pritamdeka/PubMedBERT-mnli-snli-scinli-scitail-mednli-stsb

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. It has been trained over the SNLI, MNLI, SCINLI, SCITAIL, MEDNLI and STSB datasets for providing robust sentence embeddings.

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('pritamdeka/PubMedBERT-mnli-snli-scinli-scitail-mednli-stsb')
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('pritamdeka/PubMedBERT-mnli-snli-scinli-scitail-mednli-stsb')
model = AutoModel.from_pretrained('pritamdeka/PubMedBERT-mnli-snli-scinli-scitail-mednli-stsb')

# 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 90 with parameters:

{'batch_size': 64, '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": 4,
    "evaluation_steps": 1000,
    "evaluator": "sentence_transformers.evaluation.EmbeddingSimilarityEvaluator.EmbeddingSimilarityEvaluator",
    "max_grad_norm": 1,
    "optimizer_class": "<class 'transformers.optimization.AdamW'>",
    "optimizer_params": {
        "lr": 2e-05
    },
    "scheduler": "WarmupLinear",
    "steps_per_epoch": null,
    "warmup_steps": 36,
    "weight_decay": 0.01
}

Full Model Architecture

SentenceTransformer(
  (0): Transformer({'max_seq_length': 100, '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

If you use the model kindly cite the following work

@inproceedings{deka2022evidence,
  title={Evidence Extraction to Validate Medical Claims in Fake News Detection},
  author={Deka, Pritam and Jurek-Loughrey, Anna and others},
  booktitle={International Conference on Health Information Science},
  pages={3--15},
  year={2022},
  organization={Springer}
}