AIDE v6.3.3, GPT-4.1 backend (BioML-bench)
AIDE v6.3.3, GPT-4.1 backend: AIDE (v6.3.3) with GPT-4.1 as LLM backend.
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
6 evaluations · 23 results. Different protocols are not a single leaderboard.
Sorted by Leaderboard percentile (mean over tasks in the domain; non-penalized: runs without a valid submission omitted) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
| Tested configuration | Protocol and dataset | Leaderboard percentile (mean over tasks in the domain; non-penalized: runs without a valid submission omitted) | Leaderboard percentile (mean over tasks in the domain; penalized: runs without a valid submission scored as percentile 0) | Proportion (share of tasks that yield a valid, gradable submission (Section 3.4 definition); penalized: runs without a valid submission scored as percentile 0) | Proportion (share of tasks where the agent reaches a public leaderboard medal threshold, MLE-bench definition (Section 3.4); non-penalized: runs without a valid submission omitted) | Proportion (share of tasks where the agent reaches a public leaderboard medal threshold, MLE-bench definition (Section 3.4); penalized: runs without a valid submission scored as percentile 0) | Proportion (share of tasks where the agent's mean score exceeds the median human leaderboard submission (Section 3.4 definition); non-penalized: runs without a valid submission omitted) | Proportion (share of tasks where the agent's mean score exceeds the median human leaderboard submission (Section 3.4 definition); penalized: runs without a valid submission scored as percentile 0) | Rank (mean relative rank among the five Table 4 agents (Dummy, MLAgentBench, AIDE, STELLA, Biomni) by leaderboard percentile, over tasks in the domain; non-penalized: runs without a valid submission omitted) | Rank (mean relative rank among the five Table 4 agents (Dummy, MLAgentBench, AIDE, STELLA, Biomni) by leaderboard percentile, over tasks in the domain; penalized: runs without a valid submission scored as percentile 0) |
|---|---|---|---|---|---|---|---|---|---|---|
| AIDE v6.3.3, GPT-4.1 backend (BioML-bench)Evaluation | BioML-bench single cell omics domain: agent leaderboard percentile over 5 tasks, BioML-bench v0.1-alpha single cell omics tasks (5 tasks) | 60.67 ± 11.16% (best in column) | Not reported | Not reported | 33.3 ± 19.0% (best in column) | Not reported | 58.3 ± 16.7% (best in column) | Not reported | 2.30 ± 0.54 | Not reported |
| AIDE v6.3.3, GPT-4.1 backend (BioML-bench)Evaluation | BioML-bench protein engineering domain: agent leaderboard percentile over 6 tasks, BioML-bench v0.1-alpha protein engineering tasks (6 tasks) | 35.99 ± 10.96% | Not reported | Not reported | 16.7 ± 11.4% | Not reported | 38.9 ± 15.9% | Not reported | Not reported | Not reported |
| AIDE v6.3.3, GPT-4.1 backend (BioML-bench)Evaluation | BioML-bench drug discovery domain: agent leaderboard percentile over 9 tasks, BioML-bench v0.1-alpha drug discovery tasks (9 tasks) | 31.06 ± 8.88% | Not reported | Not reported | 7.4 ± 7.4% | Not reported | 30.6 ± 13.3% | Not reported | Not reported | Not reported |
| AIDE v6.3.3, GPT-4.1 backend (BioML-bench)Evaluation | BioML-bench drug discovery domain: agent leaderboard percentile over 9 tasks, BioML-bench v0.1-alpha drug discovery tasks (9 tasks) | Not reported | 24.75 ± 7.23% | 80.6% | Not reported | 5.6 ± 5.6% | Not reported | 25.0 ± 11.0% | Not reported | Not reported |
| AIDE v6.3.3, GPT-4.1 backend (BioML-bench)Evaluation | BioML-bench protein engineering domain: agent leaderboard percentile over 6 tasks, BioML-bench v0.1-alpha protein engineering tasks (6 tasks) | Not reported | 24.50 ± 6.90% | 75% | Not reported | 12.5 ± 8.5% | Not reported | 25.0 ± 9.1% | Not reported | Not reported |
| AIDE v6.3.3, GPT-4.1 backend (BioML-bench)Evaluation | BioML-bench single cell omics domain: agent leaderboard percentile over 5 tasks, BioML-bench v0.1-alpha single cell omics tasks (5 tasks) | Not reported | 53.17 ± 14.86% (best in column) | 85% (best in column) | Not reported | 35.0 ± 18.7% (best in column) | Not reported | 55.0 ± 16.6% (best in column) | Not reported | 2.70 ± 0.44 |
All 23 result rows with coverage, uncertainty and sources
