CoolFace
Modelpublic

judithrosell/JNLPBA_ClinicalBERT_NER

sourceHugging Faceupdated 3y agoView on Hugging Face
0likes17downloads
Model Card

<!-- This model card has been generated automatically according to the information the Trainer had access to. You should probably proofread and complete it, then remove this comment. -->

JNLPBAClinicalBERTNER

This model is a fine-tuned version of medicalai/ClinicalBERT on the None dataset. It achieves the following results on the evaluation set:

  • —Loss: 0.1723
  • —Seqeval classification report: precision recall f1-score support

DNA 0.72 0.81 0.77 1351 RNA 0.71 0.86 0.78 723 cellline 0.84 0.74 0.78 582 celltype 0.72 0.75 0.73 5623 protein 0.85 0.85 0.85 3501

micro avg 0.76 0.79 0.78 11780 macro avg 0.77 0.80 0.78 11780 weighted avg 0.76 0.79 0.78 11780

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: 2e-05
  • —trainbatchsize: 16
  • —evalbatchsize: 16
  • —seed: 42
  • —gradientaccumulationsteps: 2
  • —totaltrainbatch_size: 32
  • —optimizer: Adam with betas=(0.9,0.999) and epsilon=1e-08
  • —lrschedulertype: linear
  • —num_epochs: 3

Training results

Training LossEpochStepValidation LossSeqeval classification report
0.3361.05820.1930precision recall f1-score support

DNA 0.72 0.77 0.75 1351 RNA 0.70 0.84 0.77 723 cellline 0.85 0.70 0.77 582 celltype 0.71 0.68 0.69 5623 protein 0.85 0.80 0.83 3501

micro avg 0.76 0.74 0.75 11780 macro avg 0.77 0.76 0.76 11780 weighted avg 0.76 0.74 0.75 11780 | | 0.1841 | 2.0 | 1164 | 0.1762 | precision recall f1-score support

DNA 0.73 0.78 0.76 1351 RNA 0.70 0.87 0.78 723 cellline 0.86 0.71 0.78 582 celltype 0.71 0.73 0.72 5623 protein 0.86 0.83 0.84 3501

micro avg 0.76 0.77 0.77 11780 macro avg 0.77 0.78 0.78 11780 weighted avg 0.77 0.77 0.77 11780 | | 0.1582 | 3.0 | 1746 | 0.1723 | precision recall f1-score support

DNA 0.72 0.81 0.77 1351 RNA 0.71 0.86 0.78 723 cellline 0.84 0.74 0.78 582 celltype 0.72 0.75 0.73 5623 protein 0.85 0.85 0.85 3501

micro avg 0.76 0.79 0.78 11780 macro avg 0.77 0.80 0.78 11780 weighted avg 0.76 0.79 0.78 11780 |

Framework versions

  • —Transformers 4.35.2
  • —Pytorch 2.1.0+cu121
  • —Datasets 2.15.0
  • —Tokenizers 0.15.0