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The dataset generation failed
Error code: DatasetGenerationError
Exception: CastError
Message: Couldn't cast
input_ids: list<item: int32>
child 0, item: int32
cell_types: string
organ_major: string
disease: string
length: int64
-- schema metadata --
huggingface: '{"info": {"features": {"input_ids": {"feature": {"dtype": "' + 255
to
{'input_ids': Sequence(feature=Value(dtype='int32', id=None), length=-1, id=None), 'cell_type': Value(dtype='string', id=None), 'organ_major': Value(dtype='string', id=None), 'length': Value(dtype='int64', id=None)}
because column names don't match
Traceback: Traceback (most recent call last):
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1854, in _prepare_split_single
for _, table in generator:
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 689, in wrapped
for item in generator(*args, **kwargs):
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/packaged_modules/arrow/arrow.py", line 76, in _generate_tables
yield f"{file_idx}_{batch_idx}", self._cast_table(pa_table)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/packaged_modules/arrow/arrow.py", line 59, in _cast_table
pa_table = table_cast(pa_table, self.info.features.arrow_schema)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2292, in table_cast
return cast_table_to_schema(table, schema)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2240, in cast_table_to_schema
raise CastError(
datasets.table.CastError: Couldn't cast
input_ids: list<item: int32>
child 0, item: int32
cell_types: string
organ_major: string
disease: string
length: int64
-- schema metadata --
huggingface: '{"info": {"features": {"input_ids": {"feature": {"dtype": "' + 255
to
{'input_ids': Sequence(feature=Value(dtype='int32', id=None), length=-1, id=None), 'cell_type': Value(dtype='string', id=None), 'organ_major': Value(dtype='string', id=None), 'length': Value(dtype='int64', id=None)}
because column names don't match
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1415, 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 991, in stream_convert_to_parquet
builder._prepare_split(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1741, 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 1897, in _prepare_split_single
raise DatasetGenerationError("An error occurred while generating the dataset") from e
datasets.exceptions.DatasetGenerationError: An error occurred while generating the datasetNeed help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
input_ids sequence | cell_type string | organ_major string | length int64 |
|---|---|---|---|
[
674,
7620,
16415,
2535,
10606,
17530,
10606,
10606,
2034,
17490,
3992,
1269,
4591,
5729,
7979,
17352,
2877,
744,
5323,
7682,
12050,
1262,
8737,
21382,
12630,
3516,
31119,
1180,
14397,
2710,
15228,
15968,
17571,
4358,
5633,
15553,
10024,
17353... | mature NK T cell | EX_breast | 1,183 |
[
7941,
2535,
10606,
10606,
4591,
7126,
20574,
11118,
10086,
7979,
9089,
12510,
15438,
5139,
6995,
10127,
3254,
4329,
4267,
17743,
4671,
23034,
31334,
6937,
2088,
795,
5606,
5321,
1316,
9938,
16128,
12294,
12945,
9214,
7714,
21326,
17530,
16871... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 807 |
[
2535,
10606,
2354,
10606,
5927,
8402,
10606,
10786,
12268,
10866,
8479,
7118,
11898,
10631,
2034,
731,
621,
15672,
988,
7393,
35548,
17353,
6100,
12071,
4998,
16450,
1656,
6139,
5323,
2847,
11381,
19698,
1129,
20391,
6660,
6736,
2845,
19468,
... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,075 |
[
2535,
10606,
15826,
4591,
17843,
19212,
177,
7393,
7427,
17893,
895,
174,
1906,
7979,
523,
19380,
16993,
10606,
11826,
6198,
8464,
2152,
3505,
26823,
3516,
20551,
4017,
3542,
17604,
15281,
4795,
22460,
4415,
21547,
7283,
10184,
6937,
10322,
... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,176 |
[
7941,
2535,
10606,
3993,
11016,
7061,
22718,
10606,
5519,
9612,
21611,
5619,
6213,
9615,
11118,
7689,
22916,
14004,
9751,
8557,
7947,
16925,
56061,
4442,
7283,
17883,
10024,
284,
17163,
19219,
6923,
3091,
13064,
7718,
10606,
15400,
20929,
112... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 723 |
[
2535,
10606,
7538,
14881,
16628,
6919,
5850,
2865,
12075,
17622,
19667,
6762,
10211,
10439,
12544,
13547,
1863,
4225,
13719,
16708,
2920,
8091,
37126,
11434,
3929,
17556,
2126,
681,
870,
11353,
9233,
8057,
13436,
1857,
7449,
9501,
15554,
6198... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 821 |
[
7941,
2535,
10606,
10606,
10606,
8482,
7718,
2034,
17893,
5610,
23030,
19380,
174,
604,
2187,
5733,
9260,
1102,
2046,
5776,
12244,
9378,
2103,
6500,
1713,
19212,
1269,
17719,
16925,
6198,
17635,
17352,
1020,
9214,
7714,
13166,
13586,
1036,
... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 727 |
[
2535,
10606,
8599,
10606,
10674,
4591,
19380,
284,
2034,
10606,
7393,
11436,
9204,
10322,
19298,
16363,
7948,
3011,
7979,
7689,
1906,
4078,
537,
115,
3516,
2347,
7718,
3551,
9873,
948,
7889,
11260,
21003,
3909,
4267,
10351,
9417,
3542,
424,... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,338 |
[
2535,
10606,
2034,
8283,
4591,
3643,
10462,
284,
1675,
15376,
2961,
168,
11247,
1316,
174,
2935,
15100,
2034,
6477,
7663,
4441,
10606,
10606,
1255,
16363,
31707,
8836,
7653,
8640,
7393,
8775,
177,
303,
2431,
4925,
15546,
6937,
4472,
4998,
... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 890 |
[
7941,
2535,
14849,
10606,
10606,
10410,
1255,
2662,
3022,
10895,
14163,
9870,
3415,
9712,
11410,
4953,
10817,
15438,
10272,
3190,
22916,
11247,
5141,
8633,
3783,
22460,
20746,
2320,
3940,
17353,
3578,
43233,
26823,
9204,
10954,
7689,
12182,
2... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 593 |
[
2535,
10606,
5966,
5507,
7228,
15719,
2121,
10579,
15826,
8556,
9349,
7718,
3011,
8560,
9204,
7393,
13371,
15365,
5538,
3148,
1713,
7628,
3723,
21794,
7443,
15553,
9111,
2272,
4737,
423,
5070,
146,
19357,
4757,
4978,
5401,
11765,
8367,
7398... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 504 |
[
2535,
22916,
10606,
17353,
17490,
2002,
15826,
10285,
5045,
115,
3334,
4361,
2034,
17352,
1730,
9309,
177,
11826,
15554,
174,
10606,
10606,
4004,
1906,
10,
8675,
3072,
16450,
10444,
6837,
9199,
1707,
6726,
524,
12182,
2524,
12289,
4358,
113... | mature NK T cell | EX_breast | 894 |
[
2535,
10606,
88,
6079,
10810,
10024,
853,
730,
22624,
2900,
15715,
1122,
9751,
19649,
9233,
4875,
15734,
3371,
17490,
17353,
15049,
10355,
7863,
10606,
12568,
8560,
5790,
26823,
31905,
10362,
9897,
1906,
7443,
20565,
6667,
21320,
19265,
17430... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 527 |
[
2535,
10606,
12075,
80,
12449,
1255,
1642,
6430,
3405,
5323,
8505,
12553,
12796,
1507,
1570,
17126,
4247,
7131,
2730,
8524,
9186,
7420,
22916,
1059,
8633,
15734,
10407,
5433,
10579,
9214,
13002,
31707,
17465,
523,
17353,
10462,
8775,
17296,
... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 627 |
[
2535,
10606,
10606,
17353,
4878,
15438,
17490,
19813,
1831,
63,
5752,
373,
11438,
3471,
1253,
6529,
12,
2103,
2553,
1586,
