Cambridgeltl/SapBERT-from-PubMedBERT-fulltext model: Difference between revisions

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Line 7: Line 7:
| dataset =  
| dataset =  
| language = English
| language = English
| paper =
| paper = arxiv:2010.11784
| license = arxiv:2010.11784, apache-2.0
| license = apache-2.0
| related-to = bert, biomedical, lexical semantics, bionlp, biology, science, embedding, entity linking
| related-to = bert, biomedical, lexical semantics, bionlp, biology, science, embedding, entity linking
| all-tags = Feature Extraction, PyTorch, TensorFlow, JAX, Safetensors, Transformers, English, bert, biomedical, lexical semantics, bionlp, biology, science, embedding, entity linking, arxiv:2010.11784, License: apache-2.0
| all-tags = Feature Extraction, PyTorch, TensorFlow, JAX, Safetensors, Transformers, English, bert, biomedical, lexical semantics, bionlp, biology, science, embedding, entity linking, arxiv:2010.11784, License: apache-2.0
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==Model Description==
==Model Description==
==Comments==
<comments />


==Clone Model Repository==
==Clone Model Repository==
Line 1,573: Line 1,570:


==Model Card==
==Model Card==
==Comments==
<comments />

Latest revision as of 03:24, 23 May 2023

Cambridgeltl/SapBERT-from-PubMedBERT-fulltext model

Cambridgeltl/SapBERT-from-PubMedBERT-fulltext model is a Multimodal model used for Feature Extraction.

Model Description

Clone Model Repository

#Be sure to have git-lfs installed (https://git-lfs.com)
git lfs install
git clone https://huggingface.co/cambridgeltl/SapBERT-from-PubMedBERT-fulltext
  
#To clone the repo without large files – just their pointers
#prepend git clone with the following env var:
GIT_LFS_SKIP_SMUDGE=1


#Be sure to have git-lfs installed (https://git-lfs.com)
git lfs install
git clone [email protected]:cambridgeltl/SapBERT-from-PubMedBERT-fulltext
  
#To clone the repo without large files – just their pointers
#prepend git clone with the following env var:
GIT_LFS_SKIP_SMUDGE=1

Hugging Face Transformers Library

from transformers import AutoTokenizer, AutoModel

tokenizer = AutoTokenizer.from_pretrained("cambridgeltl/SapBERT-from-PubMedBERT-fulltext")

model = AutoModel.from_pretrained("cambridgeltl/SapBERT-from-PubMedBERT-fulltext")

Deployment

Inference API

import requests

API_URL = "https://api-inference.huggingface.co/models/cambridgeltl/SapBERT-from-PubMedBERT-fulltext"
headers = {"Authorization": f"Bearer {API_TOKEN}"}

def query(payload):
	response = requests.post(API_URL, headers=headers, json=payload)
	return response.json()
	
output = query({
	"inputs": "Today is a sunny day and I'll get some ice cream.",
})


async function query(data) {
	const response = await fetch(
		"https://api-inference.huggingface.co/models/cambridgeltl/SapBERT-from-PubMedBERT-fulltext",
		{
			headers: { Authorization: "Bearer {API_TOKEN}" },
			method: "POST",
			body: JSON.stringify(data),
		}
	);
	const result = await response.json();
	return result;
}

query({"inputs": "Today is a sunny day and I'll get some ice cream."}).then((response) => {
	console.log(JSON.stringify(response));
});


curl https://api-inference.huggingface.co/models/cambridgeltl/SapBERT-from-PubMedBERT-fulltext \
	-X POST \
	-d '{"inputs": "Today is a sunny day and I'll get some ice cream."}' \
	-H "Authorization: Bearer {API_TOKEN}"

