On the extremal properties of the average eccentricity

The eccentricity of a vertex is the maximum distance from it to another vertex and the average eccentricity $ecc (G)$ of a graph $G$ is the mean value of eccentricities of all vertices of $G$. The average eccentricity is deeply connected with a topological descriptor called the eccentric connectivity index, defined as a sum of products of vertex degrees and eccentricities. In this paper we analyze extremal properties of the average eccentricity, introducing two graph transformations that increase or decrease $ecc (G)$. Furthermore, we resolve four conjectures, obtained by the system AutoGraphiX, about the average eccentricity and other graph parameters (the clique number, the Randi\' c index and the independence number), refute one AutoGraphiX conjecture about the average eccentricity and the minimum vertex degree and correct one AutoGraphiX conjecture about the domination number.Comment: 15 pages, 3 figure

ProtNN: Fast and Accurate Nearest Neighbor Protein Function Prediction based on Graph Embedding in Structural and Topological Space

Studying the function of proteins is important for understanding the molecular mechanisms of life. The number of publicly available protein structures has increasingly become extremely large. Still, the determination of the function of a protein structure remains a difficult, costly, and time consuming task. The difficulties are often due to the essential role of spatial and topological structures in the determination of protein functions in living cells. In this paper, we propose ProtNN, a novel approach for protein function prediction. Given an unannotated protein structure and a set of annotated proteins, ProtNN finds the nearest neighbor annotated structures based on protein-graph pairwise similarities. Given a query protein, ProtNN finds the nearest neighbor reference proteins based on a graph representation model and a pairwise similarity between vector embedding of both query and reference protein-graphs in structural and topological spaces. ProtNN assigns to the query protein the function with the highest number of votes across the set of k nearest neighbor reference proteins, where k is a user-defined parameter. Experimental evaluation demonstrates that ProtNN is able to accurately classify several datasets in an extremely fast runtime compared to state-of-the-art approaches. We further show that ProtNN is able to scale up to a whole PDB dataset in a single-process mode with no parallelization, with a gain of thousands order of magnitude of runtime compared to state-of-the-art approaches

Towards an Efficient Discovery of the Topological Representative Subgraphs

With the emergence of graph databases, the task of frequent subgraph discovery has been extensively addressed. Although the proposed approaches in the literature have made this task feasible, the number of discovered frequent subgraphs is still very high to be efficiently used in any further exploration. Feature selection for graph data is a way to reduce the high number of frequent subgraphs based on exact or approximate structural similarity. However, current structural similarity strategies are not efficient enough in many real-world applications, besides, the combinatorial nature of graphs makes it computationally very costly. In order to select a smaller yet structurally irredundant set of subgraphs, we propose a novel approach that mines the top-k topological representative subgraphs among the frequent ones. Our approach allows detecting hidden structural similarities that existing approaches are unable to detect such as the density or the diameter of the subgraph. In addition, it can be easily extended using any user defined structural or topological attributes depending on the sought properties. Empirical studies on real and synthetic graph datasets show that our approach is fast and scalable

Pseudo-distance-regularised graphs are distance-regular or distance-biregular

The concept of pseudo-distance-regularity around a vertex of a graph is a natural generalization, for non-regular graphs, of the standard distance-regularity around a vertex. In this note, we prove that a pseudo-distance-regular graph around each of its vertices is either distance-regular or distance-biregular. By using a combinatorial approach, the same conclusion was reached by Godsil and Shawe-Taylor for a distance-regular graph around each of its vertices. Thus, our proof, which is of an algebraic nature, can also be seen as an alternative demonstration of Godsil and Shawe-Taylor's theorem