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Information Measures to Characterize Networks

Information Measures to Characterize Networks

Matthias Dehmer (ORCID: 0000-0001-8454-5857)
  • Grant DOI 10.55776/P22029
  • Funding program Principal Investigator Projects
  • Status ended
  • Start March 1, 2010
  • End February 28, 2014
  • Funding amount € 308,658
  • Project website

Disciplines

Chemistry (25%); Mathematics (75%)

Keywords

    Information Measures, Complex Networks, Chemical Graph Theory, Structural Complexity, Chemometrics, Information Theory

Abstract Final report

Currently, network-based approaches are ubiquitous to model complex systems which occur in various scientific disciplines. Especially the fact that many real world phenomena can be modelled by using non-random network topologies, powerful methods to analyze their structural properties are essential. In our proposal, we mainly focus on structural network characterization. Network characterization is generally understood as the task of deriving characteristic (structural) features of a network under consideration to describe its structural complexity. When using information-theoretic methods, one possibility is to firstly derive a probability distribution taking structural features of the network into account. Then, classical information measures like Shannon`s-entropies can be used to quantify the structural information content and interpreted as complexity of a network. However, a major problem of some classical information measures for networks is that the time complexity of the underlying algorithms is often not appropriate for practical use. Also, mathematical properties of such information measures representing the structural information content of a graph (these are often used in mathematical chemistry) are almost unexplored so far. The goal of this research project is twofold: First we want to explore relationships and important mathematical properties of the mentioned information measures. Second, by making use of the established results, we would like to improve the usage of these measures for problems in QSPR (Quantitative Structure-Property Relationships) that is a sub-area of mathematical chemistry. Especially, we put the emphasis on applying (existing and novel) information measures to databases containing chemical structure data represented by graphs to find which measures are suitable to characterize chemical structures meaningfully.

This project dealt with structural network characterization by using information-theoretic measures. Quantitative network characterization can generally be understood as the problem of deriving characteristic (structural) features of a network under consideration to describe its structural complexity quantitatively. In our case, we used entropic quantities such as various graph entropies to do so. By using information-theoretic methods, one derives a probability distribution by taking structural features of the network into account. A still intricate question is what kind of structural complexity a given measure captures. The goal of this project was twofold: First, to investigate the mathematical apparatus and second, to (ideally) apply the findings in Chemoinformatics and for QSPR (Quantitative Structure-Property Relationships).Regarding the first part, a major result of this project dealt with proving novel relationships which describe the interaction between such information-theoretic quantities. Given the fact that numerous measures have been developed, this question has been far from trivial. Also, we extended this framework to probabilistic inequalities and obtained fascinating results. In addition, we investigated extremal properties of the information-theoretic graph measures; this problem turned out to be extremely challenging. In summary, the mentioned research contributed to the problem of measuring the complexity of networks that has been highly relevant in practice (e.g. Internet, Biology, Chemistry etc.). Another problem we tackled in this project relates to investigate how unique those information-theoretic graph measures are. With other words, we explored the ability of the measures to discriminate graphs which are structurally different. As a result, we found that most of the measures known are not unique on exhaustively generated graph. This result can be used for detecting graph isomorphism and to create unique fingerprints for graphs. In summary we believe that our theoretical results contributed to establish an Information Theory of Networks significantly. Second, we employed the achieved results to explore the measures for their use in Chemoinformatics and Chemometrics. We found interesting and important properties of descriptors which can be used to design better and efficient applications in the mentioned areas. An important finding is that most of the available molecular descriptors (we put the emphasis on structural descriptors) capture structural information very similarly and could be therefore obsolete. This result raised the question how useful molecular descriptors are.

Research institution(s)
  • Priv.-Univ. für Gesundheitswissenschaften, Medizinische Informatik und Technik - 94%
  • Technische Universität Wien - 6%
Project participants
  • Kurt Varmuza, Technische Universität Wien , associated research partner

