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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 5 new columns ({'id', 'subtype', 'task_family', 'source', 'modality'}) and 2 missing columns ({'dataset_name', 'task_name'}).
This happened while the json dataset builder was generating data using
hf://datasets/dnagpt/omnigene4-mm-corpus/train.jsonl (at revision e4a1c28a84d3f7e30043a4b5961f4317d0039b94), [/tmp/hf-datasets-cache/medium/datasets/82903343129026-config-parquet-and-info-dnagpt-omnigene4-mm-corpu-d308b770/hub/datasets--dnagpt--omnigene4-mm-corpus/snapshots/e4a1c28a84d3f7e30043a4b5961f4317d0039b94/B_chebi20/train.json (origin=hf://datasets/dnagpt/omnigene4-mm-corpus@e4a1c28a84d3f7e30043a4b5961f4317d0039b94/B_chebi20/train.json), /tmp/hf-datasets-cache/medium/datasets/82903343129026-config-parquet-and-info-dnagpt-omnigene4-mm-corpu-d308b770/hub/datasets--dnagpt--omnigene4-mm-corpus/snapshots/e4a1c28a84d3f7e30043a4b5961f4317d0039b94/train.jsonl (origin=hf://datasets/dnagpt/omnigene4-mm-corpus@e4a1c28a84d3f7e30043a4b5961f4317d0039b94/train.jsonl)], ['hf://datasets/dnagpt/omnigene4-mm-corpus@e4a1c28a84d3f7e30043a4b5961f4317d0039b94/B_chebi20/train.json', 'hf://datasets/dnagpt/omnigene4-mm-corpus@e4a1c28a84d3f7e30043a4b5961f4317d0039b94/train.jsonl']
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/python3.12/site-packages/datasets/builder.py", line 1800, in _prepare_split_single
writer.write_table(table)
File "/usr/local/lib/python3.12/site-packages/datasets/arrow_writer.py", line 765, in write_table
self._write_table(pa_table, writer_batch_size=writer_batch_size)
File "/usr/local/lib/python3.12/site-packages/datasets/arrow_writer.py", line 773, in _write_table
pa_table = table_cast(pa_table, self._schema)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2321, in table_cast
return cast_table_to_schema(table, schema)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2249, in cast_table_to_schema
raise CastError(
datasets.table.CastError: Couldn't cast
id: string
modality: list<item: string>
child 0, item: string
images: list<item: string>
child 0, item: string
messages: list<item: struct<role: string, content: string>>
child 0, item: struct<role: string, content: string>
child 0, role: string
child 1, content: string
task_family: string
source: string
subtype: string
to
{'images': List(Value('string')), 'messages': List({'role': Value('string'), 'content': Value('string')}), 'task_name': Value('string'), 'dataset_name': Value('string')}
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 1348, in compute_config_parquet_and_info_response
parquet_operations = convert_to_parquet(builder)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 980, in convert_to_parquet
builder.download_and_prepare(
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 882, in download_and_prepare
self._download_and_prepare(
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 943, in _download_and_prepare
self._prepare_split(split_generator, **prepare_split_kwargs)
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1646, in _prepare_split
for job_id, done, content in self._prepare_split_single(
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1802, 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 5 new columns ({'id', 'subtype', 'task_family', 'source', 'modality'}) and 2 missing columns ({'dataset_name', 'task_name'}).
