input_ids listlengths 2 4.1k | cell_index int64 0 4.14M | length int64 2 4.1k | species stringclasses 1
value | source_id int32 1 2.75k |
|---|---|---|---|---|
[
2,
22245,
15941,
17488,
19409,
10196,
8853,
1711,
12537,
19621,
332,
8864,
93,
7596,
12468,
8582,
76,
11281,
50,
5399,
5565,
3498,
343,
515,
14566,
14365,
17813,
1392,
6678,
6230,
2344,
6793,
6281,
4590,
20138,
420,
3715,
1069,
2555,
3647... | 154,328 | 92 | hsapiens | 389 |
[
2,
202,
7618,
16484,
16151,
17129,
7366,
16337,
701,
3165,
2512,
18625,
9502,
15048,
9328,
18105,
375,
3379,
12665,
6818,
6369,
10004,
5071,
457,
14030,
14223,
950,
504,
8939,
9555,
2638,
16621,
6919,
823,
5898,
12976,
15523,
4425,
4472,
... | 26,422 | 1,969 | hsapiens | 1,169 |
[
2,
8493,
14231,
1077,
12936,
9007,
11110,
280,
11201,
7868,
9261,
9033,
7686,
16504,
15678,
3255,
10022,
379,
4675,
1917,
9889,
14588,
9256,
13170,
9009,
845,
4454,
10001,
16975,
9465,
8742,
551,
14123,
16425,
7973,
6668,
11235,
4387,
316,
... | 12,471 | 1,875 | hsapiens | 1,633 |
[
2,
9548,
12233,
11776,
5127,
1369,
4485,
763,
19709,
4631,
8399,
1882,
13289,
4566,
15042,
5279,
292,
8266,
3954,
991,
1920,
16945,
1267,
14476,
6282,
5042,
11279,
2350,
1472,
3199,
7615,
9151,
2354,
14635,
7203,
7656,
1132,
3909,
3694,
1... | 199,184 | 53 | hsapiens | 1,109 |
[
2,
6412,
13606,
9545,
15373,
1416,
8489,
4156,
650,
9602,
14821,
9465,
16114,
15663,
3974,
9964,
15050,
12237,
10057,
13026,
9290,
3993,
10280,
14964,
9604,
11279,
9932,
12214,
12873,
9201,
15708,
7030,
11407,
1016,
11339,
16537,
1714,
410,
... | 117,813 | 4,096 | hsapiens | 614 |
[
2,
212,
3
] | 45,373 | 3 | hsapiens | 1,256 |
[
2,
7384,
5538,
11097,
16288,
573,
2624,
18011,
1920,
5097,
9596,
16719,
16690,
7343,
3790,
3012,
10698,
6016,
8939,
8434,
609,
2037,
15317,
6350,
8289,
8547,
10154,
9362,
14625,
807,
15124,
15693,
10804,
4130,
14104,
15276,
8576,
8256,
2296... | 182,430 | 2,490 | hsapiens | 1,868 |
[
2,
3974,
14967,
15373,
1416,
2641,
14821,
13016,
16699,
7656,
15140,
410,
8839,
5968,
9604,
2685,
20438,
9040,
13425,
15371,
9964,
4005,
12465,
16826,
11821,
5467,
1137,
623,
10855,
7468,
6748,
1175,
8671,
15329,
14799,
15220,
7154,
13426,
... | 3,053 | 4,096 | hsapiens | 475 |
[
2,
8151,
17978,
13372,
5505,
15340,
16963,
2772,
3641,
8521,
9384,
9855,
12333,
19253,
7228,
5187,
14771,
1755,
13037,
5217,
8854,
8172,
16583,
6593,
12432,
11731,
18467,
14005,
16278,
7551,
15534,
13386,
12926,
16561,
16646,
14319,
3256,
861... | 1,385,691 | 846 | hsapiens | 302 |
[
2,
4586,
9233,
11237,
3465,
4829,
16936,
3755,
2499,
18963,
16561,
5834,
2765,
8291,
7918,
6231,
7664,
7177,
10900,
295,
12962,
2216,
11372,
18354,
12189,
445,
2428,
7578,
1513,
9432,
335,
1142,
6383,
5273,
6255,
2293,
2580,
12691,
4263,
... | 29,315 | 484 | hsapiens | 1,193 |
[
2,
17761,
5183,
5617,
9855,
16583,
14005,
11213,
8151,
4013,
18790,
8599,
8854,
3468,
11919,
8506,
8395,
5426,
20124,
3769,
329,
14024,
2917,
3500,
1512,
15534,
1604,
853,
7097,
3481,
892,
3028,
11915,
4887,
11166,
4254,
6807,
14706,
13950,... | 2,585,486 | 1,263 | hsapiens | 718 |
[
2,
11924,
11217,
19836,
13004,
7345,
12873,
7351,
2905,
6399,
9655,
1375,
5674,
9622,
17697,
16834,
9084,
13810,
5523,
16082,
4711,
13539,
11725,
6902,
11184,
1648,
12965,
14729,
11764,
2658,
2565,
17782,
12510,
4448,
5814,
777,
5980,
13068,
... | 1,183,146 | 4,096 | hsapiens | 898 |
[
2,
12808,
15695,
11241,
3532,
3247,
20172,
4277,
15688,
4027,
5068,
13548,
14462,
1272,
12800,
12053,
13654,
16132,
2861,
1617,
5474,
15061,
4243,
16160,
14449,
12799,
8420,
9005,
15342,
3378,
17403,
12648,
12123,
13671,
3116,
3949,
6404,
705... | 166,610 | 1,181 | hsapiens | 1,303 |
[
2,
10911,
4744,
1515,
20107,
10138,
16289,
5556,
8561,
3348,
6672,
11493,
3596,
1183,
5991,
1037,
17378,
6154,
6714,
19277,
262,
13981,
9749,
15569,
13889,
6124,
6463,
16468,
12939,
7805,
16466,
14910,
6332,
2002,
19634,
3709,
12794,
6936,
... | 559,461 | 2,090 | hsapiens | 1,148 |
[
2,
9426,
104,
5607,
9860,
1813,
7451,
1109,
4008,
8854,
4369,
3434,
11915,
13418,
16583,
2094,
4013,
513,
11812,
18630,
6282,
