bio_embeddings.project

Visualize high dimensional data with t-SNE or UMAP projections or project Bert embeddings with Tucker

class bio_embeddings.project.PBTucker(model_file: Union[str, pathlib.Path], device: torch.device)

Tucker is a contrastive learning model trained to distinguish CATH superfamilies.

It consumes prottrans_bert_bfd embeddings and reduces the embedding dimensionality from 1024 to 128. See https://www.biorxiv.org/content/10.1101/2021.01.21.427551v1

To use it outside of the pipeline, first instantiate it with pb_tucker = PBTucker(“/path/to/model”, device), then project your reduced bert embedding with pb_tucker.project_reduced_embedding(bert_embedding).

__init__(model_file: Union[str, pathlib.Path], device: torch.device)

Initialize self. See help(type(self)) for accurate signature.

name: str = 'pb_tucker'

project_reduced_embedding(reduced_embedding: numpy.ndarray) → numpy.ndarray

class bio_embeddings.project.PBTuckerModel

This is the torch module behind PBTucker

__init__()

Initializes internal Module state, shared by both nn.Module and ScriptModule.

forward(data: None._VariableFunctionsClass.tensor) → None._VariableFunctionsClass.tensor

Defines the computation performed at every call.

Should be overridden by all subclasses.

Note

Although the recipe for forward pass needs to be defined within this function, one should call the Module instance afterwards instead of this since the former takes care of running the registered hooks while the latter silently ignores them.

training: bool

bio_embeddings.project.tsne_reduce(embeddings, **kwargs)

Wrapper around sklearn.manifold.TSNE() with defaults for bio_embeddings

bio_embeddings.project.umap_reduce(embeddings, **kwargs)

Wrapper around umap.UMAP() with defaults for bio_embeddings