File size: 2,371 Bytes
7c481e7 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 | run:
name: discovery_benchmark
output_dir: results/discovery_benchmark
random_seed: 20260415
batch_size: 32
adaptive_budget: 50000
baseline_budget: 50000
max_batches: 2000
allow_resume: true
enable_adaptive_early_stop: true
target:
protein_name: MDM2
target_id: mdm2_discovery
docking_reference_pdb: "4HG7"
docking_target_path: data/targets/discovery_benchmark/mdm2_4hg7.pdb
reference:
reference_id: ref_nutlin3a
pdb_id: "4HG7"
ligand_comp_id: "NUT"
benchmark_dataset:
output_dir: data/ligands/discovery_benchmark
target_size: 50000
shuffle_seed: 424242
reuse_existing: true
min_similarity_keep: 0.08
pubchem_max_records: 120000
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, 32, 30]
chembl_target_id: CHEMBL5023
chembl_max_rows: 120000
allow_generated_fallback: true
backend:
type: rdock
require_real_backend: true
n_runs: 5
mapper_radius: 6.0
command_timeout_seconds: 300
parallel_jobs: auto-minus-4
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: 50
scheduler:
init_coverage_fraction: 0.35
conservative_deprioritize: true
surrogate:
prefer_xgboost: true
n_estimators: 250
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
matrix:
naive_random_seeds: [11, 22, 33, 44, 55]
cluster_naive_seeds: [101, 202, 303, 404, 505]
include_adaptive_top1_variant: true
include_adaptive: true
include_naive_random: true
include_cluster_naive: true
modes: [docking_only, full_feature]
analysis:
analog_similarity_threshold: 0.65
rolling_window: 200
replicate_subset_size_top: 20
replicate_subset_size_borderline: 20
replicate_subset_size_clusters: 20
replicate_runs: 2
early_stop:
min_evaluated: 3000
patience_rounds: 12
min_model_weight: 0.4
quantile: 0.15
uncertainty_weight: 0.2
min_improvement: 0.015
exploration_margin: 0.45
exploitation_margin: 0.1
reference_evaluations: 50000
|