| # benchmark-triage-strategies |
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|
| ## EXECUTIVE DECISION |
| - decision: `USE cluster_only_triage` |
| - reason: `Model does not beat simple clustering in the independent benchmark.` |
| - recommended_strategy_best_hit: `random_cost_balanced` |
| - recommended_strategy_best_tradeoff: `reference_free_active_learning_v2::cluster_bandit` |
| - recommended_strategy_safest: `cluster_only_triage` |
| - recommended_strategy_final: `cluster_only_triage` |
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|
| ## Dataset validity |
| - dataset_dir: `data/datasets/rdock_3PTB_25k_pubchem_local` |
| - scientifically_valid_model_benchmark: `True` |
|
|
| ## Reference Ligand Baseline |
| - reference_ligand_available: `True` |
| - reference_ligand_baseline_score_n50: `-8.56014` |
|
|
| ## Benchmark mode |
| - independent_strategy_sampling: `true` |
| - shared_reference_stage: `false` |
| - reference_sample_docked_once_for_evaluation: `True` |
| - reference_sample_size: `300` |
| |
| ## Strategy comparison table |
| - cluster_only_triage: median_best_filtered_score `-40.17`, median_top5_mean_filtered_score `-33.229092548674544`, median_top10_mean_filtered_score `-31.733016274337267`, median_reduction_fraction `0.9492`, median_total_runs_spent `124670.0`, median_top5pct_recall `1.0` |
| - cheap_descriptor_filter_only: median_best_filtered_score `-40.1748`, median_top5_mean_filtered_score `-32.80636800080102`, median_top10_mean_filtered_score `-30.973934000400515`, median_reduction_fraction `0.95`, median_total_runs_spent `124560.0`, median_top5pct_recall `0.7333333333333333` |
| - random_cost_balanced: median_best_filtered_score `-50.1126`, median_top5_mean_filtered_score `-36.376689471691215`, median_top10_mean_filtered_score `-33.623753936310976`, median_reduction_fraction `0.9`, median_total_runs_spent `125000.0`, median_top5pct_recall `0.0` |
| - diverse_random_cost_balanced: median_best_filtered_score `-42.5011`, median_top5_mean_filtered_score `-35.63192`, median_top10_mean_filtered_score `-33.28833611220234`, median_reduction_fraction `0.9`, median_total_runs_spent `125000.0`, median_top5pct_recall `0.26666666666666666` |
| - single_fidelity_cost_balanced: median_best_filtered_score `-42.8697`, median_top5_mean_filtered_score `-35.794622588693315`, median_top10_mean_filtered_score `-32.77415209590938`, median_reduction_fraction `0.9`, median_total_runs_spent `125000.0`, median_top5pct_recall `0.3333333333333333` |
| - reference_free_active_learning_v2::cluster_bandit: median_best_filtered_score `-37.1844`, median_top5_mean_filtered_score `-34.26819999999999`, median_top10_mean_filtered_score `-32.90156`, median_reduction_fraction `0.95`, median_total_runs_spent `35345.0`, median_top5pct_recall `0.8666666666666667` |
| |
| ## Plots |
| - `results/benchmark_fixes/plots/strategy_comparison_recall_cost.png` |
| - `results/benchmark_fixes/plots/best_score_by_strategy.png` |
| - `results/benchmark_fixes/plots/false_negative_rate_by_strategy.png` |
| - `results/benchmark_fixes/plots/energy_timeline_per_strategy.png` |
| - `results/benchmark_fixes/plots/energy_timeline_per_strategy_per_seed.png` |
| - `results/benchmark_fixes/plots/energy_timeline_per_model_policy.png` |
| - `results/benchmark_fixes/plots/cumulative_best_filtered_score_vs_runs.png` |
| - `results/benchmark_fixes/plots/cumulative_best_filtered_score_vs_walltime.png` |
| - `results/benchmark_fixes/plots/topk_score_progression.png` |
| - `results/benchmark_fixes/plots/survivor_pool_size_timeline.png` |
| - `results/benchmark_fixes/plots/acquisition_component_timeline.png` |
| - `results/benchmark_fixes/plots/cluster_coverage_timeline.png` |
| - `results/benchmark_fixes/plots/promotion_funnel_per_strategy.png` |
| - `results/benchmark_fixes/plots/score_distribution_by_fidelity_and_strategy.png` |
| - `results/benchmark_fixes/plots/top_hits_component_breakdown.png` |
| - `results/benchmark_fixes/plots/top5_mean_score_by_strategy.png` |
| - `results/benchmark_fixes/plots/top10_mean_score_by_strategy.png` |
| - `results/benchmark_fixes/plots/reduction_vs_best_score_scatter.png` |
| - `results/benchmark_fixes/plots/cost_saved_vs_best_score_scatter.png` |
| - `results/benchmark_fixes/plots/cost_saved_vs_top10_score_scatter.png` |
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