Partial Least Squares Discriminant Analysis Algorithm Research Articles

Diagnostic strategy for malignant and benign thyroid nodules smaller than 10 mm based on surface-enhanced Raman spectroscopy and machine learning

The diagnostic rate of thyroid nodules has increased considerably in recent years. Malignant nodules can reduce the quality of and even endanger the lives of patients. Fine needle aspiration (FNA) with cytological diagnosis is the most common modality for diagnosing malignant and benign nodules. However, a certain percentage of nodules still cannot be diagnosed definitively, especially when they are less than 10 mm in diameter. Surface-enhanced Raman spectroscopy (SERS) is a molecule-specific analysis method suitable for tumor diagnosis. In this study, the SERS technique was used to analyze FNA samples of thyroid nodules smaller than 10 mm and combined with multiple machine learning algorithms (principal component analysis-linear discriminant analysis, partial least squares discriminant analysis (PLS-DA), and support vector machines) to develop a novel and precise diagnosis model for malignant and benign thyroid nodules. The results showed that the hyphenated method of SERS and the PLS-DA algorithm efficiently diagnosed malignant and benign thyroid nodules, with an area under the curve (AUC) of 97.479% and accuracies of 95.59% and 85.58% in the training and cross-validation sets, respectively. Moreover, the classification model outperformed cytology in diagnosing FNA samples from microscopic thyroid cancers. This study demonstrates that a novel diagnostic strategy based on SERS and machine learning can constitute a complementary diagnosis method for nodules with unknown FNA cytological findings. Furthermore, this strategy can improve the diagnostic accuracy of thyroid nodules smaller than 10 mm, achieve an early and exact diagnosis of microscopic thyroid cancer, and prevent misdiagnoses, underdiagnoses, and overtreatment of thyroid nodules.

Comparing Machine Learning and PLSDA Algorithms for Durian Pulp Classification Using Inline NIR Spectra.

The aim of this study was to evaluate and compare the performance of multivariate classification algorithms, specifically Partial Least Squares Discriminant Analysis (PLS-DA) and machine learning algorithms, in the classification of Monthong durian pulp based on its dry matter content (DMC) and soluble solid content (SSC), using the inline acquisition of near-infrared (NIR) spectra. A total of 415 durian pulp samples were collected and analyzed. Raw spectra were preprocessed using five different combinations of spectral preprocessing techniques: Moving Average with Standard Normal Variate (MA+SNV), Savitzky-Golay Smoothing with Standard Normal Variate (SG+SNV), Mean Normalization (SG+MN), Baseline Correction (SG+BC), and Multiplicative Scatter Correction (SG+MSC). The results revealed that the SG+SNV preprocessing technique produced the best performance with both the PLS-DA and machine learning algorithms. The optimized wide neural network algorithm of machine learning achieved the highest overall classification accuracy of 85.3%, outperforming the PLS-DA model, with overall classification accuracy of 81.4%. Additionally, evaluation metrics such as recall, precision, specificity, F1-score, AUC ROC, and kappa were calculated and compared between the two models. The findings of this study demonstrate the potential of machine learning algorithms to provide similar or better performance compared to PLS-DA in classifying Monthong durian pulp based on DMC and SSC using NIR spectroscopy, and they can be applied in the quality control and management of durian pulp production and storage.

Reliable classification of nutmeg fruits from some geographical origins using SWNIR spectroscopy associated with PLS-DA and SVM methods: Case Study in Aceh Province, Indonesia

Essential oils of nutmeg (Myristica fragrans) can have different qualities due to the soil and industrial process, as Indonesia’s main nutmeg production areas are enormous, especially in Aceh province. The lack of information on detecting chemical constituents and classifying nutmeg from Aceh province makes the price of nutmeg from Aceh unable to compete. Therefore, this study aims to reliably classify nutmeg fruits of some geographical origins in Aceh Province using shortwave near-infrared (SWNIR) spectroscopy associated with partial least squares discriminant analysis (PLS-DA) and support vector machine (SVM). The SWNIR used in this study has a wavelength of 381 to 1065 nm at a resolution of 3 nm and a diffuse reflectance mode. The fruit comes from four geographical areas of origin in the province of Aceh. A total of forty SWNIR spectral data were further classified using two algorithms, namely PLS-DA and SVM. The results show that SWNIR can correctly classify nutmeg from some sub-districts in Aceh province with the help of the PLS-DA and SVM algorithms. From this study, the following SVM algorithm is recommended to be used to classify nutmeg from the province of Aceh with an outstanding level of precision.