Amazon SageMaker

from sagemaker.huggingface import HuggingFaceModel
import sagemaker

role = sagemaker.get_execution_role()
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'automatic-speech-recognition'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})


from sagemaker.huggingface import HuggingFaceModel
import boto3

iam_client = boto3.client('iam')
role = iam_client.get_role(RoleName='{IAM_ROLE_WITH_SAGEMAKER_PERMISSIONS}')['Role']['Arn']
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'automatic-speech-recognition'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})


from sagemaker.huggingface import HuggingFaceModel
import sagemaker

role = sagemaker.get_execution_role()
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'conversational'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})


from sagemaker.huggingface import HuggingFaceModel
import boto3

iam_client = boto3.client('iam')
role = iam_client.get_role(RoleName='{IAM_ROLE_WITH_SAGEMAKER_PERMISSIONS}')['Role']['Arn']
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'conversational'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})


from sagemaker.huggingface import HuggingFaceModel
import sagemaker

role = sagemaker.get_execution_role()
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'feature-extraction'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})


from sagemaker.huggingface import HuggingFaceModel
import boto3

iam_client = boto3.client('iam')
role = iam_client.get_role(RoleName='{IAM_ROLE_WITH_SAGEMAKER_PERMISSIONS}')['Role']['Arn']
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'feature-extraction'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})


from sagemaker.huggingface import HuggingFaceModel
import sagemaker

role = sagemaker.get_execution_role()
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'fill-mask'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})


from sagemaker.huggingface import HuggingFaceModel
import boto3

iam_client = boto3.client('iam')
role = iam_client.get_role(RoleName='{IAM_ROLE_WITH_SAGEMAKER_PERMISSIONS}')['Role']['Arn']
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'fill-mask'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})


from sagemaker.huggingface import HuggingFaceModel
import sagemaker

role = sagemaker.get_execution_role()
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'image-classification'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})


from sagemaker.huggingface import HuggingFaceModel
import boto3

iam_client = boto3.client('iam')
role = iam_client.get_role(RoleName='{IAM_ROLE_WITH_SAGEMAKER_PERMISSIONS}')['Role']['Arn']
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'image-classification'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})


from sagemaker.huggingface import HuggingFaceModel
import sagemaker

role = sagemaker.get_execution_role()
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'question-answering'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})


from sagemaker.huggingface import HuggingFaceModel
import boto3

iam_client = boto3.client('iam')
role = iam_client.get_role(RoleName='{IAM_ROLE_WITH_SAGEMAKER_PERMISSIONS}')['Role']['Arn']
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'question-answering'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})


from sagemaker.huggingface import HuggingFaceModel
import sagemaker

role = sagemaker.get_execution_role()
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'summarization'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})


from sagemaker.huggingface import HuggingFaceModel
import boto3

iam_client = boto3.client('iam')
role = iam_client.get_role(RoleName='{IAM_ROLE_WITH_SAGEMAKER_PERMISSIONS}')['Role']['Arn']
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'summarization'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})


from sagemaker.huggingface import HuggingFaceModel
import sagemaker

role = sagemaker.get_execution_role()
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'table-question-answering'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})


from sagemaker.huggingface import HuggingFaceModel
import boto3

iam_client = boto3.client('iam')
role = iam_client.get_role(RoleName='{IAM_ROLE_WITH_SAGEMAKER_PERMISSIONS}')['Role']['Arn']
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'table-question-answering'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})


from sagemaker.huggingface import HuggingFaceModel
import sagemaker

role = sagemaker.get_execution_role()
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'text-classification'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})


from sagemaker.huggingface import HuggingFaceModel
import boto3

iam_client = boto3.client('iam')
role = iam_client.get_role(RoleName='{IAM_ROLE_WITH_SAGEMAKER_PERMISSIONS}')['Role']['Arn']
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'text-classification'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})


from sagemaker.huggingface import HuggingFaceModel
import sagemaker

role = sagemaker.get_execution_role()
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'text-generation'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})


from sagemaker.huggingface import HuggingFaceModel
import boto3

iam_client = boto3.client('iam')
role = iam_client.get_role(RoleName='{IAM_ROLE_WITH_SAGEMAKER_PERMISSIONS}')['Role']['Arn']
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'text-generation'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})


from sagemaker.huggingface import HuggingFaceModel
import sagemaker

role = sagemaker.get_execution_role()
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'text2text-generation'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})


from sagemaker.huggingface import HuggingFaceModel
import boto3

iam_client = boto3.client('iam')
role = iam_client.get_role(RoleName='{IAM_ROLE_WITH_SAGEMAKER_PERMISSIONS}')['Role']['Arn']
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'text2text-generation'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})


from sagemaker.huggingface import HuggingFaceModel
import sagemaker

role = sagemaker.get_execution_role()
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'token-classification'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})


from sagemaker.huggingface import HuggingFaceModel
import boto3

iam_client = boto3.client('iam')
role = iam_client.get_role(RoleName='{IAM_ROLE_WITH_SAGEMAKER_PERMISSIONS}')['Role']['Arn']
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'token-classification'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})


from sagemaker.huggingface import HuggingFaceModel
import sagemaker

role = sagemaker.get_execution_role()
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'translation'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})


from sagemaker.huggingface import HuggingFaceModel
import boto3

iam_client = boto3.client('iam')
role = iam_client.get_role(RoleName='{IAM_ROLE_WITH_SAGEMAKER_PERMISSIONS}')['Role']['Arn']
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'translation'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})


from sagemaker.huggingface import HuggingFaceModel
import sagemaker

role = sagemaker.get_execution_role()
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'zero-shot-classification'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})


from sagemaker.huggingface import HuggingFaceModel
import boto3

iam_client = boto3.client('iam')
role = iam_client.get_role(RoleName='{IAM_ROLE_WITH_SAGEMAKER_PERMISSIONS}')['Role']['Arn']
# Hub Model configuration. https://huggingface.co/models
hub = {
	'HF_MODEL_ID':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'HF_TASK':'zero-shot-classification'
}

# create Hugging Face Model Class
huggingface_model = HuggingFaceModel(
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	env=hub,
	role=role, 
)

# deploy model to SageMaker Inference
predictor = huggingface_model.deploy(
	initial_instance_count=1, # number of instances
	instance_type='ml.m5.xlarge' # ec2 instance type
)

predictor.predict({
	'inputs': "Today is a sunny day and I'll get some ice cream."
})

Spaces

import gradio as gr

gr.Interface.load("models/cambridgeltl/SapBERT-from-PubMedBERT-fulltext").launch()

Training

Amazon SageMaker

import sagemaker
from sagemaker.huggingface import HuggingFace

# gets role for executing training job
role = sagemaker.get_execution_role()
hyperparameters = {
	'model_name_or_path':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'output_dir':'/opt/ml/model'
	# add your remaining hyperparameters
	# more info here https://github.com/huggingface/transformers/tree/v4.17.0/examples/pytorch/language-modeling
}

# git configuration to download our fine-tuning script
git_config = {'repo': 'https://github.com/huggingface/transformers.git','branch': 'v4.17.0'}

# creates Hugging Face estimator
huggingface_estimator = HuggingFace(
	entry_point='run_clm.py',
	source_dir='./examples/pytorch/language-modeling',
	instance_type='ml.p3.2xlarge',
	instance_count=1,
	role=role,
	git_config=git_config,
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	hyperparameters = hyperparameters
)

# starting the train job
huggingface_estimator.fit()


import sagemaker
import boto3
from sagemaker.huggingface import HuggingFace

# gets role for executing training job
iam_client = boto3.client('iam')
role = iam_client.get_role(RoleName='{IAM_ROLE_WITH_SAGEMAKER_PERMISSIONS}')['Role']['Arn']
hyperparameters = {
	'model_name_or_path':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'output_dir':'/opt/ml/model'
	# add your remaining hyperparameters
	# more info here https://github.com/huggingface/transformers/tree/v4.17.0/examples/pytorch/language-modeling
}

# git configuration to download our fine-tuning script
git_config = {'repo': 'https://github.com/huggingface/transformers.git','branch': 'v4.17.0'}

