I've found a nice presentation describing PLS1 and PLS2 algorithms (pages 16-19). It's pretty clear but there is a thing confusing me.

For PLS1. Let's look at the algorithm. The first steps are

  • $w = X'y$ (which maximizes $\operatorname{cov}(Xw,y)$)
  • $w = w / ||w||$
  • $t = Xw$
  • $p = X't / t't$

On the one hand one can say $T=XW$ and $WW'=I$, but on the other hand $T=XP$ and $PP'=I$ (because we are searching for a decomposition $X=TP'$ where $PP'=I$, see page 14).

So, my question is, aren't $P$ and $W$ the same matrix? And if so, why does the algorithm need to calculate $p$ as $X't / t't$?

Why not do it this way:

  • $p = X'y$
  • $p = p / ||p||$
  • $t = Xp$

UPDATE After reading provided comments, answers, and links (thanks to @amoeba and @theGD), I get that a strict answer to my question is "No, they are not.". I almost understood why. Actually, I lost my hope to fully understand NIPALS algorthm principle. So, I decided to ask it in a differernt way: What is mathematicial task PLS NIPALS tries to solve?

For example, there is NIPALS for PCA as well. And I don't understand it fully too. But I know that it's just a computational method for solving a mathimaticial task (for one iteration): $$ {\mathbf {t}}^{T}{\mathbf {t}} = {\mathbf {w}}^{T}{\mathbf {X}}^{T}{\mathbf {Xw}} \rightarrow \max, \textrm{ given that } \Vert {\mathbf {w}}\Vert =1 $$ So, what is analogous mathematical task for PLS?

  • 2
    $\begingroup$ No, they are not the same. You can easily verify it using your own favourite programming language: generate random $X$ and $y$ (they can be very small), then carry out first steps of this algorithm: compute vector $w$, then vector $t$, then vector $p$. You will see that $w\ne p$. $\endgroup$ – amoeba says Reinstate Monica Mar 23 '17 at 12:57

The 14th page is not about PLS, it is about PCA since it refers to decomposition of $X$ alone by carrying out singular value decomposition which is an efficient way to obtain eigenvalues($D$) and eigenvectors($V$) of $\operatorname{cov}(X)$). So in PCA case, the orthogonality of $P$ is correct.

In PLS, however, the only property of $X$ loadings is each vector in $P$ matrix has unit length ($||p_i||$ = 1) whereas $W$ is orthogonal. In fact, the addition of $W$ is to ensure the orthagonality of $X$ scores($T$) and it is one of the main differences between PLS NIPALS and PCA NIPALS. Thus, as said in comments, $P$ and $W$ are not the same matrices.

As a small note I prefer SIMPLS algorithm which is faster and it provides a single vector for regression and makes interpretation a lot easier unlike NIPALS with multiple vectors each corresponding to deflated $X$ which is, in my opinion, quite counter-intuitive and hard to interpret.

The properties of PLS factors obtained by NIPALS algorithm can be found in this article: Geladi, Paul, and Bruce R. Kowalski. "Partial least-squares regression: a tutorial." Analytica chimica acta 185 (1986): 1-17.


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