Classification and determination of sulfur content in crude oil samples by infrared spectrometry

Determining and classifying the sulfur content of crude oil has long been of great importance because of its adverse economic and environmental effects. In this study, the total sulfur concentration in crude oil samples was determined and classified using attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy and chemometric methods. The methods designed for the analysis of crude oils are rapid, economical and non-destructive in the production process of the petroleum industry. Two sets of 70 and 31 samples in regression models were considered for the calibration and prediction sets, respectively. The calibration models were developed using the partial least squares regression model (PLS-R) and support vector machine regression model (SVM-R). Different pre-processing methods were also evaluated for the development of models. The preprocessing methods based on baseline correction, standard normal variate (SNV) and the auto scale were selected for regression and classification models. The use of SVM-R as a non-linear regression provided a model with significantly better root mean square error of prediction (RMSEP) values than the PLS-R model as a linear model. The ATR-FTIR spectral data were also applied by supervised classification method using the partial least squares-discriminant analysis (PLS-DA) and support vector machine-discriminant analysis (SVM-DA) for classifying crude oils based on sulfur content. The samples were classified into two classes according to the sulfur content into sweet and sour crude oil. The result of the classification found an accuracy of 96% and a classification error of 0.0384 for the prediction set in the PLS-DA algorithm. The results indicated that ATR-FTIR spectroscopy associated with multivariate calibration and classification models is a rapid and reliable approach for parallel quantification and qualification of the sulfur content present in crude oils.

Evaluation of FT-IR spectroscopy combined with SIMCA and PLS‑DA for detection of adulterants in pistachio butter

This work scrutinized the adulteration of pistachio butter with three potential edible oils using Fourier transform infrared spectroscopy (FT-IR) and multivariate classification methods. Each of the classes, including non-adulterated samples and adulterated samples consisting of pistachio butter mixed with various concentrations of peanut oil, corn oil and sunflower oil, were classified. For this purpose, multivariate methods, including soft independent modeling of class analogy (SIMCA) and partial least squares discriminant analysis (PLS-DA), were applied to classify the FTIR data. After evaluating the model on unknown samples, the results indicated that PLS-DA was better than the SIMCA model. The classification efficiency of 98% was obtained using the PLS-DA algorithm compared to the SIMCA model with 91% efficiency for prediction. According to the results FTIR spectroscopy, accompanied by multivariate classification methods, can be used as a rapid and reliable method for classifying and predicting adulteration in pistachio butter with edible oils.

Rapid detection of fumonisin B1 and B2 in ground corn samples using smartphone-controlled portable near-infrared spectrometry and chemometrics

A portable near-infrared (NIR) spectrometer coupled with chemometrics for the detection of fumonisin B1 and B2 (FBs) in ground corn samples was proposed in the present work. A total of 173 corn samples were collected, and their FB contents were determined by HPLC–MS/MS. Partial least squares (PLS), support vector machine (SVM) and local PLS based on global PLS score (LPLS-S) algorithms were employed to construct quantitative models. The performance of the SVM and LPLS-S was better than that of PLS, and the LPLS-S presented the lowest RMSEP (12.08 mg/kg) and the highest RPD (3.44). Partial least squares-discriminant analysis (PLS-DA) and support vector machine-discriminant analysis (SVM-DA) were used to classify corn samples according to the maximum residue limit (MRL) of FBs, and the discriminant accuracy of both the PLS-DA and SVM-DA algorithms was above 86.0%. Thus, the present study provided a rapid method for monitoring FB contamination in corn samples.

Differentiation of Organic Cocoa Beans and Conventional Ones by Using Handheld NIR Spectroscopy and Multivariate Classification Techniques.

