OP3 small-molecule perturbations in primary PBMC cell types, split from the NeurIPS 2023 challenge train, public and private test partitions.
8 evaluations · 55 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Biolord* | Protocol: PerturBench v4 covariate transfer of small-molecule effects across PBMC cell types on OP3 Dataset subset: OP3 (PerturBench v4 split) | 0.051 ± 5 × 10 − 3 Perturbench cosine logfc rank fraction · lower Uncertainty: SD 0.005 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBiolord ∗ on PerturBench v4 op3 lit-cells-networks-20261011-perturbench-v4-protocol-op3 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 9, row 'Biolord ∗', column 'Cosine LogFC rank' |
| Configuration: Biolord* | Protocol: PerturBench v4 covariate transfer of small-molecule effects across PBMC cell types on OP3 Dataset subset: OP3 (PerturBench v4 split) | 0.28 ± 3 × 10 − 3 Perturbench cosine logfc fraction · higher Uncertainty: SD 0.003 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBiolord ∗ on PerturBench v4 op3 lit-cells-networks-20261011-perturbench-v4-protocol-op3 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 9, row 'Biolord ∗', column 'Cosine LogFC' |
| Configuration: Biolord* | Protocol: PerturBench v4 covariate transfer of small-molecule effects across PBMC cell types on OP3 Dataset subset: OP3 (PerturBench v4 split) | 0.000 ± 0 Recall (DEG recall: fraction of the top 20 ground-truth DEGs (scanpy t-scores against controls) recalled from predicted cells) fraction · higher Uncertainty: SD 0 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBiolord ∗ on PerturBench v4 op3 lit-cells-networks-20261011-perturbench-v4-protocol-op3 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 9, row 'Biolord ∗', column 'DEG recall' |
| Configuration: Biolord* | Protocol: PerturBench v4 covariate transfer of small-molecule effects across PBMC cell types on OP3 Dataset subset: OP3 (PerturBench v4 split) | 0.92 ± 5 × 10 − 3 Perturbench energy mmd (PCA space: top 256 principal components fitted on the ground-truth test split) unit-unreported · lower Uncertainty: SD 0.005 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBiolord ∗ on PerturBench v4 op3 lit-cells-networks-20261011-perturbench-v4-protocol-op3 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 9, row 'Biolord ∗', column 'MMD PCA' |
| Configuration: Biolord* | Protocol: PerturBench v4 covariate transfer of small-molecule effects across PBMC cell types on OP3 Dataset subset: OP3 (PerturBench v4 split) | 4.6 ± 2 × 10 − 2 Perturbench energy mmd (gene expression space) unit-unreported · lower Uncertainty: SD 0.02 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBiolord ∗ on PerturBench v4 op3 lit-cells-networks-20261011-perturbench-v4-protocol-op3 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 10, row 'Biolord ∗', column 'MMD' |
| Configuration: Biolord* | Protocol: PerturBench v4 covariate transfer of small-molecule effects across PBMC cell types on OP3 Dataset subset: OP3 (PerturBench v4 split) | 0.051 ± 6 × 10 − 3 Perturbench RMSE rank fraction · lower Uncertainty: SD 0.006 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBiolord ∗ on PerturBench v4 op3 lit-cells-networks-20261011-perturbench-v4-protocol-op3 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 10, row 'Biolord ∗', column 'RMSE mean rank' |
| Configuration: Biolord* | Protocol: PerturBench v4 covariate transfer of small-molecule effects across PBMC cell types on OP3 Dataset subset: OP3 (PerturBench v4 split) | 0.038 ± 8 × 10 − 5 Perturbench RMSE of mean unit-unreported · lower Uncertainty: SD 0.00008 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBiolord ∗ on PerturBench v4 op3 lit-cells-networks-20261011-perturbench-v4-protocol-op3 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 10, row 'Biolord ∗', column 'RMSE mean' |
| Configuration: CPA* | Protocol: PerturBench v4 covariate transfer of small-molecule effects across PBMC cell types on OP3 Dataset subset: OP3 (PerturBench v4 split) | 0.091 ± 2 × 10 − 3 Perturbench cosine logfc rank fraction · lower Uncertainty: SD 0.002 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcelit-cells-networks-20261011-perturbench-v4-protocol-op3 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 9, row 'CPA ∗', column 'Cosine LogFC rank' |
| Configuration: CPA* | Protocol: PerturBench v4 covariate transfer of small-molecule effects across PBMC cell types on OP3 Dataset subset: OP3 (PerturBench v4 split) | 0.39 ± 6 × 10 − 3 Perturbench cosine logfc fraction · higher Uncertainty: SD 0.006 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcelit-cells-networks-20261011-perturbench-v4-protocol-op3 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 9, row 'CPA ∗', column 'Cosine LogFC' |
