Protocol

Ye et al. 2026 GRN reconstruction, TFs+500, 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

Rank TF-target candidate edges by absolute weight; early precision ratio scores the top K edges (K = number of reference edges) and AUPRC ratio the full ranked list, each over a random predictor, against the cell-type-specific ChIP-seq reference.

147 evaluations · 294 results

Overview

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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

147 recorded evaluations, 294 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

147 evaluations · 294 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: DeepSEM (Ye et al. 2026 baseline)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+500, cell-type-specific ChIP-seq reference Dataset subset: BEELINE hESC, TFs+500 (Ye et al. 2026)	1.07 AUPRC ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source DeepSEM GRN on hESC, TFs+500, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-500-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 6, block 'Cell-type-specific', row 'hESC', column group 'ML', column 'DeepSEM'
Configuration: DeepSEM (Ye et al. 2026 baseline)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+500, cell-type-specific ChIP-seq reference Dataset subset: BEELINE hESC, TFs+500 (Ye et al. 2026)	1.13 Early precision ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source DeepSEM GRN on hESC, TFs+500, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-500-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 4, block 'Cell-type-specific', row 'hESC', column group 'ML', column 'DeepSEM'
Configuration: Geneformer attn GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+500, cell-type-specific ChIP-seq reference Dataset subset: BEELINE hESC, TFs+500 (Ye et al. 2026)	1.11 AUPRC ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source Geneformer attn GRN on hESC, TFs+500, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-500-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 6, block 'Cell-type-specific', row 'hESC', column group 'attn', column 'Geneformer'
Configuration: Geneformer attn GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+500, cell-type-specific ChIP-seq reference Dataset subset: BEELINE hESC, TFs+500 (Ye et al. 2026)	1.07 Early precision ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source Geneformer attn GRN on hESC, TFs+500, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-500-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 4, block 'Cell-type-specific', row 'hESC', column group 'attn', column 'Geneformer'
Configuration: Geneformer coshid GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+500, cell-type-specific ChIP-seq reference Dataset subset: BEELINE hESC, TFs+500 (Ye et al. 2026)	0.985 AUPRC ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source Geneformer coshid GRN on hESC, TFs+500, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-500-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 6, block 'Cell-type-specific', row 'hESC', column group 'coshid', column 'Geneformer'
Configuration: Geneformer coshid GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+500, cell-type-specific ChIP-seq reference Dataset subset: BEELINE hESC, TFs+500 (Ye et al. 2026)	0.989 Early precision ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source Geneformer coshid GRN on hESC, TFs+500, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-500-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 4, block 'Cell-type-specific', row 'hESC', column group 'coshid', column 'Geneformer'
Configuration: Geneformer costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+500, cell-type-specific ChIP-seq reference Dataset subset: BEELINE hESC, TFs+500 (Ye et al. 2026)	0.934 AUPRC ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source Geneformer costok GRN on hESC, TFs+500, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-500-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 6, block 'Cell-type-specific', row 'hESC', column group 'costok', column 'Geneformer'
Configuration: Geneformer costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+500, cell-type-specific ChIP-seq reference Dataset subset: BEELINE hESC, TFs+500 (Ye et al. 2026)	0.792 Early precision ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source Geneformer costok GRN on hESC, TFs+500, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-500-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 4, block 'Cell-type-specific', row 'hESC', column group 'costok', column 'Geneformer'
Configuration: GENIE3 (Ye et al. 2026 baseline)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+500, cell-type-specific ChIP-seq reference Dataset subset: BEELINE hESC, TFs+500 (Ye et al. 2026)	0.978 AUPRC ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source GENIE3 GRN on hESC, TFs+500, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-500-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 6, block 'Cell-type-specific', row 'hESC', column group 'ML', column 'GENIE3'
Configuration: GENIE3 (Ye et al. 2026 baseline)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+500, cell-type-specific ChIP-seq reference Dataset subset: BEELINE hESC, TFs+500 (Ye et al. 2026)	0.979 Early precision ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source GENIE3 GRN on hESC, TFs+500, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-500-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 4, block 'Cell-type-specific', row 'hESC', column group 'ML', column 'GENIE3'
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 hESC, TFs+500 (Ye et al. 2026)	0.998 AUPRC ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source GRNboost GRN on hESC, TFs+500, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-500-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 6, block 'Cell-type-specific', row 'hESC', column group 'ML', column 'GRNboost'
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 hESC, TFs+500 (Ye et al. 2026)	0.962 Early precision ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source GRNboost GRN on hESC, TFs+500, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-500-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 4, block 'Cell-type-specific', row 'hESC', column group 'ML', column 'GRNboost'