The global market for organic cocoa beans continues to show sturdy growth. A low-cost handheld NIR spectrometer (900-1700 nm) combined with multivariate classification algorithms was used for rapid differentiation analysis of organic cocoa beans' integrity. In this research, organic and conventionally cultivated cocoa beans were collected from different locations in Ghana and scanned nondestructively with a handheld spectrometer. Different preprocessing treatments were employed. Principal component analysis (PCA) and classification analysis, RF (random forest), KNN (K-nearest neighbours), LDA (linear discriminant analysis), and PLS-DA (partial least squares-discriminant analysis) were performed comparatively to build classification models. The performance of the models was evaluated by accuracy, specificity, sensitivity, and efficiency. Second derivative preprocessing together with PLS-DA algorithm was superior to the rest of the algorithms with a classification accuracy of 100.00% in both the calibration set and prediction set. Second derivative algorithm was found to be the best preprocessing tool. The identification rates for the calibration set and prediction set were 96.15% and 98.08%, respectively, for RF, 91.35% and 92.31% for KNN, and 90.38% and 98.08% for LDA. Generally, the results showed that a handheld NIR spectrometer coupled with an appropriate multivariate algorithm could be used in situ for the differentiation of organic cocoa beans from conventional ones to ensure food integrity along the cocoa bean value chain.

Detection of Aflatoxin B1 in Peanut Oil Using Attenuated Total Reflection Fourier Transform Infrared Spectroscopy Combined with Partial Least Squares Discriminant Analysis and Support Vector Machine Models

This study was conducted to establish a rapid and accurate method for identifying aflatoxin contamination in peanut oil. Attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy combined with either partial least squares discriminant analysis (PLS-DA) or a support vector machine (SVM) algorithm were used to construct discriminative models for distinguishing between uncontaminated and aflatoxin-contaminated peanut oil. Peanut oil samples containing various concentrations of aflatoxin B1 were examined with an ATR-FTIR spectrometer. Preprocessed spectral data were input to PLS-DA and SVM algorithms to construct discriminative models for aflatoxin contamination in peanut oil. SVM penalty and kernel function parameters were optimized using grid search, a genetic algorithm, and particle swarm optimization. The PLS-DA model established using spectral data had an accuracy of 94.64% and better discrimination than did models established based on preprocessed data. The SVM model established after data normalization and grid search optimization with a penalty parameter of 16 and a kernel function parameter of 0.0359 had the best discrimination, with 98.2143% accuracy. The discriminative models for aflatoxin contamination in peanut oil established by combining ATR-FTIR spectral data and nonlinear SVM algorithm were superior to the linear PLS-DA models.

Discrimination of “Louros” wood from the Brazilian Amazon by near-infrared spectroscopy and machine learning techniques

The integration of near infrared spectroscopy (NIR) with machine learning techniques can be an adequate method for discrimination of wood species with commercial value. The aim of this study was to discriminate wood samples marketed as “Louros” from the Brazilian Amazon based on near-infrared spectroscopy and machine learning techniques. Samples of louro vermelho, louro branco, louro pimenta, louro preto, louro rosa, itauba, itauba amarela and preciosa were collected by members of two extractivist communities, Paraiso and Arimum, located in the “Green Forever” Extractivist Reserve in Para state. Near-infrared spectra were obtained in the range 4000–10,000 $$\hbox {cm}^{-1}$$ , with resolution of $$4 \hbox { cm}^{-1}$$ , directly from sample surfaces oriented in the three anatomical sections: transverse, radial and tangential. This work tests three machine learning approaches—namely support vector machine (SVM), partial least squares-discriminant analysis (PLS-DA), and k-Nearest Neighbors (k-NN). The repeated k-fold cross validation method based on stratification and blocking was used to estimate the performance of the machine learning models. To build learning models, based on near infrared spectra, two situations were considered: (1) applying spectra from all wood sections and (2) using only spectra from one wood section. In general, mean spectra of “Louros” samples were similar. In all tests, models built with PLS-DA algorithm had accuracy and F1-Score superior to 97%. When analyzing PLS-DA applying spectra from only one wood section, tangential section had results slightly superior. Discriminative patterns can be obtained by near infrared spectra independent of anatomical section. The integration from NIR and PLS-DA was an adequate approach to recognize wood from “Louros” group.

