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| { | |
| "pretty_name": "MolAS Active Learning — AI4DD 2026 benchmark and research artifacts", | |
| "language": [ | |
| "en" | |
| ], | |
| "license": "other", | |
| "license_name": "cc-by-4.0-author-content-and-upstream-terms", | |
| "license_link": "LICENSE", | |
| "size_categories": [ | |
| "10K<n<100K" | |
| ], | |
| "task_categories": [ | |
| "tabular-regression" | |
| ], | |
| "tags": [ | |
| "chemistry", | |
| "biology", | |
| "drug-discovery", | |
| "molecular-docking", | |
| "algorithm-selection", | |
| "active-learning", | |
| "runtime-aware", | |
| "benchmark", | |
| "ai4dd" | |
| ], | |
| "configs": [ | |
| { | |
| "config_name": "benchmark_cells", | |
| "data_files": [ | |
| { | |
| "split": "full", | |
| "path": "data/viewer/benchmark_cells.csv" | |
| } | |
| ], | |
| "default": true | |
| }, | |
| { | |
| "config_name": "rmsd", | |
| "data_files": [ | |
| { | |
| "split": "full", | |
| "path": "data/raw/moad_rmsd_trimmed.csv" | |
| } | |
| ] | |
| }, | |
| { | |
| "config_name": "pb_ratio", | |
| "data_files": [ | |
| { | |
| "split": "full", | |
| "path": "data/raw/moad_pb_ratio_trimmed.csv" | |
| } | |
| ] | |
| }, | |
| { | |
| "config_name": "runtime", | |
| "data_files": [ | |
| { | |
| "split": "full", | |
| "path": "data/raw/moad_runtime_trimmed.csv" | |
| } | |
| ] | |
| }, | |
| { | |
| "config_name": "acquisition_scores", | |
| "data_files": [ | |
| { | |
| "split": "full", | |
| "path": "data/targets/full_strict_score_matrix.csv" | |
| } | |
| ] | |
| }, | |
| { | |
| "config_name": "native_evaluation_scores", | |
| "data_files": [ | |
| { | |
| "split": "full", | |
| "path": "data/targets/moad_score_native_reconstructed.csv" | |
| } | |
| ] | |
| }, | |
| { | |
| "config_name": "folds", | |
| "data_files": [ | |
| { | |
| "split": "full", | |
| "path": "data/splits/moad_5fold_split_seed42.csv" | |
| } | |
| ] | |
| }, | |
| { | |
| "config_name": "physical_descriptors", | |
| "data_files": [ | |
| { | |
| "split": "full", | |
| "path": "data/descriptors/moad_physical_descriptors_filtered.csv" | |
| } | |
| ] | |
| }, | |
| { | |
| "config_name": "protein_graph_index", | |
| "data_files": [ | |
| { | |
| "split": "full", | |
| "path": "data/viewer/protein_graph_index.csv" | |
| } | |
| ] | |
| } | |
| ] | |
| } | |
| <h1 align="center">🧬 MolAS Active Learning — Dataset</h1> | |
| <p align="center"><strong>Active Learning for Molecular-Docking Algorithm Selection<br>under Heterogeneous Runtime</strong><br> | |
| Accepted at the NeurIPS 2026 Workshop on AI for Drug Discovery (AI4DD)<br> | |
| Sean Wan · Jiabao Brad Wang · Mustafa Misir — Duke Kunshan University</p> | |
| [🤗 Dataset](https://huggingface.co/datasets/SeanWan05/MolAS-Active-Learning) · [💻 Code](https://github.com/SeanWan514/MolAS_Active_Learning) · [📄 Paper](paper/AI4DD52_camera_ready.pdf) · [📝 OpenReview](https://openreview.net/forum?id=tSz3wBLABm) · [🗃️ Data dictionary](docs/data_card.md) · [🔎 Verification](provenance/final_verification.json) | |
| GitHub repository: https://github.com/SeanWan514/MolAS_Active_Learning | |
| HuggingFace repository: https://huggingface.co/datasets/SeanWan05/MolAS-Active-Learning | |
| ## 🔬 Dataset summary | |
| This dataset preserves the inputs and saved experimental artifacts for retrospective, cell-wise active learning in molecular-docking algorithm selection. It contains **3,179 protein–ligand complexes**, **seven docking engines**, fixed five-fold memberships, original molecular features, and acquisition/downstream outputs. The dataset also includes **all 3,179 original protein graph files**, which are distributed separately from the GitHub code release. | |
