S PubMedBert MedQuAD EU AI Act Compliance Profile

S-PubMedBert-MedQuAD

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.

Usage (Sentence-Transformers)

Using this model becomes easy when you have sentence-transformers installed:

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('TimKond/S-PubMedBert-MedQuAD')
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('TimKond/S-PubMedBert-MedQuAD')
model = AutoModel.from_pretrained('TimKond/S-PubMedBert-MedQuAD')

# Tokenize sentences
encoded_input = tokenizer(sentences, padding=True, truncation=True, return_tensors='pt')

# Compute token embeddings
with torch.no_grad():
    model_output

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