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: AIDE v6.3.3, GPT-4.1 backend (BioML-bench) | Protocol: BioML-bench drug discovery domain: agent leaderboard percentile over 9 tasks Dataset subset: BioML-bench v0.1-alpha drug discovery tasks (9 tasks) | 30.6 ± 13.3% Proportion (share of tasks where the agent's mean score exceeds the median human leaderboard submission (Section 3.4 definition); non-penalized: runs without a valid submission omitted) percent · higher Uncertainty: ± 13.3 (type not stated). Table 4 caption does not name the spread. Figures 2 and 4 show per-domain leaderboard percentiles as mean ± SEM across tasks; the Table 2 caption refers to the reported SEM. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDE on BioML-bench drug discovery (non-penalized) lit-agents-20261013-biomlbench-protocol-drug-discovery Aggregation: Not reported BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML · Table 4 (page 12), block 'Non-penalized', domain 'Drug Discovery', row 'AIDE', column 'Above Median (%)' |
| Configuration: AIDE v6.3.3, GPT-4.1 backend (BioML-bench) | Protocol: BioML-bench drug discovery domain: agent leaderboard percentile over 9 tasks Dataset subset: BioML-bench v0.1-alpha drug discovery tasks (9 tasks) | 7.4 ± 7.4% Proportion (share of tasks where the agent reaches a public leaderboard medal threshold, MLE-bench definition (Section 3.4); non-penalized: runs without a valid submission omitted) percent · higher Uncertainty: ± 7.4 (type not stated). Table 4 caption does not name the spread. Figures 2 and 4 show per-domain leaderboard percentiles as mean ± SEM across tasks; the Table 2 caption refers to the reported SEM. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDE on BioML-bench drug discovery (non-penalized) lit-agents-20261013-biomlbench-protocol-drug-discovery Aggregation: Not reported BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML · Table 4 (page 12), block 'Non-penalized', domain 'Drug Discovery', row 'AIDE', column 'Any Medal (%)' |
| Configuration: AIDE v6.3.3, GPT-4.1 backend (BioML-bench) | Protocol: BioML-bench drug discovery domain: agent leaderboard percentile over 9 tasks Dataset subset: BioML-bench v0.1-alpha drug discovery tasks (9 tasks) | 31.06 ± 8.88% Leaderboard percentile (mean over tasks in the domain; non-penalized: runs without a valid submission omitted) percent · higher Uncertainty: ± 8.88 (type not stated). Table 4 caption does not name the spread. Figures 2 and 4 show per-domain leaderboard percentiles as mean ± SEM across tasks; the Table 2 caption refers to the reported SEM. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDE on BioML-bench drug discovery (non-penalized) lit-agents-20261013-biomlbench-protocol-drug-discovery Aggregation: Not reported BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML · Table 4 (page 12), block 'Non-penalized', domain 'Drug Discovery', row 'AIDE', column 'Leaderboard Percentile' |
| Configuration: AIDE v6.3.3, GPT-4.1 backend (BioML-bench) | Protocol: BioML-bench drug discovery domain: agent leaderboard percentile over 9 tasks Dataset subset: BioML-bench v0.1-alpha drug discovery tasks (9 tasks) | 25.0 ± 11.0% Proportion (share of tasks where the agent's mean score exceeds the median human leaderboard submission (Section 3.4 definition); penalized: runs without a valid submission scored as percentile 0) percent · higher Uncertainty: ± 11.0 (type not stated). Table 4 caption does not name the spread. Figures 2 and 4 show per-domain leaderboard percentiles as mean ± SEM across tasks; the Table 2 caption refers to the reported SEM. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDE on BioML-bench drug discovery (penalized) lit-agents-20261013-biomlbench-protocol-drug-discovery Aggregation: Not reported BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML · Table 4 (page 12), block 'Penalized', domain 'Drug Discovery', row 'AIDE', column 'Above Median (%)' |
| Configuration: AIDE v6.3.3, GPT-4.1 backend (BioML-bench) | Protocol: BioML-bench drug discovery domain: agent leaderboard percentile over 9 tasks Dataset subset: BioML-bench v0.1-alpha drug discovery tasks (9 tasks) | 5.6 ± 5.6% Proportion (share of tasks where the agent reaches a public leaderboard medal threshold, MLE-bench definition (Section 3.4); penalized: runs without a valid submission scored as percentile 0) percent · higher Uncertainty: ± 5.6 (type not stated). Table 4 caption does not name the spread. Figures 2 and 4 show per-domain leaderboard percentiles as mean ± SEM across tasks; the Table 2 caption refers to the reported SEM. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDE on BioML-bench drug discovery (penalized) lit-agents-20261013-biomlbench-protocol-drug-discovery Aggregation: Not reported BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML · Table 4 (page 12), block 'Penalized', domain 'Drug Discovery', row 'AIDE', column 'Any Medal (%)' |
