Near infrared reflectance spectroscopy （NIRS）, a non-destructive measurement technique, was combined with partial least squares regression discrimiant analysis （PLS-DA） to discriminate the transgenic （TCTP and mi...Near infrared reflectance spectroscopy （NIRS）, a non-destructive measurement technique, was combined with partial least squares regression discrimiant analysis （PLS-DA） to discriminate the transgenic （TCTP and mi166） and wild type （Zhonghua 11） rice. Furthermore, rice lines transformed with protein gene （OsTCTP） and regulation gene （Osmi166） were also discriminated by the NIRS method. The performances of PLS-DA in spectral ranges of 4 000-8 000 cm-1 and 4 000-10 000 cm-1 were compared to obtain the optimal spectral range. As a result, the transgenic and wild type rice were distinguished from each other in the range of 4 000-10 000 cm-1, and the correct classification rate was 100.0% in the validation test. The transgenic rice TCTP and mi166 were also distinguished from each other in the range of 4 000-10 000 cm-1, and the correct classification rate was also 100.0%. In conclusion, NIRS combined with PLS-DA can be used for the discrimination of transgenic rice.展开更多
With recent advances in biotechnology, genome-wide association study （GWAS） has been widely used to identify genetic variants that underlie human complex diseases and traits. In case-control GWAS, typical statistica...With recent advances in biotechnology, genome-wide association study （GWAS） has been widely used to identify genetic variants that underlie human complex diseases and traits. In case-control GWAS, typical statistical strategy is traditional logistical regression （LR） based on single-locus analysis. However, such a single-locus analysis leads to the well-known multiplicity problem, with a risk of inflating type I error and reducing power. Dimension reduction-based techniques, such as principal component-based logistic regression （PC-LR）, partial least squares-based logistic regression （PLS-LR）, have recently gained much attention in the analysis of high dimensional genomic data. However, the perfor- mance of these methods is still not clear, especially in GWAS. We conducted simulations and real data application to compare the type I error and power of PC-LR, PLS-LR and LR applicable to GWAS within a defined single nucleotide polymorphism （SNP） set region. We found that PC-LR and PLS can reasonably control type I error under null hypothesis. On contrast, LR, which is corrected by Bonferroni method, was more conserved in all simulation settings. In particular, we found that PC-LR and PLS-LR had comparable power and they both outperformed LR, especially when the causal SNP was in high linkage disequilibrium with genotyped ones and with a small effective size in simulation. Based on SNP set analysis, we applied all three methods to analyze non-small cell lung cancer GWAS data.展开更多
In several LUCC studies, statistical methods are being used to analyze land use data. A problem using conventional statistical methods in land use analysis is that these methods assume the data to be statistically ind...In several LUCC studies, statistical methods are being used to analyze land use data. A problem using conventional statistical methods in land use analysis is that these methods assume the data to be statistically independent. But in fact, they have the tendency to be dependent, a phenomenon known as multicollinearity, especially in the cases of few observations. In this paper, a Partial Least-Squares （PLS） regression approach is developed to study relationships between land use and its influencing factors through a case study of the Suzhou-Wuxi-Changzhou region in China. Multicollinearity exists in the dataset and the number of variables is high compared to the number of observations. Four PLS factors are selected through a preliminary analysis. The correlation analyses between land use and influencing factors demonstrate the land use character of rural industrialization and urbanization in the Suzhou-Wuxi-Changzhou region, meanwhile illustrate that the first PLS factor has enough ability to best describe land use patterns quantitatively, and most of the statistical relations derived from it accord with the fact. By the decreasing capacity of the PLS factors, the reliability of model outcome decreases correspondingly.展开更多
Laser-induced breakdown spectroscopy(LIBS)has become a widely used atomic spectroscopic technique for rapid coal analysis.However,the vast amount of spectral information in LIBS contains signal uncertainty,which can a...Laser-induced breakdown spectroscopy(LIBS)has become a widely used atomic spectroscopic technique for rapid coal analysis.However,the vast amount of spectral information in LIBS contains signal uncertainty,which can affect its quantification performance.In this work,we propose a hybrid variable selection method to improve the performance of LIBS quantification.Important variables are first identified using Pearson's correlation coefficient,mutual information,least absolute shrinkage and selection operator(LASSO)and random forest,and then filtered and combined with empirical variables related to fingerprint elements of coal ash content.Subsequently,these variables are fed into a partial least squares regression(PLSR).Additionally,in some models,certain variables unrelated to ash content are removed manually to study the impact of variable deselection on model performance.The proposed hybrid strategy was tested on three LIBS datasets for quantitative analysis of coal ash