| Configuration: CPA* | Protocol: PerturBench v4 covariate transfer of small-molecule effects across PBMC cell types on OP3 Dataset subset: OP3 (PerturBench v4 split) | 0.002 ± 2 × 10 − 4 Recall (DEG recall: fraction of the top 20 ground-truth DEGs (scanpy t-scores against controls) recalled from predicted cells) fraction · higher Uncertainty: SD 0.0002 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcelit-cells-networks-20261011-perturbench-v4-protocol-op3 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 9, row 'CPA ∗', column 'DEG recall' |
| Configuration: CPA* | Protocol: PerturBench v4 covariate transfer of small-molecule effects across PBMC cell types on OP3 Dataset subset: OP3 (PerturBench v4 split) | 0.71 ± 1 × 10 − 2 Perturbench energy mmd (PCA space: top 256 principal components fitted on the ground-truth test split) unit-unreported · lower Uncertainty: SD 0.01 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcelit-cells-networks-20261011-perturbench-v4-protocol-op3 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 9, row 'CPA ∗', column 'MMD PCA' |
| Configuration: CPA* | Protocol: PerturBench v4 covariate transfer of small-molecule effects across PBMC cell types on OP3 Dataset subset: OP3 (PerturBench v4 split) | 5.3 ± 3 × 10 − 2 Perturbench energy mmd (gene expression space) unit-unreported · lower Uncertainty: SD 0.03 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcelit-cells-networks-20261011-perturbench-v4-protocol-op3 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 10, row 'CPA ∗', column 'MMD' |
| Configuration: CPA* (noAdv) | Protocol: PerturBench v4 covariate transfer of small-molecule effects across PBMC cell types on OP3 Dataset subset: OP3 (PerturBench v4 split) | 0.076 ± 3 × 10 − 3 Perturbench cosine logfc rank fraction · lower Uncertainty: SD 0.003 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCPA ∗ (noAdv) on PerturBench v4 op3 lit-cells-networks-20261011-perturbench-v4-protocol-op3 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 9, row 'CPA ∗ (noAdv)', column 'Cosine LogFC rank' |
| Configuration: CPA* (noAdv) | Protocol: PerturBench v4 covariate transfer of small-molecule effects across PBMC cell types on OP3 Dataset subset: OP3 (PerturBench v4 split) | 0.32 ± 6 × 10 − 3 Perturbench cosine logfc fraction · higher Uncertainty: SD 0.006 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCPA ∗ (noAdv) on PerturBench v4 op3 lit-cells-networks-20261011-perturbench-v4-protocol-op3 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 9, row 'CPA ∗ (noAdv)', column 'Cosine LogFC' |
| Configuration: CPA* (noAdv) | Protocol: PerturBench v4 covariate transfer of small-molecule effects across PBMC cell types on OP3 Dataset subset: OP3 (PerturBench v4 split) | 0.000 ± 0 Recall (DEG recall: fraction of the top 20 ground-truth DEGs (scanpy t-scores against controls) recalled from predicted cells) fraction · higher Uncertainty: SD 0 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCPA ∗ (noAdv) on PerturBench v4 op3 lit-cells-networks-20261011-perturbench-v4-protocol-op3 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 9, row 'CPA ∗ (noAdv)', column 'DEG recall' |
| Configuration: CPA* (noAdv) | Protocol: PerturBench v4 covariate transfer of small-molecule effects across PBMC cell types on OP3 Dataset subset: OP3 (PerturBench v4 split) | 0.86 ± 1 × 10 − 2 Perturbench energy mmd (PCA space: top 256 principal components fitted on the ground-truth test split) unit-unreported · lower Uncertainty: SD 0.01 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCPA ∗ (noAdv) on PerturBench v4 op3 lit-cells-networks-20261011-perturbench-v4-protocol-op3 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 9, row 'CPA ∗ (noAdv)', column 'MMD PCA' |
| Configuration: CPA* (noAdv) | Protocol: PerturBench v4 covariate transfer of small-molecule effects across PBMC cell types on OP3 Dataset subset: OP3 (PerturBench v4 split) | 5.7 ± 1 × 10 − 2 Perturbench energy mmd (gene expression space) unit-unreported · lower Uncertainty: SD 0.01 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCPA ∗ (noAdv) on PerturBench v4 op3 lit-cells-networks-20261011-perturbench-v4-protocol-op3 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 10, row 'CPA ∗ (noAdv)', column 'MMD' |
| Configuration: CPA* (noAdv) | Protocol: PerturBench v4 covariate transfer of small-molecule effects across PBMC cell types on OP3 Dataset subset: OP3 (PerturBench v4 split) | 0.051 ± 4 × 10 − 3 Perturbench RMSE rank fraction · lower Uncertainty: SD 0.004 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCPA ∗ (noAdv) on PerturBench v4 op3 lit-cells-networks-20261011-perturbench-v4-protocol-op3 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 10, row 'CPA ∗ (noAdv)', column 'RMSE mean rank' |
| Configuration: CPA* (noAdv) | Protocol: PerturBench v4 covariate transfer of small-molecule effects across PBMC cell types on OP3 Dataset subset: OP3 (PerturBench v4 split) | 0.034 ± 4 × 10 − 4 Perturbench RMSE of mean unit-unreported · lower Uncertainty: SD 0.0004 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCPA ∗ (noAdv) on PerturBench v4 op3 lit-cells-networks-20261011-perturbench-v4-protocol-op3 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 10, row 'CPA ∗ (noAdv)', column 'RMSE mean' |