This happened while the json dataset builder was generating data using
hf://datasets/dnagpt/omnigene4-mm-corpus/train.jsonl (at revision e4a1c28a84d3f7e30043a4b5961f4317d0039b94), [/tmp/hf-datasets-cache/medium/datasets/82903343129026-config-parquet-and-info-dnagpt-omnigene4-mm-corpu-d308b770/hub/datasets--dnagpt--omnigene4-mm-corpus/snapshots/e4a1c28a84d3f7e30043a4b5961f4317d0039b94/B_chebi20/train.json (origin=hf://datasets/dnagpt/omnigene4-mm-corpus@e4a1c28a84d3f7e30043a4b5961f4317d0039b94/B_chebi20/train.json), /tmp/hf-datasets-cache/medium/datasets/82903343129026-config-parquet-and-info-dnagpt-omnigene4-mm-corpu-d308b770/hub/datasets--dnagpt--omnigene4-mm-corpus/snapshots/e4a1c28a84d3f7e30043a4b5961f4317d0039b94/train.jsonl (origin=hf://datasets/dnagpt/omnigene4-mm-corpus@e4a1c28a84d3f7e30043a4b5961f4317d0039b94/train.jsonl)], ['hf://datasets/dnagpt/omnigene4-mm-corpus@e4a1c28a84d3f7e30043a4b5961f4317d0039b94/B_chebi20/train.json', 'hf://datasets/dnagpt/omnigene4-mm-corpus@e4a1c28a84d3f7e30043a4b5961f4317d0039b94/train.jsonl']
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.
images list | messages list | task_name string | dataset_name string |
|---|---|---|---|
[
"imgs/train/000000.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (5Z,8Z,12E)-11-hydroxy-13-[(2R,3S)-3-pentyloxiran-2-yl]trideca-5,8,12-trienoate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000001.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is tellurium-125."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000002.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is [(5R,7R,8R,9R,10R,13S,17R)-17-(furan-3-yl)-4,4,8,10,13-pentamethyl-3-oxo-5,6,7,9,11,12,16,17-octahydrocyclopenta[a]phenanthren-7-yl] acetate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000003.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is 1-methyl-1-nitrosourea."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000004.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is 2-(1H-indol-3-yl)-1,3-thiazole."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000005.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is [(2R,3S,4R)-5-[(2-azaniumylacetyl)amino]-3,4-dihydroxyoxolan-2-yl]methyl phosphate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000006.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is [(2R,3S,4S,5S)-3,4,5,6-tetrahydroxyoxan-2-yl]methyl dihydrogen phosphate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000007.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (1S,8S,9R)-8-ethenyl-1,5-dihydroxy-4,9,10-trimethoxytricyclo[7.3.1.02,7]trideca-2,4,6,10-tetraen-12-one."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000008.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is docosan-1-ol."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000009.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is [(3S,4S,5R)-3,4-dihydroxy-2-(hydroxymethyl)-5-(phosphonooxymethyl)oxolan-2-yl] dihydrogen phosphate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000010.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl] [(3S,4S,5S,6R)-6-[(1R)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-2-yl] hydrogen ph... | trans_iupac | vis_chebi20 |
[
"imgs/train/000011.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is 6,7-dichlorodibenzofuran-1-ol."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000012.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is 2-(2-methylphenyl)acetonitrile."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000013.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (2R,3R)-2,3-dihydroxybutanedioic acid;[3-[(1S)-1-(dimethylamino)ethyl]phenyl] N-ethyl-N-methylcarbamate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000014.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is 2-(3,4-dihydroxyphenyl)-6-hydroxy-3,7-dimethoxy-4-oxochromen-5-olate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000015.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is [(2R,3S,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3-[[(2R,3S,5R)-3-[[(2R,3S,5R)-3-[[(2R,3S,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3-[[(2R,3S,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3-h... | trans_iupac | vis_chebi20 |
[
