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e3c

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  1. README.md +60 -155
  2. e3c.py +16 -8
README.md CHANGED
@@ -1,160 +1,65 @@
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  ---
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  dataset_info:
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- - config_name: en
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- features:
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- - name: tokens
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- sequence: string
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- - name: ner_tags
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- sequence:
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- class_label:
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- names:
11
- "0": O
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- "1": CLINENTITY
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- "2": EVENT
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- "3": ACTOR
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- "4": BODYPART
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- "5": TIMEX3
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- "6": RML
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- splits:
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- - name: en
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- num_bytes: 507939
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- num_examples: 1520
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- download_size: 230213492
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- dataset_size: 507939
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- - config_name: es
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- features:
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- - name: tokens
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- sequence: string
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- - name: ner_tags
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- sequence:
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- class_label:
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- names:
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- "0": O
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- "1": CLINENTITY
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- "2": EVENT
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- "3": ACTOR
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- "4": BODYPART
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- "5": TIMEX3
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- "6": RML
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- splits:
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- - name: es
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- num_bytes: 501523
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- num_examples: 1134
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- download_size: 230213492
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- dataset_size: 501523
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- - config_name: eu
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- features:
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- - name: tokens
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- sequence: string
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- - name: ner_tags
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- sequence:
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- class_label:
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- names:
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- "0": O
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- "1": CLINENTITY
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- "2": EVENT
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- "3": ACTOR
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- "4": BODYPART
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- "5": TIMEX3
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- "6": RML
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- splits:
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- - name: eu
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- num_bytes: 615175
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- num_examples: 3126
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- download_size: 230213492
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- dataset_size: 615175
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- - config_name: fr
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- features:
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- - name: tokens
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- sequence: string
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- - name: ner_tags
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- sequence:
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- class_label:
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- names:
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- "0": O
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- "1": CLINENTITY
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- "2": EVENT
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- "3": ACTOR
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- "4": BODYPART
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- "5": TIMEX3
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- "6": RML
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- splits:
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- - name: fr
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- num_bytes: 506754
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- num_examples: 1109
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- download_size: 230213492
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- dataset_size: 506754
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- - config_name: it
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- features:
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- - name: tokens
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- sequence: string
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- - name: ner_tags
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- sequence:
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- class_label:
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- names:
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- "0": O
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- "1": CLINENTITY
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- "2": EVENT
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- "3": ACTOR
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- "4": BODYPART
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- "5": TIMEX3
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- "6": RML
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- splits:
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- - name: it
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- num_bytes: 516047
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- num_examples: 1146
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- download_size: 230213492
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- dataset_size: 516047
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- - config_name: e3c
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- features:
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- - name: tokens
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- sequence: string
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- - name: ner_tags
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- sequence:
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- class_label:
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- names:
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- "0": O
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- "1": CLINENTITY
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- "2": EVENT
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- "3": ACTOR
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- "4": BODYPART
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- "5": TIMEX3
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- "6": RML
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- splits:
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- - name: en.layer1
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- num_bytes: 507939
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- num_examples: 1520
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- - name: en.layer2
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- num_bytes: 1017690
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- num_examples: 2873
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- - name: es.layer1
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- num_bytes: 501523
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- num_examples: 1134
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- - name: es.layer2
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- num_bytes: 1002221
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- num_examples: 2347
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- - name: eu.layer1
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- num_bytes: 615175
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- num_examples: 3126
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- - name: eu.layer2
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- num_bytes: 342204
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- num_examples: 1594
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- - name: fr.layer1
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- num_bytes: 506754
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- num_examples: 1109
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- - name: fr.layer2
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- num_bytes: 1027933
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- num_examples: 2389
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- - name: it.layer1
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- num_bytes: 516047
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- num_examples: 1146
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- - name: it.layer2
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- num_bytes: 1071873
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- num_examples: 2436
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- download_size: 230213492
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- dataset_size: 7109359
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  ---
157
-
158
  # Dataset Card for E3C
159
 
160
  ## Dataset Description
@@ -181,4 +86,4 @@ information about clinical entities based on medical taxonomies, to be used for
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  url = {https://uts.nlm.nih.gov/uts/umls/home},
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  year = {2021},
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  }
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- ```
 
