diff --git a/.gitattributes b/.gitattributes index 28df5f900b358436f0267334b3e3e9af33f917ba..1949bcb340598fb70f8a7937f7f9b11a9fbbae88 100644 --- a/.gitattributes +++ b/.gitattributes @@ -53,3 +53,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text *.jpg filter=lfs diff=lfs merge=lfs -text *.jpeg filter=lfs diff=lfs merge=lfs -text *.webp filter=lfs diff=lfs merge=lfs -text +*.json filter=lfs diff=lfs merge=lfs -text diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..ce06304e7122e823f1f75bbf0e370cf04954a592 --- /dev/null +++ b/.gitignore @@ -0,0 +1,2 @@ +delete_tasks.sh +renumber_tasks.py \ No newline at end of file diff --git a/splits/dti/dti_bindingdb/test_tasks.txt b/splits/dti/dti_bindingdb/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..34c25e820a31474a0bdc2bb85eb4f074be0a4f96 --- /dev/null +++ b/splits/dti/dti_bindingdb/test_tasks.txt @@ -0,0 +1 @@ +task18_bindingdb_drugban_dti_test \ No newline at end of file diff --git a/splits/dti/dti_bindingdb/train_tasks.txt b/splits/dti/dti_bindingdb/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..1c371a7dac5218158529d670bb49344af267667b --- /dev/null +++ b/splits/dti/dti_bindingdb/train_tasks.txt @@ -0,0 +1 @@ +task16_bindingdb_drugban_dti_train \ No newline at end of file diff --git a/splits/dti/dti_bindingdb/validation_tasks.txt b/splits/dti/dti_bindingdb/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..ab2c3bb93bb9773acfb8fa54e4d3ffb29486fbc2 --- /dev/null +++ b/splits/dti/dti_bindingdb/validation_tasks.txt @@ -0,0 +1 @@ +task17_bindingdb_drugban_dti_valid \ No newline at end of file diff --git a/splits/dti/dti_biosnap/test_tasks.txt b/splits/dti/dti_biosnap/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..92dc65204169e98cd5da9381b2d3440d98f1097a --- /dev/null +++ b/splits/dti/dti_biosnap/test_tasks.txt @@ -0,0 +1 @@ +task21_biosnap_drugban_dti_test \ No newline at end of file diff --git a/splits/dti/dti_biosnap/train_tasks.txt b/splits/dti/dti_biosnap/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..1ddb47f436ebce6792096a6651272c41ad548d9c --- /dev/null +++ b/splits/dti/dti_biosnap/train_tasks.txt @@ -0,0 +1 @@ +task19_biosnap_drugban_dti_train \ No newline at end of file diff --git a/splits/dti/dti_biosnap/validation_tasks.txt b/splits/dti/dti_biosnap/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..dcb33f7427ea4aa97578d9c8027d190dccff6825 --- /dev/null +++ b/splits/dti/dti_biosnap/validation_tasks.txt @@ -0,0 +1 @@ +task20_biosnap_drugban_dti_valid \ No newline at end of file diff --git a/splits/dti/dti_human/test_tasks.txt b/splits/dti/dti_human/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..977a6e17fd68bb2500e4cb68badceb0381f8cc20 --- /dev/null +++ b/splits/dti/dti_human/test_tasks.txt @@ -0,0 +1 @@ +task24_human_drugban_dti_test \ No newline at end of file diff --git a/splits/dti/dti_human/train_tasks.txt b/splits/dti/dti_human/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..a718356b9b359042a132ac0d41b11f0d32f030a2 --- /dev/null +++ b/splits/dti/dti_human/train_tasks.txt @@ -0,0 +1 @@ +task22_human_drugban_dti_train \ No newline at end of file diff --git a/splits/dti/dti_human/validation_tasks.txt b/splits/dti/dti_human/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..e0713d418124014d8e09a35c3585c6ef8c0637c6 --- /dev/null +++ b/splits/dti/dti_human/validation_tasks.txt @@ -0,0 +1 @@ +task23_human_drugban_dti_valid \ No newline at end of file diff --git a/splits/mol_text/mol2text/test_tasks.txt b/splits/mol_text/mol2text/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..d9e6d17cd528ec1b04947019f0fd013978124529 --- /dev/null +++ b/splits/mol_text/mol2text/test_tasks.txt @@ -0,0 +1 @@ +task6_chebi20_mol2text_test \ No newline at end of file diff --git a/splits/mol_text/mol2text/train_tasks.txt b/splits/mol_text/mol2text/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..0062b5b8e3b3526a1ce936e79f29c57d727bea98 --- /dev/null +++ b/splits/mol_text/mol2text/train_tasks.txt @@ -0,0 +1 @@ +task4_chebi20_mol2text_train \ No newline at end of file diff --git a/splits/mol_text/mol2text/validation_tasks.txt b/splits/mol_text/mol2text/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..1c54771c66d61df695ef0e754406cdd750ef4275 --- /dev/null +++ b/splits/mol_text/mol2text/validation_tasks.txt @@ -0,0 +1 @@ +task5_chebi20_mol2text_validation \ No newline at end of file diff --git a/splits/mol_text/text2mol/test_tasks.txt b/splits/mol_text/text2mol/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..d569bad55aa0627c60088d46893a98a2db592ea1 --- /dev/null +++ b/splits/mol_text/text2mol/test_tasks.txt @@ -0,0 +1 @@ +task3_chebi20_text2mol_test \ No newline at end of file diff --git a/splits/mol_text/text2mol/train_tasks.txt b/splits/mol_text/text2mol/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..123d2b92cd04cfa956469f61c0f23a61ecf69936 --- /dev/null +++ b/splits/mol_text/text2mol/train_tasks.txt @@ -0,0 +1 @@ +task1_chebi20_text2mol_train \ No newline at end of file diff --git a/splits/mol_text/text2mol/validation_tasks.txt b/splits/mol_text/text2mol/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..5906f0cf8feb36cbb098bb5f6919e5f0159508d6 --- /dev/null +++ b/splits/mol_text/text2mol/validation_tasks.txt @@ -0,0 +1 @@ +task2_chebi20_text2mol_validation \ No newline at end of file diff --git a/splits/molnet/bace/test_tasks.txt b/splits/molnet/bace/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..ac12ef0df464ab05d7bc23dd34244b8394fd945a --- /dev/null +++ b/splits/molnet/bace/test_tasks.txt @@ -0,0 +1 @@ +task33_bace_molnet_test \ No newline at end of file diff --git a/splits/molnet/bace/train_tasks.txt b/splits/molnet/bace/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..859485a889a4d65770113c8e4dc7658bf4d189ef --- /dev/null +++ b/splits/molnet/bace/train_tasks.txt @@ -0,0 +1 @@ +task31_bace_molnet_train \ No newline at end of file diff --git a/splits/molnet/bace/validation_tasks.txt b/splits/molnet/bace/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..53e836cf4e5b1514223e9e1d21a7a41f50ac46bf --- /dev/null +++ b/splits/molnet/bace/validation_tasks.txt @@ -0,0 +1 @@ +task32_bace_molnet_valid \ No newline at end of file diff --git a/splits/molnet/bbbp/test_tasks.txt b/splits/molnet/bbbp/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..ab59ab9955e5ad8735ec45537097f77f068efb42 --- /dev/null +++ b/splits/molnet/bbbp/test_tasks.txt @@ -0,0 +1 @@ +task27_bbbp_molnet_test \ No newline at end of file diff --git a/splits/molnet/bbbp/train_tasks.txt b/splits/molnet/bbbp/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..337c7074a95ebc2ab96e2e62ccb5476b272b3144 --- /dev/null +++ b/splits/molnet/bbbp/train_tasks.txt @@ -0,0 +1 @@ +task25_bbbp_molnet_train \ No newline at end of file diff --git a/splits/molnet/bbbp/validation_tasks.txt b/splits/molnet/bbbp/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..e6d164d2a662a64b74615e21b2b621024ca6d53c --- /dev/null +++ b/splits/molnet/bbbp/validation_tasks.txt @@ -0,0 +1 @@ +task26_bbbp_molnet_valid \ No newline at end of file diff --git a/splits/molnet/clintox_ct_tox/test_tasks.txt b/splits/molnet/clintox_ct_tox/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..bf48e7e4aa6bef3606ca8af050f22584856b4bda --- /dev/null +++ b/splits/molnet/clintox_ct_tox/test_tasks.txt @@ -0,0 +1 @@ +task75_clintox_ct_tox_molnet_test \ No newline at end of file diff --git a/splits/molnet/clintox_ct_tox/train_tasks.txt b/splits/molnet/clintox_ct_tox/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..13b105bf7a0f39d2959dff2283b72c8537e168c3 --- /dev/null +++ b/splits/molnet/clintox_ct_tox/train_tasks.txt @@ -0,0 +1 @@ +task73_clintox_ct_tox_molnet_train \ No newline at end of file diff --git a/splits/molnet/clintox_ct_tox/validation_tasks.txt b/splits/molnet/clintox_ct_tox/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..674af0ca477577314ec0dfb9f5bbc465090f077d --- /dev/null +++ b/splits/molnet/clintox_ct_tox/validation_tasks.txt @@ -0,0 +1 @@ +task74_clintox_ct_tox_molnet_valid \ No newline at end of file diff --git a/splits/molnet/clintox_fda_approved/test_tasks.txt b/splits/molnet/clintox_fda_approved/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..2dab54adaf74e8e2411679d6bb77d7ff53cc62ea --- /dev/null +++ b/splits/molnet/clintox_fda_approved/test_tasks.txt @@ -0,0 +1 @@ +task72_clintox_fda_approved_molnet_test \ No newline at end of file diff --git a/splits/molnet/clintox_fda_approved/train_tasks.txt b/splits/molnet/clintox_fda_approved/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..cf5cea19b68b1f342ae6d19325b1ddda4b29394e --- /dev/null +++ b/splits/molnet/clintox_fda_approved/train_tasks.txt @@ -0,0 +1 @@ +task70_clintox_fda_approved_molnet_train \ No newline at end of file diff --git