DM840 - Algorithms in Cheminformatics

Algorithms in Cheminformatics

DM840, Spring 2017

Daniel Merkle


29.05.2017: Exam Information online. All slides / articles / book chapter are online and final now.

09.03.2017: The lecture today is in the "IMADA Methods Lab" (the meeting room just next to the terminal room).

01.03.2017: New Weekly Notes, new slides, new notes, new articles online.

01.03.2017: Schedule was updated.

13.02.2017: MěD has been updated in the terminal room, all the example files for the first assignment work as expected now.

13.02.2017: No lectures in week 7.

06.02.2017: 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 06 Introduction, Course overview, Polya enumeration (teaser), Double Pushout Approach Week 06
Week 08 Double Pushout Approach, Graph Grammars, Exploring Chemical Spaces via Graph Grammars, Subgraph Isomorphism (Ullmann algorithm), Introduction to the first mandatory project Week 08
Week 09 Graph isomorphism, McKay's Canonical Graph Labeling Algorithm, Additional information for the first Mandatory Assignment ("revive" from the strategy framework) Week 09
Week 10 Even more on graph isomorphism (traces), SMILES, starting Ring Perception tba Week 10
Week 11 Ring Perception, MCB, Horton's algorithm, de Pina's algorithm tba Week 11
Week 12 Petri Nets see Weekly Notes for Week 13
Week 13 Petri Nets, Introduction to Second Mandatory Assingnment, K Shortest Hyperpaths Week 13, Exercises
Week 14 Petri Nets, Analytic Combinatorics
Week 15 Analytic Combinatorics, Generative Functions, Polya Counting
Week 16 more on Analytic Combinatorics, Generative Functions, Polya Counting, Quantitative structure-activity relationship QSAR, Molecular Descriptors, Principal Component Analysis PCA
Week 17 more on Quantitative structure-activity relationship QSAR, Molecular Descriptors, Principal Component Analysis PCA
Week 18 (Stochastic) Process Algebras
Week 19 Chemical Organizations, Polya Counting
Week 20 Polya Counting, Repetition Exercises for Week 20 (Polya Counting)
Week 20 Repetition of topics
Week 21 Repetition of topics

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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