bio-datasets 0.0.2

Open-source collection of biology datasets and pre-trained embeddings.

bio-datasets

Open-source collection of biology datasets and pre-trained embeddings.

Description

bio-datasets is a collaborative framework that allows the user to fetch publicly available sequence-based protein datasets. For these datasets, pre-trained contextual embeddings are also available.

Installation

Install the required dependencies with pip install biodatasets.

How it works

from biodatasets import list_datasets, load_dataset

print(list_datasets())

my_dataset = load_dataset('test')
X, y = my_dataset.to_npy_arrays(input_names=['peptide'], target_names=['target'])

embeddings = my_dataset.get_embeddings(variable_name="peptide", model_name="protbert", embeddings_type="cls")