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run_everything.sh
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run_everything.sh
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#!/bin/bash
export CUDA_VISIBLE_DEVICES=0,1
######BERT Experiments######
#Mikolov Replace BERT
python run_modeling.py --batch_size 40 \
--model_name "phiyodr/bert-base-finetuned-squad2" \
--dte_lookup_table_fp "Mikolov_to_phiyodr_bert-base-finetuned-squad2.pkl" \
--lr 3e-5 \
--n_epochs 2 \
--max_len 384 \
--n_stride 196 \
--warmup_proportion 0.1 \
--use_kge T \
--n_neg_records 10 \
--gpus 0 7 \
--seed 16 \
--port 42069
#Mikolov++ Replace BERT
python run_modeling.py --batch_size 40 \
--model_name "phiyodr/bert-base-finetuned-squad2" \
--dte_lookup_table_fp "Mikolov++_to_phiyodr_bert-base-finetuned-squad2.pkl" \
--lr 3e-5 \
--n_epochs 2 \
--max_len 384 \
--n_stride 196 \
--warmup_proportion 0.1 \
--use_kge T \
--n_neg_records 10 \
--gpus 0 7 \
--seed 16 \
--port 42069
######RoBERTa Experiments######
#Random Concat with RoBERTa
python run_modeling.py --batch_size 40 \
--model_name "navteca/roberta-base-squad2" \
--dte_lookup_table_fp "Mikolov_to_navteca_roberta-base-squad2.pkl" \
--lr 3e-5 \
--n_epochs 2 \
--max_len 384 \
--n_stride 196 \
--warmup_proportion 0.1 \
--use_kge T \
--concat_kge T \
--random_kge T \
--n_neg_records 10 \
--gpus 0 1 \
--seed 16 \
--port 42069
#Mikolov Replace RoBERTa
python run_modeling.py --batch_size 40 \
--model_name "navteca/roberta-base-squad2" \
--dte_lookup_table_fp "Mikolov_to_navteca_roberta-base-squad2.pkl" \
--lr 3e-5 \
--n_epochs 2 \
--max_len 384 \
--n_stride 196 \
--warmup_proportion 0.1 \
--use_kge T \
--n_neg_records 10 \
--gpus 0 7 \
--seed 16 \
--port 42069
#Mikolov Concat RoBERTa
python run_modeling.py --batch_size 40 \
--model_name "navteca/roberta-base-squad2" \
--dte_lookup_table_fp "Mikolov_to_navteca_roberta-base-squad2.pkl" \
--lr 3e-5 \
--n_epochs 2 \
--max_len 384 \
--n_stride 196 \
--warmup_proportion 0.1 \
--use_kge T \
--concat_kge T \
--n_neg_records 10 \
--gpus 0 7 \
--seed 16 \
--port 42069
#Mikolov++ Replace RoBERTa
python run_modeling.py --batch_size 40 \
--model_name "navteca/roberta-base-squad2" \
--dte_lookup_table_fp "Mikolov++_to_navteca_roberta-base-squad2.pkl" \
--lr 3e-5 \
--n_epochs 2 \
--max_len 384 \
--n_stride 196 \
--warmup_proportion 0.1 \
--use_kge T \
--n_neg_records 10 \
--gpus 0 1 \
--seed 16 \
--port 42066
######BioBERT Experiments######
#Vanilla BioBERT FT
python run_modeling.py --batch_size 40 \
--model_name "ktrapeznikov/biobert_v1.1_pubmed_squad_v2" \
--dte_lookup_table_fp "Mikolov_to_ktrapeznikov_biobert_v1.1_pubmed_squad_v2.pkl" \
--lr 3e-5 \
--n_epochs 2 \
--max_len 384 \
--n_stride 196 \
--warmup_proportion 0.1 \
--n_neg_records 10 \
--gpus 0 1 \
--seed 16 \
--port 42069
#Random Concat with BioBERT
python run_modeling.py --batch_size 40 \
--model_name "ktrapeznikov/biobert_v1.1_pubmed_squad_v2" \
--dte_lookup_table_fp "Mikolov_to_ktrapeznikov_biobert_v1.1_pubmed_squad_v2.pkl" \
--lr 3e-5 \
--n_epochs 2 \
--max_len 384 \
--n_stride 196 \
