Quantitative Measures of Network Complexity

The first attempts to evaluate quantitatively the complexity of a system have been related to complexity of cells, organisms, and humans. Fascinated by the complex nature of the living things, a group of young mathematical biologists applied in the 1950s the Shannon theory of communications 1 to assess the information content of the living matter. The analysis made by Rashewsky 4 provided the first proof that life on earth cannot emerge as a random event, because the probability for such an event would be incredibly small. Two different approaches have been used in defining the information content. The first one proceeded from the elemental composition of the living matter (C, N, O, etc.) and is the predecessor of what is nowadays called compositional complexity. Rashewsky' topological information has been based on partitioning the atoms in a structure according to both their chemical nature and their equivalent topological neighborhoods. Mowshovitz 6 developed further these ideas to define complexity of graphs. Minoli 7

[1]  N. Trinajstic,et al.  Information theory, distance matrix, and molecular branching , 1977 .

[2]  J. Platt Prediction of Isomeric Differences in Paraffin Properties , 1952 .

[3]  Nenad Trinajstić,et al.  Isomer discrimination by topological information approach , 1981 .

[4]  Neo D. Martinez,et al.  Network structure and biodiversity loss in food webs: robustness increases with connectance , 2002, Ecology Letters.

[5]  D. Bonchev,et al.  The problems of computing molecular complexity , 1990 .

[6]  S. N. Dorogovtsev,et al.  Evolution of networks , 2001, cond-mat/0106144.

[7]  D. Bonche,et al.  Overall Molecular Descriptors. 3. Overall Zagreb Indices , 2001, SAR and QSAR in environmental research.

[8]  Danail Bonchev On the complexity of Platonic solids , 2004 .

[9]  An-Ping Zeng,et al.  Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms , 2003, Bioinform..

[10]  C Koch,et al.  Complexity and the nervous system. , 1999, Science.

[11]  E. Trucco A note on the information content of graphs , 1956 .

[12]  Danail Bonchev,et al.  Complexity index for the linear mechanisms of chemical reactions , 1987 .

[13]  Danail Bonchev,et al.  Chemical Reaction Networks: A Graph-Theoretical Approach , 1996 .

[14]  Abbe Mowshowitz,et al.  Entropy and the complexity of graphs , 1967 .

[15]  Robert B. Ash,et al.  Information Theory , 2020, The SAGE International Encyclopedia of Mass Media and Society.

[16]  N. Trinajstic Chemical Graph Theory , 1992 .

[17]  Danail Bonchev,et al.  On the complexity of linear reaction mechanisms , 1980 .

[18]  Gary D Bader,et al.  Global Mapping of the Yeast Genetic Interaction Network , 2004, Science.

[19]  Danail Bonchev,et al.  Information theoretic indices for characterization of chemical structures , 1983 .

[20]  Dennis H. Rouvray Computational chemical graph theory , 1990 .

[21]  D. Kamenski,et al.  Symmetry and information content of chemical structures , 1976 .

[22]  A. Wagner The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. , 2001, Molecular biology and evolution.

[23]  Nicola J. Rinaldi,et al.  Transcriptional Regulatory Networks in Saccharomyces cerevisiae , 2002, Science.

[24]  R. Albert,et al.  The large-scale organization of metabolic networks , 2000, Nature.

[25]  I. Gutman,et al.  Graph theory and molecular orbitals. XII. Acyclic polyenes , 1975 .

[26]  Danail Bonchev,et al.  The Overall Wiener Index-A New Tool for Characterization of Molecular Topology , 2001, J. Chem. Inf. Comput. Sci..

[27]  A. Balaban,et al.  Topological Indices and Related Descriptors in QSAR and QSPR , 2003 .

[28]  M. Newman,et al.  Random graphs with arbitrary degree distributions and their applications. , 2000, Physical review. E, Statistical, nonlinear, and soft matter physics.

[29]  Frank Harary,et al.  Graph Theory , 2016 .

[30]  M. Randic,et al.  On the Concept of Molecular Complexity , 2002 .

[31]  Danail Bonchev,et al.  Chemical Reaction Networks , 1996 .

[32]  Steven H. Bertz The bond graph , 1981 .

[33]  Danail Bonchev,et al.  Complexity Analysis of Yeast Proteome Network , 2004, Chemistry & biodiversity.

[34]  Gretchen Vogel,et al.  Ecologists Roiled by Misconduct Case , 2004, Science.

[35]  H. Wiener Structural determination of paraffin boiling points. , 1947, Journal of the American Chemical Society.

[36]  Danail Bonchev,et al.  Complexity of Protein-Protein Interaction Networks, Complexes, and Pathways , 2003 .

[37]  H. Wiener Relation of the physical properties of the isomeric alkanes to molecular structure; surface, tension, specific dispersion, and critical solution temperature in aniline. , 1948, The Journal of physical and colloid chemistry.

[38]  Danail Bonchev,et al.  Iterative procedure for the generalized graph center in polycyclic graphs , 1989, J. Chem. Inf. Comput. Sci..

[39]  Gerta Ruecker,et al.  Walk Counts, Labyrinthicity, and Complexity of Acyclic and Cyclic Graphs and Molecules. , 2000 .

[40]  U. Bhalla,et al.  Complexity in biological signaling systems. , 1999, Science.