| Configuration: AIDE v6.3.3, GPT-4.1 backend (BioML-bench) | Protocol: BioML-bench drug discovery domain: agent leaderboard percentile over 9 tasks Dataset subset: BioML-bench v0.1-alpha drug discovery tasks (9 tasks) | 80.6% Proportion (share of tasks that yield a valid, gradable submission (Section 3.4 definition); penalized: runs without a valid submission scored as percentile 0) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDE on BioML-bench drug discovery (penalized) lit-agents-20261013-biomlbench-protocol-drug-discovery Aggregation: Not reported BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML · Table 4 (page 12), block 'Penalized', domain 'Drug Discovery', row 'AIDE', column 'Completion Rate (%)' |
| Configuration: AIDE v6.3.3, GPT-4.1 backend (BioML-bench) | Protocol: BioML-bench drug discovery domain: agent leaderboard percentile over 9 tasks Dataset subset: BioML-bench v0.1-alpha drug discovery tasks (9 tasks) | 24.75 ± 7.23% Leaderboard percentile (mean over tasks in the domain; penalized: runs without a valid submission scored as percentile 0) percent · higher Uncertainty: ± 7.23 (type not stated). Table 4 caption does not name the spread. Figures 2 and 4 show per-domain leaderboard percentiles as mean ± SEM across tasks; the Table 2 caption refers to the reported SEM. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDE on BioML-bench drug discovery (penalized) lit-agents-20261013-biomlbench-protocol-drug-discovery Aggregation: Not reported BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML · Table 4 (page 12), block 'Penalized', domain 'Drug Discovery', row 'AIDE', column 'Leaderboard Percentile' |
| Configuration: AIDE v6.3.3, GPT-4.1 backend (BioML-bench) | Protocol: BioML-bench protein engineering domain: agent leaderboard percentile over 6 tasks Dataset subset: BioML-bench v0.1-alpha protein engineering tasks (6 tasks) | 38.9 ± 15.9% Proportion (share of tasks where the agent's mean score exceeds the median human leaderboard submission (Section 3.4 definition); non-penalized: runs without a valid submission omitted) percent · higher Uncertainty: ± 15.9 (type not stated). Table 4 caption does not name the spread. Figures 2 and 4 show per-domain leaderboard percentiles as mean ± SEM across tasks; the Table 2 caption refers to the reported SEM. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDE on BioML-bench protein engineering (non-penalized) lit-agents-20261013-biomlbench-protocol-protein-engineering Aggregation: Not reported BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML · Table 4 (page 12), block 'Non-penalized', domain 'Protein Engineering', row 'AIDE', column 'Above Median (%)' |
| Configuration: AIDE v6.3.3, GPT-4.1 backend (BioML-bench) | Protocol: BioML-bench protein engineering domain: agent leaderboard percentile over 6 tasks Dataset subset: BioML-bench v0.1-alpha protein engineering tasks (6 tasks) | 16.7 ± 11.4% Proportion (share of tasks where the agent reaches a public leaderboard medal threshold, MLE-bench definition (Section 3.4); non-penalized: runs without a valid submission omitted) percent · higher Uncertainty: ± 11.4 (type not stated). Table 4 caption does not name the spread. Figures 2 and 4 show per-domain leaderboard percentiles as mean ± SEM across tasks; the Table 2 caption refers to the reported SEM. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDE on BioML-bench protein engineering (non-penalized) lit-agents-20261013-biomlbench-protocol-protein-engineering Aggregation: Not reported BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML · Table 4 (page 12), block 'Non-penalized', domain 'Protein Engineering', row 'AIDE', column 'Any Medal (%)' |
