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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 1 new columns ({'BIOUG70015-D01'}) and 1 missing columns ({'BIOUG52570-G11'}).
This happened while the csv dataset builder was generating data using
zip://CLIBD_partitioning/no_split.txt::hf://datasets/bioscan-ml/clibd@6a0269ef51d1017a7fabcbdd4273a2492ff8e55e/data/BIOSCAN_1M/CLIBD_partitioning.zip
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 "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1871, in _prepare_split_single
writer.write_table(table)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 643, in write_table
pa_table = table_cast(pa_table, self._schema)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2293, in table_cast
return cast_table_to_schema(table, schema)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2241, in cast_table_to_schema
raise CastError(
datasets.table.CastError: Couldn't cast
BIOUG70015-D01: string
-- schema metadata --
pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 391
to
{'BIOUG52570-G11': Value(dtype='string', id=None)}
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 1431, in compute_config_parquet_and_info_response
parquet_operations, partial, estimated_dataset_info = stream_convert_to_parquet(
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 992, in stream_convert_to_parquet
builder._prepare_split(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1742, in _prepare_split
for job_id, done, content in self._prepare_split_single(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1873, in _prepare_split_single
raise DatasetGenerationCastError.from_cast_error(
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 1 new columns ({'BIOUG70015-D01'}) and 1 missing columns ({'BIOUG52570-G11'}).
This happened while the csv dataset builder was generating data using
zip://CLIBD_partitioning/no_split.txt::hf://datasets/bioscan-ml/clibd@6a0269ef51d1017a7fabcbdd4273a2492ff8e55e/data/BIOSCAN_1M/CLIBD_partitioning.zip
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.
BIOUG52570-G11
string |
|---|
BIOUG57567-H08
|
BIOUG57333-A05
|
BIOUG53645-B08
|
BIOUG54275-F07
|
BIOUG52306-D03
|
BIOUG52243-C09
|
BIOUG55653-E10
|
BIOUG57894-A04
|
BIOUG52552-A06
|
BIOUG61457-A09
|
BIOUG60788-F01
|
BIOUG51841-H11
|
BIOUG61510-G01
|
BIOUG59241-B12
|
BIOUG56786-B04
|
BIOUG57530-D11
|
BIOUG56081-G06
|
BIOUG68872-B05
|
BIOUG68412-B09
|
BIOUG59465-E12
|
BIOUG55980-C05
|
BIOUG67802-G05
|
BIOUG66489-H07
|
BIOUG55847-D10
|
BIOUG68224-B02
|
BIOUG56108-C07
|
BIOUG68420-C05
|
BIOUG63291-D04
|
BIOUG63498-A07
|
BIOUG54347-H08
|
BIOUG58661-H01
|
BIOUG64952-G02
|
BIOUG56450-A12
|
BIOUG63543-H08
|
BIOUG61555-H11
|
BIOUG62117-H08
|
BIOUG54347-H09
|
BIOUG65039-D11
|
BIOUG53351-B05
|
BIOUG65853-B09
|
BIOUG65877-G06
|
BIOUG66830-F07
|
BIOUG67618-A10
|
BIOUG52603-C11
|
BIOUG74244-E05
|
BIOUG51557-D08
|
BIOUG73563-D07
|
BIOUG68420-H11
|
BIOUG68227-B03
|
BIOUG61701-G01
|
BIOUG70668-E03
|
BIOUG60534-C01
|
BIOUG52296-G02
|
BIOUG51520-E03
|
BIOUG74689-G08
|
BIOUG58615-C02
|
BIOUG53622-H09
|
BIOUG58344-C11
|
BIOUG55980-H01
|
BIOUG59522-C03
|
BIOUG54491-G06
|
BIOUG73912-D04
|
BIOUG52835-F10
|
BIOUG55899-G01
|
BIOUG55987-E07
|
BIOUG55982-B01
|
BIOUG74384-C01
|
BIOUG75045-A02
|
BIOUG55847-C12
|
BIOUG60706-E05
|
BIOUG55706-A09
|
BIOUG64783-H11
|
BIOUG66041-G06
|
BIOUG65683-C04
|
BIOUG53822-D02
|
BIOUG74559-A10
|
BIOUG72927-B12
|
BIOUG72929-H02
|
BIOUG63264-A04
|
BIOUG73288-G06
|
BIOUG73282-C10
|
BIOUG55473-B11
|
BIOUG65148-E03
|
BIOUG62579-H08
|
BIOUG68198-B12
|
BIOUG62567-A02
|
BIOUG61399-D10
|
BIOUG63236-H10
|
BIOUG62571-B04
|
BIOUG62876-C03
|
BIOUG61381-G09
|
BIOUG62898-C11
|
BIOUG61390-C07
|
BIOUG61390-E05
|
BIOUG73221-F10
|
BIOUG63233-C12
|
BIOUG62898-H02
|
BIOUG73263-F02
|
BIOUG73228-F08
|
BIOUG72198-B08
|
Processed datasets for CLIBD
In this data repo we provide the pre-processed data used in the paper CLIBD: Bridging Vision and Genomics for Biodiversity Monitoring at Scale You can find more information in our github repo.
Dataset Sources
The data we used to train and test our models include BIOSCAN-1M and BIOSCAN-5M. In addition, to perform Bayesian Zero Shot Learning, we also employed the INSECT dataset that was introduced in Fine-grained ZSL with DNA as Side Information.
Download the datasets
To clone the repo:
GIT_LFS_SKIP_SMUDGE=1 git clone https://huggingface.co/datasets/bioscan-ml/bioscan-clibd
For BIOSCAN-1M:
git lfs pull --include="data/BIOSCAN_1M/**"
python merge_bioscan_1m.py
For BIOSCAN-5M:
git lfs pull --include="data/BIOSCAN_5M/**"
python merge_bioscan_5m.py
For INSECT:
git lfs pull --include="data/INSECT/**"
Acknowledgement
We would like to express our gratitude for the use of the INSECT dataset, which played a pivotal role in the completion of our experiments. Additionally, we acknowledge the use and modification of code from the Fine-Grained-ZSL-with-DNA repository, which facilitated part of our experimental work. The contributions of these resources have been invaluable to our project, and we appreciate the efforts of all developers and researchers involved.
This reseach was supported by the Government of Canada’s New Frontiers in Research Fund (NFRF) [NFRFT-2020-00073], Canada CIFAR AI Chair grants, and the Pioneer Centre for AI (DNRF grant number P1). This research was also enabled in part by support provided by the Digital Research Alliance of Canada (alliancecan.ca).
For more information, please check our paper.
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