Estimation of tea quality grade using statistical identification of key variables

The uncertainty in tea classification affects the market presence of tea and damages the related economic interests. The quick and accurate identification of tea quality grades has a significant impact on the profitability of the tea market as the prices of different grades of tea quality vary greatly. In this research, 19 chemical substances that affect the quality of Huangshan Maofeng tea were detected using stoichiometry. A model-based scheme comprising the use of the stepwise regression method (SRM) was established to estimate tea quality grades. The rationale of the filtering of sparse variables in SRM is to put the elements through the preset F-statistic test to determine the selection of variables. The results of the SRM are then compared with those of elastic net and the partial least squares discriminant analysis (PLS-DA) to demonstrate the effectiveness of the proposed scheme. Furthermore, in order to verify the stability of the model, Monte Carlo experiments were conducted on the constructed models. The predictive accuracy of the SRM, PLS-DA, and elastic net algorithms were 68.75%, 75.86%, and 71.88%, respectively. The radar diagram, which is drawn according to the sparse coefficient vector obtained using SRM, illustrates that the proposed scheme can overcome the correlation between all the detection variables. It is concluded that SRM achieves the highest prediction accuracy with the least number of features, thereby simplifying the process of chemical detection, and provides a new effective scheme for batch tea-quality-grade estimation.

Non-parametric partial least squares–discriminant analysis model based on sum of ranking difference algorithm for tea grade identification using electronic tongue data

Identifying tea grades is crucial to providing consumers with tea and ensuring consumer rights. Partial least squares–discriminant analysis (PLS-DA) is a simple and traditional classification algorithm in analyzing e-tongue data. However, the number of latent variables (LVs) in a PLS-DA model needs to be determined, and cross-validation is the most common way to identify the optimal latent variables. To overcome this obstacle, sum of ranking difference (SRD) algorithm was applied to create a non-parametric PLS-DA-SRD model. The performance of PLS-DA and PLS-DA-SRD models were then compared, and significant improvement in term of accuracy, sensitivity, and specificity was obtained when SRD was combined with PLS-DA algorithm. Moreover, no training phase was needed to identify the optimal LVs for PLS-DA, making the calculation of classification rapid and concise. The PLS-DA-SRD method demonstrated its efficiency and capability by successfully identifying the tea sample grade.

Rapid determination and classification of crude oils by ATR-FTIR spectroscopy and chemometric methods.

Classification based on °API gravity is very important to estimate the parameters related to the extraction, purification, toxicity, and pricing of crude oils. Spectroscopy methods show some advantages over ASTM and API methods for crude oil analysis. The attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy coupled with chemometric methods has been applied as a quick and non-destructive method for crude oil analysis. In this work, a new analytical method using ATR-FTIR spectroscopy associated with chemometric methods were proposed for adressing regression and classification tasks for crude oils analysis based on °API gravity values. The designed methods are rapid, economic, and nondestructive ways in production process of oil industry. The spectral data were used for estimation of °API gravity using two approaches according to PLS-R and SVM-R algorithm, separately. The ATR-FTIR spectral data were also analyzed by classification method using the partial least squares-discriminant analysis (PLS-DA) for crude oil classification. The samples were classified into three classes based on their °API gravity values. The SVM-R model showed better results than PLS-R for °API gravity values using the F-test at 95% of confidence. The result of classification, showed about 100% accuracy and a zero classification error for calibration and prediction samples in PLS-DA algorithm.

Development of a classification algorithm for efficient handling of multiple classes in sorting systems based on hyperspectral imaging

When dealing with practical applications of hyperspectral imaging, the development of efficient, fast and flexible classification algorithms is of the utmost importance. Indeed, the optimal classification method should be able, in a reasonable time, to maximise the separation between the classes of interest and, at the same time, to correctly reject possible outlier samples. To this aim, a new extension of Partial Least Squares Discriminant Analysis (PLS-DA), namely Soft PLS-DA, has been implemented. The basic engine of Soft PLS-DA is the same as PLS-DA, but class assignment is subjected to some additional criteria which allow samples not belonging to the target classes to be identified and rejected. The proposed approach was tested on a real case study of plastic waste sorting based on near infrared hyperspectral imaging. Household plastic waste objects made of the six recyclable plastic polymers commonly used for packaging were collected and imaged using a hyperspectral camera mounted on an industrial sorting system. In addition, paper and not recyclable plastics were also considered as potential foreign materials that are commonly found in plastic waste. For classification purposes, the Soft PLS-DA algorithm was integrated into a hierarchical classification tree for the discrimination of the different plastic polymers. Furthermore, Soft PLS-DA was also coupled with sparse-based variable selection to identify the relevant variables involved in the classification and to speed up the sorting process. The tree- structured classification model was successfully validated both on a test set of representative spectra of each material for a quantitative evaluation, and at the pixel level on a set of hyperspectral images for a qualitative assessment.

