Harmonised single-cell and spatial foundation model benchmark (Chen et al. 2026)
Harmonised evaluation of six single-cell and spatial foundation models (Nicheformer, CellPLM, scGPT-spatial, GenePT-w, scELMo, Novae) on zero-shot and continually pretrained clustering, supervised cell type annotation, marker-gene concordance and perturbation prediction.
Results are recorded on the linked protocols, tasks or configurations listed below. Their settings and evaluations are kept separate.
Overview
An explanatory profile has not yet been reviewed for this record.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Results on linked records
This benchmark has no results of its own in this release. 25 linked records have results. They are not assigned to the underlying benchmark: each record keeps its own settings and evaluations, and its scores are on its own page.
- Chen et al. 2026 supervised cell type annotation, ATAA Protocol · part of this benchmark · 5 evaluations · 30 results
- Chen et al. 2026 supervised cell type annotation, BMMC Protocol · part of this benchmark · 5 evaluations · 30 results
- Chen et al. 2026 supervised cell type annotation, HS Protocol · part of this benchmark · 5 evaluations · 30 results
- Chen et al. 2026 supervised cell type annotation, SEAAD Protocol · part of this benchmark · 6 evaluations · 36 results
- Chen et al. 2026 continually pretrained clustering, ATAA Protocol · part of this benchmark · 3 evaluations · 9 results
- Chen et al. 2026 continually pretrained clustering, BC Protocol · part of this benchmark · 4 evaluations · 12 results
- Chen et al. 2026 continually pretrained clustering, BMMC Protocol · part of this benchmark · 3 evaluations · 9 results
- Chen et al. 2026 continually pretrained clustering, HS Protocol · part of this benchmark · 3 evaluations · 9 results
- Chen et al. 2026 continually pretrained clustering, ME Protocol · part of this benchmark · 4 evaluations · 12 results
- Chen et al. 2026 continually pretrained clustering, MH Protocol · part of this benchmark · 4 evaluations · 12 results
- Chen et al. 2026 zero-shot clustering with k-means, ATAA Protocol · part of this benchmark · 1 evaluation · 3 results
- Chen et al. 2026 zero-shot clustering with k-means, BC Protocol · part of this benchmark · 1 evaluation · 3 results
- Chen et al. 2026 zero-shot clustering with k-means, BMMC Protocol · part of this benchmark · 1 evaluation · 3 results
- Chen et al. 2026 zero-shot clustering with k-means, HS Protocol · part of this benchmark · 1 evaluation · 3 results
- Chen et al. 2026 zero-shot clustering with k-means, ME Protocol · part of this benchmark · 1 evaluation · 3 results
- Chen et al. 2026 zero-shot clustering with k-means, MH Protocol · part of this benchmark · 1 evaluation · 3 results
- Chen et al. 2026 genetic perturbation prediction, Adamson Protocol · part of this benchmark · 4 evaluations · 24 results
- Chen et al. 2026 genetic perturbation prediction, Norman Protocol · part of this benchmark · 4 evaluations · 24 results
- Chen et al. 2026 genetic perturbation prediction, Replogle Protocol · part of this benchmark · 4 evaluations · 24 results
- Chen et al. 2026 zero-shot cell type and spatial domain clustering, ATAA Protocol · part of this benchmark · 5 evaluations · 15 results
- Chen et al. 2026 zero-shot cell type and spatial domain clustering, BC Protocol · part of this benchmark · 6 evaluations · 18 results
- Chen et al. 2026 zero-shot cell type and spatial domain clustering, BMMC Protocol · part of this benchmark · 5 evaluations · 15 results
- Chen et al. 2026 zero-shot cell type and spatial domain clustering, HS Protocol · part of this benchmark · 5 evaluations · 15 results
- Chen et al. 2026 zero-shot cell type and spatial domain clustering, ME Protocol · part of this benchmark · 6 evaluations · 18 results
- Chen et al. 2026 zero-shot cell type and spatial domain clustering, MH Protocol · part of this benchmark · 6 evaluations · 18 results
Methods and evaluation design
Procedure, tasks and evaluated configurations
Additional methodological details, tasks and evaluated configurations have not yet been extracted into a structured profile for this benchmark. Consult the linked sources and evaluation records below.
