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Roc curves #49

Merged
merged 15 commits into from
Jan 4, 2023
279 changes: 279 additions & 0 deletions config/bdgraph_pip_random-5.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,279 @@
{
"benchmark_setup": {
"data": [
{
"data_id": "example1",
"graph_id": "random-5",
"parameters_id": "gwi",
"seed_range": [
1,
1
]
}
],
"evaluation": {
"benchmarks": {
"filename_prefix": "bdgraph_pip_random5/",
"show_seed": false,
"errorbar": true,
"errorbarh": false,
"scatter": true,
"path": true,
"text": false,
"ids": [
"bdgraph_pip"
]
},
"graph_true_plots": true,
"graph_true_stats": false,
"ggally_ggpairs": false,
"graph_plots": [
"bdgraph_pip"
],
"mcmc_traj_plots": [
{
"id": "gg99",
"burn_in": 100000,
"thinning": 100,
"functional": [
"score",
"size"
],
"active": false
},
{
"id": "bdgraph",
"burn_in": 500,
"thinning": 1,
"functional": [
"size"
],
"active": false
}
],
"mcmc_heatmaps": [
{
"id": "gg99",
"burn_in": 0.5,
"active": false
},
{
"id": "bdgraph",
"burn_in": 0.5,
"active": false
},
{
"id": "bdgraph_pip",
"burn_in": 0.5,
"active": false
}
],
"mcmc_autocorr_plots": [
{
"id": "gg99",
"burn_in": 150000,
"thinning": 500,
"lags": 50,
"functional": [
"score",
"size"
],
"active": false
}
]
}
},
"resources": {
"data": {
"iid": [
{
"id": "example1",
"standardized": false,
"sample_sizes": [
200
]
}
]
},
"graph": {
"bdgraph_graphsim": [
{
"id": "lattice",
"p": 50,
"graph": "lattice",
"class": null,
"size": null,
"prob": 0.2
},
{
"id": "random-1",
"p": 50,
"graph": "random",
"class": null,
"size": null,
"prob": 0.1
},
{
"id": "random-2",
"p": 10,
"graph": "random",
"class": null,
"size": null,
"prob": 0.2
},
{
"id": "random-5",
"p": 50,
"graph": "random",
"class": null,
"size": null,
"prob": 0.5
},
{
"id": "cluster",
"p": 50,
"graph": "cluster",
"class": null,
"size": 20,
"prob": 0.2
},
{
"id": "circle",
"p": 50,
"graph": "circle",
"class": null,
"size": null,
"prob": 0.2
},
{
"id": "hub",
"p": 50,
"graph": "hub",
"class": null,
"size": null,
"prob": 0.2
},
{
"id": "scale-free",
"p": 50,
"graph": "scale-free",
"class": null,
"size": null,
"prob": 0.2
}
]
},
"parameters": {
"bdgraph_rgwish": [
{
"id": "gwi",
"b": 3,
"threshold_conv": 0.0000001
}
]
},
"structure_learning_algorithms": {
"bnlearn_tabu": [
{
"id": "tabu-bge",
"score": "bge",
"iss": 1,
"issmu": [
0.001
],
"issw": null,
"l": 5,
"k": 1,
"prior": "uniform",
"beta": 1,
"timeout": null
}
],
"bdgraph": [
{
"id": "bdgraph",
"method": "ggm",
"algo": [
"bdmcmc"
],
"iter": 30000,
"gprior": 0.5,
"dfprior": 3,
"gstart": "empty",
"timeout": null,
"mcmc_seed": [
1
],
"thresh": 0.5,
"mcmc_estimator": [
"threshold"
],
"threshold": [
0.1,
0.3,
0.5,
0.7,
0.9,
1.0
],
"burnin_frac": 0.3
}
],
"gg99_singlepair": [
{
"id": "gg99",
"n_samples": [
20000
],
"datatype": "continuous",
"randomits": 100,
"prior": "ep",
"ascore": null,
"bscore": null,
"clq": 2,
"sep": 4,
"penalty": [
0.0
],
"mcmc_seed": [
1
],
"timeout": null,
"mcmc_estimator": [
"threshold"
],
"threshold": [
0.5
],
"burnin_frac": 0.3
}
],
"bdgraph_pip": [
{
"id": "bdgraph_pip",
"method": "ggm",
"algo": [
"bdmcmc"
],
"iter": 3000,
"gprior": 0.5,
"dfprior": 3,
"startalg": "gg99",
"gstart": "empty",
"timeout": null,
"mcmc_seed": [
1
],
"thresh": 0.5,
"mcmc_estimator": [
"threshold"
],
"threshold": [
0.5
],
"burnin_frac": 0.3
}
]
}
}
}
12 changes: 8 additions & 4 deletions workflow/rules/evaluation/benchmarks/combine_ROC_data.R
Original file line number Diff line number Diff line change
Expand Up @@ -92,10 +92,14 @@ for (algorithm in active_algorithms) {
TPR_pattern_median = median(TPR_pattern),
TPR_pattern_q1 = quantile(TPR_pattern, probs = c(0.05)),
TPR_pattern_q3 = quantile(TPR_pattern, probs = c(0.95)),
FPR_pattern_mean = mean(FPRn_pattern),
FPR_pattern_median = median(FPRn_pattern),
FPR_pattern_q1 = quantile(FPRn_pattern, probs = c(0.05)),
FPR_pattern_q3 = quantile(FPRn_pattern, probs = c(0.95)),
FPR_pattern_mean = mean(FPR_pattern),
FPR_pattern_median = median(FPR_pattern),
FPR_pattern_q1 = quantile(FPR_pattern, probs = c(0.05)),
FPR_pattern_q3 = quantile(FPR_pattern, probs = c(0.95)),
FPRn_pattern_mean = mean(FPRn_pattern),
FPRn_pattern_median = median(FPRn_pattern),
FPRn_pattern_q1 = quantile(FPRn_pattern, probs = c(0.05)),
FPRn_pattern_q3 = quantile(FPRn_pattern, probs = c(0.95)),
TPR_skel_mean = mean(TP_skel / true_n_edges_skel),
TPR_skel_median = median(TP_skel / true_n_edges_skel),
TPR_skel_q1 = quantile(TP_skel / true_n_edges_skel, probs = c(0.05)),
Expand Down
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