diff --git a/downloads-generation/models_class1_allele_specific_single_kim2014_only/GENERATE.sh b/downloads-generation/models_class1_allele_specific_single_kim2014_only/GENERATE.sh index 3d7eb35498d406522bd199d440bff48e43be6bf2..80c7e46a5cf842c1b3c5e9aba1fa4b8cb547dc8b 100644 --- a/downloads-generation/models_class1_allele_specific_single_kim2014_only/GENERATE.sh +++ b/downloads-generation/models_class1_allele_specific_single_kim2014_only/GENERATE.sh @@ -40,7 +40,7 @@ time mhcflurry-class1-allele-specific-cv-and-train \ --imputer-description imputer.json \ --train-data "$(mhcflurry-downloads path data_kim2014)/bdata.2009.mhci.public.1.txt" \ --test-data "$(mhcflurry-downloads path data_kim2014)/bdata.2013.mhci.public.blind.1.txt" \ - --min-samples-per-allele 70 \ + --min-samples-per-allele 50 \ --out-cv-results cv.csv \ --out-production-results production.csv \ --out-models models \ diff --git a/downloads-generation/models_class1_allele_specific_single_kim2014_only/imputer.json b/downloads-generation/models_class1_allele_specific_single_kim2014_only/imputer.json index f761431606102dd65adadb5dcdcf036a966bee9c..c17f86cc5c2ebecb0bfcf333cab86dbb8cf1b96a 100644 --- a/downloads-generation/models_class1_allele_specific_single_kim2014_only/imputer.json +++ b/downloads-generation/models_class1_allele_specific_single_kim2014_only/imputer.json @@ -3,6 +3,6 @@ "n_burn_in": 5, "n_imputations": 50, "n_nearest_columns": 25, - "min_observations_per_peptide": 5, - "min_observations_per_allele": 100 + "min_observations_per_peptide": 2, + "min_observations_per_allele": 2 } diff --git a/downloads-generation/models_class1_allele_specific_single_kim2014_only/models.py b/downloads-generation/models_class1_allele_specific_single_kim2014_only/models.py index 6375cd4510bfebadd4df529a6884c1eb1632f162..6e20239c8185561217aa5e38e6fb4c2ac0d30677 100644 --- a/downloads-generation/models_class1_allele_specific_single_kim2014_only/models.py +++ b/downloads-generation/models_class1_allele_specific_single_kim2014_only/models.py @@ -3,13 +3,13 @@ from mhcflurry.class1_allele_specific.train import HYPERPARAMETER_DEFAULTS import json models = HYPERPARAMETER_DEFAULTS.models_grid( - #impute=[False, True], - impute=[False], + impute=[False, True], activation=["tanh"], layer_sizes=[[12], [64], [128]], embedding_output_dim=[8, 32, 64], dropout_probability=[0, .1, .25], - # fraction_negative=[0, .1, .2], + pretrain_decay=["1 / (1+epoch)**2"], + fraction_negative=[0, .1, .2], n_training_epochs=[250]) sys.stderr.write("Models: %d\n" % len(models))