Performance of multicomponent self-organizing regression (MCSOR) in QSAR, QSPR, and multivariate calibration: comparison with partial least-squares (PLS) and validation with large external data sets

A novel method for underdetermined regression problems, multicomponent self-organizing regression (MCSOR), has been recently introduced. Here, its performance is compared with partial least-squares (PLS), which is perhaps the most widely adopted multivariate method in chemometrics. A potpourri of models is presented, and MCSOR appears to provide highly predictive models that are comparable with or better than the corresponding PLS models in large internal (leave-one-out, LOO) and pseudo-external (leave-many-out, LMO) validation tests. The "blind" external predictive ability of MCSOR and PLS is demonstrated employing large melting point, factor Xa, log P and log S data sets. In a nutshell, MCSOR is fast, conceptually simple (employing multiple linear regression, MLR, as a statistical tool), and applicable to all kinds of multivariate problems with single Y-variable.     

Determination of polyphenols in oats by near-infrared spectroscopy (NIRS) and two-dimensional correlation spectroscopy

Two-dimensional correlation spectroscopy (2DCOS) and near-infrared spectroscopy (NIRS) were used to determine the polyphenol content in oat grain. A partial least squares (PLS) algorithm was used to perform the calibration. A total of 116 representative oat samples from four locations in China were prepared and the corresponding near-infrared spectra were measured. Two-dimensional correlation spectroscopy was employed to select wavelength bands for the PLS regression model for the polyphenol determination. The number of PLS components and intervals was optimized according to the coefficients of determination (R²) and root mean square error of cross validation (RMSECV) in the calibration set. The performance of the final model was evaluated using the correlation coefficient (R) and the root mean square error of validation (RMSEV) in the prediction set. The results showed the band corresponding to the optimal calibration model was between 1350 and 1848?nm and the optimal spectral preprocessing combination was second derivative with second smoothing. The optimal regression model was obtained with an R² of 0.8954 and an RMSECV of 0.06651 in the calibration set and R of 0.9614 and RMSEV of 0.04573 in the prediction set. These measurements reveal the calibration model had qualified predictive accuracy. The results demonstrated that the 2DCOS with PLS was a simple and rapid method for the quantitative determination of polyphenols in oats.     

Improving the performance of SOMFA by use of standard multivariate methods

Self-Organizing Molecular Field Analysis (SOMFA) comes with a built-in regression methodology, the Self-Organizing Regression (SOR), instead of relying on external methods such as PLS. In this article we present a proof of the equivalence between SOR and SIMPLS with one principal component. Thus, the modest performance of SOMFA on complex datasets can be primarily attributed to the low performance of the SOMFA regression methodology. A multi-component extension of the original SOR methodology (MCSOR) is introduced, and the performances of SOR, MCSOR and SIMPLS are compared using several datasets. The results indicate that in general the performance of SOMFA models is greatly improved if SOR is replaced with a more sophisticated regression method. The results obtained for the Cramer (CBG) dataset further underline the fact that it is a very poor benchmark dataset and should not be used to evaluate the performance of QSAR techniques.     

Combining orthogonal signal correction and wavelet packet transform with partial least squares to analyze overlapping spectra of three kinds of metal ions

A novel method named OSC-WPT-PLS approach based on partial least squares (PLS) regression with orthogonal signal correction (OSC) and wavelet packet transform (WPT) as pre-processed tools was proposed for the simultaneous spectrophotometric determination of Al(III), Mn(II) and Co(II). This method combines the ideas of OSC and WPT with PLS regression for enhancing the ability of extracting characteristic information and the quality of regression. OSC is used to remove information in the response matrix D by subtracting the structured noise that is orthogonal to the concentration matrix C. Wavelet packet transform was applied to perform data compression, to extract relevant information, and to eliminate noise and collinearity. PLS was applied for multivariate calibration and noise reduction by eliminating the less important latent variables. In this case, using trials, the kind of wavelet function, the decomposition level, the number of OSC components and the number of PLS factors for the OSC-WPT-PLS method were selected as Daubechies 4, 3, 2 and 3, respectively. A program (POSCWPTPLS) was designed to perform the simultaneous spectrophotometric determination of Al(III), Mn(II) and Co(II). The relative standard errors of prediction (RSEP) obtained for total elements using OSC-WPT-PLS, WPT-PLS and PLS were compared. Experimental results demonstrated that the OSC-WPT-PLS method had the best performance among the three methods and was successful even when there was severe overlap of spectra.     

A new and efficient variable selection algorithm based on ant colony optimization. Applications to near infrared spectroscopy/partial least-squares analysis

A new variable selection algorithm is described, based on ant colony optimization (ACO). The algorithm aim is to choose, from a large number of available spectral wavelengths, those relevant to the estimation of analyte concentrations or sample properties when spectroscopic analysis is combined with multivariate calibration techniques such as partial least-squares (PLS) regression. The new algorithm employs the concept of cooperative pheromone accumulation, which is typical of ACO selection methods, and optimizes PLS models using a pre-defined number of variables, employing a Monte Carlo approach to discard irrelevant sensors. The performance has been tested on a simulated system, where it shows a significant superiority over other commonly employed selection methods, such as genetic algorithms. Several near infrared spectroscopic experimental data sets have been subjected to the present ACO algorithm, with PLS leading to improved analytical figures of merit upon wavelength selection. The method could be helpful in other chemometric activities such as classification or quantitative structure-activity relationship (QSAR) problems.     

