See all my videos at www.tilestats.... 1. Introduction 2. Collinearity (01:43) 3. How PLSR works (03:14) 4. Predict (10:34) 5. Extract components(11:18)
Thank you for the amazing explanation! How would you calcualte the confidence intervals of the parameters in the final model? Or is it only possible for the coefficients of LV1 and LV2?
Fantastic video! Best explanation I’ve seen! What is the benefit of PLS over OLS? Is it simply to improve computation time? Does it tend to generalize better?
Hi thanks for the great content! how do you get the loading for the second latent variable? i assume you can optimize the coefficient for LV2 so that the dot product for LV1 and LV2 is 0? is there another way?
Great video! I read in several papers that significance of variables is calculated through the Variable Importance in Projection metric, which basically shows you how much dependent is explained by the independent. VIP is calculated for every variable in 3 components but i am unsure which to use. Should I use vip values from the first component because that's the one that explains the most variance of the dependent? Thanks!
I would study the importance on each component separately, or use some method that can combine the importance of each variable on all components. There are number of selection methods that have been developed.
In the 2d example, the PCR coefficients are very similar to the PLSR coefficients... I assume this is not always the case? Or is it often that the coefficients turn out to be same/close? If they are practically the same, I don't see the benefits of using PLSR vs. PCR.
Well it depends on the data, but I would expect that the coefficients are quite similar, but small differences may make a big change. A big difference would be seen if the dependent variable has a strong correlation with directions that have a low variance. It is said that the PLSR, usually, requires fewer components (latent variables) than PCR. Also, note that the PLSR can also be used for multivariate regression when we have more than one dependent variable. Another difference is that PLSR is a supervised method whereas PCR is unsupervised because it is only based on PCA, which does not “see” the y-variable.
Very nice explanation! The regression part on the components is only linear ß0+ß1*LV1. Would it be possible to add another term „+ß2LV1^2“ to capture quadric relationships? Since most of the data I‘m working with has a quadric relationship of predictors (intensities) on response (liking scores). With having only 1st degree linear expression this would not capture the mentioned relationship and VIPs precisely. Would this be a option or causes this problems on another side?
It is not necessary but recommended, especially if you have variables on different scales. I discuss this in this video: th-cam.com/video/dh8aTKXPKlU/w-d-xo.html
Thanks for the great video!! I was wondering how you calculate the 95% confidence intervals for the input parameters (Cholesterol and Age) @10:00. I am trying to do this with pls package in R but no luck yet.
You can for example use bootstrap confidence intervals. At the end of this video, I explain how to do that in a regression model: th-cam.com/video/AA7Jtuu9TaE/w-d-xo.html # Suggested R code library(boot) set.seed(10) bs=function(formula, data, indices){ bootstrap=data[indices,] # allows boot to select sample fit = pcr(formula, data=bootstrap,ncomp=1) return(coef(fit,intercept = TRUE)) } results = boot(data=df, statistic=bs, R=1000, formula=SBP ~Chol+Age) boot.ci(results, type="perc", index=3)# Age
Thanks for the explanation! Did I understand correctly that PLSR gives weights from which one could also infer which of the original variables/dimensions were important to the model?
@@tilestats Thanks, I just read about VIP in PLS. It seems this is what I exactly what I need (a method to check whether my model fitted to reasonable variables or mainly to noise).
Thank you! You could utilize the fact that LV1 and LV2 are orthogonal (no correlation) but have a look at, for example, the SIMPLS algorithm for the details.
Hi thanks for the answer. Anyway, you didn't standardize the predictors variables. Is there any considerations to do standardization? (Since you mentioned it in the video about PCR)
It is especially important to standardize the variables if they are on different scales, so that the scale does not impact the weights of the variables. In the example, I did not standardize because that would complicate explaining the basics of the method.
Thank you for this video but I have a question: what if I have 14 dependent variables that needs to be explained via 6 explanatory variables in the time span between 2000 and 2021? It is like to model different economic zones but keeping the set of explanatory variables constant. What kind of model can be appropriate? I know that I can model this one-by-one using OLS or something similar, but I am trying to find the most optimal model. Thank you!
