If I had a matrix $A$, what is the meaning of $A^TAx$, given $A^T$ is the transpose of $A$ and $x$ is a vector?
Is it operation on $x$ by the result of the multiplication of two matrices, or is it operation on $x$ first by $A$, then by $A^T$?
Both. Because $(A^TA)x = A^T(Ax)$.
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Both. Because $(A^TA)x = A^T(Ax)$.