About

A MCMC-based sampler to sample directed graphs G such that

• the underlying graph pr(G) is retained
• the number of directed edges is retained
• the number of simplices in its directed flag complex stays within given borders.

See TODO:ADD_PAPER for details.

Usage:

Install rust (e.g. via rustup.rs) an type

cargo build --release --bin sample

then run the code, e.g. via

target/release/sample -i input.flag -l experiment_label

for other features, call

target/release/sample --help

Roadmap:

• Fix Doku.
• Add proper citations

Citations:

• In early versions we heavily depended on flagser_count: https://github.com/luetge/flagser, but we implemented the algorithm and datastructures natively in rust. Anyway, they deserve credit.
• The example_flag_generator.py downloads data from https://github.com/lrvarshney/elegans (see https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1001066)

ToDo

• merge branches
• update readme
• decouple sampling distance from state saving interval
• save sampling distance, command line parameters, git commit hash etc in .hdf5 output file
• split state into precomputed "non"-state and actual thread-dependent state
  • ensure deterministic precomputed non-state or check for file existence
  • add command line parameters for different dirs
• enhance clo-parsing to take care of list of seeds
• clean sample.rs