Weekly Notes for Week 20

• This weeks topics:

  • Integer Linear Programming (ILP), in particular autocatalytic solutions.
  • Ring perception.
  • Minimum cycle bases: Horton’s algorithm and de Pina’s algorithm.

• Exercises:

  • Exercise Sheet 04 (preliminary)
  • Exercise Sheet 03 for the ILP part

• Reading Material:

  • Mandatory (ring perception): Franziska Berger et al., Counterexamples in Chemical Ring Perception
  • Mandatory: Hanser T, Jauffret P, Kaufmann G (1996), A New Algorithm for Exhaustive Ring Perception in a Molecular Graph. J Chem Inf Comput Sci 36(6):1146-1152.
  • Voluntary: de Pina runtime / minimum cycle bases article

• Additional slides:

  • ILP slides
  • Ring-perception notes
  • Horton / de Pina / minimum cycle bases
  • Additional cycle-basis slides
  • MOD framework addon

• Additional material:

  • ILP code fragments
  • The canonicalization and network-expansion material from week 19 remains relevant.