get pbg_metrics data frames
ingest_training_stats(
simba_ref,
gg_dirname = "graph0",
tr_output = "model",
jsonpath
)reference to simba module
character(1) the dirname specified for build_and_train_pbg, defaults to 'graph0'
character(1) the output specified for build_and_train_pbg defaults to 'model'
character(1) path to training_stats.json
a list with two data.frames of training statistics
# full run-based, commented out as too long
# p3k = get_10x3kpbmc_path(overwrite=TRUE) # allow repetition
# ref = simba_ref()
# pp = ref$read_h5ad(p3k)
# bb = basic_preproc(pp, simba_ref=ref)
# gg = build_and_train_pbg( bb, simba_ref=ref )
# ts = ingest_training_stats(ref)
# head(ts$df1)
#
# use archived pbg output
#
tpath = system.file(file.path("extdata", "pbg3k.tar.xz"), package="Simba4Bioc")
untar(tpath, exdir = tempdir())
jsonpath = paste0(tempdir(), "/pbg/graph0/model/training_stats.json")
ts = ingest_training_stats(jsonpath=jsonpath)
head(ts$df1)
#> lhs_partition rhs_partition index stats_count stats_metrics_loss
#> 1 0 0 1 2168828 22.12636
#> 2 0 0 2 2168828 21.75738
#> 3 0 0 3 2168828 21.68153
#> 4 0 0 4 2168828 21.63829
#> 5 0 0 5 2168828 21.59264
#> 6 0 0 6 2168828 21.56029
#> stats_metrics_reg stats_metrics_violators_lhs stats_metrics_violators_rhs
#> 1 0 46.32678 32.14047
#> 2 0 40.77371 28.66915
#> 3 0 39.70222 28.13866
#> 4 0 39.12694 27.83895
#> 5 0 38.54704 27.51283
#> 6 0 38.03881 27.23536
#> eval_stats_before_count eval_stats_before_metrics_loss
#> 1 114148 22.83474
#> 2 114148 21.95265
#> 3 114148 21.87745
#> 4 114148 21.87963
#> 5 114148 21.87675
#> 6 114148 21.88132
#> eval_stats_before_metrics_pos_rank eval_stats_before_metrics_mrr
#> 1 50.38945 0.05141226
#> 2 37.69553 0.07409224
#> 3 37.43978 0.07544834
#> 4 37.53849 0.07443034
#> 5 37.59927 0.07421614
#> 6 37.73723 0.07349054
#> eval_stats_before_metrics_r1 eval_stats_before_metrics_r10
#> 1 0.009500823 0.0995243
#> 2 0.015720819 0.1642123
#> 3 0.016706381 0.1666083
#> 4 0.015931072 0.1650095
#> 5 0.015865368 0.1638005
#> 6 0.015501805 0.1623594
#> eval_stats_before_metrics_r50 eval_stats_before_metrics_auc
#> 1 0.5015200 0.5064259
#> 2 0.6985668 0.6289554
#> 3 0.7022593 0.6335372
#> 4 0.7006693 0.6332349
#> 5 0.6998765 0.6336554
#> 6 0.6982426 0.6340759
#> eval_stats_after_count eval_stats_after_metrics_loss
#> 1 114148 21.95206
#> 2 114148 21.88233
#> 3 114148 21.87859
#> 4 114148 21.87929
#> 5 114148 21.88089
#> 6 114148 21.89812
#> eval_stats_after_metrics_pos_rank eval_stats_after_metrics_mrr
#> 1 37.72470 0.07398883
#> 2 37.48253 0.07540224
#> 3 37.53962 0.07441796
#> 4 37.59962 0.07433443
#> 5 37.70173 0.07379338
#> 6 37.78983 0.07285376
#> eval_stats_after_metrics_r1 eval_stats_after_metrics_r10
#> 1 0.01556313 0.1638180
#> 2 0.01670200 0.1665995
#> 3 0.01586537 0.1648868
#> 4 0.01589603 0.1642210
#> 5 0.01586537 0.1629814
#> 6 0.01508568 0.1613695
#> eval_stats_after_metrics_r50 eval_stats_after_metrics_auc epoch_idx
#> 1 0.6976469 0.6294591 0
#> 2 0.7011424 0.6343738 1
#> 3 0.7005642 0.6325691 2
#> 4 0.6997407 0.6350002 3
#> 5 0.6988559 0.6327487 4
#> 6 0.6979798 0.6325122 5
#> edge_path_idx edge_chunk_idx
#> 1 0 0
#> 2 0 0
#> 3 0 0
#> 4 0 0
#> 5 0 0
#> 6 0 0