"imgs/train/000016.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is [(3S)-3,7-dimethyloct-7-enyl] 2-phenylacetate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000017.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is nickel(2+);dichloride;hexahydrate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000018.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is nonan-1-ol."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000019.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (2-ethoxy-3,3-dimethyl-2H-1-benzofuran-5-yl) methanesulfonate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000020.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is N,N-diethyl-3-(2,4,6-trimethylphenyl)sulfonyl-1,2,4-triazole-1-carboxamide."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000021.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (4Z,7Z,11E,13Z,16Z,19Z)-10-hydroperoxydocosa-4,7,11,13,16,19-hexaenoic acid."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000022.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is N-(1-methylpiperidin-4-yl)-N-phenylpropanamide."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000023.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is 2-hydroxybutanedioic acid."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000024.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (2S)-4-[[(2R,3R,4R,5S,6R)-3-acetamido-5-[(2S,3R,4R,5S,6R)-3-acetamido-5-[(2S,3S,4S,5R,6R)-6-[[(2S,3S,4S,5R,6R)-3,5-dihydroxy-4-[(2S,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydrox... | trans_iupac | vis_chebi20 |
[
"imgs/train/000025.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is [(1R,2R,4S,5S)-9-methyl-3-oxa-9-azatricyclo[3.3.1.02,4]nonan-7-yl] (2S)-3-hydroxy-2-phenylpropanoate;trihydrate;hydrobromide."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000026.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is [hydroxy(oxido)phosphoryl]formate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000027.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is N-phenylaniline."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000028.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is sodium;3-[[N-ethyl-4-[[4-[ethyl-[(3-sulfonatophenyl)methyl]azaniumylidene]cyclohexa-2,5-dien-1-ylidene]-phenylmethyl]anilino]methyl]benzenesulfonate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000029.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (3S,8S,9R,10R,11R,13R,14S,17R)-4,4,9,13,14-pentamethyl-17-[(2R)-6-methylhept-5-en-2-yl]-2,3,7,8,10,11,12,15,16,17-decahydro-1H-cyclopenta[a]phenanthrene-3,11-diol."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000030.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is [(3aR,4R,6R,6aR)-4-(2-amino-6-oxo-1H-purin-9-yl)-2-hydroxy-2-oxo-3a,4,6,6a-tetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-6-yl]methyl dihydrogen phosphate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000031.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is N-[(2S,3R,4R,5R,6R)-2-[(2R,3S,4R,5R)-5-acetamido-4-[(2S,3S,4R,5S,6S)-4,5-dihydroxy-6-methyl-3-[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxyoxan-2-yl]oxy-6-hydro... | trans_iupac | vis_chebi20 |
[
"imgs/train/000032.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is 2-methyl-5-prop-1-en-2-ylcyclohex-2-en-1-one."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000033.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is methyl (6aR,7S,10aR)-3,6a,7,10a,12-pentahydroxy-8-methoxy-1-methyl-6,10,11-trioxo-7H-tetracene-2-carboxylate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000034.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (2-hydroxy-3-octadecoxypropyl) 2-(trimethylazaniumyl)ethyl phosphate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000035.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is 3,5-dihydroxy-7-methoxy-2-(3,4,5-trihydroxyphenyl)chromen-4-one."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000036.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is [(2S,3S)-2,3,5-trihydroxy-4-oxopentyl] dihydrogen phosphate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000037.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (2S,3S,4S,5R,6R)-3,4,5-trihydroxy-6-[[(2R,3R,4S,5R,6R)-3,4,5,6-tetrahydroxyoxan-2-yl]methoxy]oxane-2-carboxylic acid."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000038.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-2-[[[[(3R)-4-[[3-[2-[5-[(2R,3R,5R,6S)-3,5-dihydroxy-6-methyloxan-2-yl]oxypentanoylsulfanyl]ethylamino]-3-oxopropyl]amino]-3-hydroxy-2,... | trans_iupac | vis_chebi20 |
[