Configuration: LangCell attn GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+500, cell-type-specific ChIP-seq reference Dataset subset: BEELINE hESC, TFs+500 (Ye et al. 2026)	0.972 AUPRC ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source LangCell attn GRN on hESC, TFs+500, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-500-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 6, block 'Cell-type-specific', row 'hESC', column group 'attn', column 'Langcell'
Configuration: LangCell attn GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+500, cell-type-specific ChIP-seq reference Dataset subset: BEELINE hESC, TFs+500 (Ye et al. 2026)	1.02 Early precision ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source LangCell attn GRN on hESC, TFs+500, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-500-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 4, block 'Cell-type-specific', row 'hESC', column group 'attn', column 'Langcell'
Configuration: LangCell coshid GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+500, cell-type-specific ChIP-seq reference Dataset subset: BEELINE hESC, TFs+500 (Ye et al. 2026)	1.05 AUPRC ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source LangCell coshid GRN on hESC, TFs+500, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-500-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 6, block 'Cell-type-specific', row 'hESC', column group 'coshid', column 'Langcell'
Configuration: LangCell coshid GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+500, cell-type-specific ChIP-seq reference Dataset subset: BEELINE hESC, TFs+500 (Ye et al. 2026)	1.02 Early precision ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source LangCell coshid GRN on hESC, TFs+500, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-500-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 4, block 'Cell-type-specific', row 'hESC', column group 'coshid', column 'Langcell'
Configuration: LangCell costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+500, cell-type-specific ChIP-seq reference Dataset subset: BEELINE hESC, TFs+500 (Ye et al. 2026)	0.934 AUPRC ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source LangCell costok GRN on hESC, TFs+500, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-500-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 6, block 'Cell-type-specific', row 'hESC', column group 'costok', column 'Langcell'
Configuration: LangCell costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+500, cell-type-specific ChIP-seq reference Dataset subset: BEELINE hESC, TFs+500 (Ye et al. 2026)	0.789 Early precision ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source LangCell costok GRN on hESC, TFs+500, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-500-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 4, block 'Cell-type-specific', row 'hESC', column group 'costok', column 'Langcell'
Configuration: scCello attn GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+500, cell-type-specific ChIP-seq reference Dataset subset: BEELINE hESC, TFs+500 (Ye et al. 2026)	0.998 AUPRC ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source scCello attn GRN on hESC, TFs+500, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-500-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 6, block 'Cell-type-specific', row 'hESC', column group 'attn', column 'scCello'
Configuration: scCello attn GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+500, cell-type-specific ChIP-seq reference Dataset subset: BEELINE hESC, TFs+500 (Ye et al. 2026)	0.962 Early precision ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source scCello attn GRN on hESC, TFs+500, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-500-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 4, block 'Cell-type-specific', row 'hESC', column group 'attn', column 'scCello'
Configuration: scCello coshid GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+500, cell-type-specific ChIP-seq reference Dataset subset: BEELINE hESC, TFs+500 (Ye et al. 2026)	0.951 AUPRC ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source scCello coshid GRN on hESC, TFs+500, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-500-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 6, block 'Cell-type-specific', row 'hESC', column group 'coshid', column 'scello'
Configuration: scCello coshid GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+500, cell-type-specific ChIP-seq reference Dataset subset: BEELINE hESC, TFs+500 (Ye et al. 2026)	0.855 Early precision ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source scCello coshid GRN on hESC, TFs+500, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-500-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 4, block 'Cell-type-specific', row 'hESC', column group 'coshid', column 'scCello'
Configuration: scCello costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+500, cell-type-specific ChIP-seq reference Dataset subset: BEELINE hESC, TFs+500 (Ye et al. 2026)	0.99 AUPRC ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source scCello costok GRN on hESC, TFs+500, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-500-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 6, block 'Cell-type-specific', row 'hESC', column group 'costok', column 'scello'
Configuration: scCello costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+500, cell-type-specific ChIP-seq reference Dataset subset: BEELINE hESC, TFs+500 (Ye et al. 2026)	0.981 Early precision ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source scCello costok GRN on hESC, TFs+500, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-500-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 4, block 'Cell-type-specific', row 'hESC', column group 'costok', column 'scCello'
Configuration: scFoundation attn GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+500, cell-type-specific ChIP-seq reference Dataset subset: BEELINE hESC, TFs+500 (Ye et al. 2026)	1.01 AUPRC ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source scFoundation attn GRN on hESC, TFs+500, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-500-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 6, block 'Cell-type-specific', row 'hESC', column group 'attn', column 'scFoundation'

