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sample_run.sh
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sample_run.sh
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python3 -m meshsuggestlib \
--output_dir model/ \
--method ATM \
--dataset clef-tar-processed/new_query \
--cache_dir cache/ \
--output_file result/new_query_atm.tsv \
--qrel_file data/clef-tar-processed/CLEF-2017/train/data.qrels \
--email [email protected] \
--atm_key f4bc8cc0e17e8c4328c18ff0a89b5328d108 \
--depth 1 \
--device cpu
python3 -m meshsuggestlib \
--output_dir model/ \
--method MetaMAP \
--dataset clef-tar-processed/new_query \
--cache_dir cache/ \
--output_file result/new_query_metamap.tsv \
--qrel_file data/clef-tar-processed/CLEF-2017/train/data.qrels \
--depth 1 \
--device cpu
python3 -m meshsuggestlib \
--output_dir model/ \
--method UMLS \
--dataset clef-tar-processed/new_query \
--cache_dir cache/ \
--output_file result/new_query_umls.tsv \
--qrel_file data/clef-tar-processed/CLEF-2017/train/data.qrels \
--depth 1 \
--device cpu
python3 -m meshsuggestlib \
--output_dir model/ \
--method Atomic-BERT \
--dataset clef-tar-processed/new_query \
--model_dir model/checkpoint-80000/ \
--tokenizer_name_or_path dmis-lab/biobert-v1.1 \
--cache_dir cache/ \
--output_file result/new_query_atomic.tsv \
--qrel_file data/clef-tar-processed/CLEF-2017/train/data.qrels \
--email [email protected] \
--email [email protected] \
--depth 1 \
--device cpu
python3 -m meshsuggestlib \
--output_dir model/ \
--method Semantic-BERT \
--dataset clef-tar-processed/new_query \
--model_dir model/checkpoint-80000/ \
--tokenizer_name_or_path dmis-lab/biobert-v1.1 \
--semantic_model_path model/PubMed-w2v.bin \
--cache_dir cache/ \
--output_file result/new_query_semantic.tsv \
--qrel_file data/clef-tar-processed/CLEF-2017/train/data.qrels \
--email [email protected] \
--interpolation_depth 20 \
--depth 1 \
--device cpu
python3 -m meshsuggestlib \
--output_dir model/ \
--method Fragment-BERT \
--dataset clef-tar-processed/new_query \
--model_dir model/checkpoint-80000/ \
--tokenizer_name_or_path dmis-lab/biobert-v1.1 \
--cache_dir cache/ \
--output_file result/new_query_fragment.tsv \
--qrel_file data/clef-tar-processed/CLEF-2017/train/data.qrels \
--email [email protected] \
--depth 1 \
--interpolation_depth 20 \
--device cpu
#python3 -m meshsuggestlib \
#--evaluate_run \
#--output_dir model/ \
#--qrel_file data/clef-tar-processed/CLEF-2018/testing/data.qrels \
#--output_file result/semantic_bert_2018_2.tsv