whaleloops
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README.md
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license: cc-by-nc-4.0
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---
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KEPTlongfomer
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And then pretrained with Hierarchical Self-Alignment Pretrainumls (HSAP) using Knowledge Graph UMLS.
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This includes (a) Hierarchy, (b) Synonym, (c) Abbreviation. For more info, see section 3.3 in [paper](https://arxiv.org/pdf/2210.03304.pdf).
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See [
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With the following result:
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| Metric | Score |
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license: cc-by-nc-4.0
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language: "en"
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tags:
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- longformer
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- clinical
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- biomedical
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<span style="font-size:larger;">**KEPTlongfomer**</span> is a medical knowledge enhanced version of Longformer that was further pre-trained using [contrastive learning](https://arxiv.org/pdf/2210.03304.pdf).
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### Pre-training
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We initialized this model from RoBERTa-base-PM-M3-Voc-distill from Facebook [bio-lm](https://github.com/facebookresearch/bio-lm/).
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And then pretrained with Hierarchical Self-Alignment Pretrain (HSAP) using Knowledge Graph UMLS.
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This includes (a) Hierarchy, (b) Synonym, (c) Abbreviation. For more info, see section 3.3 in [paper](https://arxiv.org/pdf/2210.03304.pdf).
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The learning rate was 5e-5, weight decay was 0.01, adam epsilon was 1e-5.
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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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tokenizer = AutoTokenizer.from_pretrained("whaleloops/KEPTlongformer-PMM3")
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config = AutoConfig.from_pretrained("whaleloops/KEPTlongformer-PMM3")
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model = AutoModelForMaskedLM.from_pretrained("whaleloops/KEPTlongformer-PMM3", config=config)
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```
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See our [github](https://github.com/whaleloops/KEPT/tree/rerank300) for how to use this with prompts on auto ICD coding.
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With the following result:
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| Metric | Score |
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