Entropy of Some Models of Sparse Random Graphs With Vertex-Names

Consider the setting of sparse graphs on N vertices, where the vertices have distinct "names", which are strings of length O(log N) from a fixed finite alphabet. For many natural probability models, the entropy grows as cN log N for some model-dependent rate constant c. The mathematical content of this paper is the (often easy) calculation of c for a variety of models, in particular for various standard random graph models adapted to this setting. Our broader purpose is to publicize this particular setting as a natural setting for future theoretical study of data compression for graphs, and (more speculatively) for discussion of unorganized versus organized complexity.Comment: 31 page

Analytical maximum-likelihood method to detect patterns in real networks

In order to detect patterns in real networks, randomized graph ensembles that preserve only part of the topology of an observed network are systematically used as fundamental null models. However, their generation is still problematic. The existing approaches are either computationally demanding and beyond analytic control, or analytically accessible but highly approximate. Here we propose a solution to this long-standing problem by introducing an exact and fast method that allows to obtain expectation values and standard deviations of any topological property analytically, for any binary, weighted, directed or undirected network. Remarkably, the time required to obtain the expectation value of any property is as short as that required to compute the same property on the single original network. Our method reveals that the null behavior of various correlation properties is different from what previously believed, and highly sensitive to the particular network considered. Moreover, our approach shows that important structural properties (such as the modularity used in community detection problems) are currently based on incorrect expressions, and provides the exact quantities that should replace them.Comment: 26 pages, 10 figure

Discriminating different classes of biological networks by analyzing the graphs spectra distribution

The brain's structural and functional systems, protein-protein interaction, and gene networks are examples of biological systems that share some features of complex networks, such as highly connected nodes, modularity, and small-world topology. Recent studies indicate that some pathologies present topological network alterations relative to norms seen in the general population. Therefore, methods to discriminate the processes that generate the different classes of networks (e.g., normal and disease) might be crucial for the diagnosis, prognosis, and treatment of the disease. It is known that several topological properties of a network (graph) can be described by the distribution of the spectrum of its adjacency matrix. Moreover, large networks generated by the same random process have the same spectrum distribution, allowing us to use it as a "fingerprint". Based on this relationship, we introduce and propose the entropy of a graph spectrum to measure the "uncertainty" of a random graph and the Kullback-Leibler and Jensen-Shannon divergences between graph spectra to compare networks. We also introduce general methods for model selection and network model parameter estimation, as well as a statistical procedure to test the nullity of divergence between two classes of complex networks. Finally, we demonstrate the usefulness of the proposed methods by applying them on (1) protein-protein interaction networks of different species and (2) on networks derived from children diagnosed with Attention Deficit Hyperactivity Disorder (ADHD) and typically developing children. We conclude that scale-free networks best describe all the protein-protein interactions. Also, we show that our proposed measures succeeded in the identification of topological changes in the network while other commonly used measures (number of edges, clustering coefficient, average path length) failed

Correlation of Automorphism Group Size and Topological Properties with Program-size Complexity Evaluations of Graphs and Complex Networks

We show that numerical approximations of Kolmogorov complexity (K) applied to graph adjacency matrices capture some group-theoretic and topological properties of graphs and empirical networks ranging from metabolic to social networks. That K and the size of the group of automorphisms of a graph are correlated opens up interesting connections to problems in computational geometry, and thus connects several measures and concepts from complexity science. We show that approximations of K characterise synthetic and natural networks by their generating mechanisms, assigning lower algorithmic randomness to complex network models (Watts-Strogatz and Barabasi-Albert networks) and high Kolmogorov complexity to (random) Erdos-Renyi graphs. We derive these results via two different Kolmogorov complexity approximation methods applied to the adjacency matrices of the graphs and networks. The methods used are the traditional lossless compression approach to Kolmogorov complexity, and a normalised version of a Block Decomposition Method (BDM) measure, based on algorithmic probability theory.Comment: 15 2-column pages, 20 figures. Forthcoming in Physica A: Statistical Mechanics and its Application

Connectivity Compression for Irregular Quadrilateral Meshes

Applications that require Internet access to remote 3D datasets are often limited by the storage costs of 3D models. Several compression methods are available to address these limits for objects represented by triangle meshes. Many CAD and VRML models, however, are represented as quadrilateral meshes or mixed triangle/quadrilateral meshes, and these models may also require compression. We present an algorithm for encoding the connectivity of such quadrilateral meshes, and we demonstrate that by preserving and exploiting the original quad structure, our approach achieves encodings 30 - 80% smaller than an approach based on randomly splitting quads into triangles. We present both a code with a proven worst-case cost of 3 bits per vertex (or 2.75 bits per vertex for meshes without valence-two vertices) and entropy-coding results for typical meshes ranging from 0.3 to 0.9 bits per vertex, depending on the regularity of the mesh. Our method may be implemented by a rule for a particular splitting of quads into triangles and by using the compression and decompression algorithms introduced in [Rossignac99] and [Rossignac&Szymczak99]. We also present extensions to the algorithm to compress meshes with holes and handles and meshes containing triangles and other polygons as well as quads

Exact maximum-likelihood method to detect patterns in real networks

In order to detect patterns in real networks, randomized graph ensembles that preserve only part of the topology of an observed network are systematically used as fundamental null models. However, their generation is still problematic. The existing approaches are either computationally demanding and beyond analytic control, or analytically accessible but highly approximate. Here we propose a solution to this long-standing problem by introducing an exact and fast method that allows to obtain expectation values and standard deviations of any topological property analytically, for any binary, weighted, directed or undirected network. Remarkably, the time required to obtain the expectation value of any property is as short as that required to compute the same property on the single original network. Our method reveals that the null behavior of various correlation properties is different from what previously believed, and highly sensitive to the particular network considered. Moreover, our approach shows that important structural properties (such as the modularity used in community detection problems) are currently based on incorrect expressions, and provides the exact quantities that should replace them.