Dataset Preview
The full dataset viewer is not available (click to read why). Only showing a preview of the rows.
The dataset generation failed
Error code: DatasetGenerationError
Exception: TypeError
Message: Couldn't cast array of type
list<item: float>
to
List(Value('float32'), length=512)
Traceback: Traceback (most recent call last):
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1835, in _prepare_split_single
for key, table in generator:
^^^^^^^^^
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 621, in wrapped
for item in generator(*args, **kwargs):
~~~~~~~~~^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/hdf5/hdf5.py", line 87, in _generate_tables
yield Key(file_idx, batch_idx), cast_table_to_features(pa_table, self.info.features)
~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2288, in cast_table_to_features
arrays = [cast_array_to_feature(table[name], feature) for name, feature in features.items()]
~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 1861, in wrapper
return pa.chunked_array([func(chunk, *args, **kwargs) for chunk in array.chunks])
~~~~^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2161, in cast_array_to_feature
raise TypeError(f"Couldn't cast array of type\n{_short_str(array.type)}\nto\n{_short_str(feature)}")
TypeError: Couldn't cast array of type
list<item: float>
to
List(Value('float32'), length=512)
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 1379, in compute_config_parquet_and_info_response
parquet_operations, partial, estimated_dataset_info = stream_convert_to_parquet(
~~~~~~~~~~~~~~~~~~~~~~~~~^
builder, max_dataset_size_bytes=max_dataset_size_bytes
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 956, in stream_convert_to_parquet
builder._prepare_split(split_generator=splits_generators[split], file_format="parquet")
~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1702, in _prepare_split
for job_id, done, content in self._prepare_split_single(
~~~~~~~~~~~~~~~~~~~~~~~~~~^
gen_kwargs=gen_kwargs, job_id=job_id, **_prepare_split_args
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
):
^
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1887, 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.
coords list | features list |
|---|---|
[
12288,
0
] | [
-1.7957572937011719,
-1.1298192739486694,
-0.9496534466743469,
0.5064949989318848,
-1.9565993547439575,
0.5782869458198547,
-1.225959062576294,
-0.24500437080860138,
-0.41007548570632935,
-0.8291162848472595,
-0.7516531348228455,
-0.36806318163871765,
-1.0723514556884766,
-0.01675172522664... |
[
16384,
0
] | [
-0.825245201587677,
0.23364925384521484,
-0.3390038311481476,
0.2653384506702423,
-1.3538603782653809,
1.2502763271331787,
-1.3676358461380005,
0.08866491913795471,
0.0064229522831737995,
-1.1220154762268066,
-0.9234479069709778,
0.7753769755363464,
-0.675548255443573,
0.7089462876319885,
... |
[
20480,
0
] | [
-0.5668936967849731,
0.6237985491752625,
-0.3623184859752655,
0.25803136825561523,
-0.8546729683876038,
1.7653834819793701,
-0.897735059261322,
0.26979756355285645,
0.10804586857557297,
-1.1224285364151,
-0.8107186555862427,
0.7942233085632324,
-0.9287029504776001,
0.7671709060668945,
-0... |
[
40960,
0
] | [
-0.4216807186603546,
-0.47302424907684326,
0.9095782041549683,
-1.2285054922103882,
-1.3089661598205566,
2.224189281463623,
-1.284989595413208,
0.9497670531272888,
-0.1659606695175171,
-0.2182064652442932,
-0.7735038995742798,
-0.33270779252052307,
-0.5872527360916138,
-0.01578717306256294... |
[
45056,
0
] | [
-0.3618960678577423,
0.1522626131772995,
0.7464112043380737,
-0.48924553394317627,
-0.9361655116081238,
2.547020673751831,
-1.71893310546875,
0.7778472900390625,
-0.5627492666244507,
-0.09892577677965164,
-1.1053049564361572,
0.08282597362995148,
-0.44122084975242615,
-0.20094142854213715,... |
[
8192,
4096
] | [
-1.106291651725769,
-0.9217320680618286,
-0.631232738494873,
-0.6085933446884155,
-1.9108679294586182,
1.0509169101715088,
-1.2565668821334839,
-0.19985632598400116,
-0.8925683498382568,
-1.2898991107940674,
-0.6985352635383606,
-0.14349839091300964,
-0.8928375244140625,
0.2150673866271972... |