content and compared with the corresponding data-driven baseline method.It is significantly better than the variable selection only method based on empirical knowledge and in most cases outperforms the baseline method.The results showed that on all three datasets the hybrid strategy for variable selection combining empirical knowledge and data-driven algorithms achieved the lowest root mean square error of prediction(RMSEP)values of 1.605,3.478 and 1.647,respectively,which were significantly lower than those obtained from multiple linear regression using only 12 empirical variables,which are 1.959,3.718 and 2.181,respectively.The LASSO-PLSR model with empirical support and 20 selected variables exhibited a significantly improved performance after variable deselection,with RMSEP values dropping from 1.635,3.962 and 1.647 to 1.483,3.086 and 1.567,respectively.Such results demonstrate that using empirical knowledge as a support for datadriven variable selection can be a viable approach to improve the accuracy and reliability of LIBS quantification.展开更多
Boreal forests play an important role in global environment systems. Understanding boreal forest ecosystem structure and function requires accurate monitoring and estimating of forest canopy and biomass. We used parti...Boreal forests play an important role in global environment systems. Understanding boreal forest ecosystem structure and function requires accurate monitoring and estimating of forest canopy and biomass. We used partial least square regression （PLSR） models to relate forest parameters, i.e. canopy closure density and above ground tree biomass, to Landsat ETM＋ data. The established models were optimized according to the variable importance for projection （VIP） criterion and the bootstrap method, and their performance was compared using several statistical indices. All variables selected by the VIP criterion passed the bootstrap test （p〈0.05）. The simplified models without insignificant variables （VIP 〈1） performed as well as the full model but with less computation time. The relative root mean square error （RMSE%） was 29% for canopy closure density, and 58% for above ground tree biomass. We conclude that PLSR can be an effective method for estimating canopy closure density and above ground biomass.展开更多
With the development of mid-infrared (MIR) photoelectric devices, mid-infrared spectroscopy has become one of the important methods for non-invasive detection of blood glucose. The mid-infrared region (4000 - 400 cm&l...With the development of mid-infrared (MIR) photoelectric devices, mid-infrared spectroscopy has become one of the important methods for non-invasive detection of blood glucose. The mid-infrared region (4000 - 400 cm<sup>-1</sup>) has the well-known fingerprint region (1200 - 800 cm<sup>-1</sup>) of glucose, which has clearer characteristic absorption peaks and better specificity. There is a lot of molecular information about glucose in the MIR. The non-invasive detection of blood glucose by mid-infrared spectroscopy needs to achieve certain accuracy, and the quantitative model is an important factor affecting the accuracy of glucose detection. In this paper, the samples of imitation solution containing only glucose and the samples of imitation mixed solution are taken as the research objects, and the mid-infrared spectral data of the samples are collected. The full spectrum partial least squares Regression (PLSR) model, SNV + Ctr-PLSR model, MSC + Ctr-PLSR model, and convolutional neural networks (CNN) model of 3000 - 900 cm<sup>-1</sup> band were constructed. Full spectrum PLS model and CNN model of 1200 - 900 cm<sup>-1</sup> band were constructed. The experimental results show that the optimal model of the two bands is CNN, then the correlation coefficient of prediction set (Rp) of 3000 - 900 cm<sup>-1</sup> band is 0.95, and the root mean square error of pre-diction set (RMSEP) value is 22.10. The Rp of 1200 - 900 cm<sup>-1</sup> band is 0.95, and the RMSEP value is 22.54. The research results show that CNN is a promising method, which has higher accuracy than PLSR, and is especially suitable for modeling human complex environment. In addition, the study provides a theoretical and practical basis for CNN in feature selection and model interpretation.展开更多
基金supported by the projects under the Innovation Team of the Safety Standards and Testing Technology for Agricultural Products of Zhejiang Province, China (Grant No.2010R50028)the National Key Technologies R&D Program of China during the 11th Five-Year Plan Period (Grant No.2006BAK02A18)
文摘Near infrared reflectance spectroscopy （NIRS）, a non-destructive measurement technique, was combined with partial least squares regression discrimiant analysis （PLS-DA） to discriminate the transgenic （TCTP and mi166） and wild type （Zhonghua 11） rice. Furthermore, rice lines transformed with protein gene （OsTCTP） and regulation gene （Osmi166） were also discriminated by the NIRS method. The performances of PLS-DA in spectral ranges of 4 000-8 000 cm-1 and 4 000-10 000 cm-1 were compared to obtain the optimal spectral range. As a result, the transgenic and wild type rice were distinguished from each other in the range of 4 000-10 000 cm-1, and the correct classification rate was 100.0% in the validation test. The transgenic rice TCTP and mi166 were also distinguished from each other in the range of 4 000-10 000 cm-1, and the correct classification rate was also 100.0%. In conclusion, NIRS combined with PLS-DA can be used for the discrimination of transgenic rice.
