readme: ---
  
  language:
  - en
  
  widget:
  - text: "27 patients have been diagnosed with PKU in Iceland since 1947. Incidence 1972-2008 is 1/8400 living births."
    example_title: "Named Entity Recognition Ex. 1"
  - text: "A retrospective epidemiological study of MPSs in Estonia was undertaken, and live-birth prevalence of MPS patients born between 1985 and 2006 was estimated. The live-birth prevalence for all MPS subtypes was found to be 4.05 per 100,000 live births, which is consistent with most other European studies. MPS II had the highest calculated incidence, with 2.16 per 100,000 live births (4.2 per 100,000 male live births)"
    example_title: "Named Entity Recognition Ex. 2"
  - text: "A retrospective study conducted between January 2015 and December 2020 revealed a total of 304,086 newborns have been screened in Kuwait. Six newborns were diagnosed with classic homocystinuria with an incidence of 1:50,000, which is not as high as in Qatar but higher than the global incidence."
    example_title: "Named Entity Recognition Ex. 3"
  
  tags:
  - token-classification
  - ncats
  
  model-index:
  - name: EpiExtract4GARD-v2
    results:
    - task:
        name: NER
        type: token-classification
      metrics:
      - name: Token-Level Precision
        type: precision
        value: 
      - name: Token-Level Recall
        type: recall
        value: 
      - name: Token-Level F1 Score
        type: f_score
        value: 
      - name: Token-Level Precision
        type: precision
        value: 
      - name: Token-Level Recall
        type: recall
        value: 
      - name: Token-Level F1 Score
        type: f_score
        value: 
  datasets:
  - ncats/EpiSet4NER
  
  license: other
  
  ---
  
  ## DOCUMENTATION UPDATES IN PROGRESS
              
  ## Model description
  **EpiExtract4GARD-v2** is a fine-tuned [BioBERT-base-cased](https://huggingface.co/dmis-lab/biobert-base-cased-v1.1) model that is ready to use for **Named Entity Recognition** of locations (LOC), epidemiologic types (EPI), and epidemiologic rates (STAT). This model was fine-tuned on EpiSet4NER-v2 for epidemiological information from rare disease abstracts. See dataset documentation for details on the weakly supervised teaching methods and dataset biases and limitations. See [EpiExtract4GARD on GitHub](https://github.com/ncats/epi4GARD/tree/master/EpiExtract4GARD#epiextract4gard) for details on the entire pipeline. 
  
  #### How to use
  You can use this model with the Hosted inference API to the right with this [test sentence](https://pubmed.ncbi.nlm.nih.gov/21659675/): "27 patients have been diagnosed with PKU in Iceland since 1947. Incidence 1972-2008 is 1/8400 living births."
  
  See code below for use with Transformers *pipeline* for NER.:
  ~~~
  from transformers import pipeline, AutoModelForTokenClassification, AutoTokenizer
  model = AutoModelForTokenClassification.from_pretrained("ncats/EpiExtract4GARD")
  tokenizer = AutoTokenizer.from_pretrained("ncats/EpiExtract4GARD")
  NER_pipeline = pipeline('ner', model=model, tokenizer=tokenizer,aggregation_strategy='simple')
  
  sample = "The live-birth prevalence of mucopolysaccharidoses in Estonia. Previous studies on the prevalence of mucopolysaccharidoses (MPS) in different populations have shown considerable variations. There are, however, few data with regard to the prevalence of MPSs in Fenno-Ugric populations or in north-eastern Europe, except for a report about Scandinavian countries. A retrospective epidemiological study of MPSs in Estonia was undertaken, and live-birth prevalence of MPS patients born between 1985 and 2006 was estimated. The live-birth prevalence for all MPS subtypes was found to be 4.05 per 100,000 live births, which is consistent with most other European studies. MPS II had the highest calculated incidence, with 2.16 per 100,000 live births (4.2 per 100,000 male live births), forming 53% of all diagnosed MPS cases, and was twice as high as in other studied European populations. The second most common subtype was MPS IIIA, with a live-birth prevalence of 1.62 in 100,000 live births. With 0.27 out of 100,000 live births, MPS VI had the third-highest live-birth prevalence. No cases of MPS I were diagnosed in Estonia, making the prevalence of MPS I in Estonia much lower than in other European populations. MPSs are the third most frequent inborn error of metabolism in Estonia after phenylketonuria and galactosemia."
  sample2 = "Early Diagnosis of Classic Homocystinuria in Kuwait through Newborn Screening: A 6-Year Experience. Kuwait is a small Arabian Gulf country with a high rate of consanguinity and where a national newborn screening program was expanded in October 2014 to include a wide range of endocrine and metabolic disorders. A retrospective study conducted between January 2015 and December 2020 revealed a total of 304,086 newborns have been screened in Kuwait. Six newborns were diagnosed with classic homocystinuria with an incidence of 1:50,000, which is not as high as in Qatar but higher than the global incidence. Molecular testing for five of them has reveale