| Configuration: AIDE v6.3.3, GPT-4.1 backend (BioML-bench) | Protocol: BioML-bench protein engineering domain: agent leaderboard percentile over 6 tasks Dataset subset: BioML-bench v0.1-alpha protein engineering tasks (6 tasks) | 35.99 ± 10.96% Leaderboard percentile (mean over tasks in the domain; non-penalized: runs without a valid submission omitted) percent · higher Uncertainty: ± 10.96 (type not stated). Table 4 caption does not name the spread. Figures 2 and 4 show per-domain leaderboard percentiles as mean ± SEM across tasks; the Table 2 caption refers to the reported SEM. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDE on BioML-bench protein engineering (non-penalized) lit-agents-20261013-biomlbench-protocol-protein-engineering Aggregation: Not reported BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML · Table 4 (page 12), block 'Non-penalized', domain 'Protein Engineering', row 'AIDE', column 'Leaderboard Percentile' |
| Configuration: AIDE v6.3.3, GPT-4.1 backend (BioML-bench) | Protocol: BioML-bench protein engineering domain: agent leaderboard percentile over 6 tasks Dataset subset: BioML-bench v0.1-alpha protein engineering tasks (6 tasks) | 25.0 ± 9.1% Proportion (share of tasks where the agent's mean score exceeds the median human leaderboard submission (Section 3.4 definition); penalized: runs without a valid submission scored as percentile 0) percent · higher Uncertainty: ± 9.1 (type not stated). Table 4 caption does not name the spread. Figures 2 and 4 show per-domain leaderboard percentiles as mean ± SEM across tasks; the Table 2 caption refers to the reported SEM. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDE on BioML-bench protein engineering (penalized) lit-agents-20261013-biomlbench-protocol-protein-engineering Aggregation: Not reported BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML · Table 4 (page 12), block 'Penalized', domain 'Protein Engineering', row 'AIDE', column 'Above Median (%)' |
| Configuration: AIDE v6.3.3, GPT-4.1 backend (BioML-bench) | Protocol: BioML-bench protein engineering domain: agent leaderboard percentile over 6 tasks Dataset subset: BioML-bench v0.1-alpha protein engineering tasks (6 tasks) | 12.5 ± 8.5% Proportion (share of tasks where the agent reaches a public leaderboard medal threshold, MLE-bench definition (Section 3.4); penalized: runs without a valid submission scored as percentile 0) percent · higher Uncertainty: ± 8.5 (type not stated). Table 4 caption does not name the spread. Figures 2 and 4 show per-domain leaderboard percentiles as mean ± SEM across tasks; the Table 2 caption refers to the reported SEM. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDE on BioML-bench protein engineering (penalized) lit-agents-20261013-biomlbench-protocol-protein-engineering Aggregation: Not reported BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML · Table 4 (page 12), block 'Penalized', domain 'Protein Engineering', row 'AIDE', column 'Any Medal (%)' |
| Configuration: AIDE v6.3.3, GPT-4.1 backend (BioML-bench) | Protocol: BioML-bench protein engineering domain: agent leaderboard percentile over 6 tasks Dataset subset: BioML-bench v0.1-alpha protein engineering tasks (6 tasks) | 75% Proportion (share of tasks that yield a valid, gradable submission (Section 3.4 definition); penalized: runs without a valid submission scored as percentile 0) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDE on BioML-bench protein engineering (penalized) lit-agents-20261013-biomlbench-protocol-protein-engineering Aggregation: Not reported BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML · Table 4 (page 12), block 'Penalized', domain 'Protein Engineering', row 'AIDE', column 'Completion Rate (%)' |
| Configuration: AIDE v6.3.3, GPT-4.1 backend (BioML-bench) | Protocol: BioML-bench protein engineering domain: agent leaderboard percentile over 6 tasks Dataset subset: BioML-bench v0.1-alpha protein engineering tasks (6 tasks) | 24.50 ± 6.90% Leaderboard percentile (mean over tasks in the domain; penalized: runs without a valid submission scored as percentile 0) percent · higher Uncertainty: ± 6.90 (type not stated). Table 4 caption does not name the spread. Figures 2 and 4 show per-domain leaderboard percentiles as mean ± SEM across tasks; the Table 2 caption refers to the reported SEM. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDE on BioML-bench protein engineering (penalized) lit-agents-20261013-biomlbench-protocol-protein-engineering Aggregation: Not reported BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML · Table 4 (page 12), block 'Penalized', domain 'Protein Engineering', row 'AIDE', column 'Leaderboard Percentile' |