Fast discrimination of the geographical origins of notoginseng by near-infrared spectroscopy and chemometrics

Notoginseng is a type of highly valued Traditional Chinese medicine (TCM) due to its hemostatic and cardiovascular functions. Notoginseng of Yunnan in China usually commands a premium price and is often the subject of fraudulent practices. The feasibility of combining near-infrared (NIR) spectroscopy with chemometrics was investigated to discriminate notoginseng of different geographical origins. A total of 250 samples of four different provinces in China were collected and divided equally into the training and test sets. Principal component analysis (PCA) was used for observing possible trend of grouping. Two chemometric algorithms including partial least squares-discriminant analysis (PLSDA) and soft independent modeling of class analogy (SIMCA) were used to construct the discriminant models. Standard normal variate (SNV) and first derivative were used for pre-processing spectra. On the independent test set, the PLSDA model outperforms the SIMCA model. When combining both pre-processing methods, the constructed PLSDA model achieved 100% sensitivity and 100% specificity on both the training set and the test set. It indicates that SNV+first derivative pre-processing and PLSDA algorithm can serve as the potential tool of fast discriminating the geographical origins of notoginseng.

Mesoporosity based classification of ZSM-5 nano catalysts using DRIFT spectroscopy and chemometrics.

DRIFT spectra were used for classification of ZSM-5 catalysts according to their mesopore volumes. The spectra were pretreated by Savitzky-Golay smoothing and standard normal variate (SNV) algorithms prior to outlier detection by Hotelling T2 statistic technique. Supervised classification was applied to the spectra using partial least squares-discriminant analysis (PLS-DA) and soft independent modelling of class analogies (SIMCA) algorithms. The samples were classified into three classes related to their mesopore volumes by the proposed method and the results were in accordance with N2 physisorption textural analysis using Brunauer-Emmett-Teller (BET) model. The confusion matrix and classification efficiency parameters including sensitivity, specificity, accuracy and precision were calculated. Classification accuracy of 96% and error rate of 2% was obtained using PLS-DA algorithm while SIMCA algorithm by providing 100% classification accuracy and zero error rate proved better performance in classification of ZSM-5 catalysts.

Real-Time Monitoring of Organic Carrot (var. Romance) During Hot-Air Drying Using Near-Infrared Spectroscopy

The worldwide consumption of dried carrot (Daucus carota L.) is on a growing trend. Conventional methods for drying carrots include hot-water blanching followed by hot-air drying, which is usually uncontrolled and therefore prone to product quality deterioration. Thus, there is a need for innovative drying systems that yield high-value end products. In this study, the efficacy of NIR spectroscopy for the non-destructive monitoring of physicochemical changes and drying behaviour in organic carrot slices during 8-h hot-air drying at 40 °C was demonstrated using Partial least squares (PLS) regression and PLS discriminant analysis (PLS-DA). The impact of hot-water blanching pre-treatment (at 95 °C for 1.45 min) for enzyme inactivation on performances of both regression and classification models was also evaluated. PLS regression models were successfully developed to monitor changes in water activity (R2 = 0.91–0.96), moisture content (R2 = 0.97–0.98), total carotenoids content (R2 = 0.92–0.96), lightness for unblanched carrots (R2 = 0.80–0.83) and hue angle for blanched samples (R2 = 0.85–0.87). Soluble solids content prediction was poor for both treatments (RMSEP = 3.43–4.40). Classification models were developed to recognise dehydration phases of carrot slices on the basis of their NIR spectral profile using K-means and PLS-DA algorithms in sequence. The performance of each PLS-DA model was defined based on its accuracy, sensitivity and specificity rates. All of the selected models provided from good (> 0.85) to excellent (> 0.95) sensitivity and specificity for the predefined drying phases. Feature selection procedures yielded both regression and classification models with performances very similar to models computed from the full spectrum.

