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---
pipeline_tag: sentence-similarity
tags:
- sentence-transformers
- feature-extraction
- sentence-similarity
- transformers
datasets:
- nuvocare/WikiMedical_sentence_similarity
---
# WikiMedical_sent_biobert
This is a [sentence-transformers](https://www.SBERT.net) model: It maps sentences & paragraphs to a 768 dimensional dense vector space and can be used for tasks like clustering or semantic search.
WikiMedical_sent_bert is based on the [https://huggingface.co/dmis-lab/biobert-base-cased-v1.2](dmis-lab/biobert-base-cased-v1.2) backbone and has been trained on the [WikiMedical_sentence_simialrity](https://huggingface.co/datasets/nuvocare/WikiMedical_sentence_similarity) dataset.
The model is able to predict whether two texts are related to the same wikipedia page, with only medical topic.
## Usage (Sentence-Transformers)
Using this model becomes easy when you have [sentence-transformers](https://www.SBERT.net) installed:
```
pip install -U sentence-transformers
```
Then you can use the model like this:
```python
from sentence_transformers import SentenceTransformer
sentences = ["This is an example sentence", "Each sentence is converted"]
model = SentenceTransformer('nuvocare/WikiMedical_sent_biobert')
embeddings = model.encode(sentences)
print(embeddings)
```
## Usage (HuggingFace Transformers)
Without [sentence-transformers](https://www.SBERT.net), you can use the model like this: First, you pass your input through the transformer model, then you have to apply the right pooling-operation on-top of the contextualized word embeddings.
```python
from transformers import AutoTokenizer, AutoModel
import torch
#Mean Pooling - Take attention mask into account for correct averaging
def mean_pooling(model_output, attention_mask):
token_embeddings = model_output[0] #First element of model_output contains all token embeddings
input_mask_expanded = attention_mask.unsqueeze(-1).expand(token_embeddings.size()).float()
return torch.sum(token_embeddings * input_mask_expanded, 1) / torch.clamp(input_mask_expanded.sum(1), min=1e-9)
# Sentences we want sentence embeddings for
sentences = ['This is an example sentence', 'Each sentence is converted']
# Load model from HuggingFace Hub
tokenizer = AutoTokenizer.from_pretrained('WikiMedical_sent_biobert')
model = AutoModel.from_pretrained('WikiMedical_sent_biobert')
# Tokenize sentences
encoded_input = tokenizer(sentences, padding=True, truncation=True, return_tensors='pt')
# Compute token embeddings
with torch.no_grad():
model_output = model(**encoded_input)
# Perform pooling. In this case, mean pooling.
sentence_embeddings = mean_pooling(model_output, encoded_input['attention_mask'])
print("Sentence embeddings:")
print(sentence_embeddings)
```
## Evaluation Results
The model is evaluated on the test set of [WikiMedical_sentence_similarity](https://huggingface.co/datasets/nuvocare/WikiMedical_sentence_similarity).
It achieves a :
- cosine spearman score of 0.87
- cosine pearson score of 0.95
For an automated evaluation of this model, see the *Sentence Embeddings Benchmark*: [https://seb.sbert.net](https://seb.sbert.net?model_name=WikiMedical_sent_biobert)
## Training
The model was trained with the parameters:
**DataLoader**:
`torch.utils.data.dataloader.DataLoader` of length 3170 with parameters:
```
{'batch_size': 16, 'sampler': 'torch.utils.data.sampler.RandomSampler', 'batch_sampler': 'torch.utils.data.sampler.BatchSampler'}
```
**Loss**:
`sentence_transformers.losses.CosineSimilarityLoss.CosineSimilarityLoss`
Parameters of the fit()-Method:
```
{
"epochs": 2,
"evaluation_steps": 2000,
"evaluator": "sentence_transformers.evaluation.EmbeddingSimilarityEvaluator.EmbeddingSimilarityEvaluator",
"max_grad_norm": 1,
"optimizer_class": "<class 'torch.optim.adamw.AdamW'>",
"optimizer_params": {
"lr": 2e-05
},
"scheduler": "WarmupLinear",
"steps_per_epoch": null,
"warmup_steps": 300,
"weight_decay": 0.01
}
```
## Full Model Architecture
```
SentenceTransformer(
(0): Transformer({'max_seq_length': 256, 'do_lower_case': False}) with Transformer model: BertModel
(1): Pooling({'word_embedding_dimension': 768, 'pooling_mode_cls_token': False, 'pooling_mode_mean_tokens': True, 'pooling_mode_max_tokens': False, 'pooling_mode_mean_sqrt_len_tokens': False})
)
```
## Citing & Authors
Samuel Chaineau |