Qsar Models for Predicting the Acute Toxicity of Selected Organic Chemicals with Diverse Structures to Aquatic Non-Vertebrates and Humans

Abstract

The linear and non-linear relationships of acute toxicity (as determined on five aquatic non-vertebrates and humans) to molecular structure have been investigated on 38 structurally-diverse chemicals. The compounds selected are the organic chemicals from the 50 priority chemicals prescribed by the Multicentre Evaluation of In Vitro Cytotoxicity (MEIC) programme. The models used for the evaluations are the best combination of physico-chemical properties that could be obtained so far for each organism, using the partial least squares projection to latent structures (PLS) regression method and backpropagated neural networks (BPN). Non-linear models, whether derived from PLS regression or backpropagated neural networks, appear to be better than linear models for describing the relationship between acute toxicity and molecular structure. BPN models, in turn, outperform non-linear models obtained from PLS regression. The predictive power of BPN models for the crustacean test species are better than the model for humans (based on human lethal concentration). The physico-chemical properties found to be important to predict both human acute toxicity and the toxicity to aquatic non-vertebrates are the n?octanol water partition coefficient (Pow) and heat of formation (HF). Aside from the two former properties, the contribution of parameters that reflect size and electronic properties of the molecule to the model is also high, but the type of physico-chemical properties differs from one model to another. In all of the best BPN models, some of the principal component analysis (PCA) scores of the ¹³C-NMR spectrum, with electron withdrawing/accepting capacity (LUMO, HOMO and IP) are molecular size/volume (VDW or MS1) parameters are relevant. The chemical deviating from the QSAR models include non-pesticides as well as some of the pesticides tested. The latter type of chemical fits in a number of the QSAR models. Outliers for one species may be different from those of other test organisms.     

Performance of (consensus) kNN QSAR for predicting estrogenic activity in a large diverse set of organic compounds

A novel method (in the context of quantitative structure–activity relationship (QSAR)) based on the k nearest neighbour (kNN) principle, has recently been introduced for the derivation of predictive structure–activity relationships. Its performance has been tested for estimating the estrogen binding affinity of a diverse set of 142 organic molecules. Highly predictive models have been obtained. Moreover, it has been demonstrated that consensus-type kNN QSAR models, derived from the arithmetic mean of individual QSAR models were statistically robust and provided more accurate predictions than the great majority of the individual QSAR models. Finally, the consensus QSAR method was tested with 3D QSAR and log?P data from a widely used steroid benchmark data set.     

Variations in the chemical composition within pine (Pinus sylvestris) trunks determined by diffuse reflectance infrared spectroscopy and chemometrics

The feasibility of using DRIFT (diffuse reflectance infrared Fourier transform) spectroscopy combined with a multivariate analysis method (a PLS (projection to latent structures), regression) for predicting the distribution of the main organic constituents (cellulose, glucomannan, xylan, lignin, and extractives) within the Scots pine (Pinus sylvestris) stemwood was examined. PLS calibrations were carried out to establish a mathematical correlation between the data sets of conventional (“wet-chemistry-based”) wood analysis and the DRIFT spectra of the corresponding wood samples. Based on this approach, different surface maps on variations in the content of the main organic constituents within the stemwood matrix were shown.     

Ecotoxicological modelling of cosmetics for aquatic organisms: A QSTR approach

In this study, externally validated quantitative structure–toxicity relationship (QSTR) models were developed for toxicity of cosmetic ingredients on three different ecotoxicologically relevant organisms, namely Pseudokirchneriella subcapitata, Daphnia magna and Pimephales promelas following the OECD guidelines. The final models were developed by partial least squares (PLS) regression technique, which is more robust than multiple linear regression. The obtained model for P. subcapitata shows that molecular size and complexity have significant impacts on the toxicity of cosmetics. In case of P. promelas and D. magna, we found that the largest contribution to the toxicity was shown by hydrophobicity and van der Waals surface area, respectively. All models were validated using both internal and test compounds employing multiple strategies. For each QSTR model, applicability domain studies were also performed using the “Distance to Model in X-space” method. A comparison was made with the ECOSAR predictions in order to prove the good predictive performances of our developed models. Finally, individual models were applied to predict toxicity for an external set of 596 personal care products having no experimental data for at least one of the endpoints, and the compounds were ranked based on a decreasing order of toxicity using a scaling approach.     

Multicomponent Determination of Organophosphorus Pesticides in Grain Samples by Linear Sweep Stripping Voltammetry and Multivariate Calibration

Abstract

Organophosphorus pesticides, such as parathion methyl (PTM), fenitrothion (FT), parathion (PT), and isocarbophos (ICP), have sensitive but overlapped voltammetric peaks with peak potentials ?309, ?364, ?317, and ?480 mV, respectively, in Britton‐Robinson buffer of pH 4.8 by application of linear sweep stripping voltammetry (LSSV). In this work, two multivariate calibration methods, partial least squares (both PLS‐1 and PLS‐2), and principal component regression (PCR), were applied to quantitatively resolve the overlapping voltammogram of the mixtures of these four pesticides. The prediction results obtained from a set of independent test samples showed that PLS‐1 method performed better prediction ability than PLS‐2 and PCR methods. The proposed method was successfully applied to the determination of these four pesticides in grain samples after a pre‐extraction step with a solvent of acetone.