--warmup_proportion 0.1 \
--use_kge T \
--concat_kge T \
--random_kge T \
--n_neg_records 10 \
--gpus 0 7 \
--seed 16 \
--port 42069
#Mikolov Replace BioBERT
python run_modeling.py --batch_size 40 \
--model_name "ktrapeznikov/biobert_v1.1_pubmed_squad_v2" \
--dte_lookup_table_fp "Mikolov_to_ktrapeznikov_biobert_v1.1_pubmed_squad_v2.pkl" \
--lr 3e-5 \
--n_epochs 2 \
--max_len 384 \
--n_stride 196 \
--warmup_proportion 0.1 \
--use_kge T \
--n_neg_records 10 \
--gpus 0 7 \
--seed 16 \
--port 42069
#Mikolov Concat BioBERT
python run_modeling.py --batch_size 40 \
--model_name "ktrapeznikov/biobert_v1.1_pubmed_squad_v2" \
--dte_lookup_table_fp "Mikolov_to_ktrapeznikov_biobert_v1.1_pubmed_squad_v2.pkl" \
--lr 3e-5 \
--n_epochs 2 \
--max_len 384 \
--n_stride 196 \
--warmup_proportion 0.1 \
--use_kge T \
--concat_kge T \
--n_neg_records 10 \
--gpus 0 7 \
--seed 16 \
--port 42069
#Mikolov++ Replace BioBERT
python run_modeling.py --batch_size 40 \
--model_name "ktrapeznikov/biobert_v1.1_pubmed_squad_v2" \
--dte_lookup_table_fp "Mikolov++_to_ktrapeznikov_biobert_v1.1_pubmed_squad_v2.pkl" \
--lr 3e-5 \
--n_epochs 2 \
--max_len 384 \
--n_stride 196 \
--warmup_proportion 0.1 \
--use_kge T \
--n_neg_records 10 \
--gpus 0 7 \
--seed 16 \
--port 42069
#Mikolov++ Concat BioBERT
python run_modeling.py --batch_size 40 \
--model_name "ktrapeznikov/biobert_v1.1_pubmed_squad_v2" \
--dte_lookup_table_fp "Mikolov++_to_ktrapeznikov_biobert_v1.1_pubmed_squad_v2.pkl" \
--lr 3e-5 \
--n_epochs 2 \
--max_len 384 \
--n_stride 196 \
--warmup_proportion 0.1 \
--use_kge T \
--concat_kge T \
--n_neg_records 10 \
--gpus 0 7 \
--seed 16 \
--port 42069
######SciBERT Experiments######
#Vanilla SciBERT FT
python run_modeling.py --batch_size 40 \
--model_name "ktrapeznikov/scibert_scivocab_uncased_squad_v2" \
--dte_lookup_table_fp "Mikolov_to_ktrapeznikov_scibert_scivocab_uncased_squad_v2.pkl" \
--lr 3e-5 \
--n_epochs 2 \
--max_len 384 \
--n_stride 196 \
--warmup_proportion 0.1 \
--n_neg_records 10 \
--gpus 0 1 \
--seed 16 \
--port 42069
#Random Concat with SciBERT
python run_modeling.py --batch_size 40 \
--model_name "ktrapeznikov/scibert_scivocab_uncased_squad_v2" \
--dte_lookup_table_fp "Mikolov_to_ktrapeznikov_scibert_scivocab_uncased_squad_v2.pkl" \
--lr 3e-5 \
--n_epochs 2 \
--max_len 384 \
--n_stride 196 \
--warmup_proportion 0.1 \
--use_kge T \
--concat_kge T \
--random_kge T \
--n_neg_records 10 \
--gpus 0 7 \
--seed 16 \
--port 42069
#Mikolov Replace SciBERT
python run_modeling.py --batch_size 40 \
--model_name "ktrapeznikov/scibert_scivocab_uncased_squad_v2" \
--dte_lookup_table_fp "Mikolov_to_ktrapeznikov_scibert_scivocab_uncased_squad_v2.pkl" \
--lr 3e-5 \
--n_epochs 2 \
--max_len 384 \
--n_stride 196 \
--warmup_proportion 0.1 \
--use_kge T \
--n_neg_records 10 \
--gpus 0 7 \
--seed 16 \
--port 42069
#Mikolov Concat SciBERT
python run_modeling.py --batch_size 40 \
--model_name "ktrapeznikov/scibert_scivocab_uncased_squad_v2" \
--dte_lookup_table_fp "Mikolov_to_ktrapeznikov_scibert_scivocab_uncased_squad_v2.pkl" \
--lr 3e-5 \
--n_epochs 2 \