1
  ---
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  dataset_info:
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+ features:
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+ - name: text
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+ dtype: string
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+ - name: tokens
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+ sequence: string
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+ - name: tokens_offsets
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+ sequence:
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+ sequence: int32
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+ - name: ner_tags
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+ sequence:
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+ class_label:
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+ names:
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+ '0': O
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+ '1': B-CLINENTITY
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+ '2': B-EVENT
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+ '3': B-ACTOR
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+ '4': B-BODYPART
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+ '5': B-TIMEX3
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+ '6': B-RML
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+ '7': I-CLINENTITY
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+ '8': I-EVENT
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+ '9': I-ACTOR
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+ '10': I-BODYPART
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+ '11': I-TIMEX3
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+ '12': I-RML
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+ config_name: e3c
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+ splits:
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+ - name: en.layer1
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+ num_bytes: 1039582
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+ num_examples: 1520
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+ - name: en.layer2
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+ num_bytes: 2083098
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+ num_examples: 2873
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+ - name: es.layer1
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+ num_bytes: 1026950
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+ num_examples: 1134
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+ - name: es.layer2
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+ num_bytes: 2052073
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+ num_examples: 2347
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+ - name: eu.layer1
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+ num_bytes: 1252750
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+ num_examples: 3126
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+ - name: eu.layer2
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+ num_bytes: 697118
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+ num_examples: 1594
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+ - name: fr.layer1
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+ num_bytes: 1036878
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+ num_examples: 1109
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+ - name: fr.layer2
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+ num_bytes: 2104253
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+ num_examples: 2389
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+ - name: it.layer1
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+ num_bytes: 1055588
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+ num_examples: 1146
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+ - name: it.layer2
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+ num_bytes: 2191803
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+ num_examples: 2436
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+ download_size: 230213492
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+ dataset_size: 14540093
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
62
  ---
 
63
  # Dataset Card for E3C
64
 
65
  ## Dataset Description
 
86
  url = {https://uts.nlm.nih.gov/uts/umls/home},
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  year = {2021},
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  }
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+ ```
e3c.py CHANGED
@@ -61,12 +61,18 @@ class E3C(datasets.GeneratorBasedBuilder):
61
  datasets.features.ClassLabel(
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  names=[
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  "O",
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- "CLINENTITY",
65
- "EVENT",
66
- "ACTOR",
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- "BODYPART",
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- "TIMEX3",
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- "RML",
 
 
 
 
 
 
70
  ],
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  ),
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  ),
@@ -303,9 +309,9 @@ class E3C(datasets.GeneratorBasedBuilder):
303
  ]
304
  for idx_token in annotated_tokens:
305
  if idx_token == annotated_tokens[0]:
306
- labels[idx_token] = f"{entity_type}"
307
  else:
308
- labels[idx_token] = f"{entity_type}"
309
  yield guid, {
310
  "text": sentence[-1],
311
  "tokens": list(map(lambda tokens: tokens[2], filtered_tokens)),
@@ -313,3 +319,5 @@ class E3C(datasets.GeneratorBasedBuilder):
313
  "tokens_offsets": tokens_offsets,
314
  }
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  guid += 1
 
 
 
61
  datasets.features.ClassLabel(
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  names=[
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  "O",
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+ "B-CLINENTITY",
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+ "B-EVENT",
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+ "B-ACTOR",
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+ "B-BODYPART",
68
+ "B-TIMEX3",
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+ "B-RML",
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+ "I-CLINENTITY",
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+ "I-EVENT",
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+ "I-ACTOR",
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+ "I-BODYPART",
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+ "I-TIMEX3",
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+ "I-RML",
76
  ],
77
  ),
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  ),
 
309
  ]
310
  for idx_token in annotated_tokens:
311
  if idx_token == annotated_tokens[0]:
312
+ labels[idx_token] = f"B-{entity_type}"
313
  else:
314
+ labels[idx_token] = f"I-{entity_type}"
315
  yield guid, {
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  "text": sentence[-1],
317
  "tokens": list(map(lambda tokens: tokens[2], filtered_tokens)),
 
319
  "tokens_offsets": tokens_offsets,
320
  }
321
  guid += 1
322
+
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+ datasets.load_dataset("e3c/e3c.py")