Tool and Benchmark of Scalable Counting of Minimal Trap Spaces and Fixed Points in Boolean Networks

Content

• approxasp: ApproxASP binary
• ganak: GANAK and ApproxMC binary

Run ApproxASP

We run our experiments in a linux environment

Please make sure that approxasp, t1_244.fix.lp, IS_t1_244.fix.lp are present in the current directory

Please make sure that approxasp is executable (execute: chmod +x approxasp)

Run Approxasp for t1_244.fix.lp with independent support IS_t1_244.fix.lp

./approxasp --conf 0.35 --sparse --useind IS_t1_244.fix.lp --asp t1_244.fix.lp

The command runs approxasp for tolerance = 0.8 and confidence = 0.2

Run GANAK & ApproxMC

We run our experiments in a linux environment

Install biodivine_aeon and sympy package using command pip install biodivine_aeon sympy, related link

Please make sure that ganak, test_to_cnf.py, test_to_cnf_approx.py, t1_244.bnet are present in the current directory

Please make sure that ganak is executable (execute: chmod +x ganak)

Run GANAK for t1_244.bnet

python test_to_cnf.py t1_244.bnet

Run ApproxMC for t1_244.bnet

python test_to_cnf_approx.py t1_244.bnet

The ganak is taken from the latest model counting competition.

Benchmark:

Benchmark of the experiment is available at https://zenodo.org/records/15141045.

Sources of other counters:

• tsconj: https://github.com/daemontus/tsconj
• fASP: https://github.com/giang-trinh/fASP
• k++ADF: https://www.cs.helsinki.fi/group/coreo/k++adf/
• AEON: https://github.com/sybila/biodivine-aeon-py

How to cite

TBA