Current methods cannot tell us what the nature of the protein universe is concretely. They are based on different models of amino acid substitution and multiple sequence alignment which is an NP-hard problem and requires manual intervention. Protein structural analysis also gives a direction for mapping the protein universe. Unfortunately, now only a minuscule fraction of proteins' 3-dimensional structures are known. Furthermore, the phylogenetic tree representations are not unique for any existing tree construction methods. Here we develop a novel method to realize the nature of protein universe. We show the protein universe can be realized as a protein space in 60-dimensional Euclidean space using a distance based on a normalized distribution of amino acids. Every protein is in one-to-one correspondence with a point in protein space, where proteins with similar properties stay close together. Thus the distance between two points in protein space represents the biological distance of the corresponding two proteins. We also propose a natural graphical representation for inferring phylogenies. The representation is natural and unique based on the biological distances of proteins in protein space. This will solve the fundamental question of how proteins are distributed in the protein universe.

In this paper, we prove a necessary and sufficient condition for the edge universality of sample covariance matrices with general population. We consider sample covariance matrices of the form $\mathcal Q = TX(TX)^{*}$, where $X$ is an $M_2\times N$ random matrix with $X_{ij}=N^{-1/2}q_{ij}$ such that $q_{ij}$ are $i.i.d.$ random variables with zero mean and unit variance, and $T$ is an $M_1 \times M_2$ deterministic matrix such that $T^* T$ is diagonal. We study the asymptotic behavior of the largest eigenvalues of $\mathcal Q$ when $M:=\min\{M_1,M_2\}$ and $N$ tend to infinity with $\lim_{N \to \infty} {N}/{M}=d \in (0, \infty)$. We prove that the Tracy-Widom law holds for the largest eigenvalue of $\mathcal Q$ if and only if $\lim_{s \rightarrow \infty}s^4 \mathbb{P}(\vert q_{ij} \vert \geq s)=0$ under mild assumptions of $T$. The necessity and sufficiency of this condition for the edge universality was first proved for Wigner matrices by Lee and Yin [34].

We formulate the Riemannian calculus of the probability set embedded with L^2-Wasserstein metric. This is an initial work of transport information geometry. Our investigation starts with the probability simplex (probability manifold) supported on vertices of a finite graph. The main idea is to embed the probability manifold as a submanifold of the positive measure space with a nonlinear metric tensor. Here the nonlinearity comes from the linear weighted Laplacian operator. By this viewpoint, we establish torsion-free Christoffel symbols, Levi-Civita connections, curvature tensors, and volume forms in the probability manifold by Euclidean coordinates. As a consequence, the Jacobi equation, Laplace-Beltrami and Hessian operators on the probability manifold are derived. These geometric computations are also provided in the infinite-dimensional density space (density manifold) supported on a finite-dimensional manifold. In particular, an identity is given connecting the Baker-{É}mery Γ2 operator (carr{é} du champ it{é}r{é}) by connecting Fisher-Rao information metric and optimal transport metric. Several examples are demonstrated.

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