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config.yml
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config.yml
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profiling_pipeline_baseline:
root_dir: /data/datasets/shared_data_2/pipeline_profiling_data/
raw_data_dir: /data/datasets/shared_data_2/pipeline_profiling_data/raw_text/
suffix: baseline
generate_bio: True
encoded_text: False
ner_model:
type: bert
path: /data/datasets/zehao/sdoh/model/SDOH_bert_final
profiling_pipeline_optimized:
root_dir: /data/datasets/shared_data_2/pipeline_profiling_data/
raw_data_dir: /data/datasets/shared_data_2/pipeline_profiling_data/raw_text/
suffix: optimized
generate_bio: False
encoded_text: True # TODO: we can probably eliminate this flag by always checking if encoded text exist and generate it if not
ner_model:
type: bert
path: /data/datasets/zehao/sdoh/model/SDOH_bert_final
SDoH_pipeline:
gpu_node: 0
root_dir: /data/datasets/shared_data_2/ADRD/
raw_data_dir: /data/datasets/Tianchen/data_from_old_server/2021/ADRD_data_from_Xi/clinical_notes_all_0826/
generate_bio: False
encoded_text: True
ner_model:
type: bert
path: /data/datasets/zehao/sdoh/model/SDOH_bert_final
lungrads_ner_validation:
root_dir: /data/datasets/shared_data_2/lungrads_NER_training/
raw_data_dir: /data/datasets/shared_data_2/lungrads_NER_training/raw_text/
generate_bio: False
encoded_text: False
ner_model:
type: roberta
path: /home/jameshuang/Projects/NLP_annotation/fine_tuned_ner/mimiciii_roberta-base_10e_128b_bz=8
lungrads_ner_validation_baseline:
root_dir: /data/datasets/shared_data_2/lungrads_NER_training/
raw_data_dir: /data/datasets/shared_data_2/lungrads_NER_training/raw_text/
suffix: baseline
generate_bio: False
encoded_text: True
ner_model:
type: roberta
path: /home/jameshuang/Projects/NLP_annotation/fine_tuned_ner/mimiciii_roberta-base_10e_128b_bz=8_baseline
lungrads_pipeline:
root_dir: /data/datasets/shared_data_2/IRB201901754_lungrads
raw_data_dir: /data/datasets/shared_data_2/IRB201901754_lungrads/raw_text/
generate_bio: False
encoded_text: True
ner_model:
type: roberta
path: /home/jameshuang/Projects/NLP_annotation/fine_tuned_ner/mimiciii_roberta-base_10e_128b_bz=8