Tecnical Notes

This page contains a list of minor technical reports about my research. Mostly the notes contains results that, though interesting, are of minor importance and therefore have not made it into a paper.

I use the notes mostly as a diary, where I write down results before I leave them for some other work, either temporarily or permanently. I can then use the notes to recall my ideas later on. The notes are not really written with another audience than myself in mind, but I have put them on-line in case anyone could find them useful. (If you do, please drop me a line. I'd love to be informed of something I've missed.)

Bioinformatics

2007

1. Results for localisation accuracy and for association tests in phased and unphased data
2. Little loss of information due to unknown phase: redux
3. An extension to the HapCluster algorithm for mapping interacting genes
4. Calculating the marginal likelihood of a local phylogeny
5. An O(n²t+t²) algorithm for computing the symmetric distance between t trees of size n — the running time here is actually incorrect; you can report the shared splits in this time, but not summerize them in a distance matrix as claimed.
6. An O(n²+output) algorithm for reporting all shared quartets between two trees

2005

1. Simulating Concerted Evolution
2. Mutation- and Null-clusters in GeneRecon

2004

1. Variations on LDRecon
2. Merging Trees into a DAG
3. A Browser for Pig Genome Data

2003

1. Deviations in QuickJoin Performance — the problem discussed in this one was later solved.
2. Experimental Evaluation of QuickJoin
3. Heuristics for Speeding Up Neighbour Joining
4. MPWA: Multiple Pair-Wise Alignments

State Space Methods (Excluding the Sweep-Line Method)

2004

1. A Simple State-Space Reduction Method

The Sweep-Line Method

2002

1. A Probabilistic Cut-off Technique
2. Sweep-Line Unfolding of the Reachability Graph
3. On The Complexity of the Sweep-Line Method.
4. On Garbage Collection in SweepChecker. This technique was used in the paper A Compositional Sweep-Line State Space Exploration Method, at FORTE 2002, to improve the experimental results quite significantly.
5. On Combining the Sweep-Line and Equivalence Method.

2001

1. Abstractions and Cut-off Predicates.
2. Equivalence Based Cut-off in the Sweep-Line Method. This idea was later published at ICATPN 2002, in the paper Analysing Infinite-State Systems by Combining Equivalence Reduction and the Sweep-Line Method.

Security Protocols

2002

1. Obtaining Finite-State Representations for SPL.

2001

1. From Security Protocol Language to Coloured Petri Nets.

Module Systems for Coloured Petri Nets

2000

1. Definition of a Module system for Coloured Petri Nets. (I never got around to finishing this one, because I had to work on my part A thesis, but I've put it here anyway so I wont forget it).
2. Requirements of a Module system for Coloured Petri Nets.