feat: fix broken medical datasets #39
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The handler was missing the name of the dataset configuration and also had a feature column 'labels' instead of expected 'label'.
The handler was missing the name of the dataset configuration and also had a feature column 'labels' instead of expected 'label'.
Added the required target feature and the encoding from string to integer values.
Remove the source folder, as we want to enable fetch, copy and deletion of individual datasets no matter its source. Now, it's as easy as perform the action over the folder with the dataset title (all information related to the dataset is available in that folder).
frederik-encord
approved these changes
Mar 8, 2024
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We currently have 3 medical datasets that aren't working:
The fixes in this PR introduce the concept of
target featurewhen handling HF datasets, to explicitly mention the column we would like to use as thelabelcolumn (that may not exist in the dataset). Also, I added some handlers and conversions for out-of-the-standard content in such column.Datasets (2) and (3) are downloaded successfully and are compatible with the existing models, but dataset (1) still has an incompatibility issue when building the embeddings. We should assert if we want dataset (1) at all in this phase as its data alone occupies 85 Gb.
As part of the testing process, I found a blocker where the disk space ran out because the cache for datasets wasn't set in a sole place for all users and runs which ended up filling a drive with small capacity in the VM. Now, by default all dataset related content is stored in the
.cachedir in the project's root.