Mathematics in Computer Science

, Volume 7, Issue 3, pp 275–292 | Cite as

On the Complexity of Reconstructing Chemical Reaction Networks

  • Rolf Fagerberg
  • Christoph Flamm
  • Daniel MerkleEmail author
  • Philipp Peters
  • Peter F. Stadler


The analysis of the structure of chemical reaction networks is crucial for a better understanding of chemical processes. Such networks are well described as hypergraphs. However, due to the available methods, analyses regarding network properties are typically made on standard graphs derived from the full hypergraph description, e.g. on the so-called species and reaction graphs. However, a reconstruction of the underlying hypergraph from these graphs is not necessarily unique. In this paper, we address the problem of reconstructing a hypergraph from its species and reaction graph and show NP-completeness of the problem in its Boolean formulation. Furthermore we study the problem empirically on random and real world instances in order to investigate its computational limits in practice.


NP-completeness Hypergraph reconstruction Reduction Declarative solvers Chemical reaction network 


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Copyright information

© Springer Basel 2013

Authors and Affiliations

  • Rolf Fagerberg
    • 1
  • Christoph Flamm
    • 2
  • Daniel Merkle
    • 1
    Email author
  • Philipp Peters
    • 1
  • Peter F. Stadler
    • 2
    • 3
    • 4
    • 5
    • 6
    • 7
  1. 1.Department of Mathematics and Computer ScienceUniversity of Southern DenmarkOdense MDenmark
  2. 2.Institute for Theoretical ChemistryUniversity of ViennaViennaAustria
  3. 3.Bioinformatics Group, Department of Computer ScienceInterdisciplinary Center for BioinformaticsLeipzigGermany
  4. 4.Max Planck Institute for Mathematics in the SciencesLeipzigGermany
  5. 5.Fraunhofer Institute for Cell Therapy and ImmunologyLeipzigGermany
  6. 6.Center for non-coding RNA in Technology and HealthUniversity of CopenhagenFrederiksberg CDenmark
  7. 7.Santa Fe InstituteSanta FeUSA

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