Datasets:

ConvergeBio
/

virtual-cell-distil-bulk-example

bulk_expression list	labels int64	disease_state string	sample_id string
[0.0008312466670759022,0.008546017110347748,0.0,0.0020751995034515858,0.0018328097648918629,0.0,0.0,(...TRUNCATED)	1	sepsis	GSM5609165
[0.0018098254222422838,0.003828034969046712,0.0,0.002353789284825325,0.001552218571305275,0.00007654(...TRUNCATED)	1	sepsis	GSM5609266
[0.0034428394865244627,0.014139292761683464,0.0,0.00343943084590137,0.0020261663012206554,0.00034971(...TRUNCATED)	1	sepsis	GSM5609201
[0.001046883873641491,0.008280489593744278,0.0,0.001307089813053608,0.0,0.0,0.0,0.059794832020998,0.(...TRUNCATED)	1	sepsis	GSM5609191
[0.0016603876138105989,0.00488848052918911,0.0,0.0022213011980056763,0.0013952187728136778,0.0,0.0,0(...TRUNCATED)	1	sepsis	GSM5609173
[0.005463247653096914,0.02212451957166195,0.0,0.019359510391950607,0.019371094182133675,0.0007933034(...TRUNCATED)	0	healthy	GSM5609233
[0.015997162088751793,0.019658982753753662,0.0,0.00696159340441227,0.008670472539961338,0.0003335491(...TRUNCATED)	0	healthy	GSM5609336
[0.00854081567376852,0.020223494619131088,0.0005706815281882882,0.02250368893146515,0.01331192348152(...TRUNCATED)	0	healthy	GSM5609226
[0.0037326558958739042,0.005132290534675121,0.0,0.007907582446932793,0.0025624746922403574,0.0,0.0,0(...TRUNCATED)	0	healthy	GSM5609335
[0.0,0.0,0.0,0.0013763968599960208,0.0048539903946220875,0.0,0.0,0.05359760671854019,0.0285006780177(...TRUNCATED)	1	sepsis	GSM5609144

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Virtual Cell — Distilled Bulk Encoder Example Dataset

A minimal sample dataset for verifying the data format and running quick end-to-end checks with ConvergeBio/virtual-cell-distil-bulk.

This dataset is not intended for training or evaluation. It contains a small number of samples and is not representative of a real distribution. Metrics produced from this dataset should not be interpreted.

Dataset contents

Derived from a public sepsis bulk RNA-seq study (GSE185263). Preprocessed into the model's input format as a minimal working example.

Split	Samples	Class distribution
train	88	53 sepsis / 35 healthy
validation	22	13 sepsis / 9 healthy

Labels: 0 = healthy, 1 = sepsis.

Loading

from datasets import load_dataset

ds = load_dataset("ConvergeBio/virtual-cell-distil-bulk-example")
train_ds = ds["train"]
val_ds   = ds["validation"]

Schema

Column	Shape	Type	Description
`bulk_expression`	[18301]	float32	Log-normalised bulk gene expression, aligned to `gene_names.txt`
`labels`	scalar	int	Class index (0 = healthy, 1 = sepsis)
`disease_state`	scalar	str	Original label string
`sample_id`	scalar	str	GEO sample accession ID

Citation

If you use this dataset, please cite the original study:

@article{baghela2022sepsis,
  author  = {Baghela, A. and others},
  title   = {Predicting sepsis severity at first clinical presentation: The role of endotypes and mechanistic signatures},
  journal = {EBioMedicine},
  year    = {2022},
  volume  = {75},
  pages   = {103776},
  doi     = {10.1016/j.ebiom.2021.103776},
  note    = {GEO accession: GSE185263},
}

If you use the Virtual Cell distilled bulk encoder, please also cite:

@article{convergecell2026,
  author = {ConvergeBio},
  title  = {ConvergeCELL: An end-to-end platform from patient transcriptomics to therapeutic hypotheses},
  year   = {2026},
  note   = {Preprint available on bioRxiv},
}

License

CC BY 4.0

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