code/acquisition/README.md

Offline acquisition and matrix export

This directory packages the six-policy acquisition implementation from MolAS_AL_restart/AL_MolAS/mean_ucb_cost_5fold_paper. It queries existing docking tables in simulation; it does not execute docking engines or train the downstream MolAS selector. The numerical scoring, completion, runtime-surrogate, and acquisition functions are preserved from the inspected source. Publication packaging did not rerun acquisition or docking experiments or replace the historical feature cache.

The original source files available during packaging are preserved separately in ../../provenance/historical_acquisition_source. Its manifest records hashes for all twelve recovered historical core text files; no auxiliary source file remains unavailable. This is a snapshot of inspected source, not a claim that its exact revision generated every paper figure. The archived outputs provide additional lineage evidence described in the repository's provenance documentation.

Files and dependency boundary

File	Purpose
run_experiment.py	Six-policy acquisition, completion, and checkpoint exports
release_support.py	Portable paths, run identity, and resume safeguards
launch_all.py	Bounded parallel launcher; invoking it starts experiments
audit_inputs.py	Read-only schema and feature-order validation
finalize_audit.py	Read-only output completeness and optional incremental-log audit
summarize_results.py	Aggregate existing acquisition diagnostics; not downstream analysis
formula_tests.py	Preserved legacy finiteness checks
tests/test_release.py	Fabricated-data regression checks; no AL loop or model fitting

Python 3.10 or newer is required. Runtime dependencies are NumPy, Pandas, and scikit-learn; their normal transitive dependencies are also required. Install in an isolated environment:

python -m venv .venv
.venv/bin/python -m pip install -r code/acquisition/requirements.txt

requirements.txt preserves the original minimum-version specification. It is not a recovered historical lockfile and does not promise identical floating-point results on every platform. The release's validation record identifies the environment used for its fabricated checks. Every new run records its actual Python/package versions and source hashes.

The acquisition runner imports no other AL_MolAS source package. PyTorch, torch-geometric, pretrained feature models, and DAL-toolbox are not needed when the prepared feature array is supplied. The original feature-building functions are preserved as a non-executable provenance excerpt, with dependency notes. Data validation compares the existing cache with its source transformation; the archived cache itself is retained unchanged.

The preserved feature builder normalizes over the supplied complex IDs before random projection. The archived cache therefore must not be described as having fold-local feature preprocessing. This is separate from the runtime surrogate's StandardScaler, which is fitted only on already observed cells. The runner consumes the prepared cache unchanged. The data provenance directory records the independent alignment check of that cache against the existing molecular inputs.

Required inputs

Paths are relative to the repository by default and can be overridden explicitly.

Option	Default	Contract
--data-dir	data/raw	Three CSV matrices listed below
--features	data/features/complex_features_ligand_protein_d256_seed0.npy	Finite N × 256 numeric array, no pickle
--feature-ids	data/features/complex_feature_ids.csv	One-column CSV with producer-verified complex IDs in feature-row order
--descriptors	data/descriptors/moad_physical_descriptors_filtered.csv	Identifier plus exactly four numeric descriptors
--fold-split / --fold-file	data/splits/moad_5fold_split_seed42.csv	Identifier plus one integer fold column, encoded 0–4 or 1–5
--output-dir	outputs/acquisition	New outputs; keep historical archives separate

The three raw matrix names are moad_rmsd_trimmed.csv, moad_pb_ratio_trimmed.csv, and moad_runtime_trimmed.csv. Their first column contains complex IDs. Algorithm columns use suffixes _rmsd, _pb_ratio, and _runtime, respectively, for surfdock, unimol, diffdock, diffdock_l, gnina, autodock, and smina. Runtime values are finite nonnegative seconds. The three matrices must have identical ordered, unique identifiers.

Descriptors and folds are aligned by identifier. Molecular features require an independently established ordered-ID mapping, not merely the correct number of rows. The runner fails before acquisition if the feature ID file is missing or mismatched. Do not manufacture this file from raw-matrix order when the feature-cache order is unverified. The repository's raw-matrix ID list does not by itself prove cache alignment. All required acquisition inputs and the independently verified feature-ID mapping are included in this package; no synthetic input is substituted.

If using the documented recovered held-out membership file, supply it explicitly: --fold-split data/splits/recovered_heldout_folds_from_downstream.csv. This is not represented as recovery of the original seed-42 splitting procedure.

Validation without experiments

From the repository root, these commands do not execute an acquisition loop:

python -m unittest discover -s code/acquisition/tests -v
python code/acquisition/run_experiment.py --help
python code/acquisition/audit_inputs.py --help

Once all authentic inputs and their ordered feature mapping are available:

python code/acquisition/audit_inputs.py --fold-split PATH_TO_VERIFIED_FOLDS
python code/acquisition/run_experiment.py --validate-only --fold-split PATH_TO_VERIFIED_FOLDS

The unit suite uses temporary fabricated arrays/records. Runtime-predictor tests replace fitting with a fake predictor. No docking, SVD fitting, MLP fitting, real benchmark acquisition, or downstream selector training occurs in these checks.

