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运行文件scripts/multimodal/mtr/run_multimodal.sh出现下面的问题,使用的模型是biomedgpt-1dot6b.pth
出现的问题:
11/06/2023 09:07:16 - INFO - datasets.mtr_dataset - Num Samples: 11112
Traceback (most recent call last):
File "/media/b/DATA1/modelsDeployment/OpenBioMed/open_biomed/tasks/multi_modal_task/mtr.py", line 295, in
main(args, config)
File "/media/b/DATA1/modelsDeployment/OpenBioMed/open_biomed/tasks/multi_modal_task/mtr.py", line 213, in main
dataset = SUPPORTED_MTR_DATASETS[args.dataset](args.dataset_path, config["data"], args.dataset_mode, args.filter, args.filter_path)
File "/media/b/DATA1/modelsDeployment/OpenBioMed/open_biomed/datasets/mtr_dataset.py", line 77, in init
super(PCdes, self).init(path, config)
File "/media/b/DATA1/modelsDeployment/OpenBioMed/open_biomed/datasets/mtr_dataset.py", line 29, in init
self._featurize()
File "/media/b/DATA1/modelsDeployment/OpenBioMed/open_biomed/datasets/mtr_dataset.py", line 37, in _featurize
featurizer = MolMultiModalFeaturizer(self.config["mol"])
File "/media/b/DATA1/modelsDeployment/OpenBioMed/open_biomed/feature/mol_featurizer.py", line 760, in init
self.featurizers["text"] = SUPPORTED_TEXT_FEATURIZERconf["name"]
File "/media/b/DATA1/modelsDeployment/OpenBioMed/open_biomed/feature/text_featurizer.py", line 35, in init
self.tokenizer = name2tokenizer[config["transformer_type"]].from_pretrained(config["model_name_or_path"], model_max_length=self.max_length)
File "/home/b/anaconda3/envs/OpenBioMed/lib/python3.9/site-packages/transformers/tokenization_utils_base.py", line 1940, in from_pretrained
resolved_config_file = cached_file(
File "/home/b/anaconda3/envs/OpenBioMed/lib/python3.9/site-packages/transformers/utils/hub.py", line 429, in cached_file
resolved_file = hf_hub_download(
File "/home/b/anaconda3/envs/OpenBioMed/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 110, in _inner_fn
validate_repo_id(arg_value) File "/home/b/anaconda3/envs/OpenBioMed/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 158, in validate_repo_id
raise HFValidationError(
huggingface_hub.utils._validators.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': './ckpts/text_ckpts/gpt2-xl'. Use repo_type argument if needed.
上述的脚本文件内容:
#!/bin/bash
MODE="zero_shot"
TASK_MODE="paragraph"
MODEL="biomedgpt"
DEVICE=$1
EPOCHS=100
运行文件scripts/multimodal/mtr/run_multimodal.sh出现下面的问题,使用的模型是biomedgpt-1dot6b.pth
出现的问题:
11/06/2023 09:07:16 - INFO - datasets.mtr_dataset - Num Samples: 11112
Traceback (most recent call last):
File "/media/b/DATA1/modelsDeployment/OpenBioMed/open_biomed/tasks/multi_modal_task/mtr.py", line 295, in
main(args, config)
File "/media/b/DATA1/modelsDeployment/OpenBioMed/open_biomed/tasks/multi_modal_task/mtr.py", line 213, in main
dataset = SUPPORTED_MTR_DATASETS[args.dataset](args.dataset_path, config["data"], args.dataset_mode, args.filter, args.filter_path)
File "/media/b/DATA1/modelsDeployment/OpenBioMed/open_biomed/datasets/mtr_dataset.py", line 77, in init
super(PCdes, self).init(path, config)
File "/media/b/DATA1/modelsDeployment/OpenBioMed/open_biomed/datasets/mtr_dataset.py", line 29, in init
self._featurize()
File "/media/b/DATA1/modelsDeployment/OpenBioMed/open_biomed/datasets/mtr_dataset.py", line 37, in _featurize
featurizer = MolMultiModalFeaturizer(self.config["mol"])
File "/media/b/DATA1/modelsDeployment/OpenBioMed/open_biomed/feature/mol_featurizer.py", line 760, in init
self.featurizers["text"] = SUPPORTED_TEXT_FEATURIZERconf["name"]
File "/media/b/DATA1/modelsDeployment/OpenBioMed/open_biomed/feature/text_featurizer.py", line 35, in init
self.tokenizer = name2tokenizer[config["transformer_type"]].from_pretrained(config["model_name_or_path"], model_max_length=self.max_length)
File "/home/b/anaconda3/envs/OpenBioMed/lib/python3.9/site-packages/transformers/tokenization_utils_base.py", line 1940, in from_pretrained
resolved_config_file = cached_file(
File "/home/b/anaconda3/envs/OpenBioMed/lib/python3.9/site-packages/transformers/utils/hub.py", line 429, in cached_file
resolved_file = hf_hub_download(
File "/home/b/anaconda3/envs/OpenBioMed/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 110, in _inner_fn
validate_repo_id(arg_value)
File "/home/b/anaconda3/envs/OpenBioMed/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 158, in validate_repo_id
raise HFValidationError(
huggingface_hub.utils._validators.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': './ckpts/text_ckpts/gpt2-xl'. Use
repo_type
argument if needed.上述的脚本文件内容:
#!/bin/bash
MODE="zero_shot"
TASK_MODE="paragraph"
MODEL="biomedgpt"
DEVICE=$1
EPOCHS=100
CKPT="None"
PARAM_KEY="None"
RERANK="no_rerank"
FILTER_FILE="./datasets/mtr/momu_pretrain/pair.txt"
if [ $MODEL = "molfm" ];
then
CKPT="./ckpts/fusion_ckpts/molfm.pth"
PARAM_KEY="model"
RERANK="rerank"
elif [ $MODEL = "drugfm" ];
then
CKPT="./ckpts/fusion_ckpts/drugfm.pth"
PARAM_KEY="model"
RERANK="rerank"
elif [ $MODEL = "momu" ];
then
CKPT="./ckpts/fusion_ckpts/momu/MoMu-S.ckpt"
PARAM_KEY="state_dict"
RERANK="no_rerank"
elif [ $MODEL = "biomedgpt" ];
then
CKPT="/media/b/DATA1/modelsDeployment/OpenBioMed/ckpts/fusion_ckpts/biomedgpt-1dot6b.pth"
PARAM_KEY="None"
RERANK="no_rerank"
fi
mkdir ./ckpts/finetune_ckpts/mtr
python open_biomed/tasks/multi_modal_task/mtr.py
--device ${DEVICE}
--dataset PCdes
--dataset_path ./datasets/mtr/PCdes
--dataset_mode ${TASK_MODE}
--filter
--filter_path ${FILTER_FILE}
--config_path ./configs/mtr/${MODEL}-clip.json
--init_checkpoint ${CKPT}
--output_path ./ckpts/finetune_ckpts/mtr/${MODEL}-${TASK_MODE}-finetune.pth
--param_key ${PARAM_KEY}
--num_workers 1
--mode ${MODE}
--patience 20
--epochs ${EPOCHS}
--${RERANK}
--rerank_num 32
--alpha_m2t 0.9
--alpha_t2m 0.9
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