├── ASP └── new_wmaxsat_acyclic_causes.pl ├── R ├── .DS_Store ├── .RData ├── .Rhistory ├── bootstrap.R ├── conductIndepTests.R ├── graph_utils │ ├── cpag_to_mc.R │ ├── dag2causes.R │ ├── directed_reachable.R │ ├── pag22mag.R │ ├── pattern2dag.R │ └── unshielded_colliders.R ├── learn.R ├── load.R ├── mods │ ├── fci_mod.R │ ├── jointcont.R │ ├── jointprior.R │ ├── networkfamily.mod.R │ ├── pc.cons.intern.R │ ├── pc_mod.R │ ├── pdsep.R │ ├── source_pcalg_checkTriple.r │ ├── source_pcalg_fci.r │ └── source_pcalg_pc.cons.intern.r ├── pipeline.R ├── read_data.R ├── simulateData.R ├── simulator │ ├── .DS_Store │ ├── createData.R │ ├── divideSamples.R │ ├── experimentConfiguration.R │ ├── generateModel.R │ ├── generateSampleData.R │ └── simul_interventions.R ├── solvers │ ├── .DS_Store │ ├── .Rhistory │ ├── build_tree.R │ ├── learn.asp.R │ ├── learn.asp.iterative.R │ ├── learn.asp.short.R │ ├── learn.bnlearn.R │ ├── learn.pcalg.fci.R │ ├── objective.R │ ├── parse_ASP_solution.R │ ├── parse_asp_indeps.R │ ├── writeAspSets.R │ ├── writeAspSets.old.R │ ├── writeIndepsToFile.R │ ├── write_causal_constraint.R │ └── write_constraint.R ├── tests │ ├── .Rhistory │ ├── gaussCIcontexttest.R │ ├── test.BIC.R │ ├── test.bayes.R │ ├── test.classic.R │ ├── test.fake.R │ ├── test.logp.R │ ├── test.logp.missing.R │ └── test.oracle.R └── utils │ ├── G2st.R │ ├── combn.R │ ├── dealstring2B.R │ ├── dec.to.bin.R │ ├── find_deterministic_relations.R │ ├── getm.R │ ├── index.R │ ├── mpinv.R │ ├── next_colex_comb.R │ └── tic.R ├── README.md ├── data ├── README.md ├── batch_preprocessing │ ├── batch_preprocess.py │ ├── batch_preprocess_4var.py │ ├── batch_preprocess_filter.py │ └── batch_preprocess_filter_4var.py ├── extract_data_mice.R ├── impc_quantitative_phen_matrix.RData ├── mouse.csv ├── nan-1.csv ├── nan-2.csv ├── nan-3.csv ├── nan-4.csv ├── nan-5.csv ├── real-1.csv ├── real-2.csv ├── real-3.csv ├── real-4.csv └── real-5.csv ├── plots ├── README.md ├── boxplot_ldf.Rscript └── 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