Sentence Similarity
sentence-transformers
Safetensors
Transformers
bert
feature-extraction
biology
protein language model
text-embeddings-inference
Instructions to use monsoon-nlp/protein-matryoshka-embeddings with libraries, inference providers, notebooks, and local apps. Follow these links to get started.
- Libraries
- sentence-transformers
How to use monsoon-nlp/protein-matryoshka-embeddings with sentence-transformers:
from sentence_transformers import SentenceTransformer model = SentenceTransformer("monsoon-nlp/protein-matryoshka-embeddings") sentences = [ "That is a happy person", "That is a happy dog", "That is a very happy person", "Today is a sunny day" ] embeddings = model.encode(sentences) similarities = model.similarity(embeddings, embeddings) print(similarities.shape) # [4, 4] - Transformers
How to use monsoon-nlp/protein-matryoshka-embeddings with Transformers:
# pip install -U transformers accelerate # Load model directly from transformers import AutoTokenizer, AutoModel tokenizer = AutoTokenizer.from_pretrained("monsoon-nlp/protein-matryoshka-embeddings") model = AutoModel.from_pretrained("monsoon-nlp/protein-matryoshka-embeddings", device_map="auto") - Notebooks
- Google Colab
- Kaggle
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Example using SciKit-Learn to train on a classification task from [greenbeing-binary](https://huggingface.co/datasets/monsoon-nlp/greenbeing-binary) - https://colab.research.google.com/drive/1MCTn8f3oeIKpB6n_8mPumet3ukm7GD8a?usp=sharing
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TBD: example using Sentence-Transformers to [finetune embeddings](https://huggingface.co/blog/train-sentence-transformers) for a TAPE regression or classification task
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## Future
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This page will be updated when I have examples using it on protein classification tasks.
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Example using SciKit-Learn to train on a classification task from [greenbeing-binary](https://huggingface.co/datasets/monsoon-nlp/greenbeing-binary) - https://colab.research.google.com/drive/1MCTn8f3oeIKpB6n_8mPumet3ukm7GD8a?usp=sharing
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## Future
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This page will be updated when I have examples using it on protein classification tasks.
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