| Configuration: AIDE v6.3.3, GPT-4.1 backend (BioML-bench) | Protocol: BioML-bench single cell omics domain: agent leaderboard percentile over 5 tasks Dataset subset: BioML-bench v0.1-alpha single cell omics tasks (5 tasks) | 58.3 ± 16.7% Proportion (share of tasks where the agent's mean score exceeds the median human leaderboard submission (Section 3.4 definition); non-penalized: runs without a valid submission omitted) percent · higher Uncertainty: ± 16.7 (type not stated). Table 4 caption does not name the spread. Figures 2 and 4 show per-domain leaderboard percentiles as mean ± SEM across tasks; the Table 2 caption refers to the reported SEM. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDE on BioML-bench single cell omics (non-penalized) lit-agents-20261013-biomlbench-protocol-single-cell-omics Aggregation: Not reported BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML · Table 4 (page 12), block 'Non-penalized', domain 'Single Cell Omics', row 'AIDE', column 'Above Median (%)' |
| Configuration: AIDE v6.3.3, GPT-4.1 backend (BioML-bench) | Protocol: BioML-bench single cell omics domain: agent leaderboard percentile over 5 tasks Dataset subset: BioML-bench v0.1-alpha single cell omics tasks (5 tasks) | 33.3 ± 19.0% Proportion (share of tasks where the agent reaches a public leaderboard medal threshold, MLE-bench definition (Section 3.4); non-penalized: runs without a valid submission omitted) percent · higher Uncertainty: ± 19.0 (type not stated). Table 4 caption does not name the spread. Figures 2 and 4 show per-domain leaderboard percentiles as mean ± SEM across tasks; the Table 2 caption refers to the reported SEM. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDE on BioML-bench single cell omics (non-penalized) lit-agents-20261013-biomlbench-protocol-single-cell-omics Aggregation: Not reported BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML · Table 4 (page 12), block 'Non-penalized', domain 'Single Cell Omics', row 'AIDE', column 'Any Medal (%)' |
| Configuration: AIDE v6.3.3, GPT-4.1 backend (BioML-bench) | Protocol: BioML-bench single cell omics domain: agent leaderboard percentile over 5 tasks Dataset subset: BioML-bench v0.1-alpha single cell omics tasks (5 tasks) | 60.67 ± 11.16% Leaderboard percentile (mean over tasks in the domain; non-penalized: runs without a valid submission omitted) percent · higher Uncertainty: ± 11.16 (type not stated). Table 4 caption does not name the spread. Figures 2 and 4 show per-domain leaderboard percentiles as mean ± SEM across tasks; the Table 2 caption refers to the reported SEM. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDE on BioML-bench single cell omics (non-penalized) lit-agents-20261013-biomlbench-protocol-single-cell-omics Aggregation: Not reported BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML · Table 4 (page 12), block 'Non-penalized', domain 'Single Cell Omics', row 'AIDE', column 'Leaderboard Percentile' |
| Configuration: AIDE v6.3.3, GPT-4.1 backend (BioML-bench) | Protocol: BioML-bench single cell omics domain: agent leaderboard percentile over 5 tasks Dataset subset: BioML-bench v0.1-alpha single cell omics tasks (5 tasks) | 2.30 ± 0.54 Rank (mean relative rank among the five Table 4 agents (Dummy, MLAgentBench, AIDE, STELLA, Biomni) by leaderboard percentile, over tasks in the domain; non-penalized: runs without a valid submission omitted) unitless · lower Uncertainty: ± 0.54 (type not stated). Table 4 caption does not name the spread. Figures 2 and 4 show per-domain leaderboard percentiles as mean ± SEM across tasks; the Table 2 caption refers to the reported SEM. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDE on BioML-bench single cell omics (non-penalized) lit-agents-20261013-biomlbench-protocol-single-cell-omics Aggregation: Not reported BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML · Table 4 (page 12), block 'Non-penalized', domain 'Single Cell Omics', row 'AIDE', column 'Mean Rank' |
