aspect-based-embeddings-v3

Model Card for Model ID

This is an embedding model for clinical papers

How to Use

Simple finetuned model

from transformers import AutoTokenizer, AutoModel
import torch

DEVICE = "cuda:0" if torch.cuda.is_available() else "cpu"

PATH = "josh-oo/aspect-based-embeddings-v3"

tokenizer = AutoTokenizer.from_pretrained(PATH)
tokenizer.model_max_length = 512
model = AutoModel.from_pretrained(PATH)

dummy_text = "This is a title of a medical paper"
dummy_input = tokenizer([dummy_text], return_tensors="pt", truncation=True)

dummy_input.to(DEVICE)
model.to(DEVICE)

with torch.no_grad():
  output = model(**dummy_input)

embeddings = output.last_hidden_state[:, 0] #cls pooling

Aspect guided model

from transformers import AutoTokenizer, AutoModel
import torch

DEVICE = "cuda:0" if torch.cuda.is_available() else "cpu"

PATH = "josh-oo/aspect-based-embeddings-v3"
REVISION = "4f43387343acaacd9bfafec0a304c51ed140f078"
PREFIXES = ["<participants>","<intervention>","<condition>","<outcome>"]

tokenizer = AutoTokenizer.from_pretrained(PATH, revision=REVISION)
model = AutoModel.from_pretrained(PATH, revision=REVISION)

model.register_buffer("position_ids", torch.relu(torch.arange(model.config.max_position_embeddings + len(PREFIXES)).expand((1, -1))  - len(PREFIXES)), persistent=False)
model.register_buffer("token_type_ids", torch.zeros(model.position_ids.size(), dtype=torch.long), persistent=False) #set token type ids to 0
model.token_type_ids[:,1:1+len(PREFIXES)] = 1 #set prefix token type ids to 1

dummy_text = "".join(PREFIXES) + "This is a title of a medical paper"
dummy_input = tokenizer([dummy_text], return_tensors="pt", truncation=True)
dummy_input.pop('token_type_ids')

dummy_input.to(DEVICE)
model.to(DEVICE)

with torch.no_grad():
  output = model(**dummy_input)

embeddings = output.last_hidden_state[:, 0] #cls pooling