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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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Stable ID: lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-500-cell-type-specific-chip-seq

areas: biological-networks; single-cell
contexts: research
protocol: TFs+500 gene set; candidate space restricted to reference TFs as sources and reference-set genes as targets; cell-type-specific ChIP-seq reference network; early precision and precision-recall over ranked edges (Appendix B.2).
version: bioRxiv v1
metric: early-precision-ratio
metric direction: higher
unit: unitless
limitations: One run per dataset; dataset-level spread only.; Ratios over a random predictor depend on reference network density, so values are not comparable across references or gene sets.; The authors report near-random performance for every method on this reference and exclude it from the main comparison (Appendix B).
source locator: Tables 4-7; Section 2.2; Appendix B.2

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assessment: scCello attn GRN on mDC, TFs+500, cell-type-specific ChIP-seq
assessment: scCello coshid GRN on mDC, TFs+500, cell-type-specific ChIP-seq
assessment: scCello costok GRN on mDC, TFs+500, cell-type-specific ChIP-seq
assessment: scFoundation attn GRN on mDC, TFs+500, cell-type-specific ChIP-seq
assessment: scFoundation coshid GRN on mDC, TFs+500, cell-type-specific ChIP-seq
assessment: scFoundation costok GRN on mDC, TFs+500, cell-type-specific ChIP-seq
assessment: scGPT attn GRN on mDC, TFs+500, cell-type-specific ChIP-seq
assessment: scGPT coshid GRN on mDC, TFs+500, cell-type-specific ChIP-seq
assessment: scGPT costok GRN on mDC, TFs+500, cell-type-specific ChIP-seq
assessment: scPRINT attn GRN on mDC, TFs+500, cell-type-specific ChIP-seq
assessment: scPRINT coshid GRN on mDC, TFs+500, cell-type-specific ChIP-seq
assessment: scPRINT costok GRN on mDC, TFs+500, cell-type-specific ChIP-seq
assessment: DeepSEM GRN on mHSC-E, TFs+500, cell-type-specific ChIP-seq
assessment: Geneformer attn GRN on mHSC-E, TFs+500, cell-type-specific ChIP-seq
assessment: Geneformer coshid GRN on mHSC-E, TFs+500, cell-type-specific ChIP-seq
assessment: Geneformer costok GRN on mHSC-E, TFs+500, cell-type-specific ChIP-seq
assessment: GENIE3 GRN on mHSC-E, TFs+500, cell-type-specific ChIP-seq
assessment: GRNboost GRN on mHSC-E, TFs+500, cell-type-specific ChIP-seq
assessment: LangCell attn GRN on mHSC-E, TFs+500, cell-type-specific ChIP-seq
assessment: LangCell coshid GRN on mHSC-E, TFs+500, cell-type-specific ChIP-seq
assessment: LangCell costok GRN on mHSC-E, TFs+500, cell-type-specific ChIP-seq
assessment: scCello attn GRN on mHSC-E, TFs+500, cell-type-specific ChIP-seq
assessment: scCello coshid GRN on mHSC-E, TFs+500, cell-type-specific ChIP-seq
assessment: scCello costok GRN on mHSC-E, TFs+500, cell-type-specific ChIP-seq
assessment: scFoundation attn GRN on mHSC-E, TFs+500, cell-type-specific ChIP-seq
