S PubMedBert MS MARCO

🚀 pritamdeka/S-PubMedBert-MS-MARCO

This is a sentence-transformers model that maps sentences and paragraphs to a 768-dimensional dense vector space. It can be used for tasks such as clustering or semantic search, especially in the medical/health text domain.

🚀 Quick Start

This model is based on microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext and fine - tuned on the MS - MARCO dataset using the sentence - transformers framework. It's suitable for information retrieval tasks in the medical/health text domain.

✨ Features

• Maps sentences and paragraphs to a 768 - dimensional dense vector space.
• Applicable for clustering and semantic search tasks.
• Fine - tuned for information retrieval in the medical/health text domain.

📦 Installation

Using this model becomes easy when you have sentence-transformers installed. You can install it with the following command:

pip install -U sentence-transformers

💻 Usage Examples

Basic Usage

If you have sentence-transformers installed, you can use the model as follows:

from sentence_transformers import SentenceTransformer
sentences = ["This is an example sentence", "Each sentence is converted"]

model = SentenceTransformer('pritamdeka/S-PubMedBert-MS-MARCO')
embeddings = model.encode(sentences)
print(embeddings)

Advanced Usage

Without sentence-transformers, you need to pass the input through the transformer model and 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/S-PubMedBert-MS-MARCO')
model = AutoModel.from_pretrained('pritamdeka/S-PubMedBert-MS-MARCO')

# 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, max pooling.
sentence_embeddings = mean_pooling(model_output, encoded_input['attention_mask'])

print("Sentence embeddings:")
print(sentence_embeddings)

🔧 Technical Details

Training Parameters

The model was trained with the following parameters:

DataLoader: torch.utils.data.dataloader.DataLoader of length 31434 with parameters:

{'batch_size': 16, 'sampler': 'torch.utils.data.sampler.RandomSampler', 'batch_sampler': 'torch.utils.data.sampler.BatchSampler'}

Loss: beir.losses.margin_mse_loss.MarginMSELoss

Parameters of the fit()-Method:

{
    "callback": null,
    "epochs": 2,
    "evaluation_steps": 10000,
    "evaluator": "sentence_transformers.evaluation.SequentialEvaluator.SequentialEvaluator",
    "max_grad_norm": 1,
    "optimizer_class": "<class 'transformers.optimization.AdamW'>",
    "optimizer_params": {
        "correct_bias": false,
        "eps": 1e-06,
        "lr": 2e-05
    },
    "scheduler": "WarmupLinear",
    "steps_per_epoch": null,
    "warmup_steps": 1000,
    "weight_decay": 0.01
}

Full Model Architecture

SentenceTransformer(
  (0): Transformer({'max_seq_length': 350, '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})
)

📄 License

This model is licensed under the cc - by - nc - 2.0 license.

📚 Citing & Authors

If you use this model, please cite the following paper:

@article{deka2022improved,
  title={Improved Methods To Aid Unsupervised Evidence-Based Fact Checking For Online Health News},
  author={Deka, Pritam and Jurek-Loughrey, Anna and Deepak, P},
  journal={Journal of Data Intelligence},
  volume={3},
  number={4},
  pages={474--504},
  year={2022}
}