Biomni_Comparative_Experiments / experiments /bioagent_bench /results /by_task /transcript-quant.json
| { | |
| "evaluated_at_unix": 1778738056.609411, | |
| "task_id": "transcript-quant", | |
| "runs_root": "/225040511/project/Hypo_Bio_OS/bioagent-bench-runs", | |
| "dataset_root": "/225040511/project/bioagent-bench/dataset", | |
| "manifest": { | |
| "mcp_root": "/225040511/project/Biomni/mcp_generated", | |
| "execution_python": "/225040511/miniconda3/envs/biomni_e1/bin/python", | |
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| ] | |
| }, | |
| "500": { | |
| "config": "/225040511/project/Biomni/experiments/mcp_tool_scaling/configs/mcp_scale_500.yaml", | |
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| ] | |
| } | |
| } | |
| }, | |
| "aggregate": { | |
| "run_count": 2, | |
| "mean_retrieval_recall@1": 0.25, | |
| "mean_retrieval_recall@3": 0.5, | |
| "mean_retrieval_recall@5": 1.0, | |
| "mean_retrieval_recall@10": 1.0, | |
| "mean_retrieval_recall@20": 1.0, | |
| "mean_retrieval_recall@50": 1.0, | |
| "tool_selection_accuracy": 1.0, | |
| "workflow_validity": 1.0, | |
| "execution_success_rate": 1.0, | |
| "mean_context_tokens_rough": 900.0, | |
| "mean_planning_latency_seconds": null | |
| }, | |
| "results": [ | |
| { | |
| "task_id": "transcript-quant", | |
| "run_dir": "/225040511/project/Hypo_Bio_OS/bioagent-bench-runs/transcript-quant_20260513_065059", | |
| "retrieval_recall_at_k": { | |
| "1": 0.0, | |
| "3": 0.5, | |
| "5": 1.0, | |
| "10": 1.0, | |
| "20": 1.0, | |
| "50": 1.0 | |
| }, | |
| "tool_selection_accuracy": true, | |
| "workflow_validity": { | |
| "valid": true, | |
| "steps_matched": 4, | |
| "steps_total": 4, | |
| "matched_step_names": [ | |
| "build_transcriptome_index", | |
| "quantify_paired_reads", | |
| "extract_counts", | |
| "write_tsv" | |
| ] | |
| }, | |
| "execution_success": true, | |
| "context_tokens_rough": 886, | |
| "planning_latency_seconds": null, | |
| "retrieved_candidate_count": 612, | |
| "execution_evidence_count": 2510 | |
| }, | |
| { | |
| "task_id": "transcript-quant", | |
| "run_dir": "/225040511/project/Hypo_Bio_OS/bioagent-bench-runs/transcript-quant_20260513_105632", | |
| "retrieval_recall_at_k": { | |
| "1": 0.5, | |
| "3": 0.5, | |
| "5": 1.0, | |
| "10": 1.0, | |
| "20": 1.0, | |
| "50": 1.0 | |
| }, | |
| "tool_selection_accuracy": true, | |
| "workflow_validity": { | |
| "valid": true, | |
| "steps_matched": 4, | |
| "steps_total": 4, | |
| "matched_step_names": [ | |
| "build_transcriptome_index", | |
| "quantify_paired_reads", | |
| "extract_counts", | |
| "write_tsv" | |
| ] | |
| }, | |
| "execution_success": true, | |
| "context_tokens_rough": 914, | |
| "planning_latency_seconds": null, | |
| "retrieved_candidate_count": 619, | |
| "execution_evidence_count": 2801 | |
| } | |
| ] | |
| } |