2885,
1713,
22759,
7545,
6187,
30964,
2308,
80,
31610,
1730,
8150,
8775,
12459,
1893,
2222,
17296,
3755,
889,
11300,
... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 656 |
[
2535,
11438,
10606,
4591,
6426,
5592,
1906,
4045,
2236,
14524,
6704,
2533,
5216,
12675,
5727,
2552,
10451,
431,
567,
3351,
7718,
9204,
9955,
14019,
11118,
1558,
6274,
1713,
22916,
7327,
366,
6783,
55,
6690,
7972,
1554,
17918,
755,
12578,
... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 573 |
[
7941,
2535,
10606,
1255,
10606,
7393,
4591,
1713,
2002,
17755,
7085,
1906,
8874,
7682,
3402,
7420,
5589,
3316,
4267,
5572,
3658,
4078,
7440,
12182,
2552,
2951,
17490,
14918,
1176,
9966,
5509,
2034,
21047,
16128,
11725,
8212,
4757,
8587,
382... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 967 |
[
674,
7941,
2535,
17490,
10606,
22916,
2034,
1730,
10606,
15366,
6593,
443,
11350,
7787,
17125,
5586,
541,
1740,
20574,
7788,
11438,
4442,
1713,
8459,
17353,
16674,
8737,
9747,
10606,
7736,
4591,
6800,
3993,
11827,
21010,
2338,
10098,
3956,
... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,082 |
[
2535,
10606,
17353,
10606,
1133,
168,
17490,
36794,
16628,
22916,
2354,
10606,
1048,
316,
8560,
4505,
4561,
11866,
115,
10321,
2150,
3886,
4480,
8137,
20929,
3728,
7187,
7276,
5081,
2034,
20574,
17644,
15553,
2697,
6079,
1475,
3190,
2937,
1... | mature NK T cell | EX_breast | 833 |
[
674,
2535,
5509,
22916,
424,
2034,
11438,
17490,
10606,
15696,
11898,
8505,
13891,
3521,
11329,
1751,
9378,
16996,
11135,
88,
9593,
858,
636,
1570,
5765,
6616,
3487,
6402,
7237,
1139,
3520,
7788,
3316,
15311,
5700,
9111,
1316,
6877,
12246,
... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 777 |
[
2535,
10606,
17490,
2034,
3097,
10606,
15719,
13794,
17353,
10462,
10419,
22637,
1005,
6976,
14633,
18961,
4480,
1958,
4476,
10285,
10357,
6670,
15553,
4993,
9814,
22826,
12568,
5432,
11305,
1176,
3138,
3755,
7953,
2034,
20141,
10606,
853,
15... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 605 |
[
7941,
2535,
17353,
10606,
17490,
22916,
17158,
10606,
10606,
4267,
15438,
15243,
6079,
2002,
20574,
10462,
1713,
889,
1906,
2530,
9747,
5034,
5529,
21601,
15700,
8040,
22909,
12075,
14394,
19498,
7872,
2498,
6670,
56061,
13797,
10336,
15734,
... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,296 |
[
10606,
4078,
21794,
4475,
12568,
1906,
115,
14176,
10606,
10606,
2535,
3783,
21601,
7393,
798,
10124,
413,
4267,
7012,
2295,
5081,
3126,
4591,
10285,
9417,
54418,
7788,
8253,
15753,
5079,
6877,
10362,
15734,
15672,
1524,
16039,
9288,
17465,
... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 912 |
[
2535,
10606,
17353,
10606,
21601,
3032,
22916,
20117,
3589,
15453,
9889,
8040,
6079,
4879,
3399,
4567,
14500,
1568,
5058,
3689,
459,
2644,
7870,
11669,
7682,
2957,
1544,
8317,
6094,
4045,
16798,
9417,
1500,
4554,
20574,
1475,
6402,
51740,
1... | CD4-positive, alpha-beta T cell | EX_breast | 787 |
[
11146,
2535,
10606,
10606,
12153,
3001,
19212,
11118,
4591,
4358,
8933,
10024,
11216,
607,
1891,
8737,
7958,
1987,
2520,
10606,
16326,
1570,
15164,
4378,
21271,
4361,
1059,
7875,
3271,
7687,
43772,
2939,
7393,
8771,
15365,
12303,
19900,
6736,... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,680 |
[
2535,
10606,
2034,
14131,
10606,
5322,
11921,
2957,
12536,
16163,
7443,
6457,
16363,
621,
3284,
28222,
2162,
15890,
13586,
382,
9604,
2736,
7659,
1446,
10902,
3083,
19300,
10235,
18961,
10714,
2858,
3267,
6754,
9791,
5192,
2639,
1468,
4290,
... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,474 |
