Exploring the "Middle Earth" of Network Spectra via a Gaussian Matrix Function

We study a Gaussian matrix function of the adjacency matrix of artificial and real-world networks. We motivate the use of this function on the basis of a dynamical process modeled by the time-dependent Schrödinger equation with a squared Hamiltonian. In particular, we study the Gaussian Estrada index-an index characterizing the importance of eigenvalues close to zero. This index accounts for the information contained in the eigenvalues close to zero in the spectra of networks. Such a method is a generalization of the so-called "Folded Spectrum Method" used in quantum molecular sciences. Here, we obtain bounds for this index in simple graphs, proving that it reaches its maximum for star graphs followed by complete bipartite graphs. We also obtain formulas for the Estrada Gaussian index of Erdős-Rényi random graphs and for the Barabási-Albert graphs. We also show that in real-world networks, this index is related to the existence of important structural patterns, such as complete bipartite subgraphs (bicliques). Such bicliques appear naturally in many real-world networks as a consequence of the evolutionary processes giving rise to them. In general, the Gaussian matrix function of the adjacency matrix of networks characterizes important structural information not described in previously used matrix functions of graphs.

[1]  P ? ? ? ? ? ? ? % ? ? ? ? , 1991 .

[2]  Martí Cuquet,et al.  Entanglement percolation in quantum complex networks. , 2009, Physical review letters.

[3]  K. Havens,et al.  Scale and Structure in Natural Food Webs , 1992, Science.

[4]  Neo D. Martinez Artifacts or Attributes? Effects of Resolution on the Little Rock Lake Food Web , 1991 .

[5]  B. Berger,et al.  Herpesviral Protein Networks and Their Interaction with the Human Proteome , 2006, Science.

[6]  McIntosh,et al.  Disturbance, resource supply, and food-web architecture in streams , 1998 .

[7]  Sophie Papst Rogets Thesaurus Of English Words And Phrases , 2016 .

[8]  Manlio De Domenico,et al.  Spectral entropies as information-theoretic tools for complex network comparison , 2016, 1609.01214.

[9]  Bradford A. Hawkins,et al.  EFFECTS OF SAMPLING EFFORT ON CHARACTERIZATION OF FOOD-WEB STRUCTURE , 1999 .

[10]  Gábor Szabó,et al.  Structure of complex networks , 2005 .

[11]  S. Shen-Orr,et al.  Network motifs in the transcriptional regulation network of Escherichia coli , 2002, Nature Genetics.

[12]  Lucas Antiqueira,et al.  Analyzing and modeling real-world phenomena with complex networks: a survey of applications , 2007, 0711.3199.

[13]  Judd Harrison Michael,et al.  Modeling the communication network in a sawmill , 1997 .

[14]  R. Rothenberg,et al.  Risk network structure in the early epidemic phase of HIV transmission in Colorado Springs , 2002, Sexually transmitted infections.

[15]  Ivan Gutman,et al.  Selected topics on applications of graph spectra , 2011 .

[16]  Leo Katz,et al.  A new status index derived from sociometric analysis , 1953 .

[17]  Lin-wang Wang,et al.  Solving Schrödinger’s equation around a desired energy: Application to silicon quantum dots , 1994 .

[18]  G. Polis,et al.  Complex Trophic Interactions in Deserts: An Empirical Critique of Food-Web Theory , 1991, The American Naturalist.

[19]  Ernesto Estrada,et al.  Location in , 2010 .

[20]  Desmond J. Higham,et al.  Network Properties Revealed through Matrix Functions , 2010, SIAM Rev..

[21]  W. Zachary,et al.  An Information Flow Model for Conflict and Fission in Small Groups , 1977, Journal of Anthropological Research.

[22]  S. Perseguers,et al.  Quantum random networks , 2009, 0907.3283.

[23]  J. Roughgarden,et al.  Construction and Analysis of a Large Caribbean Food Web , 1993 .

[25]  Nicholas J. Higham,et al.  Functions of matrices - theory and computation , 2008 .

[26]  L. Zeleny,et al.  Adaptation of Research Findings in Social Leadership to College Classroom Procedures , 1950 .

[27]  Alan M. Frieze,et al.  Random graphs , 2006, SODA '06.

[28]  J. A. Rodríguez-Velázquez,et al.  Subgraph centrality in complex networks. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[29]  L. Collatz,et al.  Spektren endlicher grafen , 1957 .