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 50 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
Baseline status by linked protocol
- Chen et al. 2026 supervised cell type annotation, ATAA · 0/2 roles measured
- Chen et al. 2026 supervised cell type annotation, BMMC · 0/2 roles measured
- Chen et al. 2026 supervised cell type annotation, HS · 0/2 roles measured
- Chen et al. 2026 supervised cell type annotation, SEAAD · 0/2 roles measured
- Chen et al. 2026 continually pretrained clustering, ATAA · 0/2 roles measured
- Chen et al. 2026 continually pretrained clustering, BC · 0/2 roles measured
- Chen et al. 2026 continually pretrained clustering, BMMC · 0/2 roles measured
- Chen et al. 2026 continually pretrained clustering, HS · 0/2 roles measured
- Chen et al. 2026 continually pretrained clustering, ME · 0/2 roles measured
- Chen et al. 2026 continually pretrained clustering, MH · 0/2 roles measured
- Chen et al. 2026 zero-shot clustering with k-means, ATAA · 0/2 roles measured
- Chen et al. 2026 zero-shot clustering with k-means, BC · 0/2 roles measured
- Chen et al. 2026 zero-shot clustering with k-means, BMMC · 0/2 roles measured
- Chen et al. 2026 zero-shot clustering with k-means, HS · 0/2 roles measured
- Chen et al. 2026 zero-shot clustering with k-means, ME · 0/2 roles measured
- Chen et al. 2026 zero-shot clustering with k-means, MH · 0/2 roles measured
- Chen et al. 2026 genetic perturbation prediction, Adamson · 0/2 roles measured
- Chen et al. 2026 genetic perturbation prediction, Norman · 0/2 roles measured
- Chen et al. 2026 genetic perturbation prediction, Replogle · 0/2 roles measured
- Chen et al. 2026 zero-shot cell type and spatial domain clustering, ATAA · 0/2 roles measured
- Chen et al. 2026 zero-shot cell type and spatial domain clustering, BC · 0/2 roles measured
- Chen et al. 2026 zero-shot cell type and spatial domain clustering, BMMC · 0/2 roles measured
- Chen et al. 2026 zero-shot cell type and spatial domain clustering, HS · 0/2 roles measured
- Chen et al. 2026 zero-shot cell type and spatial domain clustering, ME · 0/2 roles measured
- Chen et al. 2026 zero-shot cell type and spatial domain clustering, MH · 0/2 roles measured
Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-10-23-5347695500ed. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
No runnable recipe has been reviewed for this benchmark. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Evidence
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Evidence table
Inspect claims, sources and review details
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Sources and history
Release 2026-10-23-5347695500ed · Record review: source checked
1 source record and release history
- Harmonised benchmarking of foundation models for single-cell and spatial transcriptomics reveals context-dependent generalisation · Original source · arXiv 2607.17227v2, updated 2026-09-17 (v1 posted 2026-07-19)
Technical metadata and extraction receipts
Stable ID: lit-cells-networks-20261011-chen2026-benchmark-harmonised-sc-spatial-fm
- areas
- single-cell; spatial-omics
- contexts
- research
- entity level
- suite
- version
- arXiv v2 (2026-09-17)
- task
- Clustering, cell type annotation and perturbation prediction from foundation model embeddings
- scope note
- No non-foundation-model baseline (for example PCA or scVI) is reported in the result tables.
- source locator
- Abstract; Methods 'Downstream evaluation tasks'; Tables 1-5
Related records
- part of: Chen et al. 2026 supervised cell type annotation, ATAA
- part of: Chen et al. 2026 supervised cell type annotation, BMMC
- part of: Chen et al. 2026 supervised cell type annotation, HS
- part of: Chen et al. 2026 supervised cell type annotation, SEAAD
- part of: Chen et al. 2026 continually pretrained clustering, ATAA
- part of: Chen et al. 2026 continually pretrained clustering, BC
- part of: Chen et al. 2026 continually pretrained clustering, BMMC
- part of: Chen et al. 2026 continually pretrained clustering, HS
- part of: Chen et al. 2026 continually pretrained clustering, ME
- part of: Chen et al. 2026 continually pretrained clustering, MH
- part of: Chen et al. 2026 zero-shot clustering with k-means, ATAA
- part of: Chen et al. 2026 zero-shot clustering with k-means, BC
- part of: Chen et al. 2026 zero-shot clustering with k-means, BMMC
- part of: Chen et al. 2026 zero-shot clustering with k-means, HS
- part of: Chen et al. 2026 zero-shot clustering with k-means, ME
- part of: Chen et al. 2026 zero-shot clustering with k-means, MH
- part of: Chen et al. 2026 genetic perturbation prediction, Adamson
- part of: Chen et al. 2026 genetic perturbation prediction, Norman
- part of: Chen et al. 2026 genetic perturbation prediction, Replogle
- part of: Chen et al. 2026 zero-shot cell type and spatial domain clustering, ATAA
- part of: Chen et al. 2026 zero-shot cell type and spatial domain clustering, BC
- part of: Chen et al. 2026 zero-shot cell type and spatial domain clustering, BMMC
- part of: Chen et al. 2026 zero-shot cell type and spatial domain clustering, HS
- part of: Chen et al. 2026 zero-shot cell type and spatial domain clustering, ME
- part of: Chen et al. 2026 zero-shot cell type and spatial domain clustering, MH