File size: 3,613 Bytes
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name: budget_efficiency_benchmark
output_dir: results/budget_efficiency_benchmark
random_seed: 20260416
batch_size: 64
allow_resume: true
max_batches: 500
budgets: [100, 500, 2500, 5000, 10000]
time_importance_values: [0.0, 0.5, 1.0]
backend:
type: rdock
require_real_backend: true
n_runs: 1
mapper_radius: 6.0
command_timeout_seconds: 240
parallel_jobs: auto-minus-4
allow_skip_failed_ligands: true
max_failed_ligands: 200
encoding:
fingerprint_radius: 2
fingerprint_bits: 1024
generate_3d: false
feature_extraction:
compute_partial_charges: false
compute_sasa: false
clustering:
butina_cutoff: 0.35
n_hyperclusters: 40
scheduler:
init_coverage_fraction: 0.35
conservative_deprioritize: true
surrogate:
prefer_xgboost: true
n_estimators: 180
min_train_samples: 20
max_depth_small: 3
max_depth_large: 6
model_weight_schedule:
sample_knots: [20, 50, 100, 200, 500]
weight_knots: [0.1, 0.3, 0.5, 0.7, 0.9]
max_weight: 0.9
min_weight: 0.05
instability_threshold: 2.0
instability_decay: 0.25
early_stop:
min_evaluated: 600
patience_rounds: 8
min_model_weight: 0.35
quantile: 0.15
uncertainty_weight: 0.2
min_improvement: 0.02
exploration_margin: 0.45
exploitation_margin: 0.1
reference_evaluations: 10000
policies:
adaptive_hard_stop: { enabled: true }
adaptive_soft_stop:
enabled: true
soft_recovery_batches: 16
soft_threshold_relax: 0.35
soft_model_weight_cap: 0.45
soft_exploration_boost: 0.25
max_soft_recoveries: 1
adaptive_no_stop: { enabled: true }
adaptive_cluster_bootstrap:
enabled: true
cluster_bootstrap_rounds: 24
adaptive_soft_stop_cluster_floor:
enabled: true
cluster_bootstrap_rounds: 20
min_cluster_coverage: 0.60
min_hypercluster_coverage: 0.55
soft_recovery_batches: 20
soft_threshold_relax: 0.40
soft_model_weight_cap: 0.40
soft_exploration_boost: 0.30
pre_floor_model_weight_cap: 0.35
max_soft_recoveries: 2
matrix:
naive_random_seeds: [11, 22, 33]
cluster_naive_seeds: [101, 202, 303]
disk_guard:
min_free_gb: 10.0
projected_output_gb: 3.0
keep_raw_batches: 6
dataset_A:
name: dataset_A
protein_name: EGFR
target_id: egfr_budget
docking_reference_pdb: "4WKQ"
docking_target_path: data/targets/budget_efficiency_benchmark_A/egfr_4wkq.pdb
reference_id: ref_gefitinib
pdb_id: "4WKQ"
ligand_comp_id: "IRE"
reference_name: Gefitinib
reference_smiles: "COC1=C(C=C2C(=C1)N=CN=C2NC3=CC(=C(C=C3)F)Cl)OCCCN4CCOCC4"
benchmark_dataset:
output_dir: data/ligands/budget_efficiency_benchmark_A
target_size: 10000
shuffle_seed: 334455
reuse_existing: true
min_similarity_keep: 0.00
pubchem_max_records: 12000
pubchem_thresholds: [80]
chembl_target_id: CHEMBL203
chembl_max_rows: 0
allow_generated_fallback: true
dataset_B:
name: dataset_B
protein_name: ABL1
target_id: abl1_budget
docking_reference_pdb: "1IEP"
docking_target_path: data/targets/budget_efficiency_benchmark_B/abl1_1iep.pdb
reference_id: ref_imatinib
pdb_id: "1IEP"
ligand_comp_id: "STI"
reference_name: Imatinib
reference_smiles: "CC1=C(C=C(C=C1)NC(=O)C2=CC=C(C=C2)CN3CCN(CC3)C)NC4=NC=CC(=N4)C5=CN=CC=C5"
benchmark_dataset:
output_dir: data/ligands/budget_efficiency_benchmark_B
target_size: 10000
shuffle_seed: 556677
reuse_existing: true
min_similarity_keep: 0.00
pubchem_max_records: 12000
pubchem_thresholds: [80]
chembl_target_id: CHEMBL1862
chembl_max_rows: 0
allow_generated_fallback: true
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