Predictive Modeling of Lignin Content for the Screening of Suitable Poplar Genotypes Based on Fourier Transform-Raman Spectrometry

Transfer learning improves predictions in lignin content of Chinese fir based on Raman spectra

Lignin in biomass plays significant role in substitution of synthetic polymer and reduction of energy expenditure, and the lignin content was usually determined by wet chemical methods. However, the methods' heavy workload, low efficiency, huge consumption of chemicals and use of toxic reagents render them unsuitable for sustainable development and environmental protection. Chinese fir, a prevalent angiosperm tree, holds immense importance for various industries. Since our previous work found that Raman spectroscopy could accurately predict the lignin content in poplar, we propose that the lignin content of Chinese fir can be estimated by similar strategy. The results suggested that the peak at 2895 cm-1 is the optimal choice of internal standard peak and algorithm of XGBoost demonstrates the highest accuracy among all algorithms. Furthermore, transfer learning was successfully introduced to enhance the accuracy and robustness of the model. Ultimately, we report that a machine learning algorithm, combining transfer learning with XGBoost or LightGBM, offers an accurate, high-efficiency and environmental friendly method for predicting the lignin content of Chinese fir using Raman spectra.

Visualization of a Machine Learning Framework toward Highly Sensitive Qualitative Analysis by SERS

Surface-enhanced Raman spectroscopy (SERS), providing near-single-molecule-level fingerprint information, is a powerful tool for the trace analysis of a target in a complicated matrix and is especially facilitated by the development of modern machine learning algorithms. However, both the high demand of mass data and the low interpretability of the mysterious black-box operation significantly limit the well-trained model to real systems in practical applications. Aiming at these two issues, we constructed a novel machine learning algorithm-based framework (Vis-CAD), integrating visual random forest, characteristic amplifier, and data augmentation. The introduction of data augmentation significantly reduced the requirement of mass data, and the visualization of the random forest clearly presented the captured features, by which one was able to determine the reliability of the algorithm. Taking the trace analysis of individual polycyclic aromatic hydrocarbons in a mixture as an example, a trustworthy accuracy no less than 99% was realized under the optimized condition. The visualization of the algorithm framework distinctly demonstrated that the captured feature was well correlated to the characteristic Raman peaks of each individual. Furthermore, the sensitivity toward the trace individual could be improved by least 1 order of magnitude as compared to that with the naked eye. The proposed algorithm distinguished by the lesser demand of mass data and the visualization of the operation process offers a new way for the indestructible application of machine learning algorithms, which would bring push-to-the-limit sensitivity toward the qualitative and quantitative analysis of trace targets, not only in the field of SERS, but also in the much wider spectroscopy world. It is implemented in the Python programming language and is open-source at https://github.com/3331822w/Vis-CAD.

Quantification of Salicylates and Flavonoids in Poplar Bark and Leaves Based on IR, NIR, and Raman Spectra

Poplar bark and leaves can be an attractive source of salicylates and other biologically active compounds used in medicine. However, the biochemical variability of poplar material requires a standardization prior to processing. The official analytical protocols used in the pharmaceutical industry rely on the extraction of active compounds, which makes their determination long and costly. An analysis of plant materials in their native state can be performed using vibrational spectroscopy. This paper presents for the first time a comparison of diffuse reflectance in the near- and mid-infrared regions, attenuated total reflection, and Raman spectroscopy used for the simultaneous determination of salicylates and flavonoids in poplar bark and leaves. Based on 185 spectra of various poplar species and hybrid powdered samples, partial least squares regression models, characterized by the relative standard errors of prediction in the 4.5-9.9% range for both calibration and validation sets, were developed. These models allow for fast and precise quantification of the studied active compounds in poplar bark and leaves without any chemical sample treatment.

Machine learning prediction of lignin content in poplar with Raman spectroscopy

Based on features extracted from Raman spectra, regularization algorithms, SVR, DT, RF, LightGBM, CatBoost, and XGBoost were used to develop prediction models for lignin content in poplar. Firstly, Raman features extracted from FT-Raman spectra after data processing were used as input of models and determined lignin contents were output. Secondly, grid-search combined with cross-validation was used to adjust the hyper-parameters of models. Finally, the predictive models were built by aforementioned algorithms. The results indicated regularization algorithms, SVR, DT held test R² were >0.80 which means the predictive values from model still deviate from measured ones. Meanwhile, RF, LightGBM, CatBoost, and XGBoost were better than above algorithms, and their test R² were >0.91 which suggesting the predictive values was nearly close to measured ones. Therefore, fast and accurate methods for predicting lignin content were obtained and will be useful for screening suitable lignocellulosic resource with expected lignin content.

Novel strategy for establishment of an FT-Raman spectroscopy based quantitative model for poplar holocellulose content determination

Raman spectroscopy is effective for studying the ultrastructure, lignin content, and cellulose crystallinity of lignocellulosic materials. However, the quantitative analysis of holocellulose in lignocellulosic materials by this technique is challenging. In this study, based on Fourier-transform Raman (FT-Raman) spectroscopy, a novel strategy for building poplar holocellulose content quantitative model was proposed. Different algorithms were applied, including Principal component regression (PCR), partial least square regression (PLSR), ridge regression (RR), lasso regression (LR), and elastic net regression (ENR). Combined with different algorithms, twelve candidates of internal standard were selected. Sixty models combined by five regression algorithms and twelve internal standards were performed by five-fold cross validation. Consequently, the models constructed through RR, LR, and ENR combined with the internal standard of peak intensity of 2945 cm^-1 were credible (R_p > 0.9, RMSE_p < 1.0, and MAE_p < 0.9). Credible models were obtained, indicating the high potential of FT-Raman spectroscopy for predicting the holocellulose content of lignocellulosic materials.

Infrared Spectroscopy and Chemometric Applications for the Qualitative and Quantitative Investigation of Grapevine Organs

The fourth agricultural revolution is leading us into a time of using data science as a tool to implement precision viticulture. Infrared spectroscopy provides the means for rapid and large-scale data collection to achieve this goal. The non-invasive applications of infrared spectroscopy in grapevines are still in its infancy, but recent studies have reported its feasibility. This review examines near infrared and mid infrared spectroscopy for the qualitative and quantitative investigation of intact grapevine organs. Qualitative applications, with the focus on using spectral data for categorization purposes, is discussed. The quantitative applications discussed in this review focuses on the methods associated with carbohydrates, nitrogen, and amino acids, using both invasive and non-invasive means of sample measurement. Few studies have investigated the use of infrared spectroscopy for the direct measurement of intact, fresh, and unfrozen grapevine organs such as berries or leaves, and these studies are examined in depth. The chemometric procedures associated with qualitative and quantitative infrared techniques are discussed, followed by the critical evaluation of the future prospects that could be expected in the field.