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README.md

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+# BioBBC BiLSTM-CRF (epoch 3)
+
+This checkpoint contains:
+- `pytorch_model.bin`: state dict for the **EmbeddingFusion → BiLSTM → Linear → CRF** model
+- `embedding_config.json`: hyperparams for embedder/backbone
+- `id2label.json`, `pos2id.json`, `char_vocab.json`
+- `tokenizer/` (if provided)
+
+**Base encoder:** microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract
+**Labels:** 3 classes
+**Notes:** Requires Flair `TransformerWordEmbeddings` with the same base model for word-level flair features.
+

char_vocab.json

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+{
+  "<PAD>": 0,
+  "C": 1,
+  "h": 2,
+  "a": 3,
+  "n": 4,
+  "g": 5,
+  "e": 6,
+  "i": 7,
+  "s": 8,
+  "p": 9,
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+  "%": 50,
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+  "5": 52,
+  ":": 53,
+  "\"": 54,
+  "D": 55,
+  "7": 56,
+  "k": 57,
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+  "=": 59,
+  "4": 60,
+  "W": 61,
+  "Y": 62,
+  ";": 63,
+  "\\": 64,
+  ">": 65,
+  "O": 66,
+  "U": 67,
+  "K": 68,
+  "9": 69,
+  "+": 70,
+  "Q": 71,
+  "z": 72,
+  "#": 73,
+  "q": 74,
+  "\u00b5": 75,
+  "J": 76,
+  "V": 77,
+  "'": 78,
+  "\u03b2": 79,
+  "[": 80,
+  "]": 81,
+  "X": 82,
+  "\u00d7": 83,
+  "<": 84,
+  "\u2264": 85,
+  "\u00b1": 86,
+  "\u03bc": 87,
+  "\u2081": 88,
+  "Z": 89,
+  "\u00ef": 90,
+  "*": 91,
+  "&": 92,
+  "\uff09": 93,
+  "\u03b3": 94,
+  "\u00e3": 95,
+  "?": 96,
+  "\u33a1": 97,
+  "\u2026": 98,
+  "\u00ae": 99,
+  "\u3016": 100,
+  "\u3017": 101,
+  "_": 102,
+  "\u03b1": 103,
+  "{": 104,
+  "}": 105,
+  "!": 106,
+  "^": 107,
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+  "\u03c0": 109,
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+  "\u00c9": 125,
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+  "\u2206": 127,
+  "\u2267": 128,
+  "\u02c2": 129,
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+  "\u0130": 171,
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+  "\u00e4": 173,
+  "\u00ac": 174,
+  "\u2083": 175,
+  "\u00e8": 176
+}

embedding_config.json

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+{
+  "embedding": {
+    "bert_model_name": "microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract",
+    "freeze_bert": false,
+    "use_pos": true,
+    "pos_emb_dim": 50,
+    "use_char": true,
+    "char_emb_dim": 50,
+    "char_hidden": 50,
+    "char_pad_idx": 0,
+    "use_flair": true,
+    "flair_dim": 768,
+    "dropout": 0.1
+  },
+  "backbone": {
+    "bilstm_hidden": 256,
+    "bilstm_layers": 1,
+    "bilstm_dropout": 0.0,
+    "out_dim": 512,
+    "num_labels": 3
+  }
+}

id2label.json

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+{
+  "0": "B-BIOMARKER",
+  "1": "I-BIOMARKER",
+  "2": "O"
+}

metrics_epoch_3.json

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+{
+  "precision": 0.9260513407862958,
+  "recall": 0.9366626372519391,
+  "f1": 0.9313267644076072
+}

pos2id.json

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+{
+  "<PAD>": 0,
+  "NN": 1
+}

pytorch_model.bin

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+version https://git-lfs.github.com/spec/v1
+oid sha256:ac2a408958da7ad4130a9647dd74e62488f46f6e8457e2bfdbc55f2b40f5e97d
+size 454155431