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Datasets:
MPRG
/
Mouse-Genecorpus-20M

Size:
10M<n<100M
Tags:
biology
License:
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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 1997, in _prepare_split_single
                  for _, table in generator:
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 688, 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 67, 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 55, 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 2302, in table_cast
                  return cast_table_to_schema(table, schema)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2256, 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 1391, 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 990, in stream_convert_to_parquet
                  builder._prepare_split(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1884, 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 2040, in _prepare_split_single
                  raise DatasetGenerationError("An error occurred while generating the dataset") from e
              datasets.exceptions.DatasetGenerationError: An error occurred while generating the dataset

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input_ids
sequence
cell_type
string
organ_major
string
length
int64
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mature NK T cell
EX_breast
1,183
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effector memory CD8-positive, alpha-beta T cell
EX_breast
807
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effector memory CD8-positive, alpha-beta T cell
EX_breast
1,075
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effector memory CD8-positive, alpha-beta T cell
EX_breast
1,176
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effector memory CD8-positive, alpha-beta T cell
EX_breast
723
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effector memory CD8-positive, alpha-beta T cell
EX_breast
821
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effector memory CD8-positive, alpha-beta T cell
EX_breast
727
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effector memory CD8-positive, alpha-beta T cell
EX_breast
1,338
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effector memory CD8-positive, alpha-beta T cell
EX_breast
890
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effector memory CD8-positive, alpha-beta T cell
EX_breast
593
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effector memory CD8-positive, alpha-beta T cell
EX_breast
504
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6724, 5751, 6139, 8358, 6325, 17612, 22739, 15349, 2905, 6033, 1167, 686, 1489, 2063, 4942, 5289, 11844, 1556, 3039, 9854, 9416, 2414, 3228, 2739, 7838, 10477, 15606, 1455, 7007, 14484, 12432, 5940, 10929, 6665, 5827, 22416, 2175, 2422, 11747, 13414, 7580, 17162, 4504, 13939, 8600, 10434, 19408, 2157, 16568, 4678, 2994, 11645, 10328, 3237, 8357, 7564, 1362, 5880, 4524, 2030, 12251, 13340, 947, 34065, 973, 11660, 5524, 9539, 9976, 16603, 5058, 13808, 3574, 8424, 2737, 5934, 14871, 318, 2239, 8062, 1389, 17936, 6381, 15570, 9715, 17482, 6821, 619, 1535, 16809, 12714, 925, 17098, 6941, 7039, 7256, 7786, 31133, 6130, 20283, 4775, 8579, 1591, 5582, 9745, 1098, 19300, 6693, 2310, 17308, 21359, 8161, 12365, 15551, 20005, 12672, 1788, 16913, 8896, 2874, 87, 11172, 12868, 9873, 16567, 14998, 8747, 14840, 9712, 7202, 6604, 186, 8003, 8227, 2719, 47359, 1170, 5780, 12268, 448, 3394, 866, 11228, 4468, 4248, 4515, 8091, 6728, 7203, 12789, 5244, 1657, 4375, 15704, 8818, 3379, 7042, 20498, 9634, 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mature NK T cell
EX_breast
894
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effector memory CD8-positive, alpha-beta T cell
EX_breast
527
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effector memory CD8-positive, alpha-beta T cell
EX_breast
627
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effector memory CD8-positive, alpha-beta T cell
EX_breast
656
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effector memory CD8-positive, alpha-beta T cell
EX_breast
573
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8959, 1802, 17975, 17397, 20088, 17987, 13940, 5288, 215, 19200, 12945, 14556, 17978, 1413, 9022, 654, 17007, 7414 ]
effector memory CD8-positive, alpha-beta T cell
EX_breast
967
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effector memory CD8-positive, alpha-beta T cell
EX_breast
1,082
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mature NK T cell
EX_breast
833
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effector memory CD8-positive, alpha-beta T cell
EX_breast