a/splits/molnet/clintox_fda_approved/validation_tasks.txt b/splits/molnet/clintox_fda_approved/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..bcbc80b66b9c83549d3a0b8f0365aa572ddd4779 --- /dev/null +++ b/splits/molnet/clintox_fda_approved/validation_tasks.txt @@ -0,0 +1 @@ +task71_clintox_fda_approved_molnet_valid \ No newline at end of file diff --git a/splits/molnet/hiv/test_tasks.txt b/splits/molnet/hiv/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..64bd29414270c2e5c219795bcd594411ae524535 --- /dev/null +++ b/splits/molnet/hiv/test_tasks.txt @@ -0,0 +1 @@ +task30_hiv_molnet_test \ No newline at end of file diff --git a/splits/molnet/hiv/train_tasks.txt b/splits/molnet/hiv/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..b4f90a43f38bda61e89d38a5c52a3af74d5d77fe --- /dev/null +++ b/splits/molnet/hiv/train_tasks.txt @@ -0,0 +1 @@ +task28_hiv_molnet_train \ No newline at end of file diff --git a/splits/molnet/hiv/validation_tasks.txt b/splits/molnet/hiv/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..3791da535d34ea4d416594ad77d74693aaae62a9 --- /dev/null +++ b/splits/molnet/hiv/validation_tasks.txt @@ -0,0 +1 @@ +task29_hiv_molnet_valid \ No newline at end of file diff --git a/splits/molnet/sider_blood_and_lymphatic_system_disorders/test_tasks.txt b/splits/molnet/sider_blood_and_lymphatic_system_disorders/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..592eb8762a65cefd7163f8790c53b8a7e016ea47 --- /dev/null +++ b/splits/molnet/sider_blood_and_lymphatic_system_disorders/test_tasks.txt @@ -0,0 +1 @@ +task123_sider_blood_and_lymphatic_system_disorders_molnet_test \ No newline at end of file diff --git a/splits/molnet/sider_blood_and_lymphatic_system_disorders/train_tasks.txt b/splits/molnet/sider_blood_and_lymphatic_system_disorders/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..410674ffe6188206e52195a03c4f2ee0d948690c --- /dev/null +++ b/splits/molnet/sider_blood_and_lymphatic_system_disorders/train_tasks.txt @@ -0,0 +1 @@ +task121_sider_blood_and_lymphatic_system_disorders_molnet_train \ No newline at end of file diff --git a/splits/molnet/sider_blood_and_lymphatic_system_disorders/validation_tasks.txt b/splits/molnet/sider_blood_and_lymphatic_system_disorders/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..5be3406fe0c3cba661930da5cd35f1f1346ef4d2 --- /dev/null +++ b/splits/molnet/sider_blood_and_lymphatic_system_disorders/validation_tasks.txt @@ -0,0 +1 @@ +task122_sider_blood_and_lymphatic_system_disorders_molnet_valid \ No newline at end of file diff --git a/splits/molnet/sider_cardiac_disorders/test_tasks.txt b/splits/molnet/sider_cardiac_disorders/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..04cfd17a05599a4d1bdfdae7859f98bfe5de9c63 --- /dev/null +++ b/splits/molnet/sider_cardiac_disorders/test_tasks.txt @@ -0,0 +1 @@ +task150_sider_cardiac_disorders_molnet_test \ No newline at end of file diff --git a/splits/molnet/sider_cardiac_disorders/train_tasks.txt b/splits/molnet/sider_cardiac_disorders/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..54a1860b5334da365b383ad185437f91b00976a9 --- /dev/null +++ b/splits/molnet/sider_cardiac_disorders/train_tasks.txt @@ -0,0 +1 @@ +task148_sider_cardiac_disorders_molnet_train \ No newline at end of file diff --git a/splits/molnet/sider_cardiac_disorders/validation_tasks.txt b/splits/molnet/sider_cardiac_disorders/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..e6c1921c8673a37cb4f48f82b3f83d2018673670 --- /dev/null +++ b/splits/molnet/sider_cardiac_disorders/validation_tasks.txt @@ -0,0 +1 @@ +task149_sider_cardiac_disorders_molnet_valid \ No newline at end of file diff --git a/splits/molnet/sider_congenital__familial_and_genetic_disorders/test_tasks.txt b/splits/molnet/sider_congenital__familial_and_genetic_disorders/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..d07bd39b8ad953492162db40902cc27e83295b8a --- /dev/null +++ b/splits/molnet/sider_congenital__familial_and_genetic_disorders/test_tasks.txt @@ -0,0 +1 @@ +task129_sider_congenital__familial_and_genetic_disorders_molnet_test \ No newline at end of file diff --git a/splits/molnet/sider_congenital__familial_and_genetic_disorders/train_tasks.txt b/splits/molnet/sider_congenital__familial_and_genetic_disorders/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..a7c2c7969aa09c2062a4b1bd514b2d42c7caf3ec --- /dev/null +++ b/splits/molnet/sider_congenital__familial_and_genetic_disorders/train_tasks.txt @@ -0,0 +1 @@ +task127_sider_congenital__familial_and_genetic_disorders_molnet_train \ No newline at end of file diff --git a/splits/molnet/sider_congenital__familial_and_genetic_disorders/validation_tasks.txt b/splits/molnet/sider_congenital__familial_and_genetic_disorders/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..1fcec1f4c6e150fecd24024a82d3da649e130ea2 --- /dev/null +++ b/splits/molnet/sider_congenital__familial_and_genetic_disorders/validation_tasks.txt @@ -0,0 +1 @@ +task128_sider_congenital__familial_and_genetic_disorders_molnet_valid \ No newline at end of file diff --git a/splits/molnet/sider_ear_and_labyrinth_disorders/test_tasks.txt b/splits/molnet/sider_ear_and_labyrinth_disorders/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..2a015587f82c204702f247a4aade015b56a80c9d --- /dev/null +++ b/splits/molnet/sider_ear_and_labyrinth_disorders/test_tasks.txt @@ -0,0 +1 @@ +task147_sider_ear_and_labyrinth_disorders_molnet_test \ No newline at end of file diff --git a/splits/molnet/sider_ear_and_labyrinth_disorders/train_tasks.txt b/splits/molnet/sider_ear_and_labyrinth_disorders/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..a8710a0a9893583c89a9c53338b4503a009550d8 --- /dev/null +++ b/splits/molnet/sider_ear_and_labyrinth_disorders/train_tasks.txt @@ -0,0 +1 @@ +task145_sider_ear_and_labyrinth_disorders_molnet_train \ No newline at end of file diff --git a/splits/molnet/sider_ear_and_labyrinth_disorders/validation_tasks.txt b/splits/molnet/sider_ear_and_labyrinth_disorders/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..d5b3c04e065175843d535cb56f693260cd0ed22e --- /dev/null +++ b/splits/molnet/sider_ear_and_labyrinth_disorders/validation_tasks.txt @@ -0,0 +1 @@ +task146_sider_ear_and_labyrinth_disorders_molnet_valid \ No newline at end of file diff --git a/splits/molnet/sider_endocrine_disorders/test_tasks.txt b/splits/molnet/sider_endocrine_disorders/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..17582e4c2a2c7b34b6061d0c7f90299f2bd7ee15 --- /dev/null +++ b/splits/molnet/sider_endocrine_disorders/test_tasks.txt @@ -0,0 +1 @@ +task114_sider_endocrine_disorders_molnet_test \ No newline at end of file diff --git a/splits/molnet/sider_endocrine_disorders/train_tasks.txt b/splits/molnet/sider_endocrine_disorders/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..57d17825423837bd58271e615d4eb691812d77c4 --- /dev/null +++ b/splits/molnet/sider_endocrine_disorders/train_tasks.txt @@ -0,0 +1 @@ +task112_sider_endocrine_disorders_molnet_train \ No newline at end of file diff --git a/splits/molnet/sider_endocrine_disorders/validation_tasks.txt b/splits/molnet/sider_endocrine_disorders/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..d4bf7949b99cc0828a108cf1dccece67849691d5 --- /dev/null +++ b/splits/molnet/sider_endocrine_disorders/validation_tasks.txt @@ -0,0 +1 @@ +task113_sider_endocrine_disorders_molnet_valid \ No newline at end of file diff --git a/splits/molnet/sider_eye_disorders/test_tasks.txt b/splits/molnet/sider_eye_disorders/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..4d119ef3d846d282c586cc4ba2a20bc1b511af24 --- /dev/null +++ b/splits/molnet/sider_eye_disorders/test_tasks.txt @@ -0,0 +1 @@ +task87_sider_eye_disorders_molnet_test \ No newline at end of file diff --git a/splits/molnet/sider_eye_disorders/train_tasks.txt b/splits/molnet/sider_eye_disorders/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..63629fc5bd2a8a3a820598073447c419951decaa --- /dev/null +++ b/splits/molnet/sider_eye_disorders/train_tasks.txt @@ -0,0 +1 @@ +task85_sider_eye_disorders_molnet_train \ No newline at end of file diff --git a/splits/molnet/sider_eye_disorders/validation_tasks.txt b/splits/molnet/sider_eye_disorders/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..720e1268e77f14c5ed5e4c525e4de98d1ecab353 --- /dev/null +++ b/splits/molnet/sider_eye_disorders/validation_tasks.txt @@ -0,0 +1 @@ +task86_sider_eye_disorders_molnet_valid \ No newline at end of file diff --git a/splits/molnet/sider_gastrointestinal_disorders/test_tasks.txt b/splits/molnet/sider_gastrointestinal_disorders/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..81c349d46db2c0e9635a4e74dc55df24d3977237 --- /dev/null +++ b/splits/molnet/sider_gastrointestinal_disorders/test_tasks.txt @@ -0,0 +1 @@ +task96_sider_gastrointestinal_disorders_molnet_test \ No newline at end of file diff --git a/splits/molnet/sider_gastrointestinal_disorders/train_tasks.txt b/splits/molnet/sider_gastrointestinal_disorders/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..dad812de3ecfaa352f36f1a22dce75be61ad8ae9 --- /dev/null +++ b/splits/molnet/sider_gastrointestinal_disorders/train_tasks.txt @@ -0,0 +1 @@ +task94_sider_gastrointestinal_disorders_molnet_train \ No newline at end of file diff --git a/splits/molnet/sider_gastrointestinal_disorders/validation_tasks.txt b/splits/molnet/sider_gastrointestinal_disorders/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..2988039521e6e1cee9f5e4cf8cf2d251ada39a29 --- /dev/null +++ b/splits/molnet/sider_gastrointestinal_disorders/validation_tasks.txt @@ -0,0 +1 @@ +task95_sider_gastrointestinal_disorders_molnet_valid \ No newline at end of file diff --git a/splits/molnet/sider_general_disorders_and_administration_site_conditions/test_tasks.txt b/splits/molnet/sider_general_disorders_and_administration_site_conditions/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..a387059371d2ce0500a57a58afe7fb73dad0ac36 --- /dev/null +++ b/splits/molnet/sider_general_disorders_and_administration_site_conditions/test_tasks.txt @@ -0,0 +1 @@ +task111_sider_general_disorders_and_administration_site_conditions_molnet_test \ No newline at end of file diff --git a/splits/molnet/sider_general_disorders_and_administration_site_conditions/train_tasks.txt b/splits/molnet/sider_general_disorders_and_administration_site_conditions/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..95b327a88138f05768ee1cb38ca435e08d42393e --- /dev/null +++ b/splits/molnet/sider_general_disorders_and_administration_site_conditions/train_tasks.txt @@ -0,0 +1 @@ +task109_sider_general_disorders_and_administration_site_conditions_molnet_train \ No newline at end of file diff --git a/splits/molnet/sider_general_disorders_and_administration_site_conditions/validation_tasks.txt b/splits/molnet/sider_general_disorders_and_administration_site_conditions/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..7d678c0068ffbd60ab057d0e1890ae769fd02b78 --- /dev/null +++ b/splits/molnet/sider_general_disorders_and_administration_site_conditions/validation_tasks.txt @@ -0,0 +1 @@ +task110_sider_general_disorders_and_administration_site_conditions_molnet_valid \ No newline at end of file diff --git a/splits/molnet/sider_hepatobiliary_disorders/test_tasks.txt b/splits/molnet/sider_hepatobiliary_disorders/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..bc1f87ada46ee13b1d444258dbdce6d15b2f028a --- /dev/null +++ b/splits/molnet/sider_hepatobiliary_disorders/test_tasks.txt @@ -0,0 +1 @@ +task78_sider_hepatobiliary_disorders_molnet_test \ No newline at end of file diff --git a/splits/molnet/sider_hepatobiliary_disorders/train_tasks.txt b/splits/molnet/sider_hepatobiliary_disorders/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..2fdd2468d9b4dffa1a1fcd2a4fd92e6e57228a04 --- /dev/null +++ b/splits/molnet/sider_hepatobiliary_disorders/train_tasks.txt @@ -0,0 +1 @@ +task76_sider_hepatobiliary_disorders_molnet_train \ No newline at end of file diff --git a/splits/molnet/sider_hepatobiliary_disorders/validation_tasks.txt b/splits/molnet/sider_hepatobiliary_disorders/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..e7053330605833688b8c4ac99686b0f1b17c14b5 --- /dev/null +++ b/splits/molnet/sider_hepatobiliary_disorders/validation_tasks.txt @@ -0,0 +1 @@ +task77_sider_hepatobiliary_disorders_molnet_valid \ No newline at end of file diff --git a/splits/molnet/sider_immune_system_disorders/test_tasks.txt b/splits/molnet/sider_immune_system_disorders/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..7b3b65a13f1d627598f259848cd34748467022da --- /dev/null +++ b/splits/molnet/sider_immune_system_disorders/test_tasks.txt @@ -0,0 +1 @@ +task102_sider_immune_system_disorders_molnet_test \ No newline at end of file diff --git a/splits/molnet/sider_immune_system_disorders/train_tasks.txt b/splits/molnet/sider_immune_system_disorders/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..f75e6bc4b67139bb47701e3807ed36fb393290b3 --- /dev/null +++ b/splits/molnet/sider_immune_system_disorders/train_tasks.txt @@ -0,0 +1 @@ +task100_sider_immune_system_disorders_molnet_train \ No newline at end of file diff --git a/splits/molnet/sider_immune_system_disorders/validation_tasks.txt b/splits/molnet/sider_immune_system_disorders/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..9e41c3860e6361aad5f6597150c44f183e9e5264 --- /dev/null +++ b/splits/molnet/sider_immune_system_disorders/validation_tasks.txt @@ -0,0 +1 @@ +task101_sider_immune_system_disorders_molnet_valid \ No newline at end of file diff --git a/splits/molnet/sider_infections_and_infestations/test_tasks.txt b/splits/molnet/sider_infections_and_infestations/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..c6755cac30876ff748ec3c16d66ab3b42b0b4402 --- /dev/null +++ b/splits/molnet/sider_infections_and_infestations/test_tasks.txt @@ -0,0 +1 @@ +task132_sider_infections_and_infestations_molnet_test \ No newline at end of file diff --git a/splits/molnet/sider_infections_and_infestations/train_tasks.txt b/splits/molnet/sider_infections_and_infestations/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..71918099209857b1ba50879fb2f33b57c5687a44 --- /dev/null +++ b/splits/molnet/sider_infections_and_infestations/train_tasks.txt @@ -0,0 +1 @@ +task130_sider_infections_and_infestations_molnet_train \ No newline at end of file diff --git a/splits/molnet/sider_infections_and_infestations/validation_tasks.txt b/splits/molnet/sider_infections_and_infestations/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..7a4a99f4b738749645b3d735bbc76d738fc36cb6 --- /dev/null +++ b/splits/molnet/sider_infections_and_infestations/validation_tasks.txt @@ -0,0 +1 @@ +task131_sider_infections_and_infestations_molnet_valid \ No newline at end of file diff --git a/splits/molnet/sider_injury__poisoning_and_procedural_complications/test_tasks.txt b/splits/molnet/sider_injury__poisoning_and_procedural_complications/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..2f71bb20bd1c644ddf237de6bc7974fed3df8500 --- /dev/null +++ b/splits/molnet/sider_injury__poisoning_and_procedural_complications/test_tasks.txt @@ -0,0 +1 @@ +task156_sider_injury__poisoning_and_procedural_complications_molnet_test \ No newline at end of file diff --git a/splits/molnet/sider_injury__poisoning_and_procedural_complications/train_tasks.txt b/splits/molnet/sider_injury__poisoning_and_procedural_complications/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..b4c070be9b3900a64d50810a663c4309791920e2 --- /dev/null +++ b/splits/molnet/sider_injury__poisoning_and_procedural_complications/train_tasks.txt @@ -0,0 +1 @@ +task154_sider_injury__poisoning_and_procedural_complications_molnet_train \ No newline at end of file diff --git a/splits/molnet/sider_injury__poisoning_and_procedural_complications/validation_tasks.txt b/splits/molnet/sider_injury__poisoning_and_procedural_complications/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..c03da4e6f8050d7c488d84120df968b50331d5ec --- /dev/null +++ b/splits/molnet/sider_injury__poisoning_and_procedural_complications/validation_tasks.txt @@ -0,0 +1 @@ +task155_sider_injury__poisoning_and_procedural_complications_molnet_valid \ No newline at end of file diff --git a/splits/molnet/sider_investigations/test_tasks.txt b/splits/molnet/sider_investigations/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..687d127b54f5106143e3eabbfdcfe788f201524c --- /dev/null +++ b/splits/molnet/sider_investigations/test_tasks.txt @@ -0,0 +1 @@ +task90_sider_investigations_molnet_test \ No newline at end of file diff --git a/splits/molnet/sider_investigations/train_tasks.txt b/splits/molnet/sider_investigations/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..3b2f86df32d7dd18cf4369107b33d39de1b38cff --- /dev/null +++ b/splits/molnet/sider_investigations/train_tasks.txt @@ -0,0 +1 @@ +task88_sider_investigations_molnet_train \ No newline at end of file diff --git a/splits/molnet/sider_investigations/validation_tasks.txt b/splits/molnet/sider_investigations/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..c800a43479ef16d1856d4294a4958e32912f415b --- /dev/null +++ b/splits/molnet/sider_investigations/validation_tasks.txt @@ -0,0 +1 @@ +task89_sider_investigations_molnet_valid \ No newline at end of file diff --git a/splits/molnet/sider_metabolism_and_nutrition_disorders/test_tasks.txt b/splits/molnet/sider_metabolism_and_nutrition_disorders/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..8dea009b976e4aa99b357e47959fe858ada0caaa --- /dev/null +++ b/splits/molnet/sider_metabolism_and_nutrition_disorders/test_tasks.txt @@ -0,0 +1 @@ +task81_sider_metabolism_and_nutrition_disorders_molnet_test \ No newline at end of file diff --git a/splits/molnet/sider_metabolism_and_nutrition_disorders/train_tasks.txt b/splits/molnet/sider_metabolism_and_nutrition_disorders/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..c6d0585754a8c9839a07738a26502b9939d1b019 --- /dev/null +++ b/splits/molnet/sider_metabolism_and_nutrition_disorders/train_tasks.txt @@ -0,0 +1 @@ +task79_sider_metabolism_and_nutrition_disorders_molnet_train \ No newline at end of file diff --git a/splits/molnet/sider_metabolism_and_nutrition_disorders/validation_tasks.txt b/splits/molnet/sider_metabolism_and_nutrition_disorders/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..4b69054e2613facf622432184ed00234e47707ce --- /dev/null +++ b/splits/molnet/sider_metabolism_and_nutrition_disorders/validation_tasks.txt @@ -0,0 +1 @@ +task80_sider_metabolism_and_nutrition_disorders_molnet_valid \ No newline at end of file diff --git a/splits/molnet/sider_musculoskeletal_and_connective_tissue_disorders/test_tasks.txt b/splits/molnet/sider_musculoskeletal_and_connective_tissue_disorders/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..fd29af308e17edfae9d0b2e2f61623b12dd19d81 --- /dev/null +++ b/splits/molnet/sider_musculoskeletal_and_connective_tissue_disorders/test_tasks.txt @@ -0,0 +1 @@ +task93_sider_musculoskeletal_and_connective_tissue_disorders_molnet_test \ No newline at end of file diff --git a/splits/molnet/sider_musculoskeletal_and_connective_tissue_disorders/train_tasks.txt b/splits/molnet/sider_musculoskeletal_and_connective_tissue_disorders/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..3f7a2ec9c64accadbbd1f56159cef69f5b3d8e3b --- /dev/null +++ b/splits/molnet/sider_musculoskeletal_and_connective_tissue_disorders/train_tasks.txt @@ -0,0 +1 @@ +task91_sider_musculoskeletal_and_connective_tissue_disorders_molnet_train \ No newline at end of file diff --git a/splits/molnet/sider_musculoskeletal_and_connective_tissue_disorders/validation_tasks.txt b/splits/molnet/sider_musculoskeletal_and_connective_tissue_disorders/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..608caac2bc0f9bc190181f939eee1bc9441d3c12 --- /dev/null +++ b/splits/molnet/sider_musculoskeletal_and_connective_tissue_disorders/validation_tasks.txt @@ -0,0 +1 @@ +task92_sider_musculoskeletal_and_connective_tissue_disorders_molnet_valid \ No newline at end of file diff --git a/splits/molnet/sider_neoplasms_benign__malignant_and_unspecified__incl_cysts_and_polyps_/test_tasks.txt b/splits/molnet/sider_neoplasms_benign__malignant_and_unspecified__incl_cysts_and_polyps_/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..4d39ab5059e862fa6a7377ab20352399b28f306b --- /dev/null +++ b/splits/molnet/sider_neoplasms_benign__malignant_and_unspecified__incl_cysts_and_polyps_/test_tasks.txt @@ -0,0 +1 @@ +task108_sider_neoplasms_benign__malignant_and_unspecified__incl_cysts_and_polyps__molnet_test \ No newline at end of file diff --git a/splits/molnet/sider_neoplasms_benign__malignant_and_unspecified__incl_cysts_and_polyps_/train_tasks.txt b/splits/molnet/sider_neoplasms_benign__malignant_and_unspecified__incl_cysts_and_polyps_/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..85d692ce2dd37bb92948afe513f78c0a0a10817e --- /dev/null +++ b/splits/molnet/sider_neoplasms_benign__malignant_and_unspecified__incl_cysts_and_polyps_/train_tasks.txt @@ -0,0 +1 @@ +task106_sider_neoplasms_benign__malignant_and_unspecified__incl_cysts_and_polyps__molnet_train \ No newline at end of file diff --git a/splits/molnet/sider_neoplasms_benign__malignant_and_unspecified__incl_cysts_and_polyps_/validation_tasks.txt b/splits/molnet/sider_neoplasms_benign__malignant_and_unspecified__incl_cysts_and_polyps_/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..d1cbdeb1c8fd4759ed0aeaae008a4470584a6bae --- /dev/null +++ b/splits/molnet/sider_neoplasms_benign__malignant_and_unspecified__incl_cysts_and_polyps_/validation_tasks.txt @@ -0,0 +1 @@ +task107_sider_neoplasms_benign__malignant_and_unspecified__incl_cysts_and_polyps__molnet_valid \ No newline at end of file diff --git a/splits/molnet/sider_nervous_system_disorders/test_tasks.txt b/splits/molnet/sider_nervous_system_disorders/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..97bed9304ecb4ff979629526e3c75edb10f87953 --- /dev/null +++ b/splits/molnet/sider_nervous_system_disorders/test_tasks.txt @@ -0,0 +1 @@ +task153_sider_nervous_system_disorders_molnet_test \ No newline at end of file diff --git a/splits/molnet/sider_nervous_system_disorders/train_tasks.txt b/splits/molnet/sider_nervous_system_disorders/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..b4e7cb9080c3a6d54e85f947e75498eaf93c67ad --- /dev/null +++ b/splits/molnet/sider_nervous_system_disorders/train_tasks.txt @@ -0,0 +1 @@ +task151_sider_nervous_system_disorders_molnet_train \ No newline at end of file diff --git a/splits/molnet/sider_nervous_system_disorders/validation_tasks.txt b/splits/molnet/sider_nervous_system_disorders/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..257733e4b23e04d5180d08d9c71737ab342d125e --- /dev/null +++ b/splits/molnet/sider_nervous_system_disorders/validation_tasks.txt @@ -0,0 +1 @@ +task152_sider_nervous_system_disorders_molnet_valid \ No newline at end of file diff --git a/splits/molnet/sider_pregnancy__puerperium_and_perinatal_conditions/test_tasks.txt b/splits/molnet/sider_pregnancy__puerperium_and_perinatal_conditions/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..e49160fa71ea3236c6218246ac4b4912757c52c1 --- /dev/null +++ b/splits/molnet/sider_pregnancy__puerperium_and_perinatal_conditions/test_tasks.txt @@ -0,0 +1 @@ +task144_sider_pregnancy__puerperium_and_perinatal_conditions_molnet_test \ No newline at end of file diff --git a/splits/molnet/sider_pregnancy__puerperium_and_perinatal_conditions/train_tasks.txt b/splits/molnet/sider_pregnancy__puerperium_and_perinatal_conditions/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..ae68dcd23064221527052bc2275dda0fb378bfc0 --- /dev/null +++ b/splits/molnet/sider_pregnancy__puerperium_and_perinatal_conditions/train_tasks.txt @@ -0,0 +1 @@ +task142_sider_pregnancy__puerperium_and_perinatal_conditions_molnet_train \ No newline at end of file diff --git a/splits/molnet/sider_pregnancy__puerperium_and_perinatal_conditions/validation_tasks.txt b/splits/molnet/sider_pregnancy__puerperium_and_perinatal_conditions/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..13193d244d7c8b589e3154ee2cd821bb0133fc1d --- /dev/null +++ b/splits/molnet/sider_pregnancy__puerperium_and_perinatal_conditions/validation_tasks.txt @@ -0,0 +1 @@ +task143_sider_pregnancy__puerperium_and_perinatal_conditions_molnet_valid \ No newline at end of file diff --git a/splits/molnet/sider_product_issues/test_tasks.txt b/splits/molnet/sider_product_issues/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..590e02041f677389b119a56334fe6ab87b679a58 --- /dev/null +++ b/splits/molnet/sider_product_issues/test_tasks.txt @@ -0,0 +1 @@ +task84_sider_product_issues_molnet_test \ No newline at end of file diff --git a/splits/molnet/sider_product_issues/train_tasks.txt b/splits/molnet/sider_product_issues/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..8553ca60e3818307b7cebff701c4474a53b2f010 --- /dev/null +++ b/splits/molnet/sider_product_issues/train_tasks.txt @@ -0,0 +1 @@ +task82_sider_product_issues_molnet_train \ No newline at end of file diff --git a/splits/molnet/sider_product_issues/validation_tasks.txt b/splits/molnet/sider_product_issues/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..5cd0dd2d02d65f3733043cf250fee9f8449408ef --- /dev/null +++ b/splits/molnet/sider_product_issues/validation_tasks.txt @@ -0,0 +1 @@ +task83_sider_product_issues_molnet_valid \ No newline at end of file diff --git a/splits/molnet/sider_psychiatric_disorders/test_tasks.txt b/splits/molnet/sider_psychiatric_disorders/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..e8d9179cc5d0a8ce52ce4d8b7f0ca4424c5d02e6 --- /dev/null +++ b/splits/molnet/sider_psychiatric_disorders/test_tasks.txt @@ -0,0 +1 @@ +task138_sider_psychiatric_disorders_molnet_test \ No newline at end of file diff --git a/splits/molnet/sider_psychiatric_disorders/train_tasks.txt b/splits/molnet/sider_psychiatric_disorders/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..b256e83603feab5ede029ce2358c42f5ab944628 --- /dev/null +++ b/splits/molnet/sider_psychiatric_disorders/train_tasks.txt @@ -0,0 +1 @@ +task136_sider_psychiatric_disorders_molnet_train \ No newline at end of file diff --git a/splits/molnet/sider_psychiatric_disorders/validation_tasks.txt b/splits/molnet/sider_psychiatric_disorders/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..86c515efa0cb8911f4414db164e1ac157d2f627f --- /dev/null +++ b/splits/molnet/sider_psychiatric_disorders/validation_tasks.txt @@ -0,0 +1 @@ +task137_sider_psychiatric_disorders_molnet_valid \ No newline at end of file diff --git a/splits/molnet/sider_renal_and_urinary_disorders/test_tasks.txt b/splits/molnet/sider_renal_and_urinary_disorders/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..2bacfa04f9d349068ffb302d61d1d5974637796e --- /dev/null +++ b/splits/molnet/sider_renal_and_urinary_disorders/test_tasks.txt @@ -0,0 +1 @@ +task141_sider_renal_and_urinary_disorders_molnet_test \ No newline at end of file diff --git a/splits/molnet/sider_renal_and_urinary_disorders/train_tasks.txt b/splits/molnet/sider_renal_and_urinary_disorders/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..95937e7f208118772848a6a8ec3b0ac9d8c7ce26 --- /dev/null +++ b/splits/molnet/sider_renal_and_urinary_disorders/train_tasks.txt @@ -0,0 +1 @@ +task139_sider_renal_and_urinary_disorders_molnet_train \ No newline at end of file diff --git a/splits/molnet/sider_renal_and_urinary_disorders/validation_tasks.txt b/splits/molnet/sider_renal_and_urinary_disorders/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..fe881dbbc3eca14fa284f2b70199a3cb5a937aa9 --- /dev/null +++ b/splits/molnet/sider_renal_and_urinary_disorders/validation_tasks.txt @@ -0,0 +1 @@ +task140_sider_renal_and_urinary_disorders_molnet_valid \ No newline at end of file diff --git a/splits/molnet/sider_reproductive_system_and_breast_disorders/test_tasks.txt b/splits/molnet/sider_reproductive_system_and_breast_disorders/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..d081ed04bb32560a14c4f5917bd2bb70777eeba9 --- /dev/null +++ b/splits/molnet/sider_reproductive_system_and_breast_disorders/test_tasks.txt @@ -0,0 +1 @@ +task105_sider_reproductive_system_and_breast_disorders_molnet_test \ No newline at end of file diff --git a/splits/molnet/sider_reproductive_system_and_breast_disorders/train_tasks.txt b/splits/molnet/sider_reproductive_system_and_breast_disorders/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..5f28634b450cb18b02abe4ac65729ef2bce89dd9 --- /dev/null +++ b/splits/molnet/sider_reproductive_system_and_breast_disorders/train_tasks.txt @@ -0,0 +1 @@ +task103_sider_reproductive_system_and_breast_disorders_molnet_train \ No newline at end of file diff --git a/splits/molnet/sider_reproductive_system_and_breast_disorders/validation_tasks.txt b/splits/molnet/sider_reproductive_system_and_breast_disorders/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..cfd3b99c5034ec5253adb5fffaa92ffbc5bf475d --- /dev/null +++ b/splits/molnet/sider_reproductive_system_and_breast_disorders/validation_tasks.txt @@ -0,0 +1 @@ +task104_sider_reproductive_system_and_breast_disorders_molnet_valid \ No newline at end of file diff --git a/splits/molnet/sider_respiratory__thoracic_and_mediastinal_disorders/test_tasks.txt b/splits/molnet/sider_respiratory__thoracic_and_mediastinal_disorders/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..50785999ab411edd9bac5e6d028d8f025589e42a --- /dev/null +++ b/splits/molnet/sider_respiratory__thoracic_and_mediastinal_disorders/test_tasks.txt @@ -0,0 +1 @@ +task135_sider_respiratory__thoracic_and_mediastinal_disorders_molnet_test \ No newline at end of file diff --git a/splits/molnet/sider_respiratory__thoracic_and_mediastinal_disorders/train_tasks.txt b/splits/molnet/sider_respiratory__thoracic_and_mediastinal_disorders/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..8240443c49903c05671d58118ec1c51be89fafe6 --- /dev/null +++ b/splits/molnet/sider_respiratory__thoracic_and_mediastinal_disorders/train_tasks.txt @@ -0,0 +1 @@ +task133_sider_respiratory__thoracic_and_mediastinal_disorders_molnet_train \ No newline at end of file diff --git a/splits/molnet/sider_respiratory__thoracic_and_mediastinal_disorders/validation_tasks.txt b/splits/molnet/sider_respiratory__thoracic_and_mediastinal_disorders/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..0ec7a6de14d3c06eab4a651d9436b749d0eb8cb1 --- /dev/null +++ b/splits/molnet/sider_respiratory__thoracic_and_mediastinal_disorders/validation_tasks.txt @@ -0,0 +1 @@ +task134_sider_respiratory__thoracic_and_mediastinal_disorders_molnet_valid \ No newline at end of file diff --git a/splits/molnet/sider_skin_and_subcutaneous_tissue_disorders/test_tasks.txt b/splits/molnet/sider_skin_and_subcutaneous_tissue_disorders/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..7f73b02a886441601dbe010e0997aaed3548a291 --- /dev/null +++ b/splits/molnet/sider_skin_and_subcutaneous_tissue_disorders/test_tasks.txt @@ -0,0 +1 @@ +task126_sider_skin_and_subcutaneous_tissue_disorders_molnet_test \ No newline at end of file diff --git a/splits/molnet/sider_skin_and_subcutaneous_tissue_disorders/train_tasks.txt b/splits/molnet/sider_skin_and_subcutaneous_tissue_disorders/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..951148f6e12084527564a1af4b3932b51632f0ff --- /dev/null +++ b/splits/molnet/sider_skin_and_subcutaneous_tissue_disorders/train_tasks.txt @@ -0,0 +1 @@ +task124_sider_skin_and_subcutaneous_tissue_disorders_molnet_train \ No newline at end of file diff --git a/splits/molnet/sider_skin_and_subcutaneous_tissue_disorders/validation_tasks.txt b/splits/molnet/sider_skin_and_subcutaneous_tissue_disorders/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..b96fc490cdea79e653505a3de08cb35a698f8052 --- /dev/null +++ b/splits/molnet/sider_skin_and_subcutaneous_tissue_disorders/validation_tasks.txt @@ -0,0 +1 @@ +task125_sider_skin_and_subcutaneous_tissue_disorders_molnet_valid \ No newline at end of file diff --git a/splits/molnet/sider_social_circumstances/test_tasks.txt b/splits/molnet/sider_social_circumstances/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..79457d7dad456fab1ac9032e7743c3b28635f50e --- /dev/null +++ b/splits/molnet/sider_social_circumstances/test_tasks.txt @@ -0,0 +1 @@ +task99_sider_social_circumstances_molnet_test \ No newline at end of file diff --git a/splits/molnet/sider_social_circumstances/train_tasks.txt b/splits/molnet/sider_social_circumstances/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..623ad9cf6fde595ea07f74f1e8a31771f76fe37d --- /dev/null +++ b/splits/molnet/sider_social_circumstances/train_tasks.txt @@ -0,0 +1 @@ +task97_sider_social_circumstances_molnet_train \ No newline at end of file diff --git a/splits/molnet/sider_social_circumstances/validation_tasks.txt b/splits/molnet/sider_social_circumstances/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..0b3a4b892b9536c6bc6f659173def6903da4dfbf --- /dev/null +++ b/splits/molnet/sider_social_circumstances/validation_tasks.txt @@ -0,0 +1 @@ +task98_sider_social_circumstances_molnet_valid \ No newline at end of file diff --git a/splits/molnet/sider_surgical_and_medical_procedures/test_tasks.txt b/splits/molnet/sider_surgical_and_medical_procedures/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..cefa179cbcb9078822ad95f8f28bdc6111344ca1 --- /dev/null +++ b/splits/molnet/sider_surgical_and_medical_procedures/test_tasks.txt @@ -0,0 +1 @@ +task117_sider_surgical_and_medical_procedures_molnet_test \ No newline at end of file diff --git a/splits/molnet/sider_surgical_and_medical_procedures/train_tasks.txt b/splits/molnet/sider_surgical_and_medical_procedures/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..65454b6247a66fffdfcad1aaad459b211687fd91 --- /dev/null +++ b/splits/molnet/sider_surgical_and_medical_procedures/train_tasks.txt @@ -0,0 +1 @@ +task115_sider_surgical_and_medical_procedures_molnet_train \ No newline at end of file diff --git a/splits/molnet/sider_surgical_and_medical_procedures/validation_tasks.txt b/splits/molnet/sider_surgical_and_medical_procedures/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..bc29c29fd58ae642d5a79c05a92d3c0200ea414f --- /dev/null +++ b/splits/molnet/sider_surgical_and_medical_procedures/validation_tasks.txt @@ -0,0 +1 @@ +task116_sider_surgical_and_medical_procedures_molnet_valid \ No newline at end of file diff --git a/splits/molnet/sider_vascular_disorders/test_tasks.txt b/splits/molnet/sider_vascular_disorders/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..f0b900b950de6cdd1a747bac227afac42e14e37d --- /dev/null +++ b/splits/molnet/sider_vascular_disorders/test_tasks.txt @@ -0,0 +1 @@ +task120_sider_vascular_disorders_molnet_test \ No newline at end of file diff --git a/splits/molnet/sider_vascular_disorders/train_tasks.txt b/splits/molnet/sider_vascular_disorders/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..745d5f4794c890d817d9c7c5e383d4da6a7a7b6a --- /dev/null +++ b/splits/molnet/sider_vascular_disorders/train_tasks.txt @@ -0,0 +1 @@ +task118_sider_vascular_disorders_molnet_train \ No newline at end of file