Research Output

  • 738 Citations
  • 39 Publications
Publications
  • 2010
    Title Network analysis using a novel highly discriminating topological index
    DOI 10.1002/cplx.20363
    Type Journal Article
    Author Diudea M
    Journal Complexity
    Pages 32-39
  • 2010
    Title A Symmetry Index for Graphs.
    Type Journal Article
    Author Dehmer M
    Journal Symmetry: Culture and Science
  • 2012
    Title Structural Discrimination of Networks by Using Distance, Degree and Eigenvalue-Based Measures
    DOI 10.1371/journal.pone.0038564
    Type Journal Article
    Author Dehmer M
    Journal PLoS ONE
    Link Publication
  • 2012
    Title On the number of transversals in random trees
    DOI 10.46298/dmtcs.2990
    Type Journal Article
    Author Gittenberger B
    Journal Discrete Mathematics & Theoretical Computer Science
    Link Publication
  • 2014
    Title The gene regulatory network for breast cancer: integrated regulatory landscape of cancer hallmarks
    DOI 10.3389/fgene.2014.00015
    Type Journal Article
    Author Emmert-Streib F
    Journal Frontiers in Genetics
    Pages 15
    Link Publication
  • 2014
    Title Probabilistic inequalities for evaluating structural network measures
    DOI 10.1016/j.ins.2014.07.018
    Type Journal Article
    Author Kraus V
    Journal Information Sciences
    Pages 220-245
  • 2014
    Title The Uniqueness of -Matrix Graph Invariants
    DOI 10.1371/journal.pone.0083868
    Type Journal Article
    Author Dehmer M
    Journal PLoS ONE
    Link Publication
  • 2012
    Title RMol: a toolset for transforming SD/Molfile structure information into R objects
    DOI 10.1186/1751-0473-7-12
    Type Journal Article
    Author Grabner M
    Journal Source Code for Biology and Medicine
    Pages 12
    Link Publication
  • 2012
    Title Uniquely Discriminating Molecular Structures Using Novel.
    Type Journal Article
    Author Dehmer M
    Journal MATCH: Communications in Mathematical and in Computer Chemistry
  • 2012
    Title An efficient heuristic approach to detecting graph isomorphism based on combinations of highly discriminating invariants
    DOI 10.1007/s10444-012-9281-0
    Type Journal Article
    Author Dehmer M
    Journal Advances in Computational Mathematics
    Pages 311-325
  • 2012
    Title Entropy and the Complexity of Graphs Revisited
    DOI 10.3390/e14030559
    Type Journal Article
    Author Mowshowitz A
    Journal Entropy
    Pages 559-570
    Link Publication
  • 2012
    Title Location of Zeros of Wiener and Distance Polynomials
    DOI 10.1371/journal.pone.0028328
    Type Journal Article
    Author Dehmer M
    Journal PLoS ONE
    Link Publication
  • 2012
    Title Redundancy analysis for characterizing the correlation between groups of variables - Applied to molecular descriptors
    DOI 10.1016/j.chemolab.2011.05.013
    Type Journal Article
    Author Varmuza K
    Journal Chemometrics and Intelligent Laboratory Systems
    Pages 31-41
  • 2012
    Title On Extremal Properties of Graph Entropies.
    Type Journal Article
    Author Dehmer M
    Journal MATCH: Communications in Mathematical and in Computer Chemistry
  • 2012
    Title Recent Developments in Quantitative Graph Theory: Information Inequalities for Networks
    DOI 10.1371/journal.pone.0031395
    Type Journal Article
    Author Dehmer M
    Journal PLoS ONE
    Link Publication
  • 2012
    Title Exploring Statistical and Population Aspects of Network Complexity
    DOI 10.1371/journal.pone.0034523
    Type Journal Article
    Author Emmert-Streib F
    Journal PLoS ONE
    Link Publication
  • 2012
    Title The Discrimination Power of Molecular Identication Numbers Revisited.
    Type Journal Article
    Author Dehmer M
    Journal MATCH: Communications in Mathematical and in Computer Chemistry
  • 2012
    Title Network-Based Methods for Computational Diagnostics by Means of R
    DOI 10.1007/978-3-7091-0947-2_11
    Type Book Chapter
    Author Mueller L
    Publisher Springer Nature
    Pages 185-197
  • 2014
    Title Netmes: Assessing Gene Network Inference Algorithms by Network-Based Measures
    DOI 10.4137/ebo.s13481
    Type Journal Article
    Author Altay G