[
12288,
4096
] | [
-0.5520032048225403,
0.4591599404811859,
0.7557553052902222,
0.747182309627533,
-0.5628012418746948,
1.5404720306396484,
-0.958993673324585,
0.34525391459465027,
0.024540899321436882,
-0.8319795727729797,
-0.4075532555580139,
0.4239293336868286,
-1.5382634401321411,
0.2626968324184418,
-... |
[
16384,
4096
] | [
-0.38798150420188904,
1.199819564819336,
1.2145167589187622,
0.7695538997650146,
0.03785739839076996,
1.743167519569397,
-0.5377309322357178,
0.4655909538269043,
-0.6230340600013733,
-1.6285823583602905,
0.07347451150417328,
0.1657762974500656,
-0.828430712223053,
0.13569943606853485,
0.... |
[
20480,
4096
] | [
-1.1615285873413086,
1.1505811214447021,
0.2761947810649872,
0.45918387174606323,
-0.41103172302246094,
1.7514151334762573,
-0.9212297201156616,
0.5736131072044373,
0.03685876727104187,
-1.3824039697647095,
-0.29975640773773193,
0.5644506216049194,
-0.9121404886245728,
0.22050020098686218,... |
[
24576,
4096
] | [
-1.1049611568450928,
0.47775399684906006,
-0.5357548594474792,
0.3389284908771515,
-1.0671778917312622,
1.2527021169662476,
-1.1959099769592285,
0.5713962316513062,
0.6881021857261658,
-1.5734859704971313,
-0.8771392107009888,
0.9501540064811707,
-0.7683668732643127,
0.30705857276916504,
... |
[
28672,
4096
] | [
-1.075869083404541,
-0.3135264217853546,
-0.441325306892395,
-0.36143961548805237,
-1.7410656213760376,
1.5485153198242188,
-0.861505389213562,
0.020187271758913994,
-0.6658623218536377,
-1.4845257997512817,
-0.722422182559967,
0.2689903974533081,
-0.10698817670345306,
0.23227138817310333,... |
[
40960,
4096
] | [
-0.07518282532691956,
0.626112699508667,
1.4714441299438477,
-2.0146777629852295,
-0.47388312220573425,
2.5829758644104004,
-0.2175826132297516,
1.203004002571106,
-0.6790719032287598,
-0.14282889664173126,
-1.064352035522461,
-0.37256407737731934,
-0.2251993864774704,
0.21129323542118073,... |
[
45056,
4096
] | [
-1.054665446281433,
-0.21559838950634003,
0.679152250289917,
-1.5050004720687866,
-0.5150777697563171,
2.2685654163360596,
-0.44136810302734375,
1.4196778535842896,
-0.8680979013442993,
0.11410179734230042,
-0.6922435164451599,
0.09398399293422699,
-0.4804758131504059,
0.2378671020269394,
... |
[
57344,
4096
] | [
1.1901925802230835,
-0.40366673469543457,
0.8878587484359741,
-0.8254520297050476,
-0.6824384927749634,
1.0284078121185303,
-0.7863653302192688,
-0.27764183282852173,
-0.7721377611160278,
-0.872539222240448,
-1.2662407159805298,
0.23605243861675262,
-1.129528284072876,
0.7953501343727112,
... |
[
61440,
4096
] | [
0.9411716461181641,
-0.6796289086341858,
0.10368836671113968,
-0.13024049997329712,
-0.5229958891868591,
0.9484580755233765,
-1.180833101272583,
-0.18426921963691711,
-2.115074872970581,
-1.0230494737625122,
-2.2658345699310303,
-0.8363968729972839,
-0.022977037355303764,
0.215541452169418... |
[
65536,
4096
] | [
0.49668237566947937,
-0.04739042744040489,
0.9852331280708313,
0.9738017320632935,
-0.6487253904342651,
0.4866473376750946,
-1.3885997533798218,
0.5924505591392517,
-0.8552286624908447,
-1.0867505073547363,
-1.3077583312988281,
-0.3850829303264618,
-0.2187052071094513,
-0.6892073750495911,... |
[
69632,
4096
] | [
-0.7005143761634827,
-0.15036381781101227,
0.8663103580474854,
0.3587208688259125,
-1.7674708366394043,
1.1697527170181274,
-2.212594509124756,
0.9178779125213623,
-0.12039157003164291,
-1.0324461460113525,
-0.8537718653678894,
0.24059616029262543,
-0.35108715295791626,
-0.6967915296554565... |
[
4096,
8192
] | [
0.08344361931085587,
0.07899317890405655,
-0.4164816737174988,
-0.22956418991088867,
-1.0714471340179443,
1.125874638557434,
-1.6902683973312378,
0.10467571020126343,
0.15676367282867432,
-1.01975679397583,
-0.8483220338821411,
0.23193661868572235,
-0.40562036633491516,
0.8328937888145447,... |
[
8192,
8192
] | [
-0.6875100135803223,
1.0146877765655518,
0.19552499055862427,
-0.012501008808612823,
-0.6509391069412231,
1.5142951011657715,
-0.5993813872337341,
0.8731749057769775,
0.11632666736841202,
-1.7335721254348755,
-0.5402262210845947,
0.31618836522102356,
-0.8754603862762451,
0.4030319154262543... |
End of preview.