Explicit experiment commands

The following commands would run new offline acquisition experiments. They are provided for future use and were not run during publication packaging. They require all authentic inputs described above; add path overrides as needed.

# One method/fold/seed, in a fresh output directory:
python code/acquisition/run_experiment.py --methods plain_mean_ucb --folds 0 --seeds 0 --output-dir outputs/new_acquisition

# All six methods, five folds, three acquisition seeds (90 runs):
python code/acquisition/launch_all.py --workers 3 --output-dir outputs/new_acquisition

--smoke-test is also a real acquisition run on the first 120 training complexes, not a data-free unit test. It writes under smoke/ rather than runs/ and is explicitly identified in metadata. The launcher retains the historical single-thread numerical-library limits in each worker. It no longer suppresses all warnings. Completed runs are skipped only after matching input/code/ environment/job provenance; an existing legacy output directory is never adopted as a validated release run.

For existing release outputs, use:

python code/acquisition/finalize_audit.py --output-dir outputs/new_acquisition --check-incremental
python code/acquisition/summarize_results.py --output-dir outputs/new_acquisition

Both accept explicit --methods, --folds, and --seeds. The summary retains the historical descriptive fold-seed means/standard deviations and requires the plain Mean-UCB baseline. These are not confidence intervals over independent replicates. The completeness audit reports file-count scope unless --check-incremental is supplied; that option additionally reads incremental logs and detects repeated prior blocks across checkpoints. Neither audit certifies historical figure lineage or downstream training.

Numerical definitions retained

• Strict score is the clipped product of the normalized RMSD sigmoid with pb_ratio == 1.0; lambda is 3. Partial PB validity is not accepted as valid.
• Acquisition uses SVD ranks 1, 2, 3, and 5, each with four completion iterations; dispersion is population standard deviation. Checkpoint matrices in this inspected implementation use rank 3 and six iterations. These code facts are not an unsupported attribution of the exact historical figure-generating run.
• Mean-UCB uses beta 1. Plain and direct cost-utility use raw utility; the other four variants use ascending average-tie percentile ranks, floored at 0.001.
• Candidate costs are min–max scaled to [1, 5] where used; numerically equal extrema map to 1. Five-tier boundaries are candidate-cost quintiles, with ties assigned to the lower tier. Direct division adds 1e-6 to predicted seconds.
• Runtime prediction fits only revealed runtimes. Each prediction is transformed from log seconds and clipped to observed 5th/95th percentile bounds. The uncertainty policy uses three models; their mean plus population SD is clipped again before cost scaling. Other policies use one model.
• The runtime MLP retains widths (32, 16) and at most ten iterations per refit. Acquisition re-ranks after batches of at most 50 cells, truncated at integer percentage checkpoint boundaries. Cumulative cost includes the warm start.

Publication changes and provenance limits

1. Portable inputs and output location. The inherited sibling-folder paths became explicit CLI options. Ordered feature IDs, finite feature values, integer fold labels, unique matrix IDs, and valid runtimes are checked. Valid scientific computations are unchanged.
2. Correct incremental export after resume. The next export starts after the last completed checkpoint, rather than the checkpoint before it. The historical defect was observed in cost-tiers/fold-0/seed-0 checkpoint 17: its incremental CSV repeated 178 earlier records. Its cumulative records and matrices remained correct. The release does not alter that archived CSV or assert that the defect changed any published figure.
3. Keep pending audit records on resume. Round diagnostics for a partly completed checkpoint are included in saved state, so resuming does not discard the earlier rounds of that checkpoint's diagnostic JSON.
4. Actual scope and run identity. Each invocation gets a separate manifest containing its selected methods/folds/seeds and smoke/resume mode. Per-run manifests bind input hashes, source hashes, actual environment, and job settings. A completed marker alone cannot silently skip a changed run. A legacy directory without release provenance is rejected; use a fresh output location. --no-resume also refuses to overwrite an existing run.
5. Focused verification. Fabricated checks cover exact formula contracts, clipping order, data identity, resume-export uniqueness, and metadata. An AST comparison verifies the scientific functions against the preserved snapshot.

The historical runtime-feature-ablation script is not the paper's engine-specific ridge-probe implementation. Neither it nor the downstream MolAS/figure pipeline is fabricated here. The exact historical training environment, source revision, and every source-to-figure link have not been recovered. Consult the repository's data and downstream documentation for available artifacts and remaining inputs.