| > This is the original GitHub source-selection audit. The HF payload adds the full graph set and explicitly indexed Viewer tables; current HF coverage is recorded in the root README and provenance/hf_source_snapshot.json. |
|
|
| # Selection of paper artifacts |
|
|
| The source workspace was inventoried by filename, size, and cloud-placeholder |
| status before copying. Its research branches are not all part of the paper. |
| No docking, acquisition campaign, selector training, or new scientific comparison |
| was run during packaging. Original workspace files were not edited. |
|
|
| | Source area | Decision and reason | |
| |---|---| |
| | `MolAS_AL_restart/AL_MolAS/mean_ucb_cost_5fold_paper` | Primary acquisition implementation candidate and six-policy, five-fold, three-acquisition-seed archive. Preserve historical source; make separately documented portable release changes. The downstream paper uses acquisition seed 0. | |
| | `port_as_results_260829/{six paper policies}` | Preserve downstream CSVs, including per-complex predictions, fold summaries, and aggregate tables. Missing cloud contents remain inventoried. | |
| | `PORT-AS_cost_aware_bare.git` and original cost-aware remote | Versioned acquisition matrix/query-log evidence. Pin the exact historical commit and content identities; do not replace it with a moving branch. | |
| | `camera_ready_final_2026-10-31` and user-supplied `SRS_2026_AL_MolAS_Docking-8.pdf` | Preserve the audited source, style, bibliography, eight figures, and supplied 12-page camera-ready PDF. | |
| | `MolAS_AL/data/raw` | Readable original raw tables; PB/runtime agree byte-for-byte with restart copies. | |
| | `MolAS_AL` legacy strict-score output and restart `ground_truth` | Preserve both existing target matrices with explicit provenance. The restart original was subsequently recovered; its values and the legacy representation were checked against the raw data without conflating their distinct file identities. | |
| | `Downloads/data/MolAS` | Original resident ligand/protein features. Copy needed structural inputs into the local data area; retain hashes and separate large-data publication requirements. | |
| | `Downloads/cost_aware_relaxed_six_methods.zip` | Complete original six-policy archive. Verify all recovered CSV identities against the pinned Git tree; losslessly deduplicate cumulative prefixes in the release. | |
| | `Downloads/MolAS_AL-main` | Recovered historical MolAS training adapter, launcher, model/data modules, embedding-generation source, and analysis notebooks. Preserve unchanged with the supplied license and hashes; it is an unversioned downloaded tree. | |
| | Original paper download's `NeurIPS2026/scripts` and `Downloads/main_results` | Additional plotting source and rendered analysis assets; only demonstrated relationships are used in the figure-lineage map. | |
| | `cost_aware_design2` and `dal_toolbox_design2` | Only the feature-cache lineage and original feature-building source are relevant dependencies. Their unrelated AL campaigns are not paper baselines. | |
| | `mean_ucb_cost_balance_100checkpoints` | Earlier design; not substituted for the paper-specific six-policy archive. | |
| | `budget_projected_gain_hybrid`, `hybrid_b1`, `hybrid_b50`, `PORT-AS_cost_aware_log_upload`, `PORT-AS_cost_aware_upload`, incomplete upload copy | Development/hybrid runs outside the evaluated six-policy study; excluded. | |
| | `design1_raw_metric_reconstruction`, `design2_score_matrix_reconstruction`, `paper_query_svd_design2`, `dl_design2_qin2025`, `cost_aware_predicted_runtime_design2` | Earlier experiments and alternative formulations. Their existence does not establish controlled baseline comparisons in the paper. Excluded from reported results. | |
| | Generic `audit` and `runtime_audit` | Earlier-design audits; not mislabeled as the paper's final runtime-probe or plotting implementation. | |
| | Early `MolAS_AL` literature/pilot reports, top-level library catalog, `docs`, `scripts/fetch_github_meta.py`, `data/repositories.yml` | Background/development materials rather than dependencies of the reported study. | |
| | `deliverables` | Earlier research report, abstract, poster-planning materials; not final paper artifacts. | |
| | Earlier camera-ready folders, compilation scratch, auxiliary LaTeX files | Superseded drafts/build products; excluded. | |
| | Virtual environments, vendored unrelated libraries, caches, nested Git metadata, `.DS_Store` | Not copied into the publication source tree. | |
|
|
| The audit includes the full accessible workspace's metadata, not a claim that |
| every cloud-only file was read. A cloud placeholder contains a name and logical |
| size but may not provide readable bytes. Missing files are explicitly identified |
| in artifact manifests rather than represented by empty files. |
|
|
| ## Evidence boundaries |
|
|
| The acquisition implementation is supported by formula checks against saved |
| records. A historical code commit and exact dependency lock were not archived |
| with every reported run. The recovered downstream source and launch script add |
| substantial protocol evidence, but launcher settings and saved filenames alone |
| do not prove every executed training configuration. The repository documents |
| these distinctions and does not claim a new end-to-end reproduction run. |
|
|
| The original acquisition report's three-seed coverage must not be confused with |
| independent selector-seed replication. The archived downstream folders are |
| `seed0`, and the manuscript describes that scope. |
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|