assessment: scFoundation coshid GRN on mHSC-E, TFs+500, cell-type-specific ChIP-seq
assessment: scFoundation costok GRN on mHSC-E, TFs+500, cell-type-specific ChIP-seq
assessment: scGPT attn GRN on mHSC-E, TFs+500, cell-type-specific ChIP-seq
assessment: scGPT coshid GRN on mHSC-E, TFs+500, cell-type-specific ChIP-seq
assessment: scGPT costok GRN on mHSC-E, TFs+500, cell-type-specific ChIP-seq
assessment: scPRINT attn GRN on mHSC-E, TFs+500, cell-type-specific ChIP-seq
assessment: scPRINT coshid GRN on mHSC-E, TFs+500, cell-type-specific ChIP-seq
assessment: scPRINT costok GRN on mHSC-E, TFs+500, cell-type-specific ChIP-seq
assessment: DeepSEM GRN on mHSC-GM, TFs+500, cell-type-specific ChIP-seq
assessment: Geneformer attn GRN on mHSC-GM, TFs+500, cell-type-specific ChIP-seq
assessment: Geneformer coshid GRN on mHSC-GM, TFs+500, cell-type-specific ChIP-seq
assessment: Geneformer costok GRN on mHSC-GM, TFs+500, cell-type-specific ChIP-seq
assessment: GENIE3 GRN on mHSC-GM, TFs+500, cell-type-specific ChIP-seq
assessment: GRNboost GRN on mHSC-GM, TFs+500, cell-type-specific ChIP-seq
assessment: LangCell attn GRN on mHSC-GM, TFs+500, cell-type-specific ChIP-seq
assessment: LangCell coshid GRN on mHSC-GM, TFs+500, cell-type-specific ChIP-seq
assessment: LangCell costok GRN on mHSC-GM, TFs+500, cell-type-specific ChIP-seq
assessment: scCello attn GRN on mHSC-GM, TFs+500, cell-type-specific ChIP-seq
assessment: scCello coshid GRN on mHSC-GM, TFs+500, cell-type-specific ChIP-seq
assessment: scCello costok GRN on mHSC-GM, TFs+500, cell-type-specific ChIP-seq
assessment: scFoundation attn GRN on mHSC-GM, TFs+500, cell-type-specific ChIP-seq
assessment: scFoundation coshid GRN on mHSC-GM, TFs+500, cell-type-specific ChIP-seq
assessment: scFoundation costok GRN on mHSC-GM, TFs+500, cell-type-specific ChIP-seq
assessment: scGPT attn GRN on mHSC-GM, TFs+500, cell-type-specific ChIP-seq
assessment: scGPT coshid GRN on mHSC-GM, TFs+500, cell-type-specific ChIP-seq
assessment: scGPT costok GRN on mHSC-GM, TFs+500, cell-type-specific ChIP-seq
assessment: scPRINT attn GRN on mHSC-GM, TFs+500, cell-type-specific ChIP-seq
assessment: scPRINT coshid GRN on mHSC-GM, TFs+500, cell-type-specific ChIP-seq
assessment: scPRINT costok GRN on mHSC-GM, TFs+500, cell-type-specific ChIP-seq
assessment: DeepSEM GRN on mHSC-L, TFs+500, cell-type-specific ChIP-seq
assessment: Geneformer attn GRN on mHSC-L, TFs+500, cell-type-specific ChIP-seq
assessment: Geneformer coshid GRN on mHSC-L, TFs+500, cell-type-specific ChIP-seq
assessment: Geneformer costok GRN on mHSC-L, TFs+500, cell-type-specific ChIP-seq
assessment: GENIE3 GRN on mHSC-L, TFs+500, cell-type-specific ChIP-seq
assessment: GRNboost GRN on mHSC-L, TFs+500, cell-type-specific ChIP-seq
assessment: LangCell attn GRN on mHSC-L, TFs+500, cell-type-specific ChIP-seq
assessment: LangCell coshid GRN on mHSC-L, TFs+500, cell-type-specific ChIP-seq
assessment: LangCell costok GRN on mHSC-L, TFs+500, cell-type-specific ChIP-seq
assessment: scCello attn GRN on mHSC-L, TFs+500, cell-type-specific ChIP-seq