WSI_Embedding
Patch and slide embeddings for whole-slide images, plus the run records used to produce them.
Original WSIs are not in this repo. They stay on HPC / the source dataset remotes. Do not expect .svs / .tif here.
Repo: thanminh01/WSI_Embedding
Top-level layout
| Path | What it is | Download when |
|---|---|---|
embeddings/<dataset>/<model>/<mag>x_<patch>px_<overlap>px_overlap/ |
Encoder tensors (.h5 / .pt / WSI-LLaVA json) and per-model TRIDENT _config_ / _logs_ |
You need features |
Run-Information/runs-report/<dataset>/ |
Job logs, VALIDATION, SLURM, perf, TRIDENT runs/*.json, cohort CSVs |
You need provenance |
Run-Information/prep/<dataset>/ |
Contours, geojson, thumbnails, wsi_states, patch-coord h5 (N,2), overlay jpgs |
You need QC / failed-mask / tiny-slide evidence |
Run-Information/parked/<dataset>/ |
Encoder files for slides excluded from the official cohort | You need the parked cases |
Selective download: pull only embeddings/DHMC-LUAD/titan/... or only Run-Information/prep/TCGA-LUAD.
Datasets
DHMC-LUAD (encoder cohort 143)
There are two HPC job directories. They are not duplicates of the same run:
| Hub name | HPC folder | Role |
|---|---|---|
DHMC-LUAD |
runs-information/full-int-DHMC-LUAD/ |
Canonical shared coords + later encoders (Virchow/PRISM/KEEP/MUSK/WSI-LLaVA/PRISM2, MUSK 1024-d redo) |
DHMC-LUAD-TITAN-CONCH |
runs-information/full-int-DHMC-LUAD (TITAN CONCH)/ |
First encoder pack: TITAN + CONCH v1.5 / v1 at 20×/512 |
Use DHMC-LUAD for current coords, masks, and later-model logs. Use DHMC-LUAD-TITAN-CONCH for the original TITAN/CONCH job (SLURM 15450381 / 15450382).
Kept encoders (see per-model folders under embeddings/DHMC-LUAD/): TITAN 768, CONCH v1.5 768, CONCH v1 512, Virchow 2560, PRISM 1280, Virchow2 2560, Virchow2 CLS 1280, PRISM2, KEEP 768, MUSK 1024-d vision CLS (ms_aug=False, no CLIP head in the stored tensor), WSI-LLaVA captions + case-bank. GigaPath tiles at 512 exist only as the WSI-LLaVA tile encoder, not as an official GigaPath product.
TCGA-LUAD (encoder cohort 531)
531 diagnostic slides after parking 10 TCGA-05 DX1 cases (tiny GDC canvas + failed tissue mask). Those 10 are not in embeddings/ tensors (except leftovers under parked/). Their wsi_states, thumbnails, contours, and coords are in Run-Information/prep/TCGA-LUAD/ so the failure stays inspectable.
Tensors for TCGA-LUAD may still be landing on HPC; this Run-Information tree is uploaded independently.
TCGA-LUSC
Not in this Run-Information snapshot: prep was still writing on the cluster at upload time. Encoder tensors are not published yet.
Canonical mag / patch
| Models | Setting |
|---|---|
| TITAN, CONCH v1.5, CONCH v1, WSI-LLaVA | 20× / 512 |
| PRISM, Virchow, Virchow2, Virchow2 CLS, PRISM2 | 20× / 224 |
| KEEP | 20× / 256 |
| MUSK | 20× / 384 |
How to download
# tensors only, one model
huggingface-cli download thanminh01/WSI_Embedding \
--repo-type dataset \
--include "embeddings/DHMC-LUAD/titan/**"
# QC / logs only
huggingface-cli download thanminh01/WSI_Embedding \
--repo-type dataset \
--include "Run-Information/**"
What is intentionally absent
- Original whole-slide images
- HPC
runs-information/full-int-*/features_*trees (those tensors live underembeddings/so they are not uploaded twice) TCGA-LUSCrun snapshot while segmentation/coords were still in flight
- Downloads last month
- 4,138