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eval_all_models.sh
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eval_all_models.sh
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# BC5CDR
# MODEL_DIR="trained_models/mesh/"
MODEL_DIR="cambridgeltl/SapBERT-from-PubMedBERT-fulltext"
DICT_PATH=/efs/davidkartchner/el-robustness-comparison/data/mesh_to_alias.txt
DATASET_NAME=bc5cdr
CUDA_VISIBLE_DEVICES=0 python3 run_bigbio_inference.py \
--model_dir $MODEL_DIR \
--dictionary_path $DICT_PATH \
--dataset_name $DATASET_NAME \
--output_dir ./output/ \
--use_cuda \
--max_length 25 \
--batch_size 32 \
--abbreviations_path /efs/davidkartchner/el-robustness-comparison/data/abbreviations.json&
# NLM Chem
# MODEL_DIR="trained_models/mesh/"
MODEL_DIR="cambridgeltl/SapBERT-from-PubMedBERT-fulltext"
DICT_PATH=/efs/davidkartchner/el-robustness-comparison/data/mesh_to_alias.txt
DATASET_NAME=nlmchem
CUDA_VISIBLE_DEVICES=1 python3 run_bigbio_inference.py \
--model_dir $MODEL_DIR \
--dictionary_path $DICT_PATH \
--dataset_name $DATASET_NAME \
--output_dir ./output/ \
--use_cuda \
--max_length 25 \
--batch_size 32 \
--abbreviations_path /efs/davidkartchner/el-robustness-comparison/data/abbreviations.json&
# NLM Gene
# MODEL_DIR="trained_models/entrez/"
MODEL_DIR="cambridgeltl/SapBERT-from-PubMedBERT-fulltext"
DICT_PATH=/efs/davidkartchner/el-robustness-comparison/data/entrez_to_alias.txt
DATASET_NAME=nlm_gene
CUDA_VISIBLE_DEVICES=2 python3 run_bigbio_inference.py \
--model_dir $MODEL_DIR \
--dictionary_path $DICT_PATH \
--dataset_name $DATASET_NAME \
--output_dir ./output/ \
--use_cuda \
--max_length 25 \
--batch_size 32 \
--abbreviations_path /efs/davidkartchner/el-robustness-comparison/data/abbreviations.json&
# GNormPlus
# MODEL_DIR="trained_models/entrez/"
MODEL_DIR="cambridgeltl/SapBERT-from-PubMedBERT-fulltext"
DICT_PATH=/efs/davidkartchner/el-robustness-comparison/data/entrez_to_alias.txt
DATASET_NAME=gnormplus
CUDA_VISIBLE_DEVICES=3 python3 run_bigbio_inference.py \
--model_dir $MODEL_DIR \
--dictionary_path $DICT_PATH \
--dataset_name $DATASET_NAME \
--output_dir ./output/ \
--use_cuda \
--max_length 25 \
--batch_size 32 \
--abbreviations_path /efs/davidkartchner/el-robustness-comparison/data/abbreviations.json
# Medmentions Full
MODEL_DIR="cambridgeltl/SapBERT-from-PubMedBERT-fulltext"
DICT_PATH=./data/medmentions/umls_dict_uncased.txt
DATASET_NAME=medmentions_full
CUDA_VISIBLE_DEVICES=0 python3 run_bigbio_inference.py \
--model_dir $MODEL_DIR \
--dictionary_path $DICT_PATH \
--dataset_name $DATASET_NAME \
--output_dir ./output/ \
--use_cuda \
--max_length 25 \
--batch_size 32 \
--abbreviations_path /efs/davidkartchner/el-robustness-comparison/data/abbreviations.json&
# --debug \
# MedMentions ST21PV
MODEL_DIR="cambridgeltl/SapBERT-from-PubMedBERT-fulltext"
DICT_PATH=/efs/davidkartchner/el-robustness-comparison/data/st21pv_to_alias.txt
DATASET_NAME=medmentions_st21pv
CUDA_VISIBLE_DEVICES=1 python3 run_bigbio_inference.py \
--model_dir $MODEL_DIR \
--dictionary_path $DICT_PATH \
--dataset_name $DATASET_NAME \
--output_dir ./output/ \
--use_cuda \
--max_length 25 \
--batch_size 32 \
--abbreviations_path /efs/davidkartchner/el-robustness-comparison/data/abbreviations.json \
# NCBI Disease
MODEL_DIR="trained_models/mesh_and_omim_disease_only/"
# MODEL_DIR="cambridgeltl/SapBERT-from-PubMedBERT-fulltext"
DICT_PATH=/efs/davidkartchner/el-robustness-comparison/data/mesh_and_omim_to_alias_disease_only.txt
DATASET_NAME=ncbi_disease
CUDA_VISIBLE_DEVICES=2 python3 run_bigbio_inference.py \
--model_dir $MODEL_DIR \
--dictionary_path $DICT_PATH \
--dataset_name $DATASET_NAME \
--output_dir ./output/ \
--use_cuda \
--max_length 25 \
--batch_size 32 \
--abbreviations_path /efs/davidkartchner/el-robustness-comparison/data/abbreviations.json
# NCBI Disease
# MODEL_DIR="trained_models/mesh_omim_disease/"
MODEL_DIR="cambridgeltl/SapBERT-from-PubMedBERT-fulltext"
DICT_PATH=/efs/davidkartchner/el-robustness-comparison/data/mesh_and_omim_to_alias_disease_only.txt
DATASET_NAME=ncbi_disease
CUDA_VISIBLE_DEVICES=3 python3 run_bigbio_inference.py \
--model_dir $MODEL_DIR \
--dictionary_path $DICT_PATH \
--dataset_name $DATASET_NAME \
--output_dir ./output/ \
--use_cuda \
--max_length 25 \
--batch_size 32 \
--abbreviations_path /efs/davidkartchner/el-robustness-comparison/data/abbreviations.json