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Update app.py
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app.py
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@@ -5,22 +5,20 @@ from typing import Any, List
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from transformers import BertTokenizer, BertConfig, TFBertModel
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MODEL_DIR = os.environ.get("MODEL_DIR", "/app/bert_tf")
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PORT = int(os.environ.get("PORT", "7860"))
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# --- Load BioBERT (TF checkpoint converted by HF loader) ---
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tok = BertTokenizer(vocab_file=f"{MODEL_DIR}/vocab.txt", do_lower_case=True)
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cfg = BertConfig.from_json_file(f"{MODEL_DIR}/config.json")
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model= TFBertModel.from_pretrained(MODEL_DIR, from_tf=True, config=cfg)
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def encode(texts: List[str]):
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ins = tok(texts, padding=True, truncation=True, return_tensors="tf", max_length=512)
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outs = model(ins)[0]
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mask = tf.cast(tf.expand_dims(ins["attention_mask"], -1), tf.float32)
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mean = tf.reduce_sum(outs
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return tf.linalg.l2_normalize(mean, axis=1).numpy().tolist()
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_ = encode(["warmup biobert embeddings"])
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app = FastAPI()
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@@ -35,8 +33,5 @@ def health():
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def embeddings(req: EmbReq):
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texts = req.input if isinstance(req.input, list) else [req.input]
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vecs = encode(texts)
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return {
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"model" : "biobert-tf-emb",
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"data" : [{"object":"embedding","index":i,"embedding":v} for i, v in enumerate(vecs)]
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}
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from transformers import BertTokenizer, BertConfig, TFBertModel
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MODEL_DIR = os.environ.get("MODEL_DIR", "/app/bert_tf")
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PORT = int(os.environ.get("PORT", "7860"))
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tok = BertTokenizer(vocab_file=f"{MODEL_DIR}/vocab.txt", do_lower_case=True)
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cfg = BertConfig.from_json_file(f"{MODEL_DIR}/config.json")
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model= TFBertModel.from_pretrained(MODEL_DIR, from_tf=True, config=cfg)
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def encode(texts: List[str]):
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ins = tok(texts, padding=True, truncation=True, return_tensors="tf", max_length=512)
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outs = model(ins)[0]
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mask = tf.cast(tf.expand_dims(ins["attention_mask"], -1), tf.float32)
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mean = tf.reduce_sum(outs*mask, axis=1) / tf.maximum(tf.reduce_sum(mask, axis=1), 1.0)
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return tf.linalg.l2_normalize(mean, axis=1).numpy().tolist()
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_ = encode(["warmup"])
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app = FastAPI()
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def embeddings(req: EmbReq):
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texts = req.input if isinstance(req.input, list) else [req.input]
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vecs = encode(texts)
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return {"object":"list","model":"biobert-tf-emb",
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"data":[{"object":"embedding","index":i,"embedding":v} for i,v in enumerate(vecs)]}
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