Dataset subset

Six BEELINE datasets, TFs+500 (Ye et al. 2026)

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

All six BEELINE scRNA-seq datasets (hESC, hHep, mDC, mHSC-E, mHSC-GM, mHSC-L) with the TFs+500 gene set; results are means across datasets.

Evaluation results

84 evaluations · 168 results. Different protocols are not a single leaderboard.

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

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: Six BEELINE datasets, TFs+500 (Ye et al. 2026)	1.05 AUPRC ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference; mean across six datasets) unitless · higher Uncertainty: SD 0.038 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 six BEELINE datasets (mean), 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 'mean', 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: Six BEELINE datasets, TFs+500 (Ye et al. 2026)	1.05 Early precision ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference; mean across six datasets) unitless · higher Uncertainty: SD 0.044 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 six BEELINE datasets (mean), 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 'mean', 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: Six BEELINE datasets, TFs+500 (Ye et al. 2026)	1.07 AUPRC ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference; mean across six datasets) unitless · higher Uncertainty: SD 0.076 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 six BEELINE datasets (mean), 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 'mean', 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: Six BEELINE datasets, TFs+500 (Ye et al. 2026)	1.16 Early precision ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference; mean across six datasets) unitless · higher Uncertainty: SD 0.259 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 six BEELINE datasets (mean), 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 'mean', 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: Six BEELINE datasets, TFs+500 (Ye et al. 2026)	0.964 AUPRC ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference; mean across six datasets) unitless · higher Uncertainty: SD 0.071 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 six BEELINE datasets (mean), 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 'mean', 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: Six BEELINE datasets, TFs+500 (Ye et al. 2026)	1.01 Early precision ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference; mean across six datasets) unitless · higher Uncertainty: SD 0.069 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 six BEELINE datasets (mean), 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 'mean', 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: Six BEELINE datasets, TFs+500 (Ye et al. 2026)	0.983 AUPRC ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference; mean across six datasets) unitless · higher Uncertainty: SD 0.031 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 six BEELINE datasets (mean), 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 'mean', 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: Six BEELINE datasets, TFs+500 (Ye et al. 2026)	0.945 Early precision ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference; mean across six datasets) unitless · higher Uncertainty: SD 0.089 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 six BEELINE datasets (mean), 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 'mean', 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: Six BEELINE datasets, TFs+500 (Ye et al. 2026)	1 AUPRC ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference; mean across six datasets) unitless · higher Uncertainty: SD 0.032 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 six BEELINE datasets (mean), 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 'mean', 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: Six BEELINE datasets, TFs+500 (Ye et al. 2026)	1.05 Early precision ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference; mean across six datasets) unitless · higher Uncertainty: SD 0.056 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 six BEELINE datasets (mean), 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 'mean', 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: Six BEELINE datasets, TFs+500 (Ye et al. 2026)	1.02 AUPRC ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference; mean across six datasets) unitless · higher Uncertainty: SD 0.044 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 six BEELINE datasets (mean), 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 'mean', 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: Six BEELINE datasets, TFs+500 (Ye et al. 2026)	0.994 Early precision ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference; mean across six datasets) unitless · higher Uncertainty: SD 0.078 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 six BEELINE datasets (mean), 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 'mean', 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: Six BEELINE datasets, TFs+500 (Ye et al. 2026)	1.05 AUPRC ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference; mean across six datasets) unitless · higher Uncertainty: SD 0.087 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 six BEELINE datasets (mean), 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 'mean', 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: Six BEELINE datasets, TFs+500 (Ye et al. 2026)	0.99 Early precision ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference; mean across six datasets) unitless · higher Uncertainty: SD 0.184 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 six BEELINE datasets (mean), 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 'mean', 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: Six BEELINE datasets, TFs+500 (Ye et al. 2026)	1.01 AUPRC ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference; mean across six datasets) unitless · higher Uncertainty: SD 0.055 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 six BEELINE datasets (mean), 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 'mean', 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: Six BEELINE datasets, TFs+500 (Ye et al. 2026)	1.01 Early precision ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference; mean across six datasets) unitless · higher Uncertainty: SD 0.052 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 six BEELINE datasets (mean), 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 'mean', 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: Six BEELINE datasets, TFs+500 (Ye et al. 2026)	0.983 AUPRC ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference; mean across six datasets) unitless · higher Uncertainty: SD 0.031 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 six BEELINE datasets (mean), 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 'mean', 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: Six BEELINE datasets, TFs+500 (Ye et al. 2026)	0.944 Early precision ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference; mean across six datasets) unitless · higher Uncertainty: SD 0.090 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 six BEELINE datasets (mean), 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 'mean', 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: Six BEELINE datasets, TFs+500 (Ye et al. 2026)	0.999 AUPRC ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference; mean across six datasets) unitless · higher Uncertainty: SD 0.020 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 six BEELINE datasets (mean), 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 'mean', 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: Six BEELINE datasets, TFs+500 (Ye et al. 2026)	1.02 Early precision ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference; mean across six datasets) unitless · higher Uncertainty: SD 0.082 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 six BEELINE datasets (mean), 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 'mean', 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: Six BEELINE datasets, TFs+500 (Ye et al. 2026)	1.01 AUPRC ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference; mean across six datasets) unitless · higher Uncertainty: SD 0.040 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 six BEELINE datasets (mean), 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 'mean', 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: Six BEELINE datasets, TFs+500 (Ye et al. 2026)	0.986 Early precision ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference; mean across six datasets) unitless · higher Uncertainty: SD 0.073 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 six BEELINE datasets (mean), 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 'mean', 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: Six BEELINE datasets, TFs+500 (Ye et al. 2026)	0.991 AUPRC ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference; mean across six datasets) unitless · higher Uncertainty: SD 0.023 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 six BEELINE datasets (mean), 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 'mean', 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: Six BEELINE datasets, TFs+500 (Ye et al. 2026)	0.981 Early precision ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference; mean across six datasets) unitless · higher Uncertainty: SD 0.045 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 six BEELINE datasets (mean), 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 'mean', 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: Six BEELINE datasets, TFs+500 (Ye et al. 2026)	1.01 AUPRC ratio (TFs+500 gene set; cell-type-specific ChIP-seq reference; mean across six datasets) unitless · higher Uncertainty: SD 0.010 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 six BEELINE datasets (mean), 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 'mean', column group 'attn', column 'scFoundation'

