readme: ---
  license: mit
  tags:
  - generated_from_trainer
  datasets:
  - ManpreetK/NDD_NER
  model-index:
  - name: BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext-NDD-NER
    results: []
  ---
  
  # BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext-NDD-NER
  
  This model is a fine-tuned version of [microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext](https://huggingface.co/microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext) on the ManpreetK/NDD_NER dataset.
  It achieves the following results on the evaluation set:
  - Overall Precision: 0.6297
  - Overall Recall: 0.7068
  - Overall F1: 0.6660
  - Overall Accuracy: 0.9044
    
  - Loss: 0.3763
    
  - Associated_Problem Precision/Recall/F1: 0.6316/0.5294/0.576
  - Associated_Problem Number: 68
    
  - Condition Precision/Recall/F1: 0.8052/0.8921/0.8464
  - Condition Number: 139
  
  - Intervention Precision/Recall/F1: 0.5159/0.6633/0.5804
  - Intervention Number: 98
    
  - Patient_Group Precision/Recall/F1: 0.5512/0.8046/0.6542
  - Patient_Group Number: 87
    
  - Test Precision/Recall/F1: 0.5882/0.4878/0.5333
  - Test Number: 82
  
  
  ## Model description
  
  More information needed
  
  ## Intended uses & limitations
  
  More information needed
  
  ## Training and evaluation data
  
  More information needed
  
  ## Training procedure
  
  ### Training hyperparameters
  
  The following hyperparameters were used during training:
  - learning_rate: 5e-05
  - train_batch_size: 32
  - eval_batch_size: 32
  - seed: 42
  - optimizer: Adam with betas=(0.9,0.999) and epsilon=1e-08
  - lr_scheduler_type: linear
  - num_epochs: 10
  
  ### Training results
  
  | Training Loss | Epoch | Step | Validation Loss | Associated Problem Precision | Associated Problem Recall | Associated Problem F1 | Associated Problem Number | Condition Precision | Condition Recall | Condition F1 | Condition Number | Intervention Precision | Intervention Recall | Intervention F1 | Intervention Number | Patient Group Precision | Patient Group Recall | Patient Group F1 | Patient Group Number | Test Precision | Test Recall | Test F1 | Test Number | Overall Precision | Overall Recall | Overall F1 | Overall Accuracy |
  |:-------------:|:-----:|:----:|:---------------:|:----------------------------:|:-------------------------:|:---------------------:|:-------------------------:|:-------------------:|:----------------:|:------------:|:----------------:|:----------------------:|:-------------------:|:---------------:|:-------------------:|:-----------------------:|:--------------------:|:----------------:|:--------------------:|:--------------:|:-----------:|:-------:|:-----------:|:-----------------:|:--------------:|:----------:|:----------------:|
  | 1.4014        | 1.0   | 11   | 0.7804          | 0.0                          | 0.0                       | 0.0                   | 68                        | 0.0                 | 0.0              | 0.0          | 139              | 0.0                    | 0.0                 | 0.0             | 98                  | 0.0                     | 0.0                  | 0.0              | 87                   | 0.0            | 0.0         | 0.0     | 82          | 0.0               | 0.0            | 0.0        | 0.7808           |
  | 0.7625        | 2.0   | 22   | 0.5575          | 0.0                          | 0.0                       | 0.0                   | 68                        | 0.7468              | 0.8273           | 0.7850       | 139              | 0.3333                 | 0.1429              | 0.2             | 98                  | 0.7627                  | 0.5172               | 0.6164           | 87                   | 0.4286         | 0.1098      | 0.1748  | 82          | 0.6630            | 0.3861         | 0.488      | 0.8546           |
  | 0.5152        | 3.0   | 33   | 0.4489          | 0.2222                       | 0.0588                    | 0.0930                | 68                        | 0.7011              | 0.9281           | 0.7988       | 139              | 0.4674                 | 0.4388              | 0.4526          | 98                  | 0.5528                  | 0.7816               | 0.6476           | 87                   | 0.5758         | 0.4634      | 0.5135  | 82          | 0.5839            | 0.5949         | 0.5893     | 0.8820           |
  | 0.3621        | 4.0   | 44   | 0.4020          | 0.2727                       | 0.1324                    | 0.1782                | 68                        | 0.7716              | 0.8993           | 0.8306       | 139              | 0.4538                 | 0.5510              | 0.4977          | 98                  | 0.5752                  | 0.7471               | 0.65             | 87                   | 0.7059         | 0.4390      | 0.5414  | 82          | 0.6046            | 0.6097         | 0.6071     | 0.8900           |
  | 0.252         | 5.0   | 55   | 0.3764          | 0.5                          | 0.5588                    | 0.5278                | 68                        | 0.8219              | 0.8633           | 0.8421       | 139      