基金founded by the National Natural Science Foundation of China(81202283,81473070,81373102 and81202267)Key Grant of Natural Science Foundation of the Jiangsu Higher Education Institutions of China(10KJA330034 and11KJA330001)+1 种基金the Research Fund for the Doctoral Program of Higher Education of China(20113234110002)the Priority Academic Program for the Development of Jiangsu Higher Education Institutions(Public Health and Preventive Medicine)
文摘With recent advances in biotechnology, genome-wide association study （GWAS） has been widely used to identify genetic variants that underlie human complex diseases and traits. In case-control GWAS, typical statistical strategy is traditional logistical regression （LR） based on single-locus analysis. However, such a single-locus analysis leads to the well-known multiplicity problem, with a risk of inflating type I error and reducing power. Dimension reduction-based techniques, such as principal component-based logistic regression （PC-LR）, partial least squares-based logistic regression （PLS-LR）, have recently gained much attention in the analysis of high dimensional genomic data. However, the perfor- mance of these methods is still not clear, especially in GWAS. We conducted simulations and real data application to compare the type I error and power of PC-LR, PLS-LR and LR applicable to GWAS within a defined single nucleotide polymorphism （SNP） set region. We found that PC-LR and PLS can reasonably control type I error under null hypothesis. On contrast, LR, which is corrected by Bonferroni method, was more conserved in all simulation settings. In particular, we found that PC-LR and PLS-LR had comparable power and they both outperformed LR, especially when the causal SNP was in high linkage disequilibrium with genotyped ones and with a small effective size in simulation. Based on SNP set analysis, we applied all three methods to analyze non-small cell lung cancer GWAS data.
基金National Natural Science Foundation of China No.40301038
文摘In several LUCC studies, statistical methods are being used to analyze land use data. A problem using conventional statistical methods in land use analysis is that these methods assume the data to be statistically independent. But in fact, they have the tendency to be dependent, a phenomenon known as multicollinearity, especially in the cases of few observations. In this paper, a Partial Least-Squares （PLS） regression approach is developed to study relationships between land use and its influencing factors through a case study of the Suzhou-Wuxi-Changzhou region in China. Multicollinearity exists in the dataset and the number of variables is high compared to the number of observations. Four PLS factors are selected through a preliminary analysis. The correlation analyses between land use and influencing factors demonstrate the land use character of rural industrialization and urbanization in the Suzhou-Wuxi-Changzhou region, meanwhile illustrate that the first PLS factor has enough ability to best describe land use patterns quantitatively, and most of the statistical relations derived from it accord with the fact. By the decreasing capacity of the PLS factors, the reliability of model outcome decreases correspondingly.