[
2535,
10606,
15735,
10606,
10786,
11118,
10606,
12318,
5358,
137,
5873,
6333,
2962,
16665,
243,
17743,
1813,
17147,
3241,
2922,
9992,
1059,
11921,
3643,
3507,
2939,
13586,
14230,
16674,
8826,
4272,
4391,
15811,
7443,
19219,
15909,
8357,
9111,... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,687 |
[
11146,
2535,
10606,
17743,
19668,
11118,
607,
10606,
10220,
17158,
15366,
3511,
4378,
11216,
382,
10582,
13371,
32071,
22916,
10606,
19782,
9025,
8357,
4491,
5820,
16629,
548,
3266,
12038,
3507,
9291,
12246,
9357,
3421,
1544,
2354,
3138,
3001... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,912 |
[
7941,
2535,
10606,
607,
15366,
2034,
10606,
10606,
10,
4591,
2034,
3001,
34995,
7714,
10658,
20777,
6298,
5784,
3017,
6280,
6333,
15049,
21310,
4078,
437,
19782,
17743,
15537,
2423,
12246,
12568,
10820,
8960,
7572,
9992,
3805,
15753,
9938,
... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,707 |
[
7941,
2535,
10606,
5727,
1987,
10606,
3849,
6402,
11932,
11438,
11001,
4154,
11469,
9788,
17346,
2034,
10786,
8556,
6903,
7393,
2575,
6237,
4658,
15966,
9214,
530,
15366,
1176,
16665,
16741,
5322,
9349,
20088,
15400,
11118,
17988,
519,
8212,
... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,625 |
[
11146,
2535,
10606,
2020,
15553,
3001,
8286,
15826,
607,
13586,
9992,
10606,
17604,
4824,
6903,
1906,
8038,
10024,
14230,
7393,
3946,
2347,
6593,
16186,
137,
976,
14475,
10606,
2092,
8111,
11609,
6237,
15221,
1585,
2034,
19380,
11921,
34995,
... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,699 |
[
2535,
10606,
10606,
607,
174,
4987,
5321,
17743,
6278,
2374,
32071,
14655,
3180,
137,
15164,
7159,
8357,
11118,
2162,
11001,
115,
11004,
537,
10,
363,
2347,
177,
5578,
9660,
7229,
15909,
17158,
11826,
21601,
6903,
499,
4930,
637,
33210,
1... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,557 |
[
2535,
10606,
2034,
10606,
10606,
10024,
10171,
4358,
15553,
3001,
9214,
11001,
8057,
10786,
12246,
2180,
3643,
2877,
11469,
8038,
9254,
5322,
4591,
2236,
11436,
15909,
15228,
11707,
137,
6229,
607,
1897,
17462,
11836,
17987,
32071,
1773,
4272... | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,666 |
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Mouse-Genecorpus-20M
Write: Keita Ito
Abstract
This repository contains the datasets of mouse-Genecorpus-20M and evaluation datasets to analysis. Mouse-Genecorpus-20M is large-scale pretraining corpus comprised of ~21 million mosue single cell transcriptomes from a broad range of tissues from publicly available data. This corpus is used for pretraining mouse-Geneformer, a pretrained transformer model that enables context-aware predictions in settings with limited data in network biology.
[bioRxiv]
Citation
If you find this repository is useful. Please cite the following references.
@article{Ito2024.09.09.611960,
author = {Ito, Keita and Hirakawa, Tsubasa and Shigenobu, Shuji and Fujiyoshi, Hironobu and Yamashita, Takayoshi},
title = {Mouse-Geneformer: A Deep Leaning Model for Mouse Single-Cell Transcriptome and Its Cross-Species Utility},
journal = {bioRxiv},
year = {2024},
URL = {https://www.biorxiv.org/content/early/2024/09/13/2024.09.09.611960}
}
How to use
You need to download datasets on your disk you want to use. After doing, you program in python as follow to use its :
from datasets inport load_from_disk
dataset = load_from_disk("/path/to/mouse-Genecorpus-20M/MLM-re_All_mouse_tokenize_dataset.dataset/")
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