9075,
5177,
12063,
832,
6630,
9066,
15801,
17671,
16013,
9855,
11221,
7287,
11192,
14629,
16324,
18467,
1827,
1104... | 70,881 | 1,993 | hsapiens | 2,650 |
[
2,
9394,
9083,
6858,
7868,
17761,
13537,
2877,
14005,
4052,
463,
5827,
2426,
5052,
6282,
2041,
2549,
7639,
18191,
11831,
16919,
6710,
13852,
3288,
4977,
8855,
9164,
7232,
9609,
5726,
9438,
2550,
5266,
3311,
476,
1669,
12921,
9972,
3672,
1... | 71,446 | 2,865 | hsapiens | 1,585 |
[
2,
11924,
11184,
11217,
21878,
9545,
2905,
19836,
4088,
14427,
13820,
15949,
7361,
6399,
13810,
18011,
1204,
7252,
15678,
4834,
13155,
14239,
2430,
15025,
2494,
9201,
3569,
10595,
733,
12965,
12698,
1017,
13249,
14041,
12728,
648,
5126,
7345,... | 133,668 | 2,823 | hsapiens | 2,228 |
[
2,
13952,
17671,
17356,
11731,
13567,
11187,
7690,
5629,
12779,
17209,
19269,
3296,
14896,
2169,
12755,
19276,
3967,
1813,
1372,
2392,
10863,
6493,
4013,
718,
5291,
777,
3703,
10647,
7660,
18856,
12052,
16011,
12574,
8567,
8721,
13294,
7188,
... | 156,303 | 1,110 | hsapiens | 824 |
[
2,
12704,
6349,
12465,
1391,
16975,
12449,
8718,
16448,
2562,
16952,
7419,
13546,
8307,
15208,
7780,
5787,
17118,
16851,
16946,
6724,
17977,
16859,
15314,
187,
4384,
13577,
767,
8366,
629,
10652,
5795,
3701,
4846,
8845,
11432,
7625,
7474,
1... | 173,167 | 2,097 | hsapiens | 1,733 |
[
2,
16583,
14005,
6575,
8721,
8755,
5919,
4231,
7808,
8506,
4055,
2925,
9855,
14185,
12687,
3462,
3481,
6384,
11496,
1126,
9164,
16196,
8854,
6807,
12317,
2058,
2550,
4174,
5431,
4413,
627,
2654,
6207,
7060,
2377,
17417,
4748,
13326,
7109,
... | 35,193 | 983 | hsapiens | 1,984 |
[
2,
8127,
7177,
16919,
5207,
1652,
15307,
11057,
14857,
1471,
8085,
13093,
17436,
5919,
1567,
2459,
3967,
2003,
3459,
1991,
16322,
16507,
2012,
3530,
9758,
7041,
5998,
3155,
5309,
5230,
2687,
15431,
1320,
7788,
13814,
9761,
3973,
10458,
1623... | 475,814 | 335 | hsapiens | 1,259 |
End of preview. Expand in Data Studio
CellxGene + scBaseCount, human, tokenized
Geneformer-style rank-value tokenized human cells: a straightforward union of two existing
public corpora, CellxGene Discover (cxg_raw_2025-11-08) and scBaseCount (2025-02-25),
deduplicated (CellxGene's own is_primary_data flag, to drop repeated cells across dataset
views) and tokenized. 211,221,738 cells. This is not an original data-collection effort --
all underlying cells were already public via CellxGene Discover and scBaseCount; this repo
is just that union in a ready-to-train tokenized form.
2026-10-19 update: rows are now globally shuffled (previously contiguous by source study
-- a streaming data loader without its own shuffle would see batches, and a leading-rows
validation split, dominated by whichever study happened to be first), and 6 genes whose
corpus median was exactly 0 have been dropped from every cell's token list (count / median = inf was forcing them to a spurious rank-1 position in ~1.8% of cells). Cell count and the
rest of each cell's ranking are unaffected.
Contents
- Repo root -- a HuggingFace
datasetsDatasetDict(singletrainsplit) saved viasave_to_disk(dataset_dict.json,train/). Columns:input_ids(large_list, Geneformer-style rank-value encoding,<cls>-prefixed, truncated to 4096 tokens),cell_index,length,species(always"hsapiens"here). vocab/hsapiens_token_dictionary.pkl-- the exact vocab these ids were tokenized against (23,260 genes + special tokens:<pad>=0, <mask>=1, <cls>=2, <eos>=3, genes 4..-- 6 fewer than the original 23,266-gene vocab, the zero-median genes above). This is not the same as the default packagedtoken_dictionary.pkl(~20k genes) -- loading with the wrong vocab silently misaligns gene ids.vocab/hsapiens_gene_medians.pkl-- non-zero median gene expression values used by the tokenizer's normalization step, computed from this same corpus/vocab.
Loading
from huggingface_hub import snapshot_download
from datasets import load_from_disk
local_dir = snapshot_download(repo_id="theislab/cellxgene-scbasecount-human-tokenized", repo_type="dataset")
ds = load_from_disk(local_dir)["train"]
- Downloads last month
- 382