[30]  M. Vignali,et al.  A protein interaction network of the malaria parasite Plasmodium falciparum , 2005, Nature.

[31]  B. Snel,et al.  Comparative assessment of large-scale data sets of protein–protein interactions , 2002, Nature.

[32]  P. Cochat,et al.  Et al , 2008, Archives de pediatrie : organe officiel de la Societe francaise de pediatrie.

[33]  Konstantin Avrachenkov,et al.  Cooperative Game Theory Approaches for Network Partitioning , 2017, COCOON.

[34]  R. Ulanowicz,et al.  The Seasonal Dynamics of The Chesapeake Bay Ecosystem , 1989 .

[35]  P. Reitsma,et al.  Predators , 2018, Journal of thrombosis and haemostasis : JTH.

[36]  Ernesto Estrada,et al.  Communicability betweenness in complex networks , 2009, 0905.4102.

[37]  Michalis Faloutsos,et al.  On power-law relationships of the Internet topology , 1999, SIGCOMM '99.

[38]  Duncan MacRae join,et al.  Direct Factor Analysis of Sociometric Data , 1960 .

[39]  Julie L. Lockwood,et al.  Assembling Ecological Communities in Time and Space , 1997 .

[40]  Michele Benzi,et al.  The Physics of Communicability in Complex Networks , 2011, ArXiv.

[41]  D. Bu,et al.  Topological structure analysis of the protein-protein interaction network in budding yeast. , 2003, Nucleic acids research.

[42]  Michele Benzi,et al.  MATRIX FUNCTIONS , 2006 .

[43]  J. A. Peña,et al.  Estimating the Estrada index , 2007 .

[44]  Ernesto Estrada,et al.  Characterization of the folding degree of proteins , 2002, Bioinform..

[45]  G. Golub,et al.  Bounds for the Entries of Matrix Functions with Applications to Preconditioning , 1999 .

[46]  J. Hirsch,et al.  Dynamic correlation functions in quantum systems: a Monte Carlo algorithm , 1983 .

[47]  Christopher R. Myers,et al.  Software systems as complex networks: structure, function, and evolvability of software collaboration graphs , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[48]  Sabre Kais,et al.  Degree distribution in quantum walks on complex networks , 2013, 1305.6078.

[49]  P. Yodzis,et al.  Local trophodynamics and the interaction of marine mammals and fisheries in the Benguela ecosystem , 1998 .

[50]  Ernesto Estrada,et al.  Communicability in complex networks. , 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

[51]  FaloutsosMichalis,et al.  On power-law relationships of the Internet topology , 1999 .

[52]  O. Sporns,et al.  Motifs in Brain Networks , 2004, PLoS biology.

[53]  Vladimir Batagelj,et al.  Exploratory Social Network Analysis with Pajek , 2005 .

[54]  Malte Doehne,et al.  Krackhardt (1999): The Ties That Torture: Simmelian Tie Analysis in Organizations , 2018, Schlüsselwerke der Netzwerkforschung.

[55]  S. Hall,et al.  Food-web patterns : lessons from a species-rich web , 1991 .

[56]  Robert R. Christian,et al.  Organizing and understanding a winter's seagrass foodweb network through effective trophic levels , 1999 .

[57]  Michael Albers,et al.  Elucidation of an Archaeal Replication Protein Network to Generate Enhanced PCR Enzymes* , 2002, The Journal of Biological Chemistry.

[58]  Ian Fleming,et al.  Frontier Orbitals and Organic Chemical Reactions , 1977 .

[59]  G. Golub,et al.  Matrices, Moments and Quadrature with Applications , 2009 .

[60]  Philip H. Warren,et al.  Spatial and temporal variation in the structure of a freshwater food web , 1989 .

[61]  Downloaded from , 1997 .

[62]  S. Opitz,et al.  Trophic interactions in Caribbean coral reefs , 1996 .

[63]  A. Rossberg,et al.  Food webs: experts consuming families of experts. , 2005, Journal of theoretical biology.

[64]  Daniel A. Spielman Graphs and networks , 2007 .

[65]  Ernesto Estrada Generalized walks-based centrality measures for complex biological networks. , 2010, Journal of theoretical biology.

[66]  Jason S. Link,et al.  Does food web theory work for marine ecosystems , 2002 .

[67]  Kenichi Fukui,et al.  A Molecular Orbital Theory of Reactivity in Aromatic Hydrocarbons , 1952 .

