Configuration

scFoundation costok GRN (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

scFoundation zero-shot GRN from cosine similarity of pretrained gene token embeddings (undirected).

56 evaluations · 112 results 2 open disagreements between studies involve its model

Overview

An explanatory profile has not yet been reviewed for this record.

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

Evaluations and results

56 evaluations · 112 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: scFoundation costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+1000, cell-type-specific ChIP-seq reference Dataset subset: BEELINE hESC, TFs+1000 (Ye et al. 2026)	0.984 AUPRC ratio (TFs+1000 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 costok GRN on hESC, TFs+1000, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-1000-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 7, block 'Cell-type-specific', row 'hESC', column group 'costok', column 'scFoundation'
Configuration: scFoundation costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+1000, cell-type-specific ChIP-seq reference Dataset subset: BEELINE hESC, TFs+1000 (Ye et al. 2026)	0.85 Early precision ratio (TFs+1000 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 costok GRN on hESC, TFs+1000, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-1000-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 5, block 'Cell-type-specific', row 'hESC', column group 'costok', column 'scFoundation'
Configuration: scFoundation costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+1000, cell-type-specific ChIP-seq reference Dataset subset: BEELINE hHep, TFs+1000 (Ye et al. 2026)	0.964 AUPRC ratio (TFs+1000 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 costok GRN on hHep, TFs+1000, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-1000-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 7, block 'Cell-type-specific', row 'hHep', column group 'costok', column 'scFoundation'
Configuration: scFoundation costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+1000, cell-type-specific ChIP-seq reference Dataset subset: BEELINE hHep, TFs+1000 (Ye et al. 2026)	1.03 Early precision ratio (TFs+1000 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 costok GRN on hHep, TFs+1000, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-1000-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 5, block 'Cell-type-specific', row 'hHep', column group 'costok', column 'scFoundation'
Configuration: scFoundation costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+1000, cell-type-specific ChIP-seq reference Dataset subset: BEELINE mDC, TFs+1000 (Ye et al. 2026)	1.08 AUPRC ratio (TFs+1000 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 costok GRN on mDC, TFs+1000, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-1000-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 7, block 'Cell-type-specific', row 'mDC', column group 'costok', column 'scFoundation'
Configuration: scFoundation costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+1000, cell-type-specific ChIP-seq reference Dataset subset: BEELINE mDC, TFs+1000 (Ye et al. 2026)	1.35 Early precision ratio (TFs+1000 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 costok GRN on mDC, TFs+1000, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-1000-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 5, block 'Cell-type-specific', row 'mDC', column group 'costok', column 'scFoundation'
Configuration: scFoundation costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+1000, cell-type-specific ChIP-seq reference Dataset subset: BEELINE mHSC-E, TFs+1000 (Ye et al. 2026)	0.9 AUPRC ratio (TFs+1000 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 costok GRN on mHSC-E, TFs+1000, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-1000-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 7, block 'Cell-type-specific', row 'mHSC-E', column group 'costok', column 'scFoundation'
Configuration: scFoundation costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+1000, cell-type-specific ChIP-seq reference Dataset subset: BEELINE mHSC-E, TFs+1000 (Ye et al. 2026)	1.04 Early precision ratio (TFs+1000 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 costok GRN on mHSC-E, TFs+1000, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-1000-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 5, block 'Cell-type-specific', row 'mHSC-E', column group 'costok', column 'scFoundation'
Configuration: scFoundation costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+1000, cell-type-specific ChIP-seq reference Dataset subset: BEELINE mHSC-GM, TFs+1000 (Ye et al. 2026)	0.883 AUPRC ratio (TFs+1000 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 costok GRN on mHSC-GM, TFs+1000, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-1000-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 7, block 'Cell-type-specific', row 'mHSC-GM', column group 'costok', column 'scFoundation'
Configuration: scFoundation costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+1000, cell-type-specific ChIP-seq reference Dataset subset: BEELINE mHSC-GM, TFs+1000 (Ye et al. 2026)	0.96 Early precision ratio (TFs+1000 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 costok GRN on mHSC-GM, TFs+1000, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-1000-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 5, block 'Cell-type-specific', row 'mHSC-GM', column group 'costok', column 'scFoundation'
Configuration: scFoundation costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+1000, cell-type-specific ChIP-seq reference Dataset subset: BEELINE mHSC-L, TFs+1000 (Ye et al. 2026)	1 AUPRC ratio (TFs+1000 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 costok GRN on mHSC-L, TFs+1000, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-1000-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 7, block 'Cell-type-specific', row 'mHSC-L', column group 'costok', column 'scFoundation'
Configuration: scFoundation costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+1000, cell-type-specific ChIP-seq reference Dataset subset: BEELINE mHSC-L, TFs+1000 (Ye et al. 2026)	1.17 Early precision ratio (TFs+1000 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 costok GRN on mHSC-L, TFs+1000, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-1000-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 5, block 'Cell-type-specific', row 'mHSC-L', column group 'costok', column 'scFoundation'
Configuration: scFoundation costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+1000, cell-type-specific ChIP-seq reference Dataset subset: Six BEELINE datasets, TFs+1000 (Ye et al. 2026)	0.968 AUPRC ratio (TFs+1000 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 scFoundation costok GRN on six BEELINE datasets (mean), TFs+1000, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-1000-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 7, block 'Cell-type-specific', row 'mean', column group 'costok', column 'scFoundation'
