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config.DOCKER-LIGHT.yaml
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base_folder: /msnovelist/
batch_size: 256
cv_fold: 1
cv_folds: 10
db_path_train:
construct_from: smiles
fp_map: /target/fingerprint_mapping_pseudo.tsv
path: /target/sirius6-ee5e71a4-77bd-487d-9508-3806ba2063c0.db
pipeline_options:
embed_X: false
fingerprint_selected: fingerprint_sampled
reload_smiles_pubchem: false
db_path_eval:
construct_from: smiles
fp_map: /target/fingerprint_mapping_pseudo.tsv
path: /target/sirius6-0ccb3c70-85f7-4aa1-9b98-7c8941910a0e.db
pipeline_options:
embed_X: false
fingerprint_selected: fingerprint_degraded
reload_smiles_pubchem: false
# db_path_template:
# construct_from: smiles
# fp_map: /contrib/fingerprinter_cli/csi_fingerid_mod.tsv
# path: /msnovelist-data/minimal-dataset/sirius6-minimal.db
# pipeline_options:
# embed_X: false
# reload_smiles_pubchem: false
db_path_sampler:
construct_from: smiles
fp_map: /target/fingerprint_mapping_pseudo.tsv
path: /target/sirius6-0ccb3c70-85f7-4aa1-9b98-7c8941910a0e.db
pipeline_options:
embed_X: false
reload_smiles_pubchem: false
db_pubchem: /msnovelist/data/pubchem-dummy/pubchem_ref_dummy.db
decoder_config:
clip_invalid_counts: false
tokenization: tokens_process
decoder_name: beam_search
epochs: 30
eval_counter: ''
eval_detail: false
eval_folder: /sirius6_db/data/results/
eval_fingerprint_all: false
eval_id: ''
eval_k: 128
eval_kk: 128
eval_n: 8
eval_n_total: 300
eval_steps: 128
eval_temperature: 1.0
eval_top_n: 1
evaluation_set: dataset
f1_cutoff: 0.5
fingerprinter_cache: /msnovelist-data/fingerprint-cache/fingerprint_cache.db
normalizer_path: /contrib/fingerprinter_cli/bin/smiles_normalizer
sirius_path: /contrib/sirius/bin/sirius
fp_map: /sirius6_db/fingerprint_mapping.tsv
fp_map_evaluation: /sirius6_db/fingerprint_mapping_pseudo.tsv
fp_overlay_method: none
fp_source: ''
hdf5_lock: 'FALSE'
log_folder: /sirius6_db/data/tensorboard/
model_config:
loss_weights:
out_nhydrogen: 0.03
out_smiles: 1
use_auxiliary_counter: true
use_fingerprint: true
use_hydrogen_estimator: true
encoder_dropout: [0.3, 0.3]
encoder_input_dropout: None
model_name: models.model_flex_20190401
model_tag: msnovelist-sirius6-weights-gamma2_nonrev_005
pipeline_encoder:
- fingerprint_selected
- mol_form
- n_hydrogen
pipeline_reference:
- smiles_canonical
- fingerprint_degraded
pipeline_x:
- fingerprint_selected
- mol_form
- tokens_X
pipeline_x_eval: []
pipeline_y:
- tokens_y
- n_hydrogen
random_seed_global: ''
rerank_sirius_results_n: 99999
#sampler_name: fp_sampling.cv_sampler_direct
sampler_name: "gamma_bitmatrix"
sampler_config:
mean: 0
stddev: 2
reverse_0_stats: false
unchanged_rate: 0.05
steps_per_epoch: -1
steps_per_epoch_validation: -1
tensorflow_trace: false
training_id: ''
training_set: train
training_verbose: 1
validation_set: validate
weights: w-20-0.069-0.074.hdf5
weights_folder: /target/evaluation/m-36719628/1