diff --git a/splits/molnet/sider_vascular_disorders/validation_tasks.txt b/splits/molnet/sider_vascular_disorders/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..ca7ab453579e04ae450c7574b05ec4021129e98b --- /dev/null +++ b/splits/molnet/sider_vascular_disorders/validation_tasks.txt @@ -0,0 +1 @@ +task119_sider_vascular_disorders_molnet_valid \ No newline at end of file diff --git a/splits/molnet/tox21_nr_ahr/test_tasks.txt b/splits/molnet/tox21_nr_ahr/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..586939d6bb52f83dcbadb8153df31d9c998aa856 --- /dev/null +++ b/splits/molnet/tox21_nr_ahr/test_tasks.txt @@ -0,0 +1 @@ +task42_tox21_nr_ahr_molnet_test \ No newline at end of file diff --git a/splits/molnet/tox21_nr_ahr/train_tasks.txt b/splits/molnet/tox21_nr_ahr/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..dd27917a21b0ce260b9c908f6847d1dfc47a6def --- /dev/null +++ b/splits/molnet/tox21_nr_ahr/train_tasks.txt @@ -0,0 +1 @@ +task40_tox21_nr_ahr_molnet_train \ No newline at end of file diff --git a/splits/molnet/tox21_nr_ahr/validation_tasks.txt b/splits/molnet/tox21_nr_ahr/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..89dd150354c681a9b661f75b36822c6764f1fed9 --- /dev/null +++ b/splits/molnet/tox21_nr_ahr/validation_tasks.txt @@ -0,0 +1 @@ +task41_tox21_nr_ahr_molnet_valid \ No newline at end of file diff --git a/splits/molnet/tox21_nr_ar/test_tasks.txt b/splits/molnet/tox21_nr_ar/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..a2439d8a9a78c4e00932bb0ebe2620442b6d2601 --- /dev/null +++ b/splits/molnet/tox21_nr_ar/test_tasks.txt @@ -0,0 +1 @@ +task36_tox21_nr_ar_molnet_test \ No newline at end of file diff --git a/splits/molnet/tox21_nr_ar/train_tasks.txt b/splits/molnet/tox21_nr_ar/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..312f1f4973f1bcb9cce2110f94108317228d80ad --- /dev/null +++ b/splits/molnet/tox21_nr_ar/train_tasks.txt @@ -0,0 +1 @@ +task34_tox21_nr_ar_molnet_train \ No newline at end of file diff --git a/splits/molnet/tox21_nr_ar/validation_tasks.txt b/splits/molnet/tox21_nr_ar/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..9a95dcb5b4099f51aa202d677a4bd26a06b2aa16 --- /dev/null +++ b/splits/molnet/tox21_nr_ar/validation_tasks.txt @@ -0,0 +1 @@ +task35_tox21_nr_ar_molnet_valid \ No newline at end of file diff --git a/splits/molnet/tox21_nr_ar_lbd/test_tasks.txt b/splits/molnet/tox21_nr_ar_lbd/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..1d8e3a27130057c99b8b0752acf7254b275ef815 --- /dev/null +++ b/splits/molnet/tox21_nr_ar_lbd/test_tasks.txt @@ -0,0 +1 @@ +task39_tox21_nr_ar_lbd_molnet_test \ No newline at end of file diff --git a/splits/molnet/tox21_nr_ar_lbd/train_tasks.txt b/splits/molnet/tox21_nr_ar_lbd/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..b7b5887c2500d20ec64aca7e84040b79c9d15ccd --- /dev/null +++ b/splits/molnet/tox21_nr_ar_lbd/train_tasks.txt @@ -0,0 +1 @@ +task37_tox21_nr_ar_lbd_molnet_train \ No newline at end of file diff --git a/splits/molnet/tox21_nr_ar_lbd/validation_tasks.txt b/splits/molnet/tox21_nr_ar_lbd/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..05ead044e7af9d07530e0977c49a40c91c4e4d35 --- /dev/null +++ b/splits/molnet/tox21_nr_ar_lbd/validation_tasks.txt @@ -0,0 +1 @@ +task38_tox21_nr_ar_lbd_molnet_valid \ No newline at end of file diff --git a/splits/molnet/tox21_nr_aromatase/test_tasks.txt b/splits/molnet/tox21_nr_aromatase/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..df221fdd83d254c1abb2f50b6e49c6445178f5ce --- /dev/null +++ b/splits/molnet/tox21_nr_aromatase/test_tasks.txt @@ -0,0 +1 @@ +task45_tox21_nr_aromatase_molnet_test \ No newline at end of file diff --git a/splits/molnet/tox21_nr_aromatase/train_tasks.txt b/splits/molnet/tox21_nr_aromatase/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..1b03f2934808b360dbcd0ceb76aba5ad398849db --- /dev/null +++ b/splits/molnet/tox21_nr_aromatase/train_tasks.txt @@ -0,0 +1 @@ +task43_tox21_nr_aromatase_molnet_train \ No newline at end of file diff --git a/splits/molnet/tox21_nr_aromatase/validation_tasks.txt b/splits/molnet/tox21_nr_aromatase/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..95c4d7e61977ccd8d0d34a2f1f238119b0e2c220 --- /dev/null +++ b/splits/molnet/tox21_nr_aromatase/validation_tasks.txt @@ -0,0 +1 @@ +task44_tox21_nr_aromatase_molnet_valid \ No newline at end of file diff --git a/splits/molnet/tox21_nr_er/test_tasks.txt b/splits/molnet/tox21_nr_er/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..cea7156047e496b607d0c9ae1b74d57a517d18c4 --- /dev/null +++ b/splits/molnet/tox21_nr_er/test_tasks.txt @@ -0,0 +1 @@ +task48_tox21_nr_er_molnet_test \ No newline at end of file diff --git a/splits/molnet/tox21_nr_er/train_tasks.txt b/splits/molnet/tox21_nr_er/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..f0351ecddc764ae4ebf416d758f06440ff308729 --- /dev/null +++ b/splits/molnet/tox21_nr_er/train_tasks.txt @@ -0,0 +1 @@ +task46_tox21_nr_er_molnet_train \ No newline at end of file diff --git a/splits/molnet/tox21_nr_er/validation_tasks.txt b/splits/molnet/tox21_nr_er/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..627a82e636a33712896b3bb4b2503c030a937914 --- /dev/null +++ b/splits/molnet/tox21_nr_er/validation_tasks.txt @@ -0,0 +1 @@ +task47_tox21_nr_er_molnet_valid \ No newline at end of file diff --git a/splits/molnet/tox21_nr_er_lbd/test_tasks.txt b/splits/molnet/tox21_nr_er_lbd/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..8a137efc126be25335400a57413ecbce635111bb --- /dev/null +++ b/splits/molnet/tox21_nr_er_lbd/test_tasks.txt @@ -0,0 +1 @@ +task51_tox21_nr_er_lbd_molnet_test \ No newline at end of file diff --git a/splits/molnet/tox21_nr_er_lbd/train_tasks.txt b/splits/molnet/tox21_nr_er_lbd/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..f3123e555530416d5a807c5b5c8d6c59783688e0 --- /dev/null +++ b/splits/molnet/tox21_nr_er_lbd/train_tasks.txt @@ -0,0 +1 @@ +task49_tox21_nr_er_lbd_molnet_train \ No newline at end of file diff --git a/splits/molnet/tox21_nr_er_lbd/validation_tasks.txt b/splits/molnet/tox21_nr_er_lbd/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..8f63d93d600734cdf818a5a4fedcd5676327eb93 --- /dev/null +++ b/splits/molnet/tox21_nr_er_lbd/validation_tasks.txt @@ -0,0 +1 @@ +task50_tox21_nr_er_lbd_molnet_valid \ No newline at end of file diff --git a/splits/molnet/tox21_nr_ppar_gamma/test_tasks.txt b/splits/molnet/tox21_nr_ppar_gamma/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..9e536b531a7689311fdc40fd5a62b937b5eb071b --- /dev/null +++ b/splits/molnet/tox21_nr_ppar_gamma/test_tasks.txt @@ -0,0 +1 @@ +task54_tox21_nr_ppar_gamma_molnet_test \ No newline at end of file diff --git a/splits/molnet/tox21_nr_ppar_gamma/train_tasks.txt b/splits/molnet/tox21_nr_ppar_gamma/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..6458c370e46585cb27cbccb497f44906e425963d --- /dev/null +++ b/splits/molnet/tox21_nr_ppar_gamma/train_tasks.txt @@ -0,0 +1 @@ +task52_tox21_nr_ppar_gamma_molnet_train \ No newline at end of file diff --git a/splits/molnet/tox21_nr_ppar_gamma/validation_tasks.txt b/splits/molnet/tox21_nr_ppar_gamma/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..a51ab1648b58ab97c3fc5a781ef52bcb5cce4568 --- /dev/null +++ b/splits/molnet/tox21_nr_ppar_gamma/validation_tasks.txt @@ -0,0 +1 @@ +task53_tox21_nr_ppar_gamma_molnet_valid \ No newline at end of file diff --git a/splits/molnet/tox21_sr_are/test_tasks.txt b/splits/molnet/tox21_sr_are/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..218cc80d5a5f65eedc76cd057402737fd7bfaf01 --- /dev/null +++ b/splits/molnet/tox21_sr_are/test_tasks.txt @@ -0,0 +1 @@ +task57_tox21_sr_are_molnet_test \ No newline at end of file diff --git a/splits/molnet/tox21_sr_are/train_tasks.txt b/splits/molnet/tox21_sr_are/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..8730bb54653bde7f5f8913c6cbd04f219ee6bf05 --- /dev/null +++ b/splits/molnet/tox21_sr_are/train_tasks.txt @@ -0,0 +1 @@ +task55_tox21_sr_are_molnet_train \ No newline at end of file diff --git a/splits/molnet/tox21_sr_are/validation_tasks.txt b/splits/molnet/tox21_sr_are/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..151b7a1b2892c3897c5c1d190ead81a5a9a507d0 --- /dev/null +++ b/splits/molnet/tox21_sr_are/validation_tasks.txt @@ -0,0 +1 @@ +task56_tox21_sr_are_molnet_valid \ No newline at end of file diff --git a/splits/molnet/tox21_sr_atad5/test_tasks.txt b/splits/molnet/tox21_sr_atad5/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..70a1066f00a97276b09d062e730c43a1bdc7e11d --- /dev/null +++ b/splits/molnet/tox21_sr_atad5/test_tasks.txt @@ -0,0 +1 @@ +task60_tox21_sr_atad5_molnet_test \ No newline at end of file diff --git a/splits/molnet/tox21_sr_atad5/train_tasks.txt b/splits/molnet/tox21_sr_atad5/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..4ab8105d1ed53d573e7a0f12bb957dfe8fe6525c --- /dev/null +++ b/splits/molnet/tox21_sr_atad5/train_tasks.txt @@ -0,0 +1 @@ +task58_tox21_sr_atad5_molnet_train \ No newline at end of file diff --git a/splits/molnet/tox21_sr_atad5/validation_tasks.txt b/splits/molnet/tox21_sr_atad5/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..074ac31c9fe033ad5df6bdb5bd42ca0c600a9050 --- /dev/null +++ b/splits/molnet/tox21_sr_atad5/validation_tasks.txt @@ -0,0 +1 @@ +task59_tox21_sr_atad5_molnet_valid \ No newline at end of file diff --git a/splits/molnet/tox21_sr_hse/test_tasks.txt b/splits/molnet/tox21_sr_hse/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..858ec003a95f3bbf4029ef34d764300311a9ce1c --- /dev/null +++ b/splits/molnet/tox21_sr_hse/test_tasks.txt @@ -0,0 +1 @@ +task63_tox21_sr_hse_molnet_test \ No newline at end of file diff --git a/splits/molnet/tox21_sr_hse/train_tasks.txt b/splits/molnet/tox21_sr_hse/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..5366dd550ca9e1d0e0fa35245bf95df7981fc1ca --- /dev/null +++ b/splits/molnet/tox21_sr_hse/train_tasks.txt @@ -0,0 +1 @@ +task61_tox21_sr_hse_molnet_train \ No newline at end of file diff --git a/splits/molnet/tox21_sr_hse/validation_tasks.txt b/splits/molnet/tox21_sr_hse/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..d9c2f45dcb9d83a68a9ab61d2d9f87be87c9d902 --- /dev/null +++ b/splits/molnet/tox21_sr_hse/validation_tasks.txt @@ -0,0 +1 @@ +task62_tox21_sr_hse_molnet_valid \ No newline at end of file diff --git a/splits/molnet/tox21_sr_mmp/test_tasks.txt b/splits/molnet/tox21_sr_mmp/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..7792827c66571bfc916bc6e89acc3b7c9a6a8cad --- /dev/null +++ b/splits/molnet/tox21_sr_mmp/test_tasks.txt @@ -0,0 +1 @@ +task66_tox21_sr_mmp_molnet_test \ No newline at end of file diff --git a/splits/molnet/tox21_sr_mmp/train_tasks.txt b/splits/molnet/tox21_sr_mmp/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..3902f96e2f4c264df882f6c780f53e7d84d7a113 --- /dev/null +++ b/splits/molnet/tox21_sr_mmp/train_tasks.txt @@ -0,0 +1 @@ +task64_tox21_sr_mmp_molnet_train \ No newline at end of file diff --git a/splits/molnet/tox21_sr_mmp/validation_tasks.txt b/splits/molnet/tox21_sr_mmp/validation_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..46216457cf70a1839b6108acfab1b4d17d431452 --- /dev/null +++ b/splits/molnet/tox21_sr_mmp/validation_tasks.txt @@ -0,0 +1 @@ +task65_tox21_sr_mmp_molnet_valid \ No newline at end of file diff --git a/splits/molnet/tox21_sr_p53/test_tasks.txt b/splits/molnet/tox21_sr_p53/test_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..464607c874581a153446952628addc5e52b8ac90 --- /dev/null +++ b/splits/molnet/tox21_sr_p53/test_tasks.txt @@ -0,0 +1 @@ +task69_tox21_sr_p53_molnet_test \ No newline at end of file diff --git a/splits/molnet/tox21_sr_p53/train_tasks.txt b/splits/molnet/tox21_sr_p53/train_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..e9dae7614f01081cb8e74ff5a17524c9a59342e3 --- /dev/null +++ b/splits/molnet/tox21_sr_p53/train_tasks.txt @@ -0,0 +1 @@ +task67_tox21_sr_p53_molnet_train \ No newline at end of file diff --git a/splits/molnet/tox21_sr_p53/validation_tasks.txt b/splits/molnet/tox21_sr_p53/validation_tasks.txt new file mode 100755 index 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a/tasks/task9_bindingdb_drugban_dti_test.json b/tasks/task9_bindingdb_drugban_dti_test.json new file mode 100755 index 0000000000000000000000000000000000000000..810fa89f5625ae207c46e77293c70f206c1b7c4e --- /dev/null +++ b/tasks/task9_bindingdb_drugban_dti_test.json @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:da330803ab95d96cc2947bff7c069293e6f616f736b7faf889499fbc615227b7 +size 31879494 diff --git a/test_task_all.py b/test_task_all.py new file mode 100755 index 0000000000000000000000000000000000000000..48483f73fcb8c67be872f51e31b5d4e3a540f0c7 --- /dev/null +++ b/test_task_all.py @@ -0,0 +1,336 @@ +#!/usr/bin/env python3 +from iso639 import languages +import json +from os import listdir +from os.path import isfile, join +import argparse +import re +import numpy as np + +# get the range of task you want to test, if specified in the command line +parser = argparse.ArgumentParser() +parser.add_argument("--task", + nargs=2, + type=int, + required=False, + help="The range of task you want to parse") + +args = parser.parse_args() +if args.task: + begin_task_number, end_task_number = args.task[0], args.task[1] + assert begin_task_number > 0, "begin task must be greater than 0" + assert end_task_number > begin_task_number, "please specify a range of task you would like to test; i.e. the end task number must be greater than beginning task number" + +# make sure that there is no json file in the root directory +root_files = [f for f in listdir('.') if isfile(join('.', f))] +for f in root_files: + assert '.json' not in f, 'looks like there is a JSON file in the main directory???' + +# read all the tasks and make sure that they're following the right pattern +tasks_path = 'tasks/' +# tasks_path = 'tasks_special_token/' + +expected_keys = [ + "Definition", + "Input_language", + "Output_language", + "Positive Examples", + "Negative Examples", + "Instances", + "Contributors", + "Categories", + "Domains", + "Source", + "URL", + "Reasoning" +] + +language_names = [ + x.name.replace('(individual language)', '').replace(" languages", "").strip() + for x in list(languages) +] + + +def assert_language_name(name): + assert name in language_names, f"Did not find `{name}` among iso639 language names: {language_names}" + + +def extract_categories(string): + """ + Get all the characters between ` and ` + """ + return set(re.findall(r'`(.*?)`', string)) + + +def dict_raise_on_duplicates(ordered_pairs): + """Reject duplicate keys.""" + d = {} + for k, v in ordered_pairs: + if k in d: + raise ValueError("duplicate key: %r" % (k,)) + else: + d[k] = v + return d + +def atoi(text): + return int(text) if text.isdigit() else text + +def natural_keys(text): + ''' + alist.sort(key=natural_keys) sorts in human order + ''' + return [ atoi(c) for c in re.split(r'(\d+)', text) ] + + +with open("tasks/README.md", 'r') as readmef: + task_readme_content = " ".join(readmef.readlines()) +with open("doc/task-hierarchy.md", 'r') as readmef: + hierarchy_content_lines = readmef.readlines() + hierarchy_content = " ".join(hierarchy_content_lines) + all_categories = extract_categories(hierarchy_content) + +# make sure there are no repeated lines in the task file +task_readme_lines = [x for x in task_readme_content.split("\n") if len(x) > 5] +if len(set(task_readme_lines)) != len(task_readme_lines): + diff = "\n --> ".join([x for x in task_readme_lines if task_readme_lines.count(x) > 1]) + assert False, f'looks like there are repeated lines in the task readme file?? \n {diff}' + +# make sure that the lines are sorted +task_numbers = [int(line.replace("`task", "").split("_")[0]) for line in task_readme_lines if "`task" in line] +for i in range(0, len(task_numbers) - 1): + num1 = task_numbers[i] + num2 = task_numbers[i + 1] + assert num1 <= num2, f"ERROR: looks like `{num1}` appears before `{num2}`." + +files = [f for f in listdir(tasks_path) if isfile(join(tasks_path, f))] +files.sort(key=natural_keys) + +# make sure anything that gets mentioned in the readme, correspond to an actual file +task_names = [line.split("`")[1] for line in task_readme_lines if '`' in line] +for name in task_names: + file_name = name + ".json" + # pqz + # assert file_name in files, f" Did not find `{file_name}` among {files}" + +# test every file (README is skipped) +if not args.task: + begin_task_number, end_task_number = 1, len(files) + +# TODO: over time, we need to fix the skew of the following tasks +skew_exclusion = [ + "150" +] + +contributor_stats = {} +categories_stats = {} +reasoning_stats = {} +domain_stats = {} +tasks_count = 0 +number_of_instances = 0 +for file in files[begin_task_number:end_task_number + 1]: + if ".json" in file: + print(f" --> testing file: {file}") + assert '.json' in file, 'the file does not seem to have a .json in it: ' + file + file_path = tasks_path + file + with open(file_path, 'r') as f: + try: + data = json.load(f) + except: + with open(file_path, 'r', encoding='utf-8') as f: + data = json.load(f, object_pairs_hook=dict_raise_on_duplicates) + for key in expected_keys: + assert key in data, f'did not find the key: {key}' + + + assert len(data['Instances']) > 25, f"there must be at least 25 instances; " \ + f"currently you have {len(data['Instances'])} instances" + # pqz + # assert len(data['Instances']) <= 6500, f"there must be at most 6.5k instances; " \ + # f"currently you have {len(data['Instances'])} instances" + + assert type(data['Definition']) == list, f'Definition must be