assessment: scCello coshid GRN on mHSC-L, TFs+500, cell-type-specific ChIP-seq
assessment: scCello costok GRN on mHSC-L, TFs+500, cell-type-specific ChIP-seq
assessment: scFoundation attn GRN on mHSC-L, TFs+500, cell-type-specific ChIP-seq
assessment: scFoundation coshid GRN on mHSC-L, TFs+500, cell-type-specific ChIP-seq
assessment: scFoundation costok GRN on mHSC-L, TFs+500, cell-type-specific ChIP-seq
assessment: scGPT attn GRN on mHSC-L, TFs+500, cell-type-specific ChIP-seq
assessment: scGPT coshid GRN on mHSC-L, TFs+500, cell-type-specific ChIP-seq
assessment: scGPT costok GRN on mHSC-L, TFs+500, cell-type-specific ChIP-seq
assessment: scPRINT attn GRN on mHSC-L, TFs+500, cell-type-specific ChIP-seq
assessment: scPRINT coshid GRN on mHSC-L, TFs+500, cell-type-specific ChIP-seq
assessment: scPRINT costok GRN on mHSC-L, TFs+500, cell-type-specific ChIP-seq
assessment: DeepSEM GRN on six BEELINE datasets (mean), TFs+500, cell-type-specific ChIP-seq
assessment: Geneformer attn GRN on six BEELINE datasets (mean), TFs+500, cell-type-specific ChIP-seq
assessment: Geneformer coshid GRN on six BEELINE datasets (mean), TFs+500, cell-type-specific ChIP-seq
assessment: Geneformer costok GRN on six BEELINE datasets (mean), TFs+500, cell-type-specific ChIP-seq
assessment: GENIE3 GRN on six BEELINE datasets (mean), TFs+500, cell-type-specific ChIP-seq
assessment: GRNboost GRN on six BEELINE datasets (mean), TFs+500, cell-type-specific ChIP-seq
assessment: LangCell attn GRN on six BEELINE datasets (mean), TFs+500, cell-type-specific ChIP-seq
assessment: LangCell coshid GRN on six BEELINE datasets (mean), TFs+500, cell-type-specific ChIP-seq
assessment: LangCell costok GRN on six BEELINE datasets (mean), TFs+500, cell-type-specific ChIP-seq
assessment: scCello attn GRN on six BEELINE datasets (mean), TFs+500, cell-type-specific ChIP-seq
assessment: scCello coshid GRN on six BEELINE datasets (mean), TFs+500, cell-type-specific ChIP-seq
assessment: scCello costok GRN on six BEELINE datasets (mean), TFs+500, cell-type-specific ChIP-seq
assessment: scFoundation attn GRN on six BEELINE datasets (mean), TFs+500, cell-type-specific ChIP-seq
assessment: scFoundation coshid GRN on six BEELINE datasets (mean), TFs+500, cell-type-specific ChIP-seq
assessment: scFoundation costok GRN on six BEELINE datasets (mean), TFs+500, cell-type-specific ChIP-seq
assessment: scGPT attn GRN on six BEELINE datasets (mean), TFs+500, cell-type-specific ChIP-seq
assessment: scGPT coshid GRN on six BEELINE datasets (mean), TFs+500, cell-type-specific ChIP-seq
assessment: scGPT costok GRN on six BEELINE datasets (mean), TFs+500, cell-type-specific ChIP-seq
assessment: scPRINT attn GRN on six BEELINE datasets (mean), TFs+500, cell-type-specific ChIP-seq
assessment: scPRINT coshid GRN on six BEELINE datasets (mean), TFs+500, cell-type-specific ChIP-seq
assessment: scPRINT costok GRN on six BEELINE datasets (mean), TFs+500, cell-type-specific ChIP-seq

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