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Datasets:
xuan-liu
/
ARIES-data

Tags:
chemistry
enzyme
reaction-site-prediction
grover
esmc
License:
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The dataset generation failed because of a cast error
Error code:   DatasetGenerationCastError
Exception:    DatasetGenerationCastError
Message:      An error occurred while generating the dataset

All the data files must have the same columns, but at some point there are 4 new columns ({'embedding_key', 'length', 'sequence', 'n_examples'}) and 4 missing columns ({'example_id', 'atom_index', 'is_legal_atom', 'label'}).

This happened while the csv dataset builder was generating data using

hf://datasets/xuan-liu/ARIES-data/brenda/esmc6b_embedding_index.csv (at revision 93d3c6a1ce15ae6963978c95c9b76412da6b7ae4), ['hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/atom_labels.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/esmc6b_embedding_index.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/examples.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/reaction.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/random_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/random_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/random_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_enzyme_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_enzyme_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_enzyme_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_substrate_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_substrate_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_substrate_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_transformation_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_transformation_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_transformation_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_transformation_substrate_enzyme_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_transformation_substrate_enzyme_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_transformation_substrate_enzyme_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_transformation_substrate_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_transformation_substrate_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_transformation_substrate_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/example_data/atom_labels.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/example_data/esmc6b_embedding_index.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/example_data/inputs.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/example_data/reaction.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/atom_labels.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/esmc6b_embedding_index.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/examples.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/reaction.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/splits/random_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/splits/random_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/splits/random_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/splits/unknown_enzyme_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/splits/unknown_enzyme_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/splits/unknown_enzyme_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/splits/unknown_enzyme_substrate_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/splits/unknown_enzyme_substrate_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/splits/unknown_enzyme_substrate_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/splits/unknown_substrate_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/splits/unknown_substrate_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/splits/unknown_substrate_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/atom_labels.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/esmc6b_embedding_index.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/examples.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/reaction.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/splits/random_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/splits/random_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/splits/random_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/splits/unknown_enzyme_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/splits/unknown_enzyme_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/splits/unknown_enzyme_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/splits/unknown_enzyme_substrate_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/splits/unknown_enzyme_substrate_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/splits/unknown_enzyme_substrate_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/splits/unknown_substrate_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/splits/unknown_substrate_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/splits/unknown_substrate_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/atom_labels.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/esmc6b_embedding_index.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/examples.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/reaction.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/splits/random_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/splits/random_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/splits/random_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/splits/unknown_enzyme_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/splits/unknown_enzyme_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/splits/unknown_enzyme_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/splits/unknown_substrate_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/splits/unknown_substrate_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/splits/unknown_substrate_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/splits/unknown_transformation_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/splits/unknown_transformation_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/splits/unknown_transformation_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/splits/unknown_transformation_substrate_enzyme_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/splits/unknown_transformation_substrate_enzyme_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/splits/unknown_transformation_substrate_enzyme_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/splits/unknown_transformation_substrate_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/splits/unknown_transformation_substrate_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/splits/unknown_transformation_substrate_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/methyltransferase/atom_labels.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/methyltransferase/esmc6b_embedding_index.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/methyltransferase/examples.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/methyltransferase/reaction.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/methyltransferase/splits/random_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/methyltransferase/splits/random_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/methyltransferase/splits/random_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/methyltransferase/splits/unknown_enzyme_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/methyltransferase/splits/unknown_enzyme_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/methyltransferase/splits/unknown_enzyme_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/methyltransferase/splits/unknown_enzyme_substrate_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/methyltransferase/splits/unknown_enzyme_substrate_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/methyltransferase/splits/unknown_enzyme_substrate_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/methyltransferase/splits/unknown_substrate_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/methyltransferase/splits/unknown_substrate_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/methyltransferase/splits/unknown_substrate_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/atom_labels.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/esmc6b_embedding_index.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/examples.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/reaction.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/splits/random_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/splits/random_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/splits/random_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/splits/unknown_enzyme_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/splits/unknown_enzyme_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/splits/unknown_enzyme_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/splits/unknown_enzyme_substrate_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/splits/unknown_enzyme_substrate_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/splits/unknown_enzyme_substrate_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/splits/unknown_substrate_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/splits/unknown_substrate_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/splits/unknown_substrate_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/atom_labels.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/esmc6b_embedding_index.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/examples.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/reaction.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/splits/random_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/splits/random_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/splits/random_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/splits/unknown_enzyme_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/splits/unknown_enzyme_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/splits/unknown_enzyme_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/splits/unknown_enzyme_substrate_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/splits/unknown_enzyme_substrate_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/splits/unknown_enzyme_substrate_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/splits/unknown_substrate_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/splits/unknown_substrate_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/splits/unknown_substrate_seed44.csv']

Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)
Traceback:    Traceback (most recent call last):
                File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1848, in _prepare_split_single
                  writer.write_table(table)
                  ~~~~~~~~~~~~~~~~~~^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/arrow_writer.py", line 784, in write_table
                  self._write_table(pa_table, writer_batch_size=writer_batch_size)
                  ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/arrow_writer.py", line 795, in _write_table
                  pa_table = table_cast(pa_table, self._schema)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2378, in table_cast
                  return cast_table_to_schema(table, schema)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2306, in cast_table_to_schema
                  raise CastError(
                  ...<3 lines>...
                  )
              datasets.table.CastError: Couldn't cast
              embedding_key: string
              sequence: string
              length: int64
              n_examples: int64
              -- schema metadata --
              pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 748
              to
              {'example_id': Value('string'), 'atom_index': Value('int64'), 'label': Value('int64'), 'is_legal_atom': Value('int64')}
              because column names don't match
              
              During handling of the above exception, another exception occurred:
              
              Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1369, in compute_config_parquet_and_info_response
                  parquet_operations, partial, estimated_dataset_info = stream_convert_to_parquet(
                                                                        ~~~~~~~~~~~~~~~~~~~~~~~~~^
                      builder, max_dataset_size_bytes=max_dataset_size_bytes
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                  )
                  ^
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 948, in stream_convert_to_parquet
                  builder._prepare_split(split_generator=splits_generators[split], file_format="parquet")
                  ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1694, in _prepare_split
                  for job_id, done, content in self._prepare_split_single(
                                               ~~~~~~~~~~~~~~~~~~~~~~~~~~^
                      gen_kwargs=gen_kwargs, job_id=job_id, **_prepare_split_args
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                  ):
                  ^
                File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1850, in _prepare_split_single
                  raise DatasetGenerationCastError.from_cast_error(
                  ...<4 lines>...
                  )
              datasets.exceptions.DatasetGenerationCastError: An error occurred while generating the dataset
              
              All the data files must have the same columns, but at some point there are 4 new columns ({'embedding_key', 'length', 'sequence', 'n_examples'}) and 4 missing columns ({'example_id', 'atom_index', 'is_legal_atom', 'label'}).
              
              This happened while the csv dataset builder was generating data using
              
              hf://datasets/xuan-liu/ARIES-data/brenda/esmc6b_embedding_index.csv (at revision 93d3c6a1ce15ae6963978c95c9b76412da6b7ae4), ['hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/atom_labels.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/esmc6b_embedding_index.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/examples.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/reaction.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/random_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/random_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/random_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_enzyme_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_enzyme_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_enzyme_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_substrate_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_substrate_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_substrate_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_transformation_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_transformation_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_transformation_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_transformation_substrate_enzyme_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_transformation_substrate_enzyme_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_transformation_substrate_enzyme_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_transformation_substrate_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_transformation_substrate_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/brenda/splits/unknown_transformation_substrate_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/example_data/atom_labels.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/example_data/esmc6b_embedding_index.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/example_data/inputs.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/example_data/reaction.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/atom_labels.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/esmc6b_embedding_index.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/examples.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/reaction.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/splits/random_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/splits/random_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/splits/random_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/splits/unknown_enzyme_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/splits/unknown_enzyme_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/splits/unknown_enzyme_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/splits/unknown_enzyme_substrate_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/splits/unknown_enzyme_substrate_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/splits/unknown_enzyme_substrate_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/splits/unknown_substrate_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/splits/unknown_substrate_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/fatty_acid_desaturase/splits/unknown_substrate_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/atom_labels.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/esmc6b_embedding_index.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/examples.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/reaction.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/splits/random_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/splits/random_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/splits/random_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/splits/unknown_enzyme_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/splits/unknown_enzyme_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/splits/unknown_enzyme_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/splits/unknown_enzyme_substrate_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/splits/unknown_enzyme_substrate_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/splits/unknown_enzyme_substrate_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/splits/unknown_substrate_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/splits/unknown_substrate_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/glycosyltransferase/splits/unknown_substrate_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/atom_labels.csv', 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'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/splits/unknown_transformation_substrate_enzyme_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/splits/unknown_transformation_substrate_enzyme_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/splits/unknown_transformation_substrate_enzyme_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/splits/unknown_transformation_substrate_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/splits/unknown_transformation_substrate_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/halogenase/splits/unknown_transformation_substrate_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/methyltransferase/atom_labels.csv', 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'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/methyltransferase/splits/unknown_enzyme_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/methyltransferase/splits/unknown_enzyme_substrate_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/methyltransferase/splits/unknown_enzyme_substrate_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/methyltransferase/splits/unknown_enzyme_substrate_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/methyltransferase/splits/unknown_substrate_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/methyltransferase/splits/unknown_substrate_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/methyltransferase/splits/unknown_substrate_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/atom_labels.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/esmc6b_embedding_index.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/examples.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/reaction.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/splits/random_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/splits/random_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/splits/random_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/splits/unknown_enzyme_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/splits/unknown_enzyme_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/splits/unknown_enzyme_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/splits/unknown_enzyme_substrate_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/splits/unknown_enzyme_substrate_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/splits/unknown_enzyme_substrate_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/splits/unknown_substrate_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/splits/unknown_substrate_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/p450/splits/unknown_substrate_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/atom_labels.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/esmc6b_embedding_index.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/examples.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/reaction.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/splits/random_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/splits/random_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/splits/random_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/splits/unknown_enzyme_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/splits/unknown_enzyme_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/splits/unknown_enzyme_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/splits/unknown_enzyme_substrate_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/splits/unknown_enzyme_substrate_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/splits/unknown_enzyme_substrate_seed44.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/splits/unknown_substrate_seed42.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/splits/unknown_substrate_seed43.csv', 'hf://datasets/xuan-liu/ARIES-data@93d3c6a1ce15ae6963978c95c9b76412da6b7ae4/prenyltransferase/splits/unknown_substrate_seed44.csv']
              
              Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)

Need help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.

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End of preview.

ARIES inference and evaluation data

This repository contains the compact public tables, exact GROVER atom and directed-bond embeddings, and ESM-C 6B residue embeddings required to run and evaluate ARIES. Model weights are available from xuan-liu/ARIES, and the package is available from the ARIES GitHub repository.

Datasets

Directory Rows Description
brenda/ 22,326 Curated BRENDA enzyme-substrate reaction-site examples.
halogenase/ 594 Curated halogenase reaction-site examples.
p450/ 3,669 Cytochrome P450 regioselectivity examples.
glycosyltransferase/ 50 Glycosyltransferase regioselectivity examples.
methyltransferase/ 54 Methyltransferase regioselectivity examples.
fatty_acid_desaturase/ 51 Fatty-acid desaturase regioselectivity examples.
prenyltransferase/ 66 Prenyltransferase regioselectivity examples.
example_data/ 21 Ready-to-run experimental inference examples.

The released specialist adapters and ARIES-XL-Hal-LoRA correspond to the random splits. The additional split protocols are included to make evaluation partitions reproducible; their inclusion does not imply that matching public fine-tuned weights are available.

Files

Every major dataset contains reaction.csv, examples.csv, atom_labels.csv, grover_exact_aries_fg.lmdb, esmc6b_residue_embeddings.lmdb, esmc6b_embedding_index.csv, and a splits/ directory. BRENDA and Halogenase include random, unknown-enzyme, unknown-substrate, unknown-transformation, unknown-transformation+substrate, and unknown-transformation+substrate+enzyme protocols. The five specialist families include random, unknown-enzyme, unknown-substrate, and joint unknown-enzyme+substrate protocols. Every protocol provides seeds 42-44.

examples.csv contains only model inputs and the example-level label. atom_labels.csv contains zero-based atom indices, ground-truth labels, and the legal-atom evaluation mask. Split files contain row_id,split assignments. reaction.csv is an independent human-readable table with the original reaction SMILES, enzyme name/accession/sequence, and EC number. EC numbers are metadata and are not consumed by ARIES.

The BRENDA and Halogenase LMDBs intentionally preserve the exact historical training-time arrays consumed by the released checkpoints. A later audit found that 1,586 collection-level ESM-C entries in those two merged caches have row counts that do not match their indexed sequences. The public files preserve these arrays for checkpoint and metric reproducibility. Newly generated caches from aries-precompute-embeddings contain one row per sequence residue.

Download 

hf download xuan-liu/ARIES-data --repo-type dataset --local-dir ARIES-data

Download one family when the full repository is not needed:

hf download xuan-liu/ARIES-data --repo-type dataset \
  --include "p450/*" --local-dir ARIES-data

Inference 

aries-inference \
  --input-csv ARIES-data/example_data/inputs.csv \
  --embedding-dir ARIES-data/example_data \
  --weights-dir model_weights/aries-xl-brenda \
  --lora-weights-dir model_weights/aries-xl-hal-lora \
  --output-csv predictions.csv \
  --device auto

For a major dataset, pass its examples.csv as --input-csv and its directory as --embedding-dir. Ground truth remains separate in atom_labels.csv.

Process raw reactions

aries-data-process performs chemical preprocessing. It converts reaction.csv into inputs.csv and atom_labels.csv by mapping reactions, selecting the principal substrate/product, extracting an ARIES reaction-site template, and deriving atom targets. It does not compute neural embeddings.

aries-data-process \
  --input-csv ARIES-data/example_data/reaction.csv \
  --output-dir processed \
  --device cuda

Run aries-precompute-embeddings afterward to create the GROVER and ESM-C LMDBs required by inference.

Split selection

ARIES accepts a split path relative to each dataset directory. For example:

aries-train \
  --data-dir ARIES-data/p450 \
  --split-relative-path splits/unknown_enzyme_seed42.csv \
  --split-seed 42 \
  --output-dir run \
  --device cuda

Data terms

The ARIES code and model licenses do not automatically relicense the underlying scientific datasets. Consult the original dataset and publication terms before redistributing or repurposing individual records.
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