"imgs/train/000039.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is methyl (1R,2S,9R,10S,11R,13R,15S)-9,15-dihydroxy-2,6,6,10,13,15-hexamethyl-17-methylidene-7,14,16-trioxotetracyclo[11.3.1.02,11.05,10]heptadec-4-ene-1-carboxylate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000040.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is [(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl] (E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enoate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000041.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (1S,2S,3S,4R,8R,9R,12S)-8-formyl-12-hydroxy-4-methyl-13-methylidenetetracyclo[10.2.1.01,9.03,8]pentadecane-2,4-dicarboxylic acid."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000042.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is N-[(2S,3R,4E,14Z)-1,3-dihydroxyoctadeca-4,14-dien-2-yl]icosanamide."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000043.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (2E,6E)-7-ethyl-9-[(2R,3S)-3-ethyl-3-methyloxiran-2-yl]-3-methylnona-2,6-dienoate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000044.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (2S,3S,4R,5R,7R)-7-[(3R,3aS,5aR,5bR,7aS,9S,11aS,11bR,13aR,13bS)-5a,5b,8,8,9,11a,13b-heptamethyl-1,2,3,3a,4,5,6,7,7a,9,10,11,11b,12,13,13a-hexadecahydrocyclopenta[a]chrysen... | trans_iupac | vis_chebi20 |
[
"imgs/train/000045.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is [(2R,5S,6R)-5-amino-6-methyloxan-2-yl] [hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000046.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is 2,8-bis(2,4-dihydroxy-6-methylphenyl)-7-hydroxy-1,9-dimethylphenoxazin-3-one."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000047.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is N,N-dimethyltrithian-5-amine."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000048.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (2S,3S,4S,5R,6R)-6-[(2R,3S,4R,5R,6S)-4,6-dihydroxy-5-(sulfoamino)-2-(sulfooxymethyl)oxan-3-yl]oxy-3,4-dihydroxy-5-sulfooxyoxane-2-carboxylic acid."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000049.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is 3-phenylpropyl acetate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000050.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (2R)-2-hydroxy-3-oxo-4-phosphonatooxybutanoate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000051.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (6Z,9Z,12Z,16E,18Z)-15-hydroxytetracosa-6,9,12,16,18-pentaenoic acid."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000052.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is [(2R)-2-hydroxy-3-phosphonooxypropyl] (9Z,12Z)-octadeca-9,12-dienoate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000053.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is decan-3-one."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000054.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is 2,3,6-trichlorobenzoic acid."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000055.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (2S)-1-[(2S,3R)-2-[[(2S)-2-[[(2S)-2-aminopropanoyl]amino]-4-methylpentanoyl]amino]-3-hydroxybutanoyl]pyrrolidine-2-carboxylic acid."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000056.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (1R,2R,4aS,6aR,6aS,6bR,8aR,10R,11R,12aR,14bS)-1,10,11-trihydroxy-9,9-bis(hydroxymethyl)-1,2,6a,6b,12a-pentamethyl-2,3,4,5,6,6a,7,8,8a,10,11,12,13,14b-tetradecahydropicene-... | trans_iupac | vis_chebi20 |
[
"imgs/train/000057.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (4S,5S)-4,5-dihydroxy-2-oxo-6-sulfohexanoic acid."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000058.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is [(2R,3R,4S)-2,3,4-trihydroxy-5-oxopentyl] dihydrogen phosphate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000059.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is [5-[(3E,5E,7E)-undeca-3,5,7-trienyl]furan-2-yl] hydrogen carbonate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000060.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is N-[(2S,3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-[(2R,3S,4R,5S,6R)-4,5,6-trihydroxy-2-(hydroxymethyl)oxan-3-yl]oxyoxan-3-yl]acetamide."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000061.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (2R)-2-[(3S)-4-[(4S,4aS,5R,7aS,8R,8aR)-4,8a-dihydroxy-2,2,5,8-tetramethyl-4a,5,6,7,7a,8-hexahydrocyclopenta[f][1]benzofuran-4-yl]-3-methyl-4-oxobutyl]-3-methyl-2H-furan-5-... | trans_iupac | vis_chebi20 |
[
"imgs/train/000062.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (2S)-2-hydroxyhexadecanoate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000063.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-hydroxyphosphoryl]oxy-2-hydroxy-3,3-dimethylbutan... | trans_iupac | vis_chebi20 |
