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protein-ligand-mlp-3

Sentence Similarity
sentence-transformers
feature-extraction
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pipeline_tag: sentence-similarity
tags:
  - sentence-transformers
  - feature-extraction
  - sentence-similarity

jglaser/protein-ligand-mlp-3

This is a sentence-transformers model: It maps sentences & paragraphs to a 1 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:

pip install -U sentence-transformers

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('jglaser/protein-ligand-mlp-3')
embeddings = model.encode(sentences)
print(embeddings)

Evaluation Results

For an automated evaluation of this model, see the Sentence Embeddings Benchmark: https://seb.sbert.net

Full Model Architecture 

SentenceTransformer(
  (0): Asym(
    (protein-0): Transformer({'max_seq_length': 2048, 'do_lower_case': False}) with Transformer model: BertModel 
    (protein-1): Pooling({'word_embedding_dimension': 1024, 'pooling_mode_cls_token': True, 'pooling_mode_mean_tokens': False, 'pooling_mode_max_tokens': False, 'pooling_mode_mean_sqrt_len_tokens': False})
    (protein-2): Dense({'in_features': 1024, 'out_features': 1024, 'bias': True, 'activation_function': 'torch.nn.modules.activation.Tanh'})
    (ligand-0): Transformer({'max_seq_length': 512, 'do_lower_case': False}) with Transformer model: BertModel 
    (ligand-1): Pooling({'word_embedding_dimension': 768, 'pooling_mode_cls_token': True, 'pooling_mode_mean_tokens': False, 'pooling_mode_max_tokens': False, 'pooling_mode_mean_sqrt_len_tokens': False})
    (ligand-2): Dense({'in_features': 768, 'out_features': 768, 'bias': True, 'activation_function': 'torch.nn.modules.activation.Tanh'})
  )
  (1): Dense({'in_features': 1792, 'out_features': 1000, 'bias': True, 'activation_function': 'torch.nn.modules.activation.GELU'})
  (2): Dense({'in_features': 1000, 'out_features': 1000, 'bias': True, 'activation_function': 'torch.nn.modules.activation.GELU'})
  (3): Dense({'in_features': 1000, 'out_features': 1000, 'bias': True, 'activation_function': 'torch.nn.modules.activation.GELU'})
  (4): Dense({'in_features': 1000, 'out_features': 1, 'bias': True, 'activation_function': 'torch.nn.modules.linear.Identity'})
  (5): Dense({'in_features': 1, 'out_features': 1, 'bias': True, 'activation_function': 'torch.nn.modules.linear.Identity'})
)

Citing & Authors