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Makefile
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Makefile
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## Model training
SAVE_DIR=./models/fine-tuned/
DATA_DIR=./data/
TRAINING_ROOT=./fine-tuning
CUDA=1
SAVING=-1
LOGGING=50
BATCH_SIZE=6
MAX_LENGTH=512
WARMUP=0
ADAM_EPS=1e-8
ADAM_BETA1=0.9
ADAM_BETA2=0.98
WEIGHT_DECAY=1e-4
GRADIENT_ACCUMULATE=1
LM=biolm-large
run_name=check
DATA_TYPE=doc
DATA_NAME=ncbi-disease
run-ner:
CUDA_LAUNCH_BLOCKING=1 CUDA_DEVICE_ORDER=PCI_BUS_ID CUDA_VISIBLE_DEVICES=$(CUDA) python3 $(TRAINING_ROOT)/run_ner.py \
--train_dir $(DATA_DIR)/$(DATA_NAME)/from_rawdata/ \
--eval_dir $(DATA_DIR)/$(DATA_NAME)/from_rawdata/ \
--model_type $(MODEL_TYPE) \
--model_name_or_path $(MODEL_NAME) \
--learning_rate $(LR) \
--weight_decay $(WEIGHT_DECAY) \
--adam_epsilon $(ADAM_EPS) \
--adam_beta1 $(ADAM_BETA1) \
--adam_beta2 $(ADAM_BETA2) \
--num_train_epochs $(EPOCH) \
--warmup_steps $(WARMUP) \
--output_dir $(SAVE_DIR)/$(DATA_NAME)/$(LM)_EP$(EPOCH)_LR$(LR)_ML$(MAX_LENGTH)_WM$(WARMUP)_$(DATA_TYPE) \
--per_gpu_train_batch_size $(BATCH_SIZE) \
--per_gpu_eval_batch_size $(BATCH_SIZE) \
--logging_steps $(LOGGING) \
--save_steps $(SAVING) \
--max_seq_length $(MAX_LENGTH) \
--gradient_accumulation_steps $(GRADIENT_ACCUMULATE) \
--do_train \
--do_eval \
--do_predict \
--evaluate_during_training \
--wandb_name $(run_name) \
--data_type $(DATA_TYPE) \
--data_name $(DATA_NAME) \
--overwrite_output_dir \
eval-ner:
CUDA_LAUNCH_BLOCKING=1 CUDA_DEVICE_ORDER=PCI_BUS_ID CUDA_VISIBLE_DEVICES=$(CUDA) python3 $(TRAINING_ROOT)/eval_ner.py \
--train_dir $(DATA_DIR)/$(DATA_NAME)/from_rawdata/ \
--eval_dir $(DATA_DIR)/$(DATA_NAME)/from_rawdata/ \
--model_type $(MODEL_TYPE) \
--model_name_or_path $(SAVE_DIR)/$(DATA_NAME)/$(LM)_EP$(EPOCH)_LR$(LR)_ML$(MAX_LENGTH)_WM$(WARMUP)_$(DATA_TYPE) \
--learning_rate $(LR) \
--weight_decay $(WEIGHT_DECAY) \
--adam_epsilon $(ADAM_EPS) \
--adam_beta1 $(ADAM_BETA1) \
--adam_beta2 $(ADAM_BETA2) \
--num_train_epochs $(EPOCH) \
--warmup_steps $(WARMUP) \
--output_dir $(SAVE_DIR)/$(DATA_NAME)/$(LM)_EP$(EPOCH)_LR$(LR)_ML$(MAX_LENGTH)_WM$(WARMUP)_$(DATA_TYPE)_eval \
--per_gpu_train_batch_size $(BATCH_SIZE) \
--per_gpu_eval_batch_size $(BATCH_SIZE) \
--logging_steps $(LOGGING) \
--save_steps $(SAVING) \
--max_seq_length $(MAX_LENGTH) \
--do_predict \
--wandb_name $(run_name) \
--data_type $(DATA_TYPE) \
--data_name $(DATA_NAME) \
--overwrite_output_dir \