[41]  Danail Bonchev,et al.  Generalization of the Graph Center Concept, and Derived Topological Centric Indexes , 1980, J. Chem. Inf. Comput. Sci..

[42]  K. Sneppen,et al.  Specificity and Stability in Topology of Protein Networks , 2002, Science.

[43]  M. Gordon,et al.  Non-random polycondensation : statistical theory of the substitution effect , 1964 .

[44]  Danail Bonchev,et al.  Overall Connectivities/Topological Complexities: A New Powerful Tool for QSPR/QSAR , 2000, J. Chem. Inf. Comput. Sci..

[45]  Danail Bonchev,et al.  The concept for the centre of a chemical structure and its applications , 1989 .

[46]  Danail Bonchev,et al.  Enumeration, Coding, and Complexity of Linear Reaction Mechanisms , 1994, J. Chem. Inf. Comput. Sci..

[47]  William C. Herndon,et al.  The Similarity of Graphs and Molecules , 1986 .

[48]  D. Bonchev On the complexity of directed biological networks , 2003, SAR and QSAR in environmental research.

[49]  D. G. Bonchev KOLMOGOROV'S INFORMATION, SHANNON'S ENTROPY, AND TOPOLOGICAL COMPLEXITY OFMOLECULES , 1995 .

[50]  S. N. Dorogovtsev,et al.  Giant strongly connected component of directed networks. , 2001, Physical review. E, Statistical, nonlinear, and soft matter physics.

[51]  Albert-László Barabási,et al.  Error and attack tolerance of complex networks , 2000, Nature.

[52]  Gerta Rücker,et al.  Walk Counts, Labyrinthicity, and Complexity of Acyclic and Cyclic Graphs and Molecules , 2000, J. Chem. Inf. Comput. Sci..

[53]  H. L. Morgan The Generation of a Unique Machine Description for Chemical Structures-A Technique Developed at Chemical Abstracts Service. , 1965 .

[54]  D. H. Rouvray Concepts in Chemistry: A Contemporary Challenge , 1996 .

[55]  D. Fell,et al.  The small world inside large metabolic networks , 2000, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[56]  D. Watts The “New” Science of Networks , 2004 .

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

[58]  R. Ozawa,et al.  A comprehensive two-hybrid analysis to explore the yeast protein interactome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[59]  Nenad Trinajstić,et al.  On the Zagreb Indices as Complexity Indices , 2000 .

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

[61]  N. Trinajstic,et al.  The Zagreb Indices 30 Years After , 2003 .

[62]  Danail Bonchev,et al.  Novel Indices for the Topological Complexity of Molecules , 1997 .

[63]  P. Bork,et al.  Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.

[64]  D. Cvetkovic,et al.  Graph theory and molecular orbitals , 1974 .

[65]  Steven H. Bertz,et al.  The first general index of molecular complexity , 1981 .

[66]  Danail Bonchev,et al.  Symmetry and information content of chemical structures , 1976 .

[67]  Claude E. Shannon,et al.  A Mathematical Theory of Communications , 1948 .

[68]  Nir Friedman,et al.  Inferring Cellular Networks Using Probabilistic Graphical Models , 2004, Science.

[69]  K. Humbel,et al.  Chemical Applications of Topology and Graph Theory, R.B. King (Ed.). Elsevier Science Publishers, Amsterdam (1983), (ISBN 0-444-42244-7). XII + 494 p. Price Dfl. 275.00 , 1985 .

[70]  Norman,et al.  Structural Models: An Introduction to the Theory of Directed Graphs. , 1966 .

[71]  H. Quastler,et al.  Essays on the use of information theory in biology , 1953 .

[72]  N. Rashevsky Life, information theory, and topology , 1955 .

[73]  James R. Knight,et al.  A Protein Interaction Map of Drosophila melanogaster , 2003, Science.

[74]  Steven H. Bertz,et al.  Rigorous mathematical approaches to strategic bonds and synthetic analysis based on conceptually simple new complexity indices , 1997 .

[75]  Paul G. Mezey,et al.  Iterated similarity sequences and shape ID numbers for molecules , 1994, J. Chem. Inf. Comput. Sci..

[76]  D. Bonchev,et al.  Overall connectivity--a next generation molecular connectivity. , 2001, Journal of molecular graphics & modelling.

[77]  J. Sutherland The Quark and the Jaguar , 1994 .

[78]  Hawoong Jeong,et al.  Modeling the Internet's large-scale topology , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[79]  A. Kolmogorov Three approaches to the quantitative definition of information , 1968 .

[80]  Gerta Rücker,et al.  Substructure, Subgraph, and Walk Counts as Measures of the Complexity of Graphs and Molecules , 2001, J. Chem. Inf. Comput. Sci..

[81]  A. Mowshowitz,et al.  Entropy and the complexity of graphs. I. An index of the relative complexity of a graph. , 1968, The Bulletin of mathematical biophysics.

[82]  Rucker Walk counts, labyrinthicity, and complexity of acyclic and cyclic graphs and molecules , 2000, Journal of chemical information and computer sciences.

[83]  Dennis H. Rouvray,et al.  Graph Theory and Topology in Chemistry , 1987 .

[84]  Martin Suter,et al.  Small World , 2002 .