Skip to main content
`Ctrl`+`K`

# 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.