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Closes part of #682 #684

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merged 6 commits into from
Oct 26, 2024
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shamikbose
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@shamikbose shamikbose commented Jun 5, 2022

medical_data updated to bigbio_pairs schema
Passes all tests

  • Confirm that this PR is linked to the dataset issue.
  • Create the dataloader script biodatasets/my_dataset/my_dataset.py (please use only lowercase and underscore for dataset naming).
  • Provide values for the _CITATION, _DATASETNAME, _DESCRIPTION, _HOMEPAGE, _LICENSE, _URLs, _SUPPORTED_TASKS, _SOURCE_VERSION, and _BIGBIO_VERSION variables.
  • Implement _info(), _split_generators() and _generate_examples() in dataloader script.
  • Make sure that the BUILDER_CONFIGS class attribute is a list with at least one BigBioConfig for the source schema and one for a bigbio schema.
  • Confirm dataloader script works with datasets.load_dataset function.
  • Confirm that your dataloader script passes the test suite run with python -m tests.test_bigbio biodatasets/my_dataset/my_dataset.py.
  • If my dataset is local, I have provided an output of the unit-tests in the PR (please copy paste). This is OPTIONAL for public datasets, as we can test these without access to the data files.

Updated to `bigbio_pairs` schema
Passes all tests
@mariosaenger mariosaenger self-assigned this Oct 23, 2024
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@phlobo Please have a look at this dataset. I refactored the implementation to the new HF-hub-based style. I'm not completely happy with the modeling - essentially it's aspect-based text classification rather than text similarity. However, the former isn't properly supported by any of the BigBio schemes.

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I would pick a different task, but apart from that, the PR looks good!

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phlobo
phlobo previously approved these changes Oct 26, 2024
@phlobo phlobo merged commit 7373ea6 into bigscience-workshop:main Oct 26, 2024
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phlobo commented Oct 26, 2024

@mariosaenger I realized the old version of the dataset is already on the hub: https://huggingface.co/datasets/bigbio/medical_data
should we delete that one?

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4 participants