a list of strings.' + assert type(data['Source']) == list, f'Sources must be a list.' + assert type(data['URL']) == list, f'URL must be a list.' + assert type(data['Contributors']) == list, f'Contributors must be a list.' + assert type(data['Categories']) == list, f'Categories must be a list.' + assert type(data['Reasoning']) == list, f'Reasoning must be a list.' + assert type(data['Domains']) == list, f'Domains must be a list.' + + number_of_instances = number_of_instances + len(data['Instances']) + for c in data['Categories']: + assert c in all_categories, f'Did not find category `{c}`' + if c not in categories_stats: + categories_stats[c] = 0 + categories_stats[c] += 1 + + for d in data['Domains']: + assert d in hierarchy_content, f'Did not find domain `{d}`' + if d not in domain_stats: + domain_stats[d] = 0 + domain_stats[d] += 1 + + for r in data['Reasoning']: + assert r in hierarchy_content, f'Did not find reasoning `{r}`' + if r not in reasoning_stats: + reasoning_stats[r] = 0 + reasoning_stats[r] += 1 + + for d in data['Definition']: + assert type(d) == str, f'Each definition must be a string.' + assert all((lan in d) for lan in data['Input_language'] if + lan != 'English'), f'Definition must contain non-English tasks language.' + assert type(data['Input_language']) == list, f'Input_language must be a list of strings.' + assert type(data['Output_language']) == list, f'Output_language must be a list of strings.' + assert type(data['Instruction_language']) == list, f'Output_language must be a list of strings.' + + assert 'instruction_language' not in data, f'Found `instruction_language`, but expected `Instruction_language`.' + assert 'input_language' not in data, f'Found `input_language`, but expected `Input_language`.' + assert 'output_language' not in data, f'Found `output_language`, but expected `Output_language`.' + + # make sure we use the standard language names + # pqz + # for lang in data['Input_language'] + data['Output_language'] + data['Instruction_language']: + # assert_language_name(lang) + + instance_ids = set() + for x in data['Instances']: + for key in ['id', 'input', 'output']: + assert key in x, f'expected the key {key} in {x}' + assert x['id'] not in instance_ids, f'found duplicate instance id: {x["id"]}' + instance_ids.add(x['id']) + assert type(x['input']) == str, f'the input of instance {x} is not a string' + assert type(x['output']) == list, f'the output of instance {x} is not a list' + assert len(x['input']) > 0, f"looks like an input `{x['input']}` is empty?" + assert len(x['output']) > 0, f"looks like an output `{x['output']}` is empty?" + for i in x['output']: + assert type(i) == str, f'the output is not a string' + # pqz + # assert len(data['Positive Examples']) > 1, "there must be at least 3 positive example" + # assert len(data['Negative Examples']) > 0, "there must be at least 2 negative example" + + for x in data['Positive Examples'] + data['Negative Examples']: + for key in ['input', 'output', 'explanation']: + assert key in x, f'expected the key {key} in {x}' + assert type(x['input']) == str, f'the input of example {x} is not a string' + assert type(x['output']) == str, f'the output of example {x} is not a string' + assert type(x['explanation']) == str, f'the explanation of example {x} is not a string' + + # Make sure there are no repeated input examples + instances = data['Instances'] + set_of_instances = {instance['input'] for instance in instances} + # Because the set length and total length are different, there must be a duplicate input + # pqz + # if len(instances) != len(set_of_instances): + # for instance in instances: + # # If the instance is a duplicate then it has already been removed from the set and a KeyError will be thrown + # try: + # set_of_instances.remove(instance['input']) + # except KeyError: + # raise Exception(f" * Looks like we have a repeated example here! " + # f"Merge outputs before removing duplicates. :-/ \n {instance}") + + # Make sure there are no link in instances + url_reg = r'http[s]?://(?:[a-zA-Z]|[0-9]|[$-_@.&+]|[!*\(\),]|(?:%[0-9a-fA-F][0-9a-fA-F]))+' + instances = data['Instances'] + for instance in instances: + ck_url = re.findall(url_reg, instance['input']) + if ck_url: + print(f'⚠️ WARNING: Looks like there is a link in the input: {ck_url}') + break + + # make sure classes are balanced + output = [ins['output'] for ins in instances] + # flattens the nested arrays + outputs = sum(output, []) + value, counts = np.unique(outputs, return_counts=True) + + task_number = file.replace("task", "").split("_")[0] + # TODO: drop this condition + if int(task_number) not in [902, 903]: + assert len(value) > 1, f" Looks like all the instances are mapped to a single output: {value}" + + if task_number not in skew_exclusion and len(value) < 15: + norm_counts = counts / counts.sum() + entropy = -(norm_counts * np.log(norm_counts) / np.log(len(value))).sum() + # pqz + # assert entropy > 0.8, f"Looks like this task is heavily skewed!\n 📋 classes: {value} \n 📋 Norm_counts: {norm_counts} \n 📋 Distribution of classes: {counts} \n 📊 entropy= {entropy}" + # Make sure there are no examples repeated across instances and positive examples + examples = [ex['input'] for ex in data['Positive Examples']] + for instance in instances: + if instance['input'] in examples: + raise Exception(f" * Looks like we have a same example across positive examples and instances! " + f"Drop the example from the instances. :-/ \n {instance}") + + assert len(instance['output']) > 0, "all the instances must have at least one output" + + true_file = file.replace(".json", "") + for char in true_file: + if char.isupper(): + raise Exception(f" * Looks like there is an uppercase letter in `{true_file}`. " + f"All letters should be lowercased.") + + if file in task_readme_content: + raise Exception(f" * Looks like the .json file extension ending is " + f"present with the task name in `tasks/README.md` when it should just be `{true_file}`") + + # pqz + # if true_file not in task_readme_content: + # raise Exception(f' * Looks like the task name `{true_file}` is not included ' + # f'in the task file `tasks/README.md`') + + if task_readme_content.count(true_file) > 1: + raise Exception(f' * Looks like the task name `{true_file}` is repeated in ' + f'the task file `tasks/README.md`') + + for c in data['Contributors']: + if c not in contributor_stats: + contributor_stats[c] = 0 + contributor_stats[c] += 1 + tasks_count = tasks_count + 1 + +# test the the official splits +# pqz +# for split_name in ["mol_text"]: + # train_tasks = [l.strip() for l in open(f"splits/{split_name}/train_tasks.txt")] + # test_tasks = [l.strip() for l in open(f"splits/{split_name}/test_tasks.txt")] + # excluded_tasks = [l.strip() for l in open(f"splits/{split_name}/excluded_tasks.txt")] + + # make east task in the split actually exists + # pqz + # for task in train_tasks + test_tasks + excluded_tasks: + # assert task in task_names, f" Task {task} doesn't exist, but it's included in the {split_name} split." + # make sure each task appears in the split + # pqz + # for task in task_names: + # assert task in train_tasks + test_tasks + excluded_tasks, f" Task {task} is missing in the {split_name} split." + # make sure there is no overlap between test and train task names in the splits files. + # assert len(set(train_tasks) & set(test_tasks)) == 0, f" {split_name} split has overlap tasks in the train & test sets." + # assert len(set(train_tasks) & set(excluded_tasks)) == 0, f" {split_name} split has overlap tasks in the train & excluded sets." + # assert len(set(test_tasks) & set(excluded_tasks)) == 0, f" {split_name} split has overlap tasks in the test & excluded sets." + +print("Did not find any errors! ✅") + +print("\n - - - - - Contributors >= 25 tasks - - - - - ") +keyvalues = sorted(list(contributor_stats.items()), key=lambda x: x[1]) +for author, count in keyvalues: + if count >= 25: + print(f" ✍️ {author} -> {count}") + +print("\n - - - - - Category Stats - - - - - ") +keyvalues = sorted(list(categories_stats.items()), key=lambda x: x[1]) +for cat, count in categories_stats.items(): + print(f" ✍️ {cat} -> {count}") + +print("\n - - - - - Domain Stats - - - - - ") +keyvalues = sorted(list(domain_stats.items()), key=lambda x: x[1]) +for dom, count in domain_stats.items(): + print(f" ✍️ {dom} -> {count}") + +print("\n - - - - - Reasoning Stats - - - - - ") +keyvalues = sorted(list(reasoning_stats.items()), key=lambda x: x[1]) +for res, count in reasoning_stats.items(): + print(f" ✍️ {res} -> {count}") + +print("\n - - - - - Instances Stats - - - - - ") +average_number_of_instances = number_of_instances / tasks_count +print(f" ✍️ Average number of Instances -> {average_number_of_instances}") \ No newline at end of file