‐MSC‐CARS‐PLS‐DA was optimal, with a Root Mean Square Error of Prediction (RMSEP) of 0.0658; among the SVM models Partial‐Standard Normal Variable (SNV‐SPA‐SVM was the best, with a kernel parameter of 0.1768 and the lowest number of support vectors; among the RF models Partial‐SNV‐RF is optimal, but not as effective as the first two models. The loss value of the ResNet model built based on effective information is 0.001, and the model building time is short and directly uses the original data. Therefore, the ResNet model based on feature bands is the most suitable for practical application compared with other models.

Indonesian Meteorology, Climatology, and Geophysics Agency (BMKG) uses Numerical Weather Prediction (NWP) for short-term weather forecast but it gives biased result. Therefore, this study implements Univariate Partial Least Square (PLS) as Model Output Statistics (MOS) for temperature and humidity forecast. This study uses the maximum temperature (Tmax), minimum temperature (Tmin), and relative humidity (RH) which are called response variables and NWP as predictor variable. The results show that the performance of the model based on Root Mean Square Error of Prediction (RMSEP) are considered to be good and intermediate. The RMSEP for Tmax in all stations is intermediate (0.9-1.2), Tmin in three stations is good (0.5-0.8), and humidity in three stations is also good (2.6-5.0). The prediction result from the PLS is more accurate than the NWP model and able to correct an 89.94% of the biased NWP for Tmin forecasting.

Quantification of mineral oil contamination in corn oil by Fourier transform near-infrared spectroscopy: Comparison of linear and nonlinear multi-calibration methods