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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.
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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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tokenizer = AutoTokenizer.from_pretrained("yikuan8/Clinical-Longformer")
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model = AutoModelForMaskedLM.from_pretrained("yikuan8/Clinical-Longformer")
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If you find our model helps, please consider citing this :)
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```
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@article{li2022clinicallongformer,
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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. Those downstream experiments broadly cover named entity recognition (NER), question answering (QA), natural language inference (NLI) and text classification tasks. For more details, please refer to [our paper](https://arxiv.org/pdf/2201.11838.pdf).
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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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tokenizer = AutoTokenizer.from_pretrained("yikuan8/Clinical-Longformer")
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model = AutoModelForMaskedLM.from_pretrained("yikuan8/Clinical-Longformer")
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```
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### Citing
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If you find our model helps, please consider citing this :)
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```
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@article{li2022clinicallongformer,
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