Configuration: scFoundation costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+1000, cell-type-specific ChIP-seq reference Dataset subset: Six BEELINE datasets, TFs+1000 (Ye et al. 2026)	1.07 Early precision ratio (TFs+1000 gene set; cell-type-specific ChIP-seq reference; mean across six datasets) unitless · higher Uncertainty: SD 0.175 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 costok GRN on six BEELINE datasets (mean), TFs+1000, cell-type-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-1000-cell-type-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 5, block 'Cell-type-specific', row 'mean', column group 'costok', column 'scFoundation'
Configuration: scFoundation costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+1000, non-specific ChIP-seq reference Dataset subset: BEELINE hESC, TFs+1000 (Ye et al. 2026)	0.981 AUPRC ratio (TFs+1000 gene set; non-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 costok GRN on hESC, TFs+1000, non-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-1000-non-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 7, block 'Nonspecific', row 'hESC', column group 'costok', column 'scFoundation'
Configuration: scFoundation costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+1000, non-specific ChIP-seq reference Dataset subset: BEELINE hESC, TFs+1000 (Ye et al. 2026)	1.32 Early precision ratio (TFs+1000 gene set; non-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 costok GRN on hESC, TFs+1000, non-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-1000-non-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 5, block 'Nonspecific', row 'hESC', column group 'costok', column 'scFoundation'
Configuration: scFoundation costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+1000, non-specific ChIP-seq reference Dataset subset: BEELINE hHep, TFs+1000 (Ye et al. 2026)	1.08 AUPRC ratio (TFs+1000 gene set; non-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 costok GRN on hHep, TFs+1000, non-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-1000-non-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 7, block 'Nonspecific', row 'hHep', column group 'costok', column 'scFoundation'
Configuration: scFoundation costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+1000, non-specific ChIP-seq reference Dataset subset: BEELINE hHep, TFs+1000 (Ye et al. 2026)	0.879 Early precision ratio (TFs+1000 gene set; non-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 costok GRN on hHep, TFs+1000, non-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-1000-non-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 5, block 'Nonspecific', row 'hHep', column group 'costok', column 'scFoundation'
Configuration: scFoundation costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+1000, non-specific ChIP-seq reference Dataset subset: BEELINE mDC, TFs+1000 (Ye et al. 2026)	1.23 AUPRC ratio (TFs+1000 gene set; non-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 costok GRN on mDC, TFs+1000, non-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-1000-non-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 7, block 'Nonspecific', row 'mDC', column group 'costok', column 'scFoundation'
Configuration: scFoundation costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+1000, non-specific ChIP-seq reference Dataset subset: BEELINE mDC, TFs+1000 (Ye et al. 2026)	1.1 Early precision ratio (TFs+1000 gene set; non-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 costok GRN on mDC, TFs+1000, non-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-1000-non-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 5, block 'Nonspecific', row 'mDC', column group 'costok', column 'scFoundation'
Configuration: scFoundation costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+1000, non-specific ChIP-seq reference Dataset subset: BEELINE mHSC-E, TFs+1000 (Ye et al. 2026)	1.15 AUPRC ratio (TFs+1000 gene set; non-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 costok GRN on mHSC-E, TFs+1000, non-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-1000-non-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 7, block 'Nonspecific', row 'mHSC-E', column group 'costok', column 'scFoundation'
Configuration: scFoundation costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+1000, non-specific ChIP-seq reference Dataset subset: BEELINE mHSC-E, TFs+1000 (Ye et al. 2026)	1.38 Early precision ratio (TFs+1000 gene set; non-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 costok GRN on mHSC-E, TFs+1000, non-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-1000-non-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 5, block 'Nonspecific', row 'mHSC-E', column group 'costok', column 'scFoundation'
Configuration: scFoundation costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+1000, non-specific ChIP-seq reference Dataset subset: BEELINE mHSC-GM, TFs+1000 (Ye et al. 2026)	1.23 AUPRC ratio (TFs+1000 gene set; non-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 costok GRN on mHSC-GM, TFs+1000, non-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-1000-non-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 7, block 'Nonspecific', row 'mHSC-GM', column group 'costok', column 'scFoundation'
Configuration: scFoundation costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+1000, non-specific ChIP-seq reference Dataset subset: BEELINE mHSC-GM, TFs+1000 (Ye et al. 2026)	1.22 Early precision ratio (TFs+1000 gene set; non-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 costok GRN on mHSC-GM, TFs+1000, non-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-1000-non-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 5, block 'Nonspecific', row 'mHSC-GM', column group 'costok', column 'scFoundation'
Configuration: scFoundation costok GRN (Ye et al. 2026)	Protocol: Ye et al. 2026 GRN reconstruction, TFs+1000, non-specific ChIP-seq reference Dataset subset: BEELINE mHSC-L, TFs+1000 (Ye et al. 2026)	1.02 AUPRC ratio (TFs+1000 gene set; non-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 costok GRN on mHSC-L, TFs+1000, non-specific ChIP-seq lit-cells-networks-20261011-ye2026grn-protocol-tf-plus-1000-non-specific-chip-seq Aggregation: Not reported Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models · Table 7, block 'Nonspecific', row 'mHSC-L', column group 'costok', 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-config-scfoundation-costok

areas: biological-networks; single-cell
contexts: research
method types: foundation_model
reported name: scFoundation costok
foundation model eligible: true
training setting: Zero-shot; pretrained weights, no fine-tuning
representation: cosine similarity of pretrained gene token embeddings (undirected)
source locator: Section 2.2; Table 3; Appendix A.2
missing metadata: version: reason: unreported; note: Source names no checkpoint; Table 3 gives size, layers and pretraining cells

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