    Journal Evolutionary Bioinformatics
    Link Publication
  • 2013
    Title MULTIVARIATE LINEAR QSPR/QSAR MODELS: RIGOROUS EVALUATION OF VARIABLE SELECTION FOR PLS
    DOI 10.5936/csbj.201302007
    Type Journal Article
    Author Varmuza K
    Journal Computational and Structural Biotechnology Journal
    Pages 1-10
    Link Publication
  • 2013
    Title Enhancing systems medicine beyond genotype data by dynamic patient signatures: having information and using it too
    DOI 10.3389/fgene.2013.00241
    Type Journal Article
    Author Emmert-Streib F
    Journal Frontiers in Genetics
    Pages 241
    Link Publication
  • 2013
    Title On Sphere-Regular Graphs and the Extremality of Information-Theoretic Network Measures.
    Type Journal Article
    Author Kraus V
    Journal MATCH: Communications in Mathematical and in Computer Chemistry
  • 2013
    Title [COMMODE] a large-scale database of molecular descriptors using compounds from PubChem
    DOI 10.1186/1751-0473-8-22
    Type Journal Article
    Author Dander A
    Journal Source Code for Biology and Medicine
    Pages 22
    Link Publication
  • 2013
    Title The Discrimination Power of Structural SuperIndices
    DOI 10.1371/journal.pone.0070551
    Type Journal Article
    Author Dehmer M
    Journal PLoS ONE
    Link Publication
  • 2013
    Title Large-scale analysis of structural branching measures
    DOI 10.1007/s10910-013-0294-9
    Type Journal Article
    Author Schutte M
    Journal Journal of Mathematical Chemistry
    Pages 805-819
  • 2014
    Title A computational approach to construct a multivariate complete graph invariant
    DOI 10.1016/j.ins.2013.11.008
    Type Journal Article
    Author Dehmer M
    Journal Information Sciences
    Pages 200-208
  • 2012
    Title Towards Information Inequalities for Generalized Graph Entropies
    DOI 10.1371/journal.pone.0038159
    Type Journal Article
    Author Sivakumar L
    Journal PLoS ONE
    Link Publication
  • 2012
    Title Information Indices with High Discriminative Power for Graphs
    DOI 10.1371/journal.pone.0031214
    Type Journal Article
    Author Dehmer M
    Journal PLoS ONE
    Link Publication
  • 2011
    Title Generalized graph entropies
    DOI 10.1002/cplx.20379
    Type Journal Article
    Author Dehmer M
    Journal Complexity
    Pages 45-50
  • 2011
    Title Connections between Classical and Parametric Network Entropies
    DOI 10.1371/journal.pone.0015733
    Type Journal Article
    Author Dehmer M
    Journal PLoS ONE
    Link Publication
  • 2011
    Title On Distance-Based Entropy Measures.
    Type Book Chapter
    Author Dehmer M
  • 2011
    Title Structural Measures for Network Biology Using QuACN
    DOI 10.1186/1471-2105-12-492
    Type Journal Article
    Author Mueller L
    Journal BMC Bioinformatics
    Pages 492
    Link Publication
  • 2011
    Title Quantifying Structural Complexity of Graphs: Information Measures in Mathematical Chemistry.
    Type Book Chapter
    Author Dehmer M
  • 2011
    Title Information Theory of Networks
    DOI 10.3390/sym3040767
    Type Journal Article
    Author Dehmer M
    Journal Symmetry
    Pages 767-779
    Link Publication
  • 2013
    Title B-cell lymphoma gene regulatory networks: biological consistency among inference methods
    DOI 10.3389/fgene.2013.00281
    Type Journal Article
    Author De Matos Simoes R
    Journal Frontiers in Genetics
    Pages 281
    Link Publication
  • 2013
    Title Quantitative Network Measures as Biomarkers for Classifying Prostate Cancer Disease States: A Systems Approach to Diagnostic Biomarkers
    DOI 10.1371/journal.pone.0077602
    Type Journal Article
    Author Dehmer M
    Journal PLoS ONE
    Link Publication
  • 2013
    Title Large-Scale Evaluation of Molecular Descriptors by Means of Clustering
    DOI 10.1371/journal.pone.0083956
    Type Journal Article
    Author Dehmer M
    Journal PLoS ONE
    Link Publication
  • 0
    Title Advances in Network complexity.
    Type Other
    Author Dehmer M
  • 0
    Title Statistical Modeling of Molecular Descriptors in QSAR/QSPR.
    Type Other
    Author Bonchev D Et Al

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