Result

Adjusted rand index of Nicheformer (zero-shot, Chen et al. 2026) on BC (Chen et al. 2026)

0.27 Adjusted rand index

Methods

Tested configuration: Nicheformer (zero-shot, Chen et al. 2026)
Protocol: Chen et al. 2026 zero-shot cell type and spatial domain clustering, BC
Dataset subset: BC (Chen et al. 2026)
Procedure: Chen et al. 2026 zero-shot cell type and spatial domain clustering, BC
Evaluation: Nicheformer on Chen et al. 2026 zero-shot cell type and spatial domain clustering, BC
Coverage: Not reported scored / Not reported eligible
Uncertainty: Not reported by the source
Evidence: Independent external evaluation · source checkedHarmonised benchmarking of foundation models for single-cell and spatial transcriptomics reveals context-dependent generalisation · Table 2, model 'Nicheformer', dataset 'BC', column 'ARI'

A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.

Reproduction

Split: All cells (unsupervised clustering)
Adaptation: frozen pretrained embeddings, Leiden clustering with resolution tuned to the number of reference labels, seed 42
Scoring implementation: Not reported

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

1 evidence row matching the loaded filters

Claims, original sources and review scope · Release 2026-10-23-5347695500ed
Property and statement	Original source and location	Review and provenance
Reported result 0.27 Individual claims	Harmonised benchmarking of foundation models for single-cell and spatial transcriptomics reveals context-dependent generalisation Original source ↗ Table 2, model 'Nicheformer', dataset 'BC', column 'ARI' Version: arXiv 2607.17227v2, updated 2026-09-17 (v1 posted 2026-07-19) Retrieved: 2026-10-11T21:29:34Z	source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-12 independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Extraction: Parsed the pdftotext -layout text of the pinned PDF with extract_chen2026.py: data rows matched by dataset code and number count, model labels assigned to fixed blocks in printed order with labels and block sizes asserted. Table 2, model 'Nicheformer', dataset 'BC', column 'ARI'. Independent review 2026-10-12: value, locator, metric, unit, direction and linked configuration and protocol checked by the reviewer's own parse of all Tables 2-5 and S2 cells and a hand check of 45 values against the rendered pages. Corrections from the review applied by the extractor as listed in review.md. Field: `attributes.printed_value` Source artifact SHA-256: `8137338c6146f570a6546f30707d4244baca9dab848b32c51539665a5ba539da` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact Extraction artifact SHA-256: `8137338c6146f570a6546f30707d4244baca9dab848b32c51539665a5ba539da` Extraction artifact

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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)

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Technical metadata and extraction receipts

Stable ID: lit-cells-networks-20261011-chen2026-result-zs-cluster-bc-nicheformer-ari

metric: adjusted-rand-index
metric direction: higher
unit: unitless
printed value: 0.27
source locator: Table 2, model 'Nicheformer', dataset 'BC', column 'ARI'
review: method: source-hash-verification; deterministic-table-parse; independent-cell-check; method note: Parsed the pdftotext -layout text of the pinned PDF with extract_chen2026.py: data rows matched by dataset code and number count, model labels assigned to fixed blocks in printed order with labels and block sizes asserted. Table 2, model 'Nicheformer', dataset 'BC', column 'ARI'; reviewer: claude; reviewer note: Claude review agent reviewer-cn-2, independent of the extractor lit-cells-networks; no human review claimed; date: 2026-10-12; artifact sha256: 8137338c6146f570a6546f30707d4244baca9dab848b32c51539665a5ba539da; retrieval url: https://arxiv.org/pdf/2607.17227v2; note: Extraction: Parsed the pdftotext -layout text of the pinned PDF with extract_chen2026.py: data rows matched by dataset code and number count, model labels assigned to fixed blocks in printed order with labels and block sizes asserted. Table 2, model 'Nicheformer', dataset 'BC', column 'ARI'. Independent review 2026-10-12: value, locator, metric, unit, direction and linked configuration and protocol checked by the reviewer's own parse of all Tables 2-5 and S2 cells and a hand check of 45 values against the rendered pages. Corrections from the review applied by the extractor as listed in review.md.
numeric value: 0.27
missing metadata: uncertainty: reason: unreported

Related records

evaluation: Nicheformer on Chen et al. 2026 zero-shot cell type and spatial domain clustering, BC

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