| Configuration: AIDE v6.3.3, GPT-4.1 backend (BioML-bench) | Protocol: BioML-bench single cell omics domain: agent leaderboard percentile over 5 tasks Dataset subset: BioML-bench v0.1-alpha single cell omics tasks (5 tasks) | 55.0 ± 16.6% Proportion (share of tasks where the agent's mean score exceeds the median human leaderboard submission (Section 3.4 definition); penalized: runs without a valid submission scored as percentile 0) percent · higher Uncertainty: ± 16.6 (type not stated). Table 4 caption does not name the spread. Figures 2 and 4 show per-domain leaderboard percentiles as mean ± SEM across tasks; the Table 2 caption refers to the reported SEM. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDE on BioML-bench single cell omics (penalized) lit-agents-20261013-biomlbench-protocol-single-cell-omics Aggregation: Not reported BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML · Table 4 (page 12), block 'Penalized', domain 'Single Cell Omics', row 'AIDE', column 'Above Median (%)' |
| Configuration: AIDE v6.3.3, GPT-4.1 backend (BioML-bench) | Protocol: BioML-bench single cell omics domain: agent leaderboard percentile over 5 tasks Dataset subset: BioML-bench v0.1-alpha single cell omics tasks (5 tasks) | 35.0 ± 18.7% Proportion (share of tasks where the agent reaches a public leaderboard medal threshold, MLE-bench definition (Section 3.4); penalized: runs without a valid submission scored as percentile 0) percent · higher Uncertainty: ± 18.7 (type not stated). Table 4 caption does not name the spread. Figures 2 and 4 show per-domain leaderboard percentiles as mean ± SEM across tasks; the Table 2 caption refers to the reported SEM. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDE on BioML-bench single cell omics (penalized) lit-agents-20261013-biomlbench-protocol-single-cell-omics Aggregation: Not reported BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML · Table 4 (page 12), block 'Penalized', domain 'Single Cell Omics', row 'AIDE', column 'Any Medal (%)' |
| Configuration: AIDE v6.3.3, GPT-4.1 backend (BioML-bench) | Protocol: BioML-bench single cell omics domain: agent leaderboard percentile over 5 tasks Dataset subset: BioML-bench v0.1-alpha single cell omics tasks (5 tasks) | 85% Proportion (share of tasks that yield a valid, gradable submission (Section 3.4 definition); penalized: runs without a valid submission scored as percentile 0) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDE on BioML-bench single cell omics (penalized) lit-agents-20261013-biomlbench-protocol-single-cell-omics Aggregation: Not reported BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML · Table 4 (page 12), block 'Penalized', domain 'Single Cell Omics', row 'AIDE', column 'Completion Rate (%)' |
| Configuration: AIDE v6.3.3, GPT-4.1 backend (BioML-bench) | Protocol: BioML-bench single cell omics domain: agent leaderboard percentile over 5 tasks Dataset subset: BioML-bench v0.1-alpha single cell omics tasks (5 tasks) | 53.17 ± 14.86% Leaderboard percentile (mean over tasks in the domain; penalized: runs without a valid submission scored as percentile 0) percent · higher Uncertainty: ± 14.86 (type not stated). Table 4 caption does not name the spread. Figures 2 and 4 show per-domain leaderboard percentiles as mean ± SEM across tasks; the Table 2 caption refers to the reported SEM. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDE on BioML-bench single cell omics (penalized) lit-agents-20261013-biomlbench-protocol-single-cell-omics Aggregation: Not reported BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML · Table 4 (page 12), block 'Penalized', domain 'Single Cell Omics', row 'AIDE', column 'Leaderboard Percentile' |
| Configuration: AIDE v6.3.3, GPT-4.1 backend (BioML-bench) | Protocol: BioML-bench single cell omics domain: agent leaderboard percentile over 5 tasks Dataset subset: BioML-bench v0.1-alpha single cell omics tasks (5 tasks) | 2.70 ± 0.44 Rank (mean relative rank among the five Table 4 agents (Dummy, MLAgentBench, AIDE, STELLA, Biomni) by leaderboard percentile, over tasks in the domain; penalized: runs without a valid submission scored as percentile 0) unitless · lower Uncertainty: ± 0.44 (type not stated). Table 4 caption does not name the spread. Figures 2 and 4 show per-domain leaderboard percentiles as mean ± SEM across tasks; the Table 2 caption refers to the reported SEM. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDE on BioML-bench single cell omics (penalized) lit-agents-20261013-biomlbench-protocol-single-cell-omics Aggregation: Not reported BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML · Table 4 (page 12), block 'Penalized', domain 'Single Cell Omics', row 'AIDE', column 'Mean Rank' |
Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.
