File size: 4,214 Bytes
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name: multifidelity_regularized
output_dir: results/multifidelity_regularized
random_seed: 20260416
budgets: [50, 100, 150, 200, 250, 300, 400, 500, 750, 1000, 1500, 2000, 2500, 5000, 10000]
haddock_budgets: [250]
dynamic_predock_batch_size: 256
dynamic_predock_max_batches: 4
dynamic_predock_flush_every_batches: 1
wall_time_per_dock: 0.5
max_wall_time_seconds: 7200
n_baseline_seeds: 3
allow_resume: true
parameters:
max_budget: 10000
min_budget: 100
epsilon_quality_target: 0.10
time_importance: 0.6
shortlist_fraction: 0.35
haddock_shortlist_size: 4
stopping:
target_rank_percentile: 1.0
peak_patience: 32
min_improvement_delta: 0.02
exploration:
stagnation_patience: 20
diversity_boost_strength: 0.5
dominant_window: 128
uncertainty:
uncertainty_low_threshold: 0.35
uncertainty_patience: 32
expected_gain_threshold: 0.03
backend:
require_real_backend: true
rdock:
n_runs: 1
mapper_radius: 6.0
command_timeout_seconds: 20
parallel_jobs: auto-minus-4
allow_skip_failed_ligands: true
max_failed_ligands: 3000
haddock:
enabled: false
command_timeout_seconds: 90
haddock_env_bin_dir: .venv_haddock/bin
disk_guard:
min_free_gb: 10.0
projected_output_gb: 3.0
keep_raw_batches: 4
datasets:
A:
name: dataset_A
target_name: EGFR
target_path: data/targets/budget_efficiency_benchmark_A/egfr_4wkq.pdb
shared_library_path: data/ligands/budget_efficiency_benchmark_A/shared_library_shuffled.csv
predock_master_path: results/budget_efficiency_benchmark/dataset_A/bootstrap/predock/parsed_scores_master.csv
adaptive_no_stop_run_path: results/budget_efficiency_benchmark/dataset_A/replay_cache/dataset_A__adaptive_no_stop__ti0.50__evaluated.csv
naive_glob: results/budget_efficiency_benchmark/dataset_A/replay_cache/dataset_A__naive_random_s*__evaluated.csv
cluster_glob: results/budget_efficiency_benchmark/dataset_A/replay_cache/dataset_A__cluster_naive_s*__evaluated.csv
B:
name: dataset_B
target_name: ABL1
target_path: data/targets/budget_efficiency_benchmark_B/abl1_1iep.pdb
shared_library_path: data/ligands/budget_efficiency_benchmark_B/shared_library_shuffled.csv
predock_master_path: results/budget_efficiency_benchmark/dataset_B/bootstrap/predock/parsed_scores_master.csv
adaptive_no_stop_run_path: results/budget_efficiency_benchmark/dataset_B/replay_cache/dataset_B__adaptive_no_stop__ti0.50__evaluated.csv
naive_glob: results/budget_efficiency_benchmark/dataset_B/replay_cache/dataset_B__naive_random_s*__evaluated.csv
cluster_glob: results/budget_efficiency_benchmark/dataset_B/replay_cache/dataset_B__cluster_naive_s*__evaluated.csv
C:
name: dataset_C
target_name: MDM2
target_id: mdm2_mf_c
target_pdb: "4HG7"
target_path: data/targets/multifidelity_benchmark_C/mdm2_4hg7.pdb
reference_id: ref_nutlin3a_c
reference_name: Nutlin-3a
ligand_comp_id: NUT
reference_smiles: "CC1=C(C(C)=NN1)C2=CC=C(C=C2)C3=NC(C)(C)C4=CC(Cl)=CC(Cl)=C34"
benchmark_dataset:
output_dir: data/ligands/multifidelity_benchmark_C
target_size: 10000
shuffle_seed: 909001
reuse_existing: false
min_similarity_keep: 0.0
pubchem_max_records: 20000
pubchem_thresholds: [95, 92, 90, 88, 85, 82, 80, 77, 75, 72, 70, 67, 65, 62, 60, 57, 55, 52, 50, 47, 45, 42, 40, 37, 35]
chembl_target_id: CHEMBL5023
chembl_max_rows: 40000
allow_generated_fallback: true
D:
name: dataset_D
target_name: CDK2
target_id: cdk2_mf_d
target_pdb: "1H1Q"
target_path: data/targets/multifidelity_benchmark_D/cdk2_1h1q.pdb
reference_id: ref_stauro_d
reference_name: Staurosporine
ligand_comp_id: STU
benchmark_dataset:
output_dir: data/ligands/multifidelity_benchmark_D
target_size: 10000
shuffle_seed: 909101
reuse_existing: true
min_similarity_keep: 0.0
pubchem_max_records: 20000
pubchem_thresholds: [95, 92, 90, 88, 85, 82, 80, 77, 75, 72, 70, 67, 65, 62, 60, 57, 55, 52, 50, 47, 45, 42, 40, 37, 35]
chembl_target_id: CHEMBL301
chembl_max_rows: 40000
allow_generated_fallback: true
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