Combining NMR and LC/MS Using Backward Variable Elimination: Metabolomics Analysis of Colorectal Cancer, Polyps, and Healthy Controls.

Both nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) play important roles in metabolomics. The complementary features of NMR and MS make their combination very attractive; however, currently the vast majority of metabolomics studies use either NMR or MS separately, and variable selection that combines NMR and MS for biomarker identification and statistical modeling is still not well developed. In this study focused on methodology, we developed a backward variable elimination partial least-squares discriminant analysis algorithm embedded with Monte Carlo cross validation (MCCV-BVE-PLSDA), to combine NMR and targeted liquid chromatography (LC)/MS data. Using the metabolomics analysis of serum for the detection of colorectal cancer (CRC) and polyps as an example, we demonstrate that variable selection is vitally important in combining NMR and MS data. The combined approach was better than using NMR or LC/MS data alone in providing significantly improved predictive accuracy in all the pairwise comparisons among CRC, polyps, and healthy controls. Using this approach, we selected a subset of metabolites responsible for the improved separation for each pairwise comparison, and we achieved a comprehensive profile of altered metabolite levels, including those in glycolysis, the TCA cycle, amino acid metabolism, and other pathways that were related to CRC and polyps. MCCV-BVE-PLSDA is straightforward, easy to implement, and highly useful for studying the contribution of each individual variable to multivariate statistical models. On the basis of these results, we recommend using an appropriate variable selection step, such as MCCV-BVE-PLSDA, when analyzing data from multiple analytical platforms to obtain improved statistical performance and a more accurate biological interpretation, especially for biomarker discovery. Importantly, the approach described here is relatively universal and can be easily expanded for combination with other analytical technologies.

Rapid elemental analysis and provenance study of Blumea balsamifera DC using laser-induced breakdown spectroscopy.

Laser-induced breakdown spectroscopy (LIBS) was applied to perform a rapid elemental analysis and provenance study of Blumea balsamifera DC. Principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were implemented to exploit the multivariate nature of the LIBS data. Scores and loadings of computed principal components visually illustrated the differing spectral data. The PLS-DA algorithm showed good classification performance. The PLS-DA model using complete spectra as input variables had similar discrimination performance to using selected spectral lines as input variables. The down-selection of spectral lines was specifically focused on the major elements of B. balsamifera samples. Results indicated that LIBS could be used to rapidly analyze elements and to perform provenance study of B. balsamifera.

Determination of Quality Parameters in Moist Wood Chips by Near Infrared Spectroscopy Combining PLS-DA and Support Vector Machines

In this work, studies are described using near infrared spectroscopy and chemometrics for determination of quality parameters in moist wood chips, such as basic density, lignin content, and extractives. A classification model using partial least squares—discriminant analysis (PLS-DA) was developed to determine the level of moisture in the samples. Then, for each moisture level, a calibration model was built for quality parameter predictions using least squares support vector machines (LS-SVM). Multivariate calibration was performed for a data set of 92 wood chip samples. The PLS-DA algorithm was able to classify the samples in the correct class with a small error (lower than 6%) and it was possible to develop a LS-SVM model for quality parameter determination for each class of moisture content with only a few samples and with average relative errors comparable to those obtained by conventional analysis.

Detecting bunch withering disorder in date fruit by near infrared spectroscopy

This study introduces the application of near infrared spectroscopy (NIRs) to detect bunch withering disorder in date fruit (cv. Mazafati). The samples included intact as well as infected date fruits at different stages of ripening. Chemometric evaluation of the data was performed by soft independent modeling of class analogy (SIMCA), partial least squares discriminant analysis (PLS-DA), and principal components analysis combined with artificial neural networks (PCA–ANN). The PLS-DA algorithm was able to provide models with the best classification performance, followed by SIMCA and then PCA–ANN. The maturity stage of samples influenced the performance of the classification methods. The classification accuracy for the late harvested samples was better than those harvested at normal time and the combined data set in all classification analyses. The total accuracies of 82%, 93% and 86%, respectively for normal, late and combined data sets demonstrate that NIRs with PLS-DA has a strong potential to detect the bunch withering disorder in date fruit.