Try rare probabilitic masking to reinforce context-dependency

Use relevant bits from anonym2 branch. Maybe mask with proba=0.1. Important: use validation set where no masking. The idea is to monitor the effect of masking on the generalization of unmasked data and compare with no masking on unmaked (the usual setup).

[tlemberger]

proba masking

smtag-convert2th -c 190414 -f 5X_L1200_fig_article_embeddings_128_proba_masking -X5 -L1200 -E ".//fig/caption" -A ".//sd-tag[@type='molecule']",".//sd-tag[@type='gene']",".//sd-tag[@type='protein']",".//sd-tag[@type='subcellular']",".//sd-tag[@type='cell']",".//sd-tag[@type='tissue']",".//sd-tag[@type='organism']",".//sd-tag[@category='assay']"  --noocr --noviz -p rack

Build a composite training set where train/ is probabilitically (10%) masked and valid/ and test/ are unmasked.

Train

smtag-meta -f composite_train_proba_valid_normal -E50 -Z32 -R0.005 -D0.2 -o small_molecule,geneprod,subcellular,cell,tissue,organism,assay -k 7,7,7,7,7,7,7,7,7,7 -n 128,128,128,128,128,128,128,128,128,128 -g 3,3,3,3,3,3,3,3,3,3 -p rack

composite_train_proba_valid_normal_small_molecule_geneprod_subcellular_cell_tissue_organism_assay_2019-09-10-22-32.

compared to

smtag-meta -f 5X_L1200_article_embeddings_128 -E20 -Z32 -R0.005 -D0.2 -o small_molecule,geneprod,subcellular,cell,tissue,organism,assay -k 7,7,7,7,7,7,7,7,7,7 -n 128,128,128,128,128,128,128,128,128,128 -g 3,3,3,3,3,3,3,3,3,3

[tlemberger]

no difference :-(