Extending the Datasets
While the core of PyKEEN uses the
pykeen.triples.TriplesFactory for handling sets of triples,
the definition of a training, validation, and testing trichotomy for a given dataset is very useful
for reproducible benchmarking. The internal
pykeen.datasets.base.Dataset class can be considered
as a three-tuple of datasets (though it’s implemented as a class such that it can be extended). There
are several datasets included in PyKEEN already, each coming from sources that look different. This
tutorial gives some insight into implementing your own Dataset class.
Unpacked Remote Dataset
Use this tutorial if you have three separate URLs for the respective training, testing, and validation
sets that are each 3 column TSV files. A good example can be found at
https://github.com/ZhenfengLei/KGDatasets/tree/master/DBpedia50. There’s a base class called
pykeen.datasets.base.UnpackedRemoteDataset that can be used to wrap it like the following:
from pykeen.datasets.base import UnpackedRemoteDataset TEST_URL = 'https://raw.githubusercontent.com/ZhenfengLei/KGDatasets/master/DBpedia50/test.txt' TRAIN_URL = 'https://raw.githubusercontent.com/ZhenfengLei/KGDatasets/master/DBpedia50/train.txt' VALID_URL = 'https://raw.githubusercontent.com/ZhenfengLei/KGDatasets/master/DBpedia50/valid.txt' class DBpedia50(UnpackedRemoteDataset): def __init__(self, **kwargs): super().__init__( training_url=TRAIN_URL, testing_url=TEST_URL, validation_url=VALID_URL, **kwargs, )
Use this tutorial if you have a single URL for a TSV dataset that needs to be automatically split into
training, testing, and validation. A good example can be found at
https://github.com/hetio/hetionet/raw/master/hetnet/tsv. There’s a base class called
pykeen.datasets.base.SingleTabbedDataset that can be used to wrap it like the following:
from pykeen.datasets.base import SingleTabbedDataset URL = 'https://github.com/hetio/hetionet/raw/master/hetnet/tsv/hetionet-v1.0-edges.sif.gz' class Hetionet(SingleTabbedDataset): def __init__(self, **kwargs): super().__init__(url=URL, **kwargs)
The value for URL can be anything that can be read by
pandas.read_csv(). Additional options
can be passed through to the reading function, such as
sep=',', with the keyword argument
read_csv_kwargs=dict(sep=','). Note that the default separator for Pandas is a comma, but PyKEEN
overrides it to be a tab, so you’ll have to explicitly set it if you want a comma. Since there’s a random
aspect to this process, you can also set the seed used for splitting with the
Whether you’re making a pull request against PyKEEN or implementing a dataset in your own package,
you can use Python entrypoints to register your dataset with PyKEEN. Below is an example of the
entrypoints that register
and others that appear in the PyKEEN setup.cfg.
pykeen.datasets header, you can pick whatever name you want for the dataset as the key
(appearing on the left side of the equals, e.g.
hetionet) and the path to the class (appearing on
the right side of the equals, e.g.,
pykeen.datasets.hetionet:Hetionet). The right side
is constructed by the path to the module, the colon
:, then the name of the class.
# setup.cfg ... [options.entry_points] console_scripts = pykeen = pykeen.cli:main pykeen.datasets = hetionet = pykeen.datasets.hetionet:Hetionet conceptnet = pykeen.datasets.conceptnet:ConceptNet drkg = pykeen.datasets.drkg:DRKG ...
If you’re working on a development version of PyKEEN, you also need to run
pykeen readme in the shell
to update the README.md file.