# creates Hugging Face estimator
huggingface_estimator = HuggingFace(
	entry_point='run_clm.py',
	source_dir='./examples/pytorch/language-modeling',
	instance_type='ml.p3.2xlarge',
	instance_count=1,
	role=role,
	git_config=git_config,
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	hyperparameters = hyperparameters
)

# starting the train job
huggingface_estimator.fit()


import sagemaker
from sagemaker.huggingface import HuggingFace

# gets role for executing training job
role = sagemaker.get_execution_role()
hyperparameters = {
	'model_name_or_path':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'output_dir':'/opt/ml/model'
	# add your remaining hyperparameters
	# more info here https://github.com/huggingface/transformers/tree/v4.17.0/examples/pytorch/language-modeling
}

# git configuration to download our fine-tuning script
git_config = {'repo': 'https://github.com/huggingface/transformers.git','branch': 'v4.17.0'}

# creates Hugging Face estimator
huggingface_estimator = HuggingFace(
	entry_point='run_mlm.py',
	source_dir='./examples/pytorch/language-modeling',
	instance_type='ml.p3.2xlarge',
	instance_count=1,
	role=role,
	git_config=git_config,
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	hyperparameters = hyperparameters
)

# starting the train job
huggingface_estimator.fit()


import sagemaker
import boto3
from sagemaker.huggingface import HuggingFace

# gets role for executing training job
iam_client = boto3.client('iam')
role = iam_client.get_role(RoleName='{IAM_ROLE_WITH_SAGEMAKER_PERMISSIONS}')['Role']['Arn']
hyperparameters = {
	'model_name_or_path':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'output_dir':'/opt/ml/model'
	# add your remaining hyperparameters
	# more info here https://github.com/huggingface/transformers/tree/v4.17.0/examples/pytorch/language-modeling
}

# git configuration to download our fine-tuning script
git_config = {'repo': 'https://github.com/huggingface/transformers.git','branch': 'v4.17.0'}

# creates Hugging Face estimator
huggingface_estimator = HuggingFace(
	entry_point='run_mlm.py',
	source_dir='./examples/pytorch/language-modeling',
	instance_type='ml.p3.2xlarge',
	instance_count=1,
	role=role,
	git_config=git_config,
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	hyperparameters = hyperparameters
)

# starting the train job
huggingface_estimator.fit()


import sagemaker
from sagemaker.huggingface import HuggingFace

# gets role for executing training job
role = sagemaker.get_execution_role()
hyperparameters = {
	'model_name_or_path':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'output_dir':'/opt/ml/model'
	# add your remaining hyperparameters
	# more info here https://github.com/huggingface/transformers/tree/v4.17.0/examples/pytorch/question-answering
}

# git configuration to download our fine-tuning script
git_config = {'repo': 'https://github.com/huggingface/transformers.git','branch': 'v4.17.0'}

# creates Hugging Face estimator
huggingface_estimator = HuggingFace(
	entry_point='run_qa.py',
	source_dir='./examples/pytorch/question-answering',
	instance_type='ml.p3.2xlarge',
	instance_count=1,
	role=role,
	git_config=git_config,
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	hyperparameters = hyperparameters
)

# starting the train job
huggingface_estimator.fit()


import sagemaker
import boto3
from sagemaker.huggingface import HuggingFace

# gets role for executing training job
iam_client = boto3.client('iam')
role = iam_client.get_role(RoleName='{IAM_ROLE_WITH_SAGEMAKER_PERMISSIONS}')['Role']['Arn']
hyperparameters = {
	'model_name_or_path':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'output_dir':'/opt/ml/model'
	# add your remaining hyperparameters
	# more info here https://github.com/huggingface/transformers/tree/v4.17.0/examples/pytorch/question-answering
}

# git configuration to download our fine-tuning script
git_config = {'repo': 'https://github.com/huggingface/transformers.git','branch': 'v4.17.0'}

# creates Hugging Face estimator
huggingface_estimator = HuggingFace(
	entry_point='run_qa.py',
	source_dir='./examples/pytorch/question-answering',
	instance_type='ml.p3.2xlarge',
	instance_count=1,
	role=role,
	git_config=git_config,
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	hyperparameters = hyperparameters
)

