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Characteristics and Interrelations between Methods for Comparing Relational Structures

Characteristics and Interrelations between Methods for Comparing Relational Structures

Matthias Dehmer (ORCID: 0000-0001-8454-5857)
  • Grant DOI 10.55776/P26142
  • Funding program Principal Investigator Projects
  • Status ended
  • Start December 1, 2013
  • End November 30, 2018
  • Funding amount € 197,956
  • Project website

Disciplines

Mathematics (100%)

Keywords

    Similarity, Relational Structures, Graph Measures, Discrete Mathematics, Graph Theory

Abstract Final report

To develop methods for analyzing graphs is a multidisciplinary problem because the underlying research problems have been widely spread over scientific disciplines. Particularly after the hype dealing with examining global properties of complex networks, it turned out that quantitative methods for exploring graphs such as graph similarity and other graph measures are crucial. In this project, we put the emphasis on investigating methods to measure the structural similarity of graphs generally referred to as graph matching. Particularly we explore mathematical properties of such methods in depth. Early contributions deal with exploring isomorphic and subgraph isomorphic relations between graphs. But the resulting graph similarity measures or metrics are, for general graphs, computationally inefficient because the isomorphism and subgraph isomorphism problems are known for their non-feasible time complexity. Consequently, other approaches based on error-tolerant graph comparison have also been developed and investigated. Importantly, all these techniques have been spread across a range of disciplines but a thorough analysis of their mathematical properties has not been performed so far. The goal of this research project to investigate mathematical properties of graph comparison methods as there is a lack of rather deep results in this field. For instance, this relates to prove interrelations between the graph comparison methods and examining their structural interpretation.

The goal of this research project was to investigate mathematical properties of graph comparison methods. Our results comprise developing new graph similarity techniques as well as investigating their relationships. For instance, this relates to prove inequalities between the graph comparison methods representing graph similarity or distance measures and examining their structural interpretation. Developing comparative graph methods is a multidisciplinary problem because the underlying research problems have been widely spread over scientific disciplines. Particularly after the hype dealing with examining global properties of complex networks, it turned out that quantitative methods for exploring graphs such as graph similarity and other graph measures are crucial. In this project, we have investigated methods to measure the structural similarity of graphs generally referred to as graph matching. Also, we explored mathematical properties of such methods in depth. Also, we have investigated topological indices which often serve as an important component to define graph similarity or distance. Given the fact that early contributions dealt with exploring isomorphic and subgraph isomorphic relations between graphs, we here put the emphasis on methods without computing graph isomorphism. Hence, other approaches based on error-tolerant graph comparison have also been developed and investigated. So, all these techniques have been spread across a range of disciplines and we performed a thorough analysis of mathematical properties of selected comparative methods.

Research institution(s)
  • Priv.-Univ. für Gesundheitswissenschaften, Medizinische Informatik und Technik - 100%
International project participants
  • Terry Caelli, University of Queensland - Australia
  • Frank Emmert-Streib, Tampere University - Finland
  • Zsolt Tuza, University of Pannonia - Hungary
  • Abbe Mowshowitz, New York City College - USA

Research Output

  • 2188 Citations
  • 46 Publications
Publications
  • 2016
    Title samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files
    DOI 10.1093/bioinformatics/btw475
    Type Journal Article
    Author Stupnikov A
    Journal Bioinformatics
    Pages 3345-3347
    Link Publication
  • 2016
    Title The Process of Analyzing Data is the Emergent Feature of Data Science
    DOI 10.3389/fgene.2016.00012
    Type Journal Article
    Author Emmert-Streib F
    Journal Frontiers in Genetics
    Pages 12
    Link Publication
  • 2015
    Title The Hosoya Entropy of a Graph
    DOI 10.3390/e17031054
    Type Journal Article
    Author Mowshowitz A
    Journal Entropy
    Pages 1054-1062
    Link Publication
  • 2015
    Title Discrimination power of graph measures based on complex zeros of the partial Hosoya polynomial
    DOI 10.1016/j.amc.2014.10.048
    Type Journal Article
    Author Dehmer M
    Journal Applied Mathematics and Computation
    Pages 352-355
  • 2018
    Title Interplay between SIR-based disease spreading and awareness diffusion on multiplex networks
    DOI 10.1016/j.jpdc.2018.01.001
    Type Journal Article
    Author Zheng C
    Journal Journal of Parallel and Distributed Computing
    Pages 20-28
  • 2018
    Title Harnessing the biological complexity of Big Data from LINCS gene expression signatures
    DOI 10.1371/journal.pone.0201937
    Type Journal Article
    Author Musa A
    Journal PLOS ONE
    Link Publication
  • 2018
    Title Graph measures with high discrimination power revisited: A random polynomial approach
    DOI 10.1016/j.ins.2018.07.072
    Type Journal Article
    Author Dehmer M
    Journal Information Sciences
    Pages 407-414
  • 2018
    Title Identifying anticancer peptides by using a generalized chaos game representation
    DOI 10.1007/s00285-018-1279-x
    Type Journal Article
    Author Ge L
    Journal Journal of Mathematical Biology
    Pages 441-463
  • 2015
    Title Encoding structural information uniquely with polynomial-based descriptors by employing the Randic matrix
    DOI 10.1016/j.amc.2015.04.115
    Type Journal Article
    Author Dehmer M
    Journal Applied Mathematics and Computation
    Pages 164-168
  • 2014
    Title A case study of cracks in the scientific enterprise: Reinvention of information-theoretic measures for graphs
    DOI 10.1002/cplx.21540
    Type Journal Article
    Author Dehmer M
    Journal Complexity
    Pages 10-14
  • 2014
    Title Functional and genetic analysis of the colon cancer network
    DOI 10.1186/1471-2105-15-s6-s6
    Type Journal Article
    Author Emmert-Streib F
    Journal BMC Bioinformatics
    Link Publication
  • 2014
    Title Untangling statistical and biological models to understand network inference: the need for a genomics network ontology
    DOI 10.3389/fgene.2014.00299
    Type Journal Article
    Author Emmert-Streib F
    Journal Frontiers in Genetics
    Pages 299
    Link Publication
  • 2017
    Title Lessons from the Human Genome Project: Modesty, Honesty, and Realism
    DOI 10.3389/fgene.2017.00184
    Type Journal Article
    Author Emmert-Streib F
    Journal Frontiers in Genetics
    Pages 184
    Link Publication
  • 2017
    Title Prediction of therapeutic peptides by incorporating q-Wiener index into Chou’s general PseAAC
    DOI 10.1016/j.jbi.2017.09.011
    Type Journal Article
    Author Xu C
    Journal Journal of Biomedical Informatics
    Pages 63-69
  • 2017
    Title sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters
    DOI 10.1186/s12859-017-1731-8
    Type Journal Article
    Author Tripathi S
    Journal BMC Bioinformatics
    Pages 325
    Link Publication
  • 2017
    Title Quantitative Graph Theory: A new branch of graph theory and network science
    DOI 10.1016/j.ins.2017.08.009
    Type Journal Article
    Author Dehmer M
    Journal Information Sciences
    Pages 575-580
    Link Publication
  • 2017
    Title A review of connectivity map and computational approaches in pharmacogenomics
    DOI 10.1093/bib/bbw112
    Type Journal Article
    Author Musa A
    Journal Briefings in Bioinformatics
    Pages 506-523
    Link Publication
  • 2019
    Title A new coupled disease-awareness spreading model with mass media on multiplex networks
    DOI 10.1016/j.ins.2018.08.050
    Type Journal Article
    Author Xia C
    Journal Information Sciences
    Pages 185-200
  • 2018
    Title A calculus for measuring the elegance of abstract graphs
    DOI 10.1016/j.amc.2017.09.023
    Type Journal Article
    Author Mowshowitz A
    Journal Applied Mathematics and Computation
    Pages 142-148
  • 2018
    Title Feature selection of gene expression data for Cancer classification using double RBF-kernels
    DOI 10.1186/s12859-018-2400-2
    Type Journal Article
    Author Liu S
    Journal BMC Bioinformatics
    Pages 396
    Link Publication
  • 2017
    Title Principal minor version of Matrix-Tree theorem for mixed graphs
    DOI 10.1016/j.amc.2017.03.034
    Type Journal Article
    Author Yu G
    Journal Applied Mathematics and Computation
    Pages 27-30
  • 2017
    Title A comparative analysis of new graph distance measures and graph edit distance
    DOI 10.1016/j.ins.2017.03.036
    Type Journal Article
    Author Li T
    Journal Information Sciences
    Pages 15-21
  • 2017
    Title Protein Sequence Comparison Based on Physicochemical Properties and the Position-Feature Energy Matrix
    DOI 10.1038/srep46237
    Type Journal Article
    Author Yu L
    Journal Scientific Reports
    Pages 46237
    Link Publication
  • 2017
    Title Highly unique network descriptors based on the roots of the permanental polynomial
    DOI 10.1016/j.ins.2017.04.041
    Type Journal Article
    Author Dehmer M
    Journal Information Sciences
    Pages 176-181
  • 2017
    Title Network Entropies Based on Independent Sets and Matchings
    DOI 10.1016/j.amc.2017.02.021
    Type Journal Article
    Author Cao S
    Journal Applied Mathematics and Computation
    Pages 265-270
  • 2016
    Title Fifty years of graph matching, network alignment and network comparison
    DOI 10.1016/j.ins.2016.01.074
    Type Journal Article
    Author Emmert-Streib F
    Journal Information Sciences
    Pages 180-197
  • 2016
    Title Comparison of module detection algorithms in protein networks and investigation of the biological meaning of predicted modules
    DOI 10.1186/s12859-016-0979-8
    Type Journal Article
    Author Tripathi S
    Journal BMC Bioinformatics
    Pages 129
    Link Publication
  • 2015
    Title Biological networks: the microscope of the twenty-first century?
    DOI 10.3389/fgene.2015.00307
    Type Journal Article
    Author Emmert-Streib F
    Journal Frontiers in Genetics
    Pages 307
    Link Publication
  • 2015
    Title Discrimination Power of Polynomial-Based Descriptors for Graphs by Using Functional Matrices
    DOI 10.1371/journal.pone.0139265
    Type Journal Article
    Author Dehmer M
    Journal PLOS ONE
    Link Publication
  • 2015
    Title Graph distance measures based on topological indices revisited
    DOI 10.1016/j.amc.2015.05.072
    Type Journal Article
    Author Dehmer M
    Journal Applied Mathematics and Computation
    Pages 623-633
  • 2015
    Title Degree-based entropies of networks revisited
    DOI 10.1016/j.amc.2015.03.046
    Type Journal Article
    Author Cao S
    Journal Applied Mathematics and Computation
    Pages 141-147
  • 2015
    Title A method for inferring inequalities for probability values applied to complex networks
    DOI 10.1002/cplx.21718
    Type Journal Article
    Author Dehmer M
    Journal Complexity
    Pages 113-115
  • 2015
    Title A comparative analysis of the Tanimoto index and graph edit distance for measuring the topological similarity of trees
    DOI 10.1016/j.amc.2015.02.042
    Type Journal Article
    Author Dehmer M
    Journal Applied Mathematics and Computation
    Pages 242-250
  • 2015
    Title Entropy of Weighted Graphs with Randic Weights
    DOI 10.3390/e17063710
    Type Journal Article
    Author Chen Z
    Journal Entropy
    Pages 3710-3723
    Link Publication
  • 2015
    Title Bounds for degree-based network entropies
    DOI 10.1016/j.amc.2015.06.003
    Type Journal Article
    Author Chen Z
    Journal Applied Mathematics and Computation
    Pages 983-993
  • 2016
    Title Against Dataism and for Data Sharing of Big Biomedical and Clinical Data with Research Parasites
    DOI 10.3389/fgene.2016.00154
    Type Journal Article
    Author Emmert-Streib F
    Journal Frontiers in Genetics
    Pages 154
    Link Publication
  • 2014
    Title A Note on Distance-based Graph Entropies
    DOI 10.3390/e16105416
    Type Journal Article
    Author Chen Z
    Journal Entropy
    Pages 5416-5427
    Link Publication
  • 2014
    Title Extremality of degree-based graph entropies
    DOI 10.1016/j.ins.2014.03.133
    Type Journal Article
    Author Cao S
    Journal Information Sciences
    Pages 22-33
  • 2014
    Title Interrelations of Graph Distance Measures Based on Topological Indices
    DOI 10.1371/journal.pone.0094985
    Type Journal Article
    Author Dehmer M
    Journal PLoS ONE
    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 Structural Differentiation of Graphs Using Hosoya-Based Indices
    DOI 10.1371/journal.pone.0102459
    Type Journal Article
    Author Dehmer M
    Journal PLoS ONE
    Link Publication
  • 2014
    Title Entropy bounds for dendrimers
    DOI 10.1016/j.amc.2014.05.105
    Type Journal Article
    Author Chen Z
    Journal Applied Mathematics and Computation
    Pages 462-472
  • 2014
    Title NetBioV: an R package for visualizing large network data in biology and medicine
    DOI 10.1093/bioinformatics/btu384
    Type Journal Article
    Author Tripathi S
    Journal Bioinformatics
    Pages 2834-2836
    Link Publication
  • 2014
    Title Connections between generalized graph entropies and graph energy
    DOI 10.1002/cplx.21539
    Type Journal Article
    Author Dehmer M
    Journal Complexity
    Pages 35-41
  • 2018
    Title Properties of graph distance measures by means of discrete inequalities
    DOI 10.1016/j.apm.2018.01.027
    Type Journal Article
    Author Dehmer M
    Journal Applied Mathematical Modelling
    Pages 739-749
    Link Publication
  • 2014
    Title Gene regulatory networks and their applications: understanding biological and medical problems in terms of networks
    DOI 10.3389/fcell.2014.00038
    Type Journal Article
    Author Emmert-Streib F
    Journal Frontiers in Cell and Developmental Biology
    Pages 38
    Link Publication

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+43 1 505 67 40

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