Biological Embeddings (skbio.embedding)

This module provides support for storing embeddings for biological objects, such as protein embeddings outputted from protein language models (pLMs).

Embedding types

Embedding	Embedding for a biological object.
SequenceEmbedding	Embedding for a biological sequence.
ProteinEmbedding	Embedding of a protein sequence.

Embedding vector types

EmbeddingVector	Vector representation for a biological entity.
SequenceVector	Vector representation for a biological sequence.
ProteinVector	Vector representation for a protein sequence.

Embedding vector utilities

embed_vec_to_numpy	Convert an iterable of EmbeddingVector objects to a NumPy array.
embed_vec_to_distances	Convert EmbeddingVector objects to a DistanceMatrix object.
embed_vec_to_ordination	Convert EmbeddingVector objects to an Ordination object.
embed_vec_to_dataframe	Convert a list of SequenceVector objects to a pandas DataFrame.