Well you do not need to worry about multicollinearity in PLS. The main thing to look for is outliers that may have a large effect on the results. For prediction, it also makes sense that you have linearity.
That is because you use the rounded values of LV1 that are shown in the last column. Use the equation for LV1 to get more exact values for LV1, and then use regression on these more exact values.
@@tilestats thanks for replying Sir just one thing once we calculate slope and intercept then can we conclude the answer or it is necessary to try example two times
@@tilestats basically what I wanted to say is that you run the example for a value of alpha i.e. 0.1 and then complete for 0.5 Should we try both or just one Time Kindly let me know
I have to say, this explanation is amazing! Thanks!
Great video. This video explained PLS in such a simple way. Hope you keep making more videos like this!
Thank you for this video! I just joined a lab that does mixture modeling and they use this method a lot
Thank you so very much! This is amazingly helpful and clear to understand!!!
Thanks for the simple but useful video!
Very clearly explained. Thank you so much for the teaching.
Amazing explanation. Thanks alot
Best explanation!
Extremely helpful. Thank you!
Thank you for the amazing explanation!
How would you calcualte the confidence intervals of the parameters in the final model? Or is it only possible for the coefficients of LV1 and LV2?
Thank you for your content !
Muy buen video. Tiene conceptos muy claros
Fantastic video! Best explanation I’ve seen! What is the benefit of PLS over OLS? Is it simply to improve computation time? Does it tend to generalize better?
Thank you! The benefits are mainly described in the video before this, which is about PCR:
th-cam.com/video/SWfucxnOF8c/w-d-xo.html
very beautifully explained....kudos
Thank you!
Thanks a lot!
This is awesome! Would you mind providing details on how you found the optimal weights using the SIMPLS algorithm?
I did not implement the algorithm, I simply used the pls package in R.
@@tilestats Okay
I am having trouble in finding the SIMPLS algorithm besides the payed Sijmen de Jong article, do you have any?
Hi thanks for the great content! how do you get the loading for the second latent variable? i assume you can optimize the coefficient for LV2 so that the dot product for LV1 and LV2 is 0? is there another way?
To understand the details, I suggest to check how the NIPALS and the SIMPLS algorithms work
thanks a lot
Great video! I read in several papers that significance of variables is calculated through the Variable Importance in Projection metric, which basically shows you how much dependent is explained by the independent. VIP is calculated for every variable in 3 components but i am unsure which to use. Should I use vip values from the first component because that's the one that explains the most variance of the dependent? Thanks!
I would study the importance on each component separately, or use some method that can combine the importance of each variable on all components. There are number of selection methods that have been developed.
In the 2d example, the PCR coefficients are very similar to the PLSR coefficients... I assume this is not always the case? Or is it often that the coefficients turn out to be same/close? If they are practically the same, I don't see the benefits of using PLSR vs. PCR.
I share your confusion:(
Well it depends on the data, but I would expect that the coefficients are quite similar, but small differences may make a big change. A big difference would be seen if the dependent variable has a strong correlation with directions that have a low variance. It is said that the PLSR, usually, requires fewer components (latent variables) than PCR. Also, note that the PLSR can also be used for multivariate regression when we have more than one dependent variable. Another difference is that PLSR is a supervised method whereas PCR is unsupervised because it is only based on PCA, which does not “see” the y-variable.
Very clear, thank you
Thank you!
very nice video thank you so much! But it only explained how to calculate LV1 by maximizing x and y covariances, how to calculate LV2?
In this example, you can use the fact that LV1 and LV2 are orthogonal, which means that their dot product should be equal to zero.
Excellent!!! Thank you!
Thank you!
Very nice explanation! The regression part on the components is only linear ß0+ß1*LV1. Would it be possible to add another term „+ß2LV1^2“ to capture quadric relationships? Since most of the data I‘m working with has a quadric relationship of predictors (intensities) on response (liking scores). With having only 1st degree linear expression this would not capture the mentioned relationship and VIPs precisely. Would this be a option or causes this problems on another side?
I know that there are nonlinear PLS variants, such as kernel PLS.
In summary, when I want to do dimension reduction + regression, is PLSR always better than PCR?
Generally, yes, but I have had data where PCR has done better, based on the RMSEP, with the same number of components.
Is it not necessary to use normalised data for each independent variable when calculating PC1?
It is not necessary but recommended, especially if you have variables on different scales.
I discuss this in this video:
th-cam.com/video/dh8aTKXPKlU/w-d-xo.html
Thanks for the great video!! I was wondering how you calculate the 95% confidence intervals for the input parameters (Cholesterol and Age) @10:00. I am trying to do this with pls package in R but no luck yet.
You can for example use bootstrap confidence intervals. At the end of this video, I explain how to do that in a regression model:
th-cam.com/video/AA7Jtuu9TaE/w-d-xo.html
# Suggested R code
library(boot)
set.seed(10)
bs=function(formula, data, indices){
bootstrap=data[indices,] # allows boot to select sample
fit = pcr(formula, data=bootstrap,ncomp=1)
return(coef(fit,intercept = TRUE))
}
results = boot(data=df, statistic=bs, R=1000, formula=SBP ~Chol+Age)
boot.ci(results, type="perc", index=3)# Age
@@tilestats Amazing, thank you so much! Just had to switch to using plsr instead of pcr and it worked great. Cheers!
Thanks for the explanation! Did I understand correctly that PLSR gives weights from which one could also infer which of the original variables/dimensions were important to the model?
There are special methods for VIP associated with PLS. I have previously used the plsVarSel package in R.
@@tilestats Thanks, I just read about VIP in PLS. It seems this is what I exactly what I need (a method to check whether my model fitted to reasonable variables or mainly to noise).
Awesome. Very clear explanation. But can you give explanation in determining the alphas(weights) in LV2? Thank you
Thank you! You could utilize the fact that LV1 and LV2 are orthogonal (no correlation) but have a look at, for example, the SIMPLS algorithm for the details.
Hi thanks for the answer. Anyway, you didn't standardize the predictors variables.
Is there any considerations to do standardization? (Since you mentioned it in the video about PCR)
It is especially important to standardize the variables if they are on different scales, so that the scale does not impact the weights of the variables. In the example, I did not standardize because that would complicate explaining the basics of the method.
Awesome. Thanks you very much!
You made that easy!
Great
Thank you for this video but I have a question: what if I have 14 dependent variables that needs to be explained via 6 explanatory variables in the time span between 2000 and 2021? It is like to model different economic zones but keeping the set of explanatory variables constant. What kind of model can be appropriate? I know that I can model this one-by-one using OLS or something similar, but I am trying to find the most optimal model. Thank you!
Have a look at this video to see if that kind of model fits your problem
th-cam.com/video/4bGG02Jsjyc/w-d-xo.html
does PLS follow same assumptions as OLS? Such as linearity, normality etc. ?
Well you do not need to worry about multicollinearity in PLS. The main thing to look for is outliers that may have a large effect on the results. For prediction, it also makes sense that you have linearity.
HOW TO FIND VALUES OF B0 AND B1.
PLEASE LET ME KNOW FORMULAS
because when i am calculating slope my answer is 2.01416 where as yours is 1.958
That is because you use the rounded values of LV1 that are shown in the last column. Use the equation for LV1 to get more exact values for LV1, and then use regression on these more exact values.
@@tilestats thanks for replying
Sir just one thing once we calculate slope and intercept then can we conclude the answer or it is necessary to try example two times
@@tilestats basically what I wanted to say is that you run the example for a value of alpha i.e. 0.1 and then complete for 0.5
Should we try both or just one Time
Kindly let me know
Just one in the case when there is 2 weights. But please use a software to compute pls. I just illustrate with a simple example to explain the method.