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README.md
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<span style="font-size:larger;">**Clinical-Longformer**</span> is a clinical knowledge enriched version of Longformer that was further pre-trained using MIMIC-III clinical notes. It allows up to 4,096 tokens as the model input.
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### Pre-training
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We initialized Clinical-Longformer from the pre-trained weights of the base version of Longformer. The pre-training process was distributed in parallel to 6 32GB Tesla V100 GPUs. FP16 precision was enabled to accelerate training. We pre-trained Clinical-Longformer for 200,000 steps with batch size of 6×3. The learning rates were 3e-5 for both models. The entire pre-training process took more than 2 weeks.
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### Down-stream Tasks
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Clinical-Longformer consistently out-perform ClinicalBERT across 10 baseline dataset for at least 2 percent. The dataset broadly cover NER, QA and text classification tasks. For more details, please refer to:
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### Usage
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Load the model directly from Transformers:
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```
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from transformers import AutoTokenizer, AutoModelForMaskedLM
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model = AutoModelForMaskedLM.from_pretrained("yikuan8/Clinical-Longformer", use_auth_token=True)
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If you find our
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@inproceedings{li2020comparison,
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title={A comparison of pre-trained vision-and-language models for multimodal representation learning across medical images and reports},
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<span style="font-size:larger;">**Clinical-Longformer**</span> is a clinical knowledge enriched version of Longformer that was further pre-trained using MIMIC-III clinical notes. It allows up to 4,096 tokens as the model input. Clinical-Longformer consistently out-performs ClinicalBERT across 10 baseline dataset for at least 2 percent. The dataset broadly cover clinical NER, QA and text classification tasks. For more details, please refer to:
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### Pre-training
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We initialized Clinical-Longformer from the pre-trained weights of the base version of Longformer. The pre-training process was distributed in parallel to 6 32GB Tesla V100 GPUs. FP16 precision was enabled to accelerate training. We pre-trained Clinical-Longformer for 200,000 steps with batch size of 6×3. The learning rates were 3e-5 for both models. The entire pre-training process took more than 2 weeks.
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### Usage
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Load the model directly from Transformers:
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```
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from transformers import AutoTokenizer, AutoModelForMaskedLM
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model = AutoModelForMaskedLM.from_pretrained("yikuan8/Clinical-Longformer", use_auth_token=True)
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```
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If you find our model helps, please consider citing this :)
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```
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@inproceedings{li2020comparison,
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title={A comparison of pre-trained vision-and-language models for multimodal representation learning across medical images and reports},
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