Result

Early precision ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference) of GRNBoost (Ye et al. 2026 baseline) on BEELINE mHSC-GM, TFs+500 (Ye et al. 2026)

1.02 Early precision ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference)

Evidence concern: excluded from comparisons

Table 1 labels its middle reference column 'ChIP-seq' and the caption names cell-type-specific ChIP-seq, but its values equal the 'Nonspecific ChIP-seq' mean and std rows of Tables 4 and 6 (for example scGPT costok EPR 4.211±1.703), and Appendix B says cell-type-specific ChIP-seq is excluded from the main comparison. Table 1 is therefore not extracted; Tables 4-7 carry the reference labels.Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 1 caption and column header; Tables 4 and 6, 'Nonspecific ChIP-seq' mean rows; Appendix B text before Table 4

Table 6 is titled 'AUPR' and Table 7 'AUPRC', but both print ratios over a random predictor (values above 1), matching the 'AUPRC ratio' of Table 1; both are recorded as auprc-ratio.Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 6 and Table 7 captions; Table 1 caption

Table 7 (TFs+1000 AUPRC) repeats Table 6 (TFs+500 AUPR) exactly in the GENIE3 column of the STRING, Cell-type-specific ChIP-seq and Nonspecific ChIP-seq blocks: all 18 dataset values and the three mean and std rows are identical (for example STRING hESC 1.6241, mean 3.301, std 2.244). Only the OmniPath block differs. Every other column, and GENIE3 in the EPR Tables 4 and 5, differs between the two gene sets, and the Table 6 values match Table 1. These 21 Table 7 GENIE3 values are likely a copy of the TFs+500 values and should not be compared.Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 7, column group 'ML', column 'GENIE3', blocks 'STRING', 'Cell-type-specific' and 'Nonspecific'; Table 6, same cells; Table 1, GENIE3 AUPRC ratio

Methods

Tested configuration: GRNBoost (Ye et al. 2026 baseline)
Protocol: Ye et al. 2026 GRN reconstruction, TFs+500, cell-type-specific ChIP-seq reference
Dataset subset: BEELINE mHSC-GM, TFs+500 (Ye et al. 2026)
Procedure: Ye et al. 2026 GRN reconstruction, TFs+500, cell-type-specific ChIP-seq reference
Evaluation: GRNboost GRN on mHSC-GM, TFs+500, cell-type-specific ChIP-seq
Coverage: Not reported scored / Not reported eligible
Uncertainty: Not reported by the source
Evidence: Independent external evaluation · source checkedBenchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 4, block 'Cell-type-specific', row 'mHSC-GM', column group 'ML', column 'GRNboost'

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: No train/test split; networks inferred from each full expression matrix
Adaptation: Foundation models zero-shot from pretrained weights; GENIE3, DeepSEM and GRNBoost fitted to each expression matrix
Scoring implementation: Early precision ratio and AUPRC ratio over a random predictor (Appendix B.2)

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 1.0225 Individual claims	Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models Original source ↗ Table 4, block 'Cell-type-specific', row 'mHSC-GM', column group 'ML', column 'GRNboost' Version: bioRxiv preprint version 1, posted 2026-05-20 Retrieved: 2026-10-11T21:36:31Z	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_ye2026.py: rows of exactly 21 numbers taken in printed order, 8 rows (six datasets, mean, std) per reference block, dataset and reference labels asserted where printed, column headers asserted. Table 4, block 'Cell-type-specific', row 'mHSC-GM', column group 'ML', column 'GRNboost'. Independent review 2026-10-12: value, locator, metric, unit, direction, uncertainty and linked configuration, protocol and dataset checked by the reviewer's own parse of all Tables 4-7 cells and a hand check of 48 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: `a6c3aae569b1f1614c71569efb0692f15700aea473c64c7bc0bc660e81330dc7` Hash scope: Exact bytes of one download. bioRxiv serves slightly different PDF bytes per download (41 bytes differed between two downloads 2 minutes apart; pdftotext output identical), so the gzip copy in artifacts/ is the reference. Inspected artifact Extraction artifact SHA-256: `a6c3aae569b1f1614c71569efb0692f15700aea473c64c7bc0bc660e81330dc7` Extraction artifact

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Sources and history

Release 2026-10-23-5347695500ed · Record review: source checked

1 source record and release history

Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Original source · bioRxiv preprint version 1, posted 2026-05-20

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Technical metadata and extraction receipts

Stable ID: lit-cells-networks-20261011-ye2026grn-result-tf-plus-500-cell-type-specific-chip-seq-mhsc-gm-grnboost-early-precision-ratio

metric: early-precision-ratio
metric direction: higher
unit: unitless
printed value: 1.0225
source locator: Table 4, block 'Cell-type-specific', row 'mHSC-GM', column group 'ML', column 'GRNboost'
review: method: source-hash-verification; deterministic-table-parse; independent-cell-check; method note: Parsed the pdftotext -layout text of the pinned PDF with extract_ye2026.py: rows of exactly 21 numbers taken in printed order, 8 rows (six datasets, mean, std) per reference block, dataset and reference labels asserted where printed, column headers asserted. Table 4, block 'Cell-type-specific', row 'mHSC-GM', column group 'ML', column 'GRNboost'; reviewer: claude; reviewer note: Claude review agent reviewer-cn-1, independent of the extractor lit-cells-networks; no human review claimed; date: 2026-10-12; artifact sha256: a6c3aae569b1f1614c71569efb0692f15700aea473c64c7bc0bc660e81330dc7; retrieval url: https://www.biorxiv.org/content/10.64898/2026.05.17.725083v1.full.pdf; note: Extraction: Parsed the pdftotext -layout text of the pinned PDF with extract_ye2026.py: rows of exactly 21 numbers taken in printed order, 8 rows (six datasets, mean, std) per reference block, dataset and reference labels asserted where printed, column headers asserted. Table 4, block 'Cell-type-specific', row 'mHSC-GM', column group 'ML', column 'GRNboost'. Independent review 2026-10-12: value, locator, metric, unit, direction, uncertainty and linked configuration, protocol and dataset checked by the reviewer's own parse of all Tables 4-7 cells and a hand check of 48 values against the rendered pages. Corrections from the review applied by the extractor as listed in review.md.
numeric value: 1.0225
metric qualifier: TFs+500 gene set; cell-type-specific ChIP-seq reference
missing metadata: uncertainty: reason: unreported

Related records

evaluation: GRNboost GRN on mHSC-GM, TFs+500, cell-type-specific ChIP-seq

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