It is known that every complex square matrix with nonnega-tive determinant is the product of positive semi-definite matrices. There are characterizations of matrices that require two or five positive semi-definite matrices in the product. However, the characterizations of matrices that require three or four positive semi-definite matrices in the product are lacking. In this paper, we give a complete characterization of these two types of matrices. With these results, we give an algorithm to determine whether a square matrix can be expressed as the product of kpositive semi-definite matrices but not fewer, for k=1, 2, 3, 4, 5.

Denote by Mnthe set of n ×ncomplex matrices. Let f:Mn→[0, ∞)be a continuous map such that f(μUAU∗) =f(A)for any complex unit μ, A ∈Mnand unitary U∈Mn, f(X) =0if and only if X=0and the induced map t →f(tX)is monotonically increasing on [0, ∞)for any rank onenilpotent X∈Mn. Characterization is given for surjective maps φon Mnsatisfying f(AB−BA) =f(φ(A)φ(B) −φ(B)φ(A)). The general theorem isthen used to deduce results on special cases when the function is the pseudo spectrum and the pseudo spectral radius.

Protein universe is a complex system with critical problem of protein evolution to be analyzed. Early studies have used geometric distances and polygenetic-trees to solve this problem. However, the traditional methods are bivariate, whose taxonomy classification relies on bivariate branching. This is not sufficient to describe the complex nature of protein universe. Therefore, we propose a novel approach on multivariate protein classification. The new method bases on the theory of information and network, can be used to analyze multivariate relationships of proteins. The new method is alignment-free and have wide-applications to both sequences and 3D structures. We demonstrate the new method on six protein examples, results show that the new method is efficient and can potentially be used for future protein classifications.