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, ids, **kwargs)	Embedding for a biological object.
SequenceEmbedding(embedding, sequence, **kwargs)	Embedding for a biological sequence.
ProteinEmbedding(embedding, sequence[, ...])	Embedding of a protein sequence.

Embedding vector types

EmbeddingVector(vector, obj, **kwargs)	Vector representation for a biological entity.
SequenceVector(vector, sequence, **kwargs)	Vector representation for a biological sequence.
ProteinVector(vector, sequence, **kwargs)	Vector representation for a protein sequence.

Embedding vector utilities

embed_vec_to_numpy(vectors[, validate])	Convert an iterable of EmbeddingVector objects to a NumPy array.
embed_vec_to_distances(vectors[, metric, ...])	Convert EmbeddingVector objects to a DistanceMatrix object.
embed_vec_to_ordination(vectors[, validate])	Convert EmbeddingVector objects to an Ordination object.
embed_vec_to_dataframe(vectors[, validate])	Convert a list of SequenceVector objects to a pandas DataFrame.