Information Measures to Characterize Networks
Information Measures to Characterize Networks
Disciplines
Chemistry (25%); Mathematics (75%)
Keywords
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Information Measures,
Complex Networks,
Chemical Graph Theory,
Structural Complexity,
Chemometrics,
Information Theory
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.
- Kurt Varmuza, Technische Universität Wien , associated research partner
Research Output
- 738 Citations
- 39 Publications
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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