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--- |
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license: other |
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widget: |
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- text: Ḣ Q V Q [MASK] E |
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tags: |
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- biology |
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- medical |
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--- |
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## AntiBERTa2-CSSP 🧬 |
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AntiBERTa2 is an antibody-specific language model based on the [RoFormer model](https://arxiv.org/abs/2104.09864) - it is pre-trained using masked language modelling. |
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We also provide a multimodal version of AntiBERTa2, AntiBERTa2-CSSP, that has been trained using a contrastive objective, similar to the [CLIP method](https://arxiv.org/abs/2103.00020). |
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Further details on both AntiBERTa2 and AntiBERTa2-CSSP are described in our [paper](https://www.mlsb.io/papers_2023/Enhancing_Antibody_Language_Models_with_Structural_Information.pdf) accepted at the NeurIPS MLSB Workshop 2023. |
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Both AntiBERTa2 models are only available for non-commercial use. Output antibody sequences (e.g. from infilling via masked language models) can only be used for |
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non-commercial use. For any users seeking commercial use of our model and generated antibodies, please reach out to us at [info@alchemab.com](mailto:info@alchemab.com). |
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| Model variant | Parameters | Config | |
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| ------------- | ---------- | ------ | |
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| [AntiBERTa2](https://huggingface.co/alchemab/antiberta2) | 202M | 16L, 16H, 1024d | |
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| [AntiBERTa2-CSSP](https://huggingface.co/alchemab/antiberta2-cssp) | 202M | 16L, 16H, 1024d | |
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## Example usage |
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``` |
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>>> from transformers import ( |
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RoFormerModel, |
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RoFormerTokenizer, |
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RoFormerForSequenceClassification |
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) |
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>>> tokenizer = RoFormerTokenizer.from_pretrained("alchemab/antiberta2-cssp") |
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>>> model = RoFormerModel.from_pretrained("alchemab/antiberta2-cssp") |
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>>> model(**tokenizer("Ḣ Q V Q ... T V S S", return_tensors='pt')).last_hidden_state... # etc |
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>>> new_model = RoFormerForSequenceClassification.from_pretrained( |
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"alchemab/antiberta2-cssp") # this will of course raise warnings |
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# that a new linear layer will be added |
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# and randomly initialized |
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``` |