| The default `benchmark_cells` configuration contains **22,253 rows**, one per complex–algorithm cell. It is a deterministic reshaping of the unchanged original tables, with original outer-fold assignments. No docking, feature inference, acquisition campaign, or selector training was executed to prepare this release. | |
| ## ✨ Included artifacts | |
| | Artifact | Contents | | |
| |---|---| | |
| | Raw outcomes | Aligned RMSD, PoseBusters-validity ratio, and runtime tables: 3,179 × 7 each | | |
| | Targets | Continuous acquisition scores; the explicitly reconstructed native MolAS evaluation scores; preserved earlier target serialization | | |
| | Splits and descriptors | Original five outer folds and four physical descriptor columns | | |
| | Small features | Original 3,179 × 256 projected cache, its verified row IDs, and 3,179 × 384 ligand embeddings | | |
| | Protein graphs | **3,179 original PyTorch/PyG graph files; 14,985,036,224 bytes** | | |
| | Acquisition artifacts | **90 run archives** covering six policies × five folds × three acquisition seeds; **27,000 original CSV identities** | | |
| | Downstream artifacts | **4,508 original CSV payloads** in six ZIPs and 1,771 readable summary mirrors; acquisition seed 0 | | |
| | Research context | Paper PDF/source/figures, source-code mirror, data dictionary, historical provenance, and portable inspection utilities | | |
| The GitHub repository is the primary code reference. The source mirror here is pinned to the GitHub commit recorded in `provenance/hf_source_snapshot.json`. The acquisition archive uses lossless storage deduplication: earlier cumulative CSVs are exact prefixes of final ledgers, with original byte identities recorded and verified. Extraction utilities recover the original CSV streams; a duplicate multi-gigabyte transport ZIP is unnecessary. | |
| ## 🚀 Inspect the dataset | |
| For the loading/download examples, install `datasets` and `huggingface_hub` (`python3 -m pip install -r requirements-hub.txt`). The standalone file/data validators require only Python’s standard library. | |
| The Dataset Viewer is explicitly configured for nine independent CSV tables. The binary graphs/features and compressed result archives are download assets and are not automatically deserialized by the Viewer. Every configuration has a split named **`full`**. | |
| ```python | |
| from datasets import load_dataset | |
| repo_id = "SeanWan05/MolAS-Active-Learning" | |
| cells = load_dataset(repo_id, "benchmark_cells", split="full") | |
| runtime = load_dataset(repo_id, "runtime", split="full") | |
| graphs = load_dataset(repo_id, "protein_graph_index", split="full") | |
| ``` | |
| Available configurations: `benchmark_cells` (default), `rmsd`, `pb_ratio`, `runtime`, `acquisition_scores`, `native_evaluation_scores`, `folds`, `physical_descriptors`, and `protein_graph_index`. Their paths and row counts are in `provenance/hf_viewer_configurations.json`. | |
| ### Default cellwise schema | |
| | Column | Meaning | | |
| |---|---| | |
| | `PDB_CCD_ID` | Original complex identifier; preserve as a string | | |
| | `algorithm` | One of the seven engine IDs listed below | | |
| | `outer_test_fold` | Original test-fold membership, integers 0–4 | | |
| | `rmsd_angstrom` | Original docking RMSD, interpreted in Å by the paper | | |
| | `pb_ratio` | Original PoseBusters validity ratio; strict validity requires exact equality to 1 | | |
| | `runtime_seconds` | Original runtime, treated as seconds by the experiment code | | |
| | `acquisition_strict_score` | Original continuous acquisition target | | |
| | `native_evaