Questions tagged [partial-least-squares]

A class of linear methods for modeling the relationship between two groups of variables, X and Y. Includes PLS regression.

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390 views

What, if any, dissimilarity is preserved in partial least squares (PLS)?

When we perform a principal components analysis (PCA) on a multivariate data set we are interested in finding orthogonal components that explain maximal variance in the data set. We can form a biplot ...
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95 views

Is it possible to combine bayesian SEM with PLS SEM?

I have already read some books about both two structural equation models. It seems both SEMs are suitable to the situation with small observations and large variables. I assume to use combine both ...
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115 views

Partial Least Squares Regression : deflation of the Y matrix

I am digging deep into the PLSR algorithms and while I have found multiple flavours of if (different normalisations, SIMPLS,..), there is always something in the Y deflation that is throwing me off ...
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419 views

PLS using a kernel matrix

I would like to use a kernel matrix generated with a custom kernel function to fit a PLS-DA model (I am thinking of caret's PLS-DA at the moment), with only one binary response variable in the Y block....
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455 views

How to choose between different options in partial least square regression?

There seem to be several methods of performing partial least square regression. For example in pls pacakge in R, following are available: ...
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919 views

Multivariate outlier detection for PLS model

I am working with a PLS model (library pls) in R, where I am developing calibration models for NIRS data. I have been using other commercial software before that allowed me to detect outliers based on ...
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153 views

Define the number of components for PLSR when RMCEP doesn't stabilize

According to pls package, you can define the number of components of plsr using RMCEP. I tried to do the same for the df, using this code ...
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45 views

PLS between error and negative loglikelihood in classification models?

Consider a large but finite output space $\mathcal{Y}$. Let $\Delta$ denote a loss function between $y^*$ and $\hat{y}$, i.e. $\Delta : \mathcal{Y} \times \mathcal{Y} \rightarrow \mathbb{R_{+}}$. One ...
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379 views

How to compute percent of variance explained in X and Y for each component of a PLSR?

I am not a mathematician and my question is probably trivial but I did not manage to find an answer on the web. I need to compute the percent of variance explained (eigenvalues?) in X and Y for each ...
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474 views

How to pre-process data for partial least square PLS regression in R?

I have a data frame that is consisted of 20 observations and 35 variables. I want to prepare the data for partial least square regression PLS in R. Many authors suggest: 1)Check whether the ...
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1answer
33 views

Moderated moderation (3-way interaction) with latent variables

I would appreciate some help in deciding the analysis method for my research. I have 7 variables: one DV, one IV, two moderators, one moderator/moderating moderator plus 2 controls. My overall ...
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38 views

How to interpret output from RMSEP in R

I have a dataset with 15 columns and 500 rows. I have developed a plsr model as "plsr_model" and I have a testing dataset as "train.data". I want to find the Root mean square error of prediction (RMSE)...
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22 views

Different PLS model when using plsr() function in R or Minitab PLS regression menu

I have a PLS model made in R with plsr() function (from package pls); I have chosen the right number of components with cross ...
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17 views

Are there constraints on the ratio of dependent variables to independent variables for PLS regression?

I will begin with a disclaimer that while I understand the general underlying principles behind PLS, my linear algebra background is rather limited. I have trouble with the details of constraints on ...
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26 views

Why is there an inconsistency between PLS projections and energy statistic output?

On R, I use the mixOmics package to run a repeated measures ("multilevel") Partial Least Squares analysis. I'm able to plot the 2-dimensional PLS projections such ...
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55 views

How should predicted probabilities be interpreted in a binary classification model?

I ran a PLS-DA model with 10-fold cross-validation to classify data in 2 groups (using the Caret package in R). The predicted probabilities are close to 0.5 (the highest propbability is just 0.7). The ...
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57 views

meaning of projection subspace in a PLSDA plot

I have a dataset with a handful of predictors and one output variable which is categorical and can only be C or N. I am working ...
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26 views

How is this standard error obtained?

I am working through the exercises in Kuhn and Johnson's "Applied Predictive Modelling" and cannot reproduce one of their results in the exercises. Looking at 4.3 we have ... find the number of ...
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72 views

Is there a theoretical basis for using partial least squares with categorical responses

I am using what is called PLS-DA in JMP to find a model for predicting a categorical (Positive/Negative) response. The documentation says that the responses are simply coded as 0/1, thereby ...
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34 views

Partial Least Square vs Principle Component Regression

Is it the case where PLS, when compared to PCR with all things equal, generally gives lower bias but higher variance when regressed against a response Y, since PLS relates to/makes use of Y but PCR ...
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97 views

PLS (Partial Least Squares) deflation and graphics

I have been working with pls for a little while now. I have a question in terms of the deflation of both the $X$ and $Y$ matrices. In the literature I have found different methods over which deflation ...
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28 views

How to compute/plot the contribution of each original descriptor in a final PLA regression model?

New to scikit-learn. I am using v 20.2. I am developing PLS regression models.I would like to know how important each of the original predictors/descriptors are in predicting the response. The ...
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24 views

Will PLSR work on nonlinear dataset?

Im new to this topic and a bit confused. When I read about PLSR on the web I only see examples where the original plot shows a somewhat linear relationship in the data set, but in my case I have a ...
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70 views

What is the point of using PRESS instead of RMSECV?

What is the point of using predicted residual sum of squares (PRESS) instead of root-mean-squared-error-of-cross-validation(RMSECV)? In many books, especially in the area of chemometrics, the authors ...
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28 views

Partial least square different maximization programs

PLS regression is a regression method based based on latent variables in order to handle collinearity or violation of full rank assumption in linear regression. Latent variables called components are ...
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31 views

Inference using model with low goodness of fit.