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Claims, original sources and review scope · Release 2026-10-23-5347695500ed
Property and statement	Original source and location	Review and provenance
Source location Section 2.1; Appendix A.1 Context-only references	Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models Original source ↗ Section 2.1; Appendix A.1 Version: bioRxiv preprint version 1, posted 2026-05-20 Retrieved: 2026-10-11T21:36:31Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.source_locator` 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
Split No train/test split; zero-shot network inference on each full expression matrix Context-only references	Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models Original source ↗ Section 2.1; Appendix A.1 Version: bioRxiv preprint version 1, posted 2026-05-20 Retrieved: 2026-10-11T21:36:31Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.split` 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
Description All six BEELINE scRNA-seq datasets (hESC, hHep, mDC, mHSC-E, mHSC-GM, mHSC-L) with the TFs+500 gene set; results are means across datasets. Context-only references	Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models Original source ↗ Section 2.1; Appendix A.1 Version: bioRxiv preprint version 1, posted 2026-05-20 Retrieved: 2026-10-11T21:36:31Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `description` 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
Name Six BEELINE datasets, TFs+500 (Ye et al. 2026) Context-only references	Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models Original source ↗ Section 2.1; Appendix A.1 Version: bioRxiv preprint version 1, posted 2026-05-20 Retrieved: 2026-10-11T21:36:31Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `name` 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

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

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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-data-tf-plus-500-six-datasets

areas: biological-networks; single-cell
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split: No train/test split; zero-shot network inference on each full expression matrix
source locator: Section 2.1; Appendix A.1
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