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biobart/.gitattributes

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biobart/README.md

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+---
+language: 
+  - en
+license: apache-2.0
+
+tags:
+- bart
+- biobart
+- biomedical
+
+inference: true
+
+widget:
+- text: "Influenza is a <mask> disease."
+- type: "text-generation"
+
+---
+
+Paper: [BioBART: Pretraining and Evaluation of A Biomedical Generative Language Model](https://arxiv.org/pdf/2204.03905.pdf)
+
+V2 adopts a new biomedical vocab.
+
+```
+@misc{BioBART,
+  title={BioBART: Pretraining and Evaluation of A Biomedical Generative Language Model},
+  author={Hongyi Yuan and Zheng Yuan and Ruyi Gan and Jiaxing Zhang and Yutao Xie and Sheng Yu},
+  year={2022},
+  eprint={2204.03905},
+  archivePrefix={arXiv}
+}
+```

biobart/config.json

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+{
+  "_name_or_path": "checkpoint_global_step_200000",
+  "activation_dropout": 0.1,
+  "activation_function": "gelu",
+  "add_bias_logits": false,
+  "add_final_layer_norm": false,
+  "architectures": [
+    "BartForConditionalGeneration"
+  ],
+  "attention_dropout": 0.1,
+  "bos_token_id": 0,
+  "classif_dropout": 0.1,
+  "classifier_dropout": 0.0,
+  "d_model": 768,
+  "decoder_attention_heads": 12,
+  "decoder_ffn_dim": 3072,
+  "decoder_layerdrop": 0.0,
+  "decoder_layers": 6,
+  "decoder_start_token_id": 2,
+  "dropout": 0.1,
+  "early_stopping": true,
+  "encoder_attention_heads": 12,
+  "encoder_ffn_dim": 3072,
+  "encoder_layerdrop": 0.0,
+  "encoder_layers": 6,
+  "eos_token_id": 2,
+  "forced_eos_token_id": 2,
+  "gradient_checkpointing": false,
+  "id2label": {
+    "0": "LABEL_0",
+    "1": "LABEL_1",
+    "2": "LABEL_2"
+  },
+  "init_std": 0.02,
+  "is_encoder_decoder": true,
+  "label2id": {
+    "LABEL_0": 0,
+    "LABEL_1": 1,
+    "LABEL_2": 2
+  },
+  "max_position_embeddings": 1024,
+  "model_type": "bart",
+  "no_repeat_ngram_size": 3,
+  "normalize_before": false,
+  "normalize_embedding": true,
+  "num_beams": 4,
+  "num_hidden_layers": 6,
+  "pad_token_id": 1,
+  "scale_embedding": false,
+  "task_specific_params": {
+    "summarization": {
+      "length_penalty": 1.0,
+      "max_length": 128,
+      "min_length": 12,
+      "num_beams": 4
+    },
+    "summarization_cnn": {
+      "length_penalty": 2.0,
+      "max_length": 142,
+      "min_length": 56,
+      "num_beams": 4
+    },
+    "summarization_xsum": {
+      "length_penalty": 1.0,
+      "max_length": 62,
+      "min_length": 11,
+      "num_beams": 6
+    }
+  },
+  "torch_dtype": "float32",
+  "transformers_version": "4.11.3",
+  "use_cache": true,
+  "vocab_size": 85401
+}

biobart/model.safetensors

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biobart/special_tokens_map.json

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+{"bos_token": {"content": "<s>", "single_word": false, "lstrip": false, "rstrip": false, "normalized": true}, "eos_token": {"content": "</s>", "single_word": false, "lstrip": false, "rstrip": false, "normalized": true}, "unk_token": {"content": "<unk>", "single_word": false, "lstrip": false, "rstrip": false, "normalized": true}, "sep_token": {"content": "</s>", "single_word": false, "lstrip": false, "rstrip": false, "normalized": true}, "pad_token": {"content": "<pad>", "single_word": false, "lstrip": false, "rstrip": false, "normalized": true}, "cls_token": {"content": "<s>", "single_word": false, "lstrip": false, "rstrip": false, "normalized": true}, "mask_token": {"content": "<mask>", "single_word": false, "lstrip": true, "rstrip": false, "normalized": true}}

biobart/tokenizer_config.json

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+{"errors": "replace", "unk_token": {"content": "<unk>", "single_word": false, "lstrip": false, "rstrip": false, "normalized": true, "__type": "AddedToken"}, "bos_token": {"content": "<s>", "single_word": false, "lstrip": false, "rstrip": false, "normalized": true, "__type": "AddedToken"}, "eos_token": {"content": "</s>", "single_word": false, "lstrip": false, "rstrip": false, "normalized": true, "__type": "AddedToken"}, "add_prefix_space": false, "sep_token": {"content": "</s>", "single_word": false, "lstrip": false, "rstrip": false, "normalized": true, "__type": "AddedToken"}, "cls_token": {"content": "<s>", "single_word": false, "lstrip": false, "rstrip": false, "normalized": true, "__type": "AddedToken"}, "pad_token": {"content": "<pad>", "single_word": false, "lstrip": false, "rstrip": false, "normalized": true, "__type": "AddedToken"}, "mask_token": {"content": "<mask>", "single_word": false, "lstrip": true, "rstrip": false, "normalized": true, "__type": "AddedToken"}, "special_tokens_map_file": null, "name_or_path": "checkpoint_global_step_200000", "tokenizer_file": null, "tokenizer_class": "BartTokenizer"}