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.

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In this paper, we consider the harmonic extension problem, which is widely used in many applications of machine learning. We formulate the harmonic extension as solving a Laplace-Beltrami equation with Dirichlet boundary condition. We use the point integral method (PIM) to solve the Laplace-Beltrami equation. The basic idea of the PIM method is to approximate the Laplace equation using an integral equation, which is easy to be discretized from points. Based on the integral equation, we found that traditional graph Laplacian method (GLM) may fail to approximate the harmonic functions in the classical sense. For the Laplace-Beltrami equation with Dirichlet boundary, we can prove the convergence of the point integral method. The point integral method is also very easy to implement, which only requires a minor modification of the graph Laplacian. One important application of the harmonic extension in machine learning is semi-supervised learning. We run a popular semi-supervised learning algorithm by Zhu et al. over a couple of well-known datasets and compare the performance of the aforementioned approaches. Our experiments show the PIM performs the best. We also apply PIM to an image recovery problem and show it outperforms GLM. Finally, on a model problem of Laplace-Beltrami equation with Dirichlet boundary, we prove the convergence of the point integral method.

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No abstract uploaded!