777
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effector memory CD8-positive, alpha-beta T cell
EX_breast
605
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19841, 8737, 3516, 31707, 9564, 4272, 1741, 8775, 1866, 3001, 9759, 1857, 9788, 1897, 2180, 10, 1632, 791, 5439, 12428, 15301, 2034, 7720, 32071, 17987, 5526 ]
effector memory CD8-positive, alpha-beta T cell
EX_breast
1,296
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effector memory CD8-positive, alpha-beta T cell
EX_breast
912
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5721, 17255 ]
CD4-positive, alpha-beta T cell
EX_breast
787
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effector memory CD8-positive, alpha-beta T cell
EX_breast
1,680
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effector memory CD8-positive, alpha-beta T cell
EX_breast
1,474
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effector memory CD8-positive, alpha-beta T cell
EX_breast
1,687
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633, 4791, 8093, 3575, 8882, 5106, 1121, 1905, 15272, 7914, 4501, 8956, 7367, 1830, 304, 8243, 11361, 16135, 16123, 8884, 4616, 7350, 5925, 4114, 9891, 1261, 2613, 13746, 4811, 6954, 1656, 6972, 1446, 4820, 6578, 16251, 6007, 17074, 17656, 506, 16479, 7498, 11721, 19953, 3176, 5199, 12539, 17788, 12505, 14686, 5706, 18981, 2547, 1637, 11751, 10445, 3398, 4892, 4618, 4604, 3225, 7180, 8105, 17835, 1841, 8596, 10905, 6216, 8937, 11013, 9343, 2898, 4707, 10222, 6474, 8280, 11698, 20078, 8717, 3419, 2361, 11697, 12784, 8320, 4194, 16141, 4384, 5003, 2469, 3641, 1894, 11127, 5751, 14209, 197, 6325, 9318, 1114, 10549, 7672, 3744, 10902, 10915, 2698, 2905, 317, 10602, 3210, 11874, 7579, 1489, 6506, 12616, 2855, 9906, 4704, 17880, 5359, 19355, 8095, 10859, 18954, 10343, 9090, 1005, 1350, 6275, 13535, 7387, 4175, 1455, 22726, 6765, 3498, 17330, 254, 10177, 454, 10337, 9365, 2145, 2871, 3953, 6248, 4326, 3430, 2144, 19292, 5711, 438, 20148, 1691, 10551, 9989, 5427, 19903, 8316, 5094, 22525, 6102, 16333, 10678, 16684, 4702, 3971, 3657, 2450, 3324, 9460, 3936, 3427, 10434, 1992, 2731, 10210, 5110, 9013, 572, 4678, 8652, 8570, 22804, 2110, 63, 12448, 11458, 11358, 804, 11743, 10211, 4652, 11341, 10822, 17725, 19623, 9652, 3272, 15449, 4445, 12682, 2904, 4374, 15393, 1199, 5363, 920, 6889, 223, 9521, 14603, 15229, 378, 7157, 288, 2927, 7021, 15981, 2562, 947, 653, 8803, 2867, 2954, 6947, 5524, 4981, 6408, 20992, 6916, 14527, 1737, 7182, 13663, 11819, 8204, 6158, 12002, 8982, 981, 9581, 7424, 14285, 4565, 116, 10913, 19415, 10093, 1087, 5507, 17936, 11381, 35344, 2426, 4002, 10346, 17482, 5099, 10668, 7264, 12453, 3278, 17817, 32344, 5326, 1910, 10248, 590, 10745, 12494, 6076, 19307, 10651, 17563, 730, 4275, 6426, 930, 509, 7310, 12544, 8311, 10078, 3221, 10513, 12628, 7210, 12589, 3320, 6593, 8977, 8218, 8676, 12059, 12084, 9260, 132, 12501, 6666, 10377, 8734, 19300, 577, 3726, 2310, 4051, 373, 14071, 990, 21359, 746, 2747, 15551, 12650, 8605, 17137, 8161, 16851, 20833, 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17689, 3589, 802, 34614, 6079, 21601, 2642, 6352, 2104, 791, 5509, 2034, 2298, 8959 ]
effector memory CD8-positive, alpha-beta T cell
EX_breast
1,912
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1127, 31161, 2865, 5322, 6340, 8294, 5898, 10580, 13293, 33210, 6300, 17147, 8149, 15700, 11412, 2298, 3699, 17988, 1891, 6847, 20126, 11436, 6849, 12075, 5350, 12016, 16629, 31777, 14079, 31250, 14079, 12050, 3399, 17255, 3230, 14785, 1484, 15966, 9146, 6365, 1332, 11469, 6774, 14310, 1086, 2935, 1558, 6274, 17475, 9897, 382, 3075, 16993, 12303, 17571, 4021, 15750, 20029, 359, 4778, 3955, 1544, 22916, 7302, 4612, 7327, 6323, 15810, 5610, 11668, 15731, 15553, 5578, 31640, 8310, 16278, 6198, 15273, 20565, 4475, 3180, 4004, 2231, 5355, 12153, 6397, 6475, 5680, 2710, 12679, 8556, 451, 8419, 11831, 13697, 5790, 17111, 7682, 6819, 6990, 12388, 9564, 4272, 15909, 12318, 15643, 6381, 3589, 802, 4899, 1413, 8590, 8408, 2642, 791, 7905, 12428, 13257, 4206, 8959, 17149, 14630, 20088, 5288, 17848 ]
effector memory CD8-positive, alpha-beta T cell
EX_breast
1,707
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effector memory CD8-positive, alpha-beta T cell
EX_breast
1,625
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effector memory CD8-positive, alpha-beta T cell
EX_breast
1,699
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effector memory CD8-positive, alpha-beta T cell
EX_breast
1,557
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effector memory CD8-positive, alpha-beta T cell
EX_breast
1,666
End of preview.

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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