Update README.md

README.md

@@ -8,51 +8,80 @@ model-index:
   results: []
 ---
 
-<!-- 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. -->
+# WhereIsAI/pubmed-angle-base-en
 
-[<img src="https://raw.githubusercontent.com/wandb/assets/main/wandb-github-badge-28.svg" alt="Visualize in Weights & Biases" width="200" height="32"/>]()
-# pre-pubmedbert-base-embedding
+This model is an example model for the Chinese blog post [title](#) and [angle tutorial](https://angle.readthedocs.io/en/latest/notes/tutorial.html#tutorial). 
 
-This model is a fine-tuned version of [microsoft/BiomedNLP-BiomedBERT-base-uncased-abstract-fulltext](https://huggingface.co/microsoft/BiomedNLP-BiomedBERT-base-uncased-abstract-fulltext) on an unknown dataset.
+It was fine-tuned with [AnglE Loss](https://arxiv.org/abs/2309.12871) using the official [angle-emb](https://github.com/SeanLee97/AnglE).
 
-## Model description
+Here are the details:
 
-More information needed
+- Base model: [microsoft/BiomedNLP-BiomedBERT-base-uncased-abstract-fulltext](https://huggingface.co/microsoft/BiomedNLP-BiomedBERT-base-uncased-abstract-fulltext)
+- Training Data: [WhereIsAI/medical-triples](https://huggingface.co/datasets/WhereIsAI/medical-triples), processed from [PubMedQA](https://huggingface.co/datasets/qiaojin/PubMedQA).
+- Test Data: [WhereIsAI/pubmedqa-test-angle-format-a](https://huggingface.co/datasets/WhereIsAI/pubmedqa-test-angle-format-a)
 
-## Intended uses & limitations
+**Performance:**
 
-More information needed
+| Model                                  | Pooling Strategy | Spearman's Correlation |
+|----------------------------------------|------------------|:----------------------:|
+| tavakolih/all-MiniLM-L6-v2-pubmed-full | avg              | 84.56                  |
+| NeuML/pubmedbert-base-embeddings       | avg              | 84.88                  |
+| **WhereIsAI/pubmed-angle-base-en**     | cls              | 86.01                  |
+| WhereIsAI/pubmed-angle-large-en        | cls              | 86.21                  |
 
-## Training and evaluation data
 
-More information needed
+## Usage
 
-## Training procedure
+### via angle-emb
 
-### Training hyperparameters
+```bash
+python -m pip install -U angle-emb
+```
 
-The following hyperparameters were used during training:
-- learning_rate: 1e-06
-- train_batch_size: 64
-- eval_batch_size: 8
-- seed: 42
-- distributed_type: multi-GPU
-- num_devices: 3
-- total_train_batch_size: 192
-- total_eval_batch_size: 24
-- optimizer: Adam with betas=(0.9,0.999) and epsilon=1e-08
-- lr_scheduler_type: linear
-- lr_scheduler_warmup_steps: 50
-- num_epochs: 1
+Example:
 
-### Training results
+```python
+from angle_emb import AnglE
+from angle_emb.utils import cosine_similarity
 
+angle = AnglE.from_pretrained('WhereIsAI/pubmed-angle-base-en', pooling_strategy='cls').cuda()
 
+query = 'How to treat childhood obesity and overweight?'
+docs = [
+    query,
+    'The child is overweight. Parents should relieve their children\'s symptoms through physical activity and healthy eating. First, they can let them do some aerobic exercise, such as jogging, climbing, swimming, etc. In terms of diet, children should eat more cucumbers, carrots, spinach, etc. Parents should also discourage their children from eating fried foods and dried fruits, which are high in calories and fat. Parents should not let their children lie in bed without moving after eating. If their children\'s condition is serious during the treatment of childhood obesity, parents should go to the hospital for treatment under the guidance of a doctor in a timely manner.',
+    'If you want to treat tonsillitis better, you can choose some anti-inflammatory drugs under the guidance of a doctor, or use local drugs, such as washing the tonsil crypts, injecting drugs into the tonsils, etc. If your child has a sore throat, you can also give him or her some pain relievers. If your child has a fever, you can give him or her antipyretics. If the condition is serious, seek medical attention as soon as possible. If the medication does not have a good effect and the symptoms recur, the author suggests surgical treatment. Parents should also make sure to keep their children warm to prevent them from catching a cold and getting tonsillitis again.',
+]
 
-### Framework versions
+embeddings = angle.encode(docs)
+query_emb = embeddings[0]
 
-- Transformers 4.42.3
-- Pytorch 2.3.0+cu121
-- Datasets 2.19.1
-- Tokenizers 0.19.1
+for doc, emb in zip(docs[1:], embeddings[1:]):
+    print(cosine_similarity(query_emb, emb))
+
+# 0.8029839020052982
+# 0.4260630076818197
+```
+
+
+### via sentence-transformers
+
+Install sentence-transformers
+
+```bash
+python -m pip install -U sentence-transformers
+```
+
+
+## Citation
+
+If you use this model for academic papers, please cite angle's paper, as follows:
+
+```bibtext
+@article{li2023angle,
+  title={AnglE-optimized Text Embeddings},
+  author={Li, Xianming and Li, Jing},
+  journal={arXiv preprint arXiv:2309.12871},
+  year={2023}
+}
+```