[68]  David Lusseau,et al.  The emergent properties of a dolphin social network , 2003, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[69]  Chia-Ling Chen,et al.  hp-DPI: Helicobacter pylori Database of Protein Interactomes-embracing experimental and inferred interactions , 2005, Bioinform..

[70]  Keith Yates,et al.  Huckel Molecular Orbital Theory , 1978 .

[71]  M. Benzi,et al.  Quadrature rule-based bounds for functions of adjacency matrices , 2010 .

[72]  A. Barabasi,et al.  Spectra of "real-world" graphs: beyond the semicircle law. , 2001, Physical review. E, Statistical, nonlinear, and soft matter physics.

[73]  Lin-wang Wang,et al.  Parallel Empirical Pseudopotential Electronic Structure Calculations for Million Atom Systems , 2000 .

[74]  E. Wigner Characteristic Vectors of Bordered Matrices with Infinite Dimensions I , 1955 .

[75]  S. Shen-Orr,et al.  Network motifs: simple building blocks of complex networks. , 2002, Science.

[76]  M. Huxham,et al.  Do Parasites Reduce the Chances of Triangulation in a Real Food Web , 1996 .

[77]  J. Cirac,et al.  Entanglement percolation in quantum networks , 2006, quant-ph/0612167.

[78]  Kenichi Fukui,et al.  The Role of Frontier Orbitals in Chemical Reactions (Nobel Lecture) , 1982 .

[79]  Hongzhong Deng,et al.  Vulnerability of complex networks under intentional attack with incomplete information , 2007 .

[80]  Michele Benzi,et al.  Decay Properties of Spectral Projectors with Applications to Electronic Structure , 2012, SIAM Rev..

[81]  Neo D. Martinez,et al.  Predators, parasitoids and pathogens: species richness, trophic generality and body sizes in a natural food web , 2000 .

[82]  Jetta Carol Culpepper,et al.  ODLIS: Online Dictionary of Library and Information Science , 2013 .

[83]  Guy Theraulaz,et al.  Topological efficiency in three-dimensional gallery networks of termite nests , 2008 .

[84]  M. Noirot-Gros,et al.  Protein interaction networks in bacteria. , 2004, Current opinion in microbiology.

[85]  Duncan J. Watts,et al.  Collective dynamics of ‘small-world’ networks , 1998, Nature.

[86]  Albert,et al.  Emergence of scaling in random networks , 1999, Science.

[87]  Geisel,et al.  Slow decay of temporal correlations in quantum systems with Cantor spectra. , 1992, Physical review letters.

[88]  Michele Benzi,et al.  Updating and Downdating Techniques for Optimizing Network Communicability , 2014, SIAM J. Sci. Comput..

[89]  S. Shen-Orr,et al.  Superfamilies of Evolved and Designed Networks , 2004, Science.

[90]  W. Marsden I and J , 2012 .

[91]  L. Freeman,et al.  Analyzing the Structure of the Centrality-Productivity Literature Created Between 1948 and 1979 , 1990 .

[92]  Michele Benzi,et al.  On the Limiting Behavior of Parameter-Dependent Network Centrality Measures , 2013, SIAM J. Matrix Anal. Appl..

[93]  Guy Theraulaz,et al.  Efficiency and robustness in ant networks of galleries , 2004 .

[94]  Benny Sudakov,et al.  The Largest Eigenvalue of Sparse Random Graphs , 2001, Combinatorics, Probability and Computing.

[95]  G. Naumis,et al.  Doped graphene: the interplay between localization and frustration due to the underlying triangular symmetry , 2011, Journal of physics. Condensed matter : an Institute of Physics journal.

[96]  P. Yodzis,et al.  DIFFUSE EFFECTS IN FOOD WEBS , 2000 .

[97]  Werner Kutzelnigg,et al.  What I like about Hückel theory , 2007, J. Comput. Chem..

[98]  Bo Zhou,et al.  ON ESTRADA INDEX , 2008 .

[99]  M E J Newman Assortative mixing in networks. , 2002, Physical review letters.

[100]  A. Emili,et al.  Interaction network containing conserved and essential protein complexes in Escherichia coli , 2005, Nature.

[101]  Mauricio Barahona,et al.  Robustness of regular ring lattices based on natural connectivity , 2011, Int. J. Syst. Sci..

[102]  Robert B. Waide,et al.  The food web of a tropical rain forest , 1997 .