# starting the train job
huggingface_estimator.fit()


import sagemaker
from sagemaker.huggingface import HuggingFace

# gets role for executing training job
role = sagemaker.get_execution_role()
hyperparameters = {
	'model_name_or_path':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'output_dir':'/opt/ml/model'
	# add your remaining hyperparameters
	# more info here https://github.com/huggingface/transformers/tree/v4.17.0/examples/pytorch/seq2seq
}

# git configuration to download our fine-tuning script
git_config = {'repo': 'https://github.com/huggingface/transformers.git','branch': 'v4.17.0'}

# creates Hugging Face estimator
huggingface_estimator = HuggingFace(
	entry_point='run_summarization.py',
	source_dir='./examples/pytorch/seq2seq',
	instance_type='ml.p3.2xlarge',
	instance_count=1,
	role=role,
	git_config=git_config,
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	hyperparameters = hyperparameters
)

# starting the train job
huggingface_estimator.fit()


import sagemaker
import boto3
from sagemaker.huggingface import HuggingFace

# gets role for executing training job
iam_client = boto3.client('iam')
role = iam_client.get_role(RoleName='{IAM_ROLE_WITH_SAGEMAKER_PERMISSIONS}')['Role']['Arn']
hyperparameters = {
	'model_name_or_path':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'output_dir':'/opt/ml/model'
	# add your remaining hyperparameters
	# more info here https://github.com/huggingface/transformers/tree/v4.17.0/examples/pytorch/seq2seq
}

# git configuration to download our fine-tuning script
git_config = {'repo': 'https://github.com/huggingface/transformers.git','branch': 'v4.17.0'}

# creates Hugging Face estimator
huggingface_estimator = HuggingFace(
	entry_point='run_summarization.py',
	source_dir='./examples/pytorch/seq2seq',
	instance_type='ml.p3.2xlarge',
	instance_count=1,
	role=role,
	git_config=git_config,
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	hyperparameters = hyperparameters
)

# starting the train job
huggingface_estimator.fit()


import sagemaker
from sagemaker.huggingface import HuggingFace

# gets role for executing training job
role = sagemaker.get_execution_role()
hyperparameters = {
	'model_name_or_path':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'output_dir':'/opt/ml/model'
	# add your remaining hyperparameters
	# more info here https://github.com/huggingface/transformers/tree/v4.17.0/examples/pytorch/text-classification
}

# git configuration to download our fine-tuning script
git_config = {'repo': 'https://github.com/huggingface/transformers.git','branch': 'v4.17.0'}

# creates Hugging Face estimator
huggingface_estimator = HuggingFace(
	entry_point='run_glue.py',
	source_dir='./examples/pytorch/text-classification',
	instance_type='ml.p3.2xlarge',
	instance_count=1,
	role=role,
	git_config=git_config,
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	hyperparameters = hyperparameters
)

# starting the train job
huggingface_estimator.fit()


import sagemaker
import boto3
from sagemaker.huggingface import HuggingFace

# gets role for executing training job
iam_client = boto3.client('iam')
role = iam_client.get_role(RoleName='{IAM_ROLE_WITH_SAGEMAKER_PERMISSIONS}')['Role']['Arn']
hyperparameters = {
	'model_name_or_path':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'output_dir':'/opt/ml/model'
	# add your remaining hyperparameters
	# more info here https://github.com/huggingface/transformers/tree/v4.17.0/examples/pytorch/text-classification
}

# git configuration to download our fine-tuning script
git_config = {'repo': 'https://github.com/huggingface/transformers.git','branch': 'v4.17.0'}

# creates Hugging Face estimator
huggingface_estimator = HuggingFace(
	entry_point='run_glue.py',
	source_dir='./examples/pytorch/text-classification',
	instance_type='ml.p3.2xlarge',
	instance_count=1,
	role=role,
	git_config=git_config,
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	hyperparameters = hyperparameters
)

