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I wonder if there is any inequality (or even equality) relating $Trace(AB (AB)^T)$ and $Trace(AA^T)$, where $A, B$ are both general square matrices of dimension $p$, and $B$ is positive semidefinite (thus symmetric). I did not find much discussion on this, and I tried thinking of it in terms of trace as an inner product, but haven't made much progress yet. Any help or pointer to books is appreciated!

Yang
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Yes, using the cyclic property of the trace, one has $$\operatorname{tr}(AB(AB)^T)=\operatorname{tr}(ABB^TA^T)=\operatorname{tr}(A^T A B B^T).$$ Since both $A^T A$ and $B B^T$ are positive semidefinite (try proving this), one can use the following inequality for positive semidefinite matrices $C,D$: $$\operatorname{tr}(CD)\leq \operatorname{tr}(C)\operatorname{tr}(D).$$ Therefore $$\operatorname{tr}(AB(AB)^T)\leq \operatorname{tr}(A^T A)\operatorname{tr}(BB^T)=\operatorname{tr}(AA^T)\operatorname{tr}(B^2).$$