Update README.md
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README.md
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@@ -93,6 +93,58 @@ The output will be a list of recognized entities with their entity type, score,
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```
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**Use Cases:**
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- Extracting clinical information from unstructured text in medical records.
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- Structuring data for downstream biomedical research or applications.
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```
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In some cases, we are getting multiple same entity groups so to join please use below code:
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```python
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def merge_consecutive_entities(entities):
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entities = sorted(entities, key=lambda x: x['start'])
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merged_entities = []
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current_entity = None
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for entity in entities:
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if current_entity is None:
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current_entity = entity
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elif (
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entity['entity_group'] == current_entity['entity_group'] and
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(entity['start'] <= current_entity['end'])
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):
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new_word = entity['word']
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if not current_entity['word'].endswith(new_word):
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current_entity['word'] += " " + new_word
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current_entity['end'] = max(current_entity['end'], entity['end'])
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current_entity['score'] = (current_entity['score'] + entity['score']) / 2
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else:
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merged_entities.append(current_entity)
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current_entity = entity
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if current_entity:
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merged_entities.append(current_entity)
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return merged_entities
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from transformers import pipeline
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# Load the model
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model_path = "Helios9/BIOMed_NER"
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pipe = pipeline(
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task="token-classification",
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model=model_path,
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tokenizer=model_path,
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aggregation_strategy="simple"
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)
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# Test the pipeline
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text = ("A 48-year-old female presented with vaginal bleeding and abnormal Pap smears. "
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"Upon diagnosis of invasive non-keratinizing SCC of the cervix, she underwent a radical "
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"hysterectomy with salpingo-oophorectomy which demonstrated positive spread to the pelvic "
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"lymph nodes and the parametrium.")
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result = pipe(text)
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final_result=merge_consecutive_entities(result)
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print(final_result)
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```
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**Use Cases:**
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- Extracting clinical information from unstructured text in medical records.
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- Structuring data for downstream biomedical research or applications.
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