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Evidence
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Evidence table
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2 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Parameters AIDE (v6.3.3) with GPT-4.1 as LLM backend. The repository installs it from the fork github.com/AIxBio/aideml_bmlb (agents/aide/requirements.txt). Individual claims | science-machine/biomlbench repository at commit 673f3d8 Repository agents/aide/config.yaml and agents/aide/requirements.txt at commit 673f3d8 Version: Git commit 673f3d8d3462fc6cdcbbd9695fba612b9332ca65 (2025-09-14, head of main at retrieval); README title 'BioML-bench (v0.1-alpha)' | conflicting claim ["source-hash-verification","independent-cell-check"] · 2026-10-13 Audit detailsIndependent review 2026-10-13: matched the cited repository file at commit 673f3d8. Conflicting source claim: Field: Claim: lit-agents-20261013-biomlbench-claim-aide-repo-llm Source artifact SHA-256: Hash scope: SHA-256 of the codeload tar.gz archive for the commit; two downloads gave identical bytes. Per-file hashes of the files cited are in sources.md. Extraction artifact SHA-256: |
| Version v6.3.3 Individual claims | BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML Section 3.3 Version: bioRxiv 2025.09.01.673319 version 3, posted 2025-09-28 (versions 1 and 2 posted 2025-09-04 and 2025-09-07) | conflicting claim ["source-hash-verification","pdf-text-parse","independent-cell-check"] · 2026-10-13 Audit detailsIndependent review 2026-10-13: wording found at the locator. Conflicting source claim: Field: Claim: lit-agents-20261013-biomlbench-claim-aide-version Source artifact SHA-256: Hash scope: SHA-256 of the PDF bytes as downloaded 2026-10-13T12:38:42Z. bioRxiv rewrites the XMP dates and document IDs, the Info ModDate and the trailer /ID on download, so a re-download does not reproduce the hash; the review found a fresh copy differing only in those 43 bytes, with an identical text layer. Extraction artifact SHA-256: |
Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
2 source records and release history
- BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML · Original source · bioRxiv 2025.09.01.673319 version 3, posted 2025-09-28 (versions 1 and 2 posted 2025-09-04 and 2025-09-07)
- science-machine/biomlbench repository at commit 673f3d8 · Original source · Git commit 673f3d8d3462fc6cdcbbd9695fba612b9332ca65 (2025-09-14, head of main at retrieval); README title 'BioML-bench (v0.1-alpha)'
Technical metadata and extraction receipts
Stable ID: lit-agents-20261013-biomlbench-config-aide-gpt-4-1
- areas
- molecular-interactions; protein-function; single-cell
- contexts
- research
- method types
- foundation_model
- reported name
- AIDE
- version
- v6.3.3
- parameters
- AIDE (v6.3.3) with GPT-4.1 as LLM backend. The repository installs it from the fork github.com/AIxBio/aideml_bmlb (agents/aide/requirements.txt).
- source locator
- Section 3.3; repository agents/aide/requirements.txt
- access reuse
- Open-source agent; LLM backend is a hosted API
- limitations
- Run by the BioML-bench authors in the configuration described in Section 3.3; four replicate runs per task.
- provenance note
- Agent configuration as run in BioML-bench (bioRxiv v3).
Related records
- configuration of: AIDE
- uses model: GPT-4.1
- subject: config-aide-gpt-4-1: attributes.parameters
- subject: config-aide-gpt-4-1: attributes.version
- system: AIDE on BioML-bench drug discovery (non-penalized)
- system: AIDE on BioML-bench drug discovery (penalized)
- system: AIDE on BioML-bench protein engineering (non-penalized)
- system: AIDE on BioML-bench protein engineering (penalized)
- system: AIDE on BioML-bench single cell omics (non-penalized)
- system: AIDE on BioML-bench single cell omics (penalized)