[
"imgs/train/000064.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (6R,7S)-7-[[2-[(2S)-2-amino-2-carboxyethyl]sulfanylacetyl]amino]-7-methoxy-3-[(1-methyltetrazol-5-yl)sulfanylmethyl]-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic... | trans_iupac | vis_chebi20 |
[
"imgs/train/000065.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (2E,4E,6E,8E,10E,12E,14E,16E,18E,20E,22E)-2,6,10,15,19,23-hexamethyltetracosa-2,4,6,8,10,12,14,16,18,20,22-undecaenedioic acid."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000066.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is [(1S,4aR,11R,11aR,12S,12aR)-3-carbamoyl-4,4a,6,7,12-pentahydroxy-11-methyl-2,5-dioxo-11,11a,12,12a-tetrahydro-1H-tetracen-1-yl]-dimethylazanium;ethanol;dichloride;hydrate.... | trans_iupac | vis_chebi20 |
[
"imgs/train/000067.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is 5,7-dihydroxy-2-(4-hydroxy-3-methoxyphenyl)-6-methoxychromen-4-one."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000068.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (Z)-7-[(1R,4S,5R,6R)-6-[(E,3S)-3-hydroperoxyoct-1-enyl]-2,3-dioxabicyclo[2.2.1]heptan-5-yl]hept-5-enoic acid."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000069.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is [(1S,2S,6R,10S,11R,13S,14R,15R)-13-acetyloxy-1,6-dihydroxy-8-(hydroxymethyl)-4,12,12,15-tetramethyl-5-oxo-14-tetracyclo[8.5.0.02,6.011,13]pentadeca-3,8-dienyl] tetradecano... | trans_iupac | vis_chebi20 |
[
"imgs/train/000070.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (2S,6R)-6-[(3S,8S,9S,10R,13R,14S,17R)-3-hydroxy-10,13-dimethyl-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-17-yl]-2-methylheptanoate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000071.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (2S,5R,6R)-3,3-dimethyl-7-oxo-6-(2-phenoxypropanoylamino)-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000072.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (2S)-2-amino-5-[(N'-methylcarbamimidoyl)amino]pentanoic acid."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000073.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is methyl N-[2-[[1-(4-chlorophenyl)pyrazol-3-yl]oxymethyl]phenyl]-N-methoxycarbamate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000074.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is 2-[[(4R)-4-[(3R,5R,8R,9S,10S,13R,14S,17R)-10,13-dimethyl-3-sulfooxy-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-17-yl]pentanoyl]amino]etha... | trans_iupac | vis_chebi20 |
[
"imgs/train/000075.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is sodium;[(Z,1R)-1-carboxytricos-16-en-2-ynyl] sulfate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000076.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (4E,6E,8E,10E,12E)-8-methyl-13-phenyltrideca-4,6,8,10,12-pentaen-3-one."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000077.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (Z)-12,13-dihydroxyoctadec-9-enoate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000078.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is [(2R)-2-hydroxy-3-icosanoyloxypropyl] 2-(trimethylazaniumyl)ethyl phosphate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000079.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (13Z,16Z)-docosa-13,16-dienoate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000080.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is ethylazanium;nitrate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000081.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (2S)-2-[[2-(1H-indol-3-yl)acetyl]amino]propanoic acid."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000082.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-hydroxyphosphoryl]oxy-2-hydroxy-3,3-dimethylbutan... | trans_iupac | vis_chebi20 |
[
"imgs/train/000083.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is N-[(E,2S,3R)-1,3-dihydroxy-15-methylhexadec-4-en-2-yl]octadecanamide."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000084.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is disodium;[2,7-dibromo-9-(2-carboxylatophenyl)-3-oxido-6-oxoxanthen-4-yl]mercury;hydrate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000085.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoic acid."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000086.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (4aS,6aR,6aR,6bR,8aR,12aR,14aS)-2,2,6a,6b,9,9,12a-heptamethyl-10-oxo-4,5,6,6a,7,8,8a,11,12,13,14,14a-dodecahydro-3H-picene-4a-carboxylic acid."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000087.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is 5-hydroxy-3-(hydroxymethyl)-2-[3-hydroxy-4-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyphenyl]-7-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)o... | trans_iupac | vis_chebi20 |
