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Fix PubChemBatched dataset#170

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sfluegel05 merged 6 commits into
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fix/pubchem-batched
Jun 26, 2026
Merged

Fix PubChemBatched dataset#170
sfluegel05 merged 6 commits into
devfrom
fix/pubchem-batched

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@sfluegel05

@sfluegel05 sfluegel05 commented May 28, 2026

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When changing the PubChem dataset to dynamic in #167, I forgot that the PubChemBatched dataset actually isn't that dynamic (i.e., has different files for train/val/test). To make things more complicated, the train set is split across multiple files.

Therefore, we need to

  • overwrite load_processed_data with the custom data loading scheme
  • create a splits.csv file and enable loading a dataset from this file

@sfluegel05

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This is working. I uploaded the generated dataset to Hugging Face: https://huggingface.co/datasets/chebai/PubChem

I also trained an ELECTRA on this dataset: https://huggingface.co/chebai/electra_pubchem_123m

@sfluegel05 sfluegel05 marked this pull request as ready for review June 26, 2026 08:53
@sfluegel05 sfluegel05 merged commit 190ad0a into dev Jun 26, 2026
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@sfluegel05 sfluegel05 deleted the fix/pubchem-batched branch June 26, 2026 08:53
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