基金financial supports from National Natural Science Foundation of China(No.62205172)Huaneng Group Science and Technology Research Project(No.HNKJ22-H105)Tsinghua University Initiative Scientific Research Program and the International Joint Mission on Climate Change and Carbon Neutrality。
文摘Laser-induced breakdown spectroscopy(LIBS)has become a widely used atomic spectroscopic technique for rapid coal analysis.However,the vast amount of spectral information in LIBS contains signal uncertainty,which can affect its quantification performance.In this work,we propose a hybrid variable selection method to improve the performance of LIBS quantification.Important variables are first identified using Pearson's correlation coefficient,mutual information,least absolute shrinkage and selection operator(LASSO)and random forest,and then filtered and combined with empirical variables related to fingerprint elements of coal ash content.Subsequently,these variables are fed into a partial least squares regression(PLSR).Additionally,in some models,certain variables unrelated to ash content are removed manually to study the impact of variable deselection on model performance.The proposed hybrid strategy was tested on three LIBS datasets for quantitative analysis of coal ash content and compared with the corresponding data-driven baseline method.It is significantly better than the variable selection only method based on empirical knowledge and in most cases outperforms the baseline method.The results showed that on all three datasets the hybrid strategy for variable selection combining empirical knowledge and data-driven algorithms achieved the lowest root mean square error of prediction(RMSEP)values of 1.605,3.478 and 1.647,respectively,which were significantly lower than those obtained from multiple linear regression using only 12 empirical variables,which are 1.959,3.718 and 2.181,respectively.The LASSO-PLSR model with empirical support and 20 selected variables exhibited a significantly improved performance after variable deselection,with RMSEP values dropping from 1.635,3.962 and 1.647 to 1.483,3.086 and 1.567,respectively.Such results demonstrate that using empirical knowledge as a support for datadriven variable selection can be a viable approach to improve the accuracy and reliability of LIBS quantification.
基金supported by the 948 Program of the State Forestry Administration (2009-4-43)the National Natura Science Foundation of China (No.30870420)
文摘Boreal forests play an important role in global environment systems. Understanding boreal forest ecosystem structure and function requires accurate monitoring and estimating of forest canopy and biomass. We used partial least square regression （PLSR） models to relate forest parameters, i.e. canopy closure density and above ground tree biomass, to Landsat ETM＋ data. The established models were optimized according to the variable importance for projection （VIP） criterion and the bootstrap method, and their performance was compared using several statistical indices. All variables selected by the VIP criterion passed the bootstrap test （p〈0.05）. The simplified models without insignificant variables （VIP 〈1） performed as well as the full model but with less computation time. The relative root mean square error （RMSE%） was 29% for canopy closure density, and 58% for above ground tree biomass. We conclude that PLSR can be an effective method for estimating canopy closure density and above ground biomass.
文摘With the development of mid-infrared (MIR) photoelectric devices, mid-infrared spectroscopy has become one of the important methods for non-invasive detection of blood glucose. The mid-infrared region (4000 - 400 cm<sup>-1</sup>) has the well-known fingerprint region (1200 - 800 cm<sup>-1</sup>) of glucose, which has clearer characteristic absorption peaks and better specificity. There is a lot of molecular information about glucose in the MIR. The non-invasive detection of blood glucose by mid-infrared spectroscopy needs to achieve certain accuracy, and the quantitative model is an important factor affecting the accuracy of glucose detection. In this paper, the samples of imitation solution containing only glucose and the samples of imitation mixed solution are taken as the research objects, and the mid-infrared spectral data of the samples are collected. The full spectrum partial least squares Regression (PLSR) model, SNV + Ctr-PLSR model, MSC + Ctr-PLSR model, and convolutional neural networks (CNN) model of 3000 - 900 cm<sup>-1</sup> band were constructed. Full spectrum PLS model and CNN model of 1200 - 900 cm<sup>-1</sup> band were constructed. The experimental results show that the optimal model of the two bands is CNN, then the correlation coefficient of prediction set (Rp) of 3000 - 900 cm<sup>-1</sup> band is 0.95, and the root mean square error of pre-diction set (RMSEP) value is 22.10. The Rp of 1200 - 900 cm<sup>-1</sup> band is 0.95, and the RMSEP value is 22.54. The research results show that CNN is a promising method, which has higher accuracy than PLSR, and is especially suitable for modeling human complex environment. In addition, the study provides a theoretical and practical basis for CNN in feature selection and model interpretation.