[
"imgs/train/000088.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is [(2R)-3-hydroxy-2-[(5Z,8Z,11Z,13E,15S)-15-hydroxyicosa-5,8,11,13-tetraenoyl]oxypropyl] 2-(trimethylazaniumyl)ethyl phosphate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000089.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is [(2R,3S,4R,5R)-3,4,6-trihydroxy-5-[(2-hydroxyacetyl)amino]oxan-2-yl]methyl dihydrogen phosphate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000090.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is 3-[(7Z,10Z,13Z,16Z)-docosa-7,10,13,16-tetraenoyl]oxy-4-(trimethylazaniumyl)butanoate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000091.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is 4,5,6,7-tetrachloro-2-benzofuran-1,3-dione."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000092.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is [(2R,3S,4R,5R)-5-[2-(dimethylamino)-7-methyl-6-oxo-1H-purin-9-ium-9-yl]-3,4-dihydroxyoxolan-2-yl]methyl phosphate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000093.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is 4-[3-(4-carbamimidoylphenoxy)propoxy]benzenecarboximidamide;2-hydroxyethanesulfonic acid."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000094.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is [(1S,4R)-4-[2-amino-6-(cyclopropylamino)purin-9-yl]cyclopent-2-en-1-yl]methanol;sulfuric acid."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000095.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is [(2R)-3-icosanoyloxy-2-[(Z)-icos-11-enoyl]oxypropyl] 2-(trimethylazaniumyl)ethyl phosphate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000096.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is propyl acetate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000097.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is 2-hydroxy-3-methylpentanoate."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000098.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is 1-[4-[4-[[(2R,4R)-2-(2,4-dichlorophenyl)-2-(imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy]phenyl]piperazin-1-yl]ethanone."
}
] | trans_iupac | vis_chebi20 |
[
"imgs/train/000099.png"
] | [
{
"role": "user",
"content": "<image> What is the IUPAC of the molecule?"
},
{
"role": "assistant",
"content": "The IUPAC is (2S,4S,5R,6R)-5-acetamido-2-[(2S,3R,4R,5S,6R)-5-[(2S,3R,4R,5R,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-2-[(2R,3S,4R,5R,6R)-4,5-dihydroxy-2-(hydroxymeth... | trans_iupac | vis_chebi20 |
End of preview.
OmniGene-4-MM unified corpus
Multi-modal training corpus used for the OmniGene-4-MM Stages 1–3 (see https://github.com/maris205/omnigene4 ).
Each row is a JSON object with messages (chat-format), images
(list of relative image paths), and modality field. Vision rows
reference images that live in the source datasets:
- Vis-CheBI20 (PharMolix/Vis-CheBI20)
- PubMedVision (FreedomIntelligence/PubMedVision)
- HPA10M (Human Protein Atlas microscopy)
- ChartQA (HuggingFaceM4/ChartQA)
- Synthetic biomedical visual tasks (project-internal)
To reproduce the MM training, download the source vision datasets to
matching local paths and run omnigene5/scripts/02-fix_image_paths.py
to remap.
Files
| File | Rows | Notes |
|---|---|---|
train.jsonl |
~280K | Used by 30-train_omnigene5_stage1.py (vision warmup) and the mixed-stage pools downstream |
val.jsonl |
~5K | Held-out validation slice |
meta.json |
— | Per-modality counts and split sizes |
B_chebi20/train.json |
~26K | Vis-CheBI20 train split (project copy of PharMolix/Vis-CheBI20). Five OCSU subtasks: struct_recog, struct_cap, general_desp, trans_iupac, trans_smiles. |
B_chebi20/test.json |
~3K | Vis-CheBI20 test split, same five subtasks. Used by 60-eval_stage2.py, 91-eval_stage3v2.py, 92-eval_stage3v3.py, 95-qualitative_demo_stage3v3.py. |
Citation
@article{wang2026omnigene4,
author = {Wang, Liang},
title = {{OmniGene-4}: A Unified Bio-Language MoE Model with Router-Level
Interpretability and Modality-Invariant Transfer},
year = {2026},
journal = {bioRxiv},
doi = {10.64898/2026.05.12.724542}
}
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