--max_len 384 \
--n_stride 196 \
--warmup_proportion 0.1 \
--use_kge T \
--concat_kge T \
--n_neg_records 10 \
--gpus 0 7 \
--seed 16 \
--port 42069
#Mikolov++ Replace SciBERT
python run_modeling.py --batch_size 40 \
--model_name "ktrapeznikov/scibert_scivocab_uncased_squad_v2" \
--dte_lookup_table_fp "Mikolov++_to_ktrapeznikov_scibert_scivocab_uncased_squad_v2.pkl" \
--lr 3e-5 \
--n_epochs 2 \
--max_len 384 \
--n_stride 196 \
--warmup_proportion 0.1 \
--use_kge T \
--n_neg_records 10 \
--gpus 0 7 \
--seed 16 \
--port 42069
#Mikolov++ Concat SciBERT
python run_modeling.py --batch_size 40 \
--model_name "ktrapeznikov/scibert_scivocab_uncased_squad_v2" \
--dte_lookup_table_fp "Mikolov++_to_ktrapeznikov_scibert_scivocab_uncased_squad_v2.pkl" \
--lr 3e-5 \
--n_epochs 2 \
--max_len 384 \
--n_stride 196 \
--warmup_proportion 0.1 \
--use_kge T \
--concat_kge T \
--n_neg_records 10 \
--gpus 0 7 \
--seed 16 \
--port 42069
######PubMedBERT Experiments######
#Vanilla PubMedBERT FT
python run_modeling.py --batch_size 40 \
--model_name "franklu/pubmed_bert_squadv2" \
--dte_lookup_table_fp "Mikolov_to_franklu_pubmed_bert_squadv2.pkl" \
--lr 3e-5 \
--n_epochs 2 \
--max_len 384 \
--n_stride 196 \
--warmup_proportion 0.1 \
--n_neg_records 10 \
--gpus 0 1 \
--seed 16 \
--port 42069
#Random Concat with PubMedBERT
python run_modeling.py --batch_size 40 \
--model_name "franklu/pubmed_bert_squadv2" \
--dte_lookup_table_fp "Mikolov_to_franklu_pubmed_bert_squadv2.pkl" \
--lr 3e-5 \
--n_epochs 2 \
--max_len 384 \
--n_stride 196 \
--warmup_proportion 0.1 \
--use_kge T \
--concat_kge T \
--random_kge T \
--n_neg_records 10 \
--gpus 0 7 \
--seed 16 \
--port 42069
#Mikolov Replace PubMedBERT
python run_modeling.py --batch_size 40 \
--model_name "franklu/pubmed_bert_squadv2" \
--dte_lookup_table_fp "Mikolov_to_franklu_pubmed_bert_squadv2.pkl" \
--lr 3e-5 \
--n_epochs 2 \
--max_len 384 \
--n_stride 196 \
--warmup_proportion 0.1 \
--use_kge T \
--n_neg_records 10 \
--gpus 0 7 \
--seed 16 \
--port 42069
#Mikolov Concat PubMedBERT
python run_modeling.py --batch_size 40 \
--model_name "franklu/pubmed_bert_squadv2" \
--dte_lookup_table_fp "Mikolov_to_franklu_pubmed_bert_squadv2.pkl" \
--lr 3e-5 \
--n_epochs 2 \
--max_len 384 \
--n_stride 196 \
--warmup_proportion 0.1 \
--use_kge T \
--concat_kge T \
--n_neg_records 10 \
--gpus 0 7 \
--seed 16 \
--port 42069
#Mikolov++ Replace PubMedBERT
python run_modeling.py --batch_size 40 \
--model_name "franklu/pubmed_bert_squadv2" \
--dte_lookup_table_fp "Mikolov++_to_franklu_pubmed_bert_squadv2.pkl" \
--lr 3e-5 \
--n_epochs 2 \
--max_len 384 \
--n_stride 196 \
--warmup_proportion 0.1 \
--use_kge T \
--n_neg_records 10 \
--gpus 0 7 \
--seed 16 \
--port 42069
#Mikolov++ Concat PubMedBERT
python run_modeling.py --batch_size 40 \
--model_name "franklu/pubmed_bert_squadv2" \
--dte_lookup_table_fp "Mikolov++_to_franklu_pubmed_bert_squadv2.pkl" \
--lr 3e-5 \
--n_epochs 2 \
--max_len 384 \
--n_stride 196 \
--warmup_proportion 0.1 \
--use_kge T \
--concat_kge T \
--n_neg_records 10 \
--gpus 0 7 \
--seed 16 \
--port 42069