Assuming a model is correctly specified, would it be appropriate to draw inferences based on a model with a low Goodness of Fit (~0.15)? Of course, using such a model to make predictions is likely ...
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185 views

Items measured with 5 and 7 point Likert scale in PLS-SEM analysis

Some items in the questionnaire were measured with the 7-point Likert scale and some with the 5-point one. I am doing PLS-SEM analysis of the data in SmartPLS. Are there any additional steps to take ...
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49 views

PLS Structural equation modelling

In PLS structural equation modelling when dealing with the outer model (relationship between latent variable and its items) if there is a variable which does not meet the quality criteria should I ...
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121 views

Partial Least Squares NIPALS Algorithm when Y has more than one column (PLS2)

I wanted to exactly understand how Partial Least Squares Regression works and thus got my hands onto a paper called "A Simple Explanation of Partial Least Squares". After some thinking and consulting ...
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377 views

Partial least squares regression component selection based on Q2

I am working on high dimensional biological data and I am trying to use PLSR to build a model and identify important variables. The dataset has 427 X variables and 1 response variable for 16 ...
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162 views

Does PLS have a corresponding objective function to PCA's?

Paraphrased from Understanding Machine Learning by Shalev-Shwartz: Let $\mathbf{x}_1, \dots, \mathbf{x}_m \in \mathbb{R}^d$, $\mathbf{W}$ an $n \times d$ matrix with real entries, and $\mathbf{U}$...
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817 views

Interpreting a PLS-DA model with Caret

I'm train a Partial Least Squares Discrimination Analysis with caret package. My dataset dimensions are 80K rows, 50 continuous explanatory variables, and one ...
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1answer
55 views

Fundamental query on mediation and indirect effect

Am trying to understand the basics of mediation and am confused between an actual indirect effect and mediation effect. My query is what if A causes B and B causes C, but there is no direct effect ...
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314 views

PLS regression - My X and Y blocks are obtained at different sampling frequencies. Should I trim the X block or smooth and interpolate the Y block?

PLS (partial least squares) regression is the tool that I'm using to express each Y block variable as a linear function of the X block variables. The overall goal of this project is to create a model ...
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1answer
89 views

Eliminating latent variables in structural model using PLS-SEM

I have a very simple structural model, with 11 exogenous constructs predicting 1 endogenous latent variable. I examined my structural model with PLS, and I got very poor results - none of the 11 paths ...
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143 views

Can model variance be concluded using boxplot of error estimates?

I have three statistical models, partial least square(PLS), random forest (RF) and support vector machine (SMV). I have divided my three datasets (e.g. leaf, canopy, shrub) randomly 1000 times into ...
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448 views

is Q2 a good parameter to evaluate PLS regression?

I have built a PLS model on a training set and I have tried to predict a validation set. From the correlation between real values and predicted, the PLS model seems to have some predictive ...
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319 views

Explanation of output in OPLS-DA

I am dealing with metabolomics data, and using OPLS-DA to determine if 2+ groups cluster. I've used the ropls package in R to create the following image. This is ...
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83 views

How does R handle Observation fewer than Variable problem in PCA

Got a dataset of 63 observations of 900 variables. The Variable data is arranged as 63x900. I'm trying to build a prediction model based on this dataset. Three methods have been tried: PCR, PLSR, and ...
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117 views

cutoff for selected variables using spls package

I used the spls R-package to select relevant variables from a list of 1600 continuous predictor variables (genes). The response variable is expression of another ...
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1answer
178 views

Validation of modeling step of PLS

How can i validate the modeling step of my dataset with PLS regression? In other words can i calculate an X_hat and Y_hat using the modeling factors (T,P,Q,U,B,W) and compare it with the original X ...
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574 views

Converting PLS-DA to O-PLS-DA for feature selection

I have a very big data which have 210k variables and 90 samples. Among the supervised classification methods, partial least squares discriminant analysis(PLS-DA) provided me the best separation. ...
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394 views

Contradictory p-value and confidence interval in permutation test

I am using the MICOM procedure to test for measurement invariance among groups in PLS SEM modelling [1]. This procedure consists of 3 steps, where in step 3 one tests for equality of composite means ...
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365 views

If there is only one variable in Y, does the first PLS component go in the exact same direction?

In partial least squares (PLS), I have multiple variables in X and only one variable in Y. If I only choose one PLS component to use for the PLS model, can I assume that this PLS component is in the ...
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81 views

Diagnostics for PLSR?

I am trying to apply sPLS2 type pf regression my matrix y has a set of clinical variables and matrix X has some gene data. I am using mixOmics package in R. My question is how to decide that my ...
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23 views

Partial Least Squares for validating a Framework

I understand that PLS can indicate the cronbach's alpha between two variables in a Framework. (i) For instance, can PLS tell us, based on the direction of the arrows, if there is causation (i.e. one ...
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130 views

Neural network partial least square

I'm trying to use neural network partial least square proposed by Qin and McAvoy. The whole network trained based on the scaled values. I want to know how can I rewrite the general neural network ...
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174 views

Best method of analysis for negatively skewed longitudinal environmental data?

I have a dataset composed of a dependent variable (species percent cover) and a range of abiotic variables (salinity, temperature, pH, water movement etc). It is a longitudinal study, in which species ...
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95 views

Individual factor significance in multilevel sPLS-DA

I recently was asked by reviewers to "include p-values" with my multilevel sparse partial least squares analysis. In brief, I have a nested design with two factors, say treatment and sampling region. ...
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123 views

Include confounder into partial least squares regression

I am wondering, when using partial least squares regression to investigate a research question, there is predictor component (T) and response component (U), if I want to adjust for confounders (C), do ...