# starting the train job
huggingface_estimator.fit()


import sagemaker
from sagemaker.huggingface import HuggingFace

# gets role for executing training job
role = sagemaker.get_execution_role()
hyperparameters = {
	'model_name_or_path':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'output_dir':'/opt/ml/model'
	# add your remaining hyperparameters
	# more info here https://github.com/huggingface/transformers/tree/v4.17.0/examples/pytorch/token-classification
}

# git configuration to download our fine-tuning script
git_config = {'repo': 'https://github.com/huggingface/transformers.git','branch': 'v4.17.0'}

# creates Hugging Face estimator
huggingface_estimator = HuggingFace(
	entry_point='run_ner.py',
	source_dir='./examples/pytorch/token-classification',
	instance_type='ml.p3.2xlarge',
	instance_count=1,
	role=role,
	git_config=git_config,
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	hyperparameters = hyperparameters
)

# starting the train job
huggingface_estimator.fit()


import sagemaker
import boto3
from sagemaker.huggingface import HuggingFace

# gets role for executing training job
iam_client = boto3.client('iam')
role = iam_client.get_role(RoleName='{IAM_ROLE_WITH_SAGEMAKER_PERMISSIONS}')['Role']['Arn']
hyperparameters = {
	'model_name_or_path':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'output_dir':'/opt/ml/model'
	# add your remaining hyperparameters
	# more info here https://github.com/huggingface/transformers/tree/v4.17.0/examples/pytorch/token-classification
}

# git configuration to download our fine-tuning script
git_config = {'repo': 'https://github.com/huggingface/transformers.git','branch': 'v4.17.0'}

# creates Hugging Face estimator
huggingface_estimator = HuggingFace(
	entry_point='run_ner.py',
	source_dir='./examples/pytorch/token-classification',
	instance_type='ml.p3.2xlarge',
	instance_count=1,
	role=role,
	git_config=git_config,
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	hyperparameters = hyperparameters
)

# starting the train job
huggingface_estimator.fit()


import sagemaker
from sagemaker.huggingface import HuggingFace

# gets role for executing training job
role = sagemaker.get_execution_role()
hyperparameters = {
	'model_name_or_path':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'output_dir':'/opt/ml/model'
	# add your remaining hyperparameters
	# more info here https://github.com/huggingface/transformers/tree/v4.17.0/examples/pytorch/seq2seq
}

# git configuration to download our fine-tuning script
git_config = {'repo': 'https://github.com/huggingface/transformers.git','branch': 'v4.17.0'}

# creates Hugging Face estimator
huggingface_estimator = HuggingFace(
	entry_point='run_translation.py',
	source_dir='./examples/pytorch/seq2seq',
	instance_type='ml.p3.2xlarge',
	instance_count=1,
	role=role,
	git_config=git_config,
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	hyperparameters = hyperparameters
)

# starting the train job
huggingface_estimator.fit()


import sagemaker
import boto3
from sagemaker.huggingface import HuggingFace

# gets role for executing training job
iam_client = boto3.client('iam')
role = iam_client.get_role(RoleName='{IAM_ROLE_WITH_SAGEMAKER_PERMISSIONS}')['Role']['Arn']
hyperparameters = {
	'model_name_or_path':'cambridgeltl/SapBERT-from-PubMedBERT-fulltext',
	'output_dir':'/opt/ml/model'
	# add your remaining hyperparameters
	# more info here https://github.com/huggingface/transformers/tree/v4.17.0/examples/pytorch/seq2seq
}

# git configuration to download our fine-tuning script
git_config = {'repo': 'https://github.com/huggingface/transformers.git','branch': 'v4.17.0'}

# creates Hugging Face estimator
huggingface_estimator = HuggingFace(
	entry_point='run_translation.py',
	source_dir='./examples/pytorch/seq2seq',
	instance_type='ml.p3.2xlarge',
	instance_count=1,
	role=role,
	git_config=git_config,
	transformers_version='4.17.0',
	pytorch_version='1.10.2',
	py_version='py38',
	hyperparameters = hyperparameters
)

# starting the train job
huggingface_estimator.fit()

Model Card

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