| Configuration: CPA* | Protocol: PerturBench v4 covariate transfer of small-molecule effects across PBMC cell types on OP3 Dataset subset: OP3 (PerturBench v4 split) | 0.062 ± 4 × 10 − 3 Perturbench RMSE rank fraction · lower Uncertainty: SD 0.004 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcelit-cells-networks-20261011-perturbench-v4-protocol-op3 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 10, row 'CPA ∗', column 'RMSE mean rank' |
| Configuration: CPA* | Protocol: PerturBench v4 covariate transfer of small-molecule effects across PBMC cell types on OP3 Dataset subset: OP3 (PerturBench v4 split) | 0.032 ± 2 × 10 − 4 Perturbench RMSE of mean unit-unreported · lower Uncertainty: SD 0.0002 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcelit-cells-networks-20261011-perturbench-v4-protocol-op3 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 10, row 'CPA ∗', column 'RMSE mean' |
| Configuration: Decoder | Protocol: PerturBench v4 covariate transfer of small-molecule effects across PBMC cell types on OP3 Dataset subset: OP3 (PerturBench v4 split) | 0.070 ± 5 × 10 − 3 Perturbench cosine logfc rank fraction · lower Uncertainty: SD 0.005 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcelit-cells-networks-20261011-perturbench-v4-protocol-op3 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 9, row 'Decoder', column 'Cosine LogFC rank' |
| Configuration: Decoder | Protocol: PerturBench v4 covariate transfer of small-molecule effects across PBMC cell types on OP3 Dataset subset: OP3 (PerturBench v4 split) | 0.32 ± 6 × 10 − 3 Perturbench cosine logfc fraction · higher Uncertainty: SD 0.006 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcelit-cells-networks-20261011-perturbench-v4-protocol-op3 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 9, row 'Decoder', column 'Cosine LogFC' |
| Configuration: Decoder | Protocol: PerturBench v4 covariate transfer of small-molecule effects across PBMC cell types on OP3 Dataset subset: OP3 (PerturBench v4 split) | 4.4 ± 1 × 10 − 2 Perturbench energy mmd (PCA space: top 256 principal components fitted on the ground-truth test split) unit-unreported · lower Uncertainty: SD 0.01 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcelit-cells-networks-20261011-perturbench-v4-protocol-op3 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 9, row 'Decoder', column 'MMD PCA' |
| Configuration: Decoder | Protocol: PerturBench v4 covariate transfer of small-molecule effects across PBMC cell types on OP3 Dataset subset: OP3 (PerturBench v4 split) | 11.0 ± 5 × 10 − 3 Perturbench energy mmd (gene expression space) unit-unreported · lower Uncertainty: SD 0.005 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcelit-cells-networks-20261011-perturbench-v4-protocol-op3 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 10, row 'Decoder', column 'MMD' |
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| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Source location Table 1; Appendix D.4 'OP3 splits' Context-only references | PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) Table 1; Appendix D.4 'OP3 splits' Version: arXiv 2408.10609v4, posted 2025-10-24 (NeurIPS 2025 Datasets and Benchmarks Track version) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact bytes of the arXiv HTML rendering of v4 as retrieved; arXiv may regenerate HTML, so the hash describes this retrieval. |
| Split OP3 small-molecule perturbations in primary PBMC cell types, split from the NeurIPS 2023 challenge train, public and private test partitions. Context-only references | PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) Table 1; Appendix D.4 'OP3 splits' Version: arXiv 2408.10609v4, posted 2025-10-24 (NeurIPS 2025 Datasets and Benchmarks Track version) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact bytes of the arXiv HTML rendering of v4 as retrieved; arXiv may regenerate HTML, so the hash describes this retrieval. |
| Description OP3 small-molecule perturbations in primary PBMC cell types, split from the NeurIPS 2023 challenge train, public and private test partitions. Context-only references | PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) Table 1; Appendix D.4 'OP3 splits' Version: arXiv 2408.10609v4, posted 2025-10-24 (NeurIPS 2025 Datasets and Benchmarks Track version) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact bytes of the arXiv HTML rendering of v4 as retrieved; arXiv may regenerate HTML, so the hash describes this retrieval. |
| Name OP3 (PerturBench v4 split) Context-only references | PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) Table 1; Appendix D.4 'OP3 splits' Version: arXiv 2408.10609v4, posted 2025-10-24 (NeurIPS 2025 Datasets and Benchmarks Track version) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact bytes of the arXiv HTML rendering of v4 as retrieved; arXiv may regenerate HTML, so the hash describes this retrieval. |
Release 2026-10-23-5347695500ed · Record review: source checked
Stable ID: lit-cells-networks-20261011-perturbench-v4-data-op3