DM840 - Algorithms in Cheminformatics

Algorithms in Cheminformatics

DM840, Spring 2018

Daniel Merkle


05.11.2018: New Weekly Notes, slides and new articles are online.

24.10.2018: The second mandatory assignment is announced.

22.10.2018: New Weekly Notes are online. Deadline for the first project was finalised to October 31.

11.10.2018: New Weekly Notes, slides and new articles are online.

01.10.2018: New Weekly Notes, slides and new articles are online.

24.09.2018: New Weekly Notes, new slides are online.

17.09.2018: New Weekly Notes, new slides, new notes, and additional material for the first mandatort assignment is online.

10.09.2018: New Weekly Notes, new slides, new notes, new articles online.

29.08.2018: Site Launch.


The lectures will always start 15 minutes after the full hour.

All lectures, unless stated explicitly, are in the IMADA seminar room.

Weekly Notes

The slides material presented in the lectures can be found in the Blackboard System.

DateTopicWeekly Notes
Week 36 Introduction, Course overview, Polya enumeration (teaser), Double Pushout Approach Week 36
Week 37 Double Pushout Approach, Graph Grammars, Exploring Chemical Spaces via Graph Grammars, Subgraph Isomorphism (Ullmann algorithm), Introduction to the first mandatory project Week 37
Week 38 ILP formulation for autocatalysis, Graph isomorphism, McKay's Canonical Graph Labeling Algorithm, Additional information for the first Mandatory Assignment ("revive" from the strategy framework) Week 38
Week 39 Even more on graph canonicalisation (traces), SMILES, starting Ring Perception Week 39
Week 40 Ring Perception, MCB, Horton's algorithm, de Pina's algorithm Week 40
Week 41 FinishingRing Perception, Starting Petri Nets Week 41
Week 43 Petri Nets Week 43
Week 44 Petri Nets, Introduction to Mandatory Assignment 2 Exercises
Week 45 K Shortest Hyperpaths (Synthesis Planning), Introduction to Mandatory Assignment 2 Week 45

Office Hours

Just write a short mail, and come by.

  • Office: IMADA, ě14-602b-2 map.
  • Phone: 2322
  • E-mail: daniel


In addition to the books we will use original articles as a source of information.

Course Description

The official course description can be found here.

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