eladogruyol/pubmedbert-base-embeddings-base-sentence-transformer
This is a sentence-transformers model: It maps sentences & paragraphs to a 768 dimensional dense vector space and can be used for tasks like clustering or semantic search.
This model is created with the base of "https://huggingface.co/NeuML/pubmedbert-base-embeddings". This pre-trained model is trained with approximately 1100 interview questions data collected by our team. Our aim is to be able to get more accurate similarity rates about answers given to interview questions for our project.
Usage (Sentence-Transformers)
Using this model becomes easy when you have sentence-transformers installed:
pip install -U sentence-transformers
Then you can use the model like this:
from sentence_transformers import SentenceTransformer
sentences = ["This is an example sentence", "Each sentence is converted"]
model = SentenceTransformer('eladogruyol/pubmedbert-base-embeddings-base-sentence-transformer')
embeddings = model.encode(sentences)
print(embeddings)
Usage (HuggingFace Transformers)
Without sentence-transformers, 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.
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('eladogruyol/pubmedbert-base-embeddings-base-sentence-transformer')
model = AutoModel.from_pretrained('eladogruyol/pubmedbert-base-embeddings-base-sentence-transformer')
# 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
For an automated evaluation of this model, see the Sentence Embeddings Benchmark: https://seb.sbert.net
Training
The model was trained with the parameters:
DataLoader:
torch.utils.data.dataloader.DataLoader
of length 23 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": 10,
"evaluation_steps": 0,
"evaluator": "NoneType",
"max_grad_norm": 1,
"optimizer_class": "<class 'torch.optim.adamw.AdamW'>",
"optimizer_params": {
"lr": 2e-05
},
"scheduler": "WarmupLinear",
"steps_per_epoch": null,
"warmup_steps": 23,
"weight_decay": 0.01
}
Full Model Architecture
SentenceTransformer(
(0): Transformer({'max_seq_length': 512, '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, 'pooling_mode_weightedmean_tokens': False, 'pooling_mode_lasttoken': False, 'include_prompt': True})
)
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