Characteristics and Interrelations between Methods for Comparing Relational Structures
Characteristics and Interrelations between Methods for Comparing Relational Structures
Disciplines
Mathematics (100%)
Keywords
-
Similarity,
Relational Structures,
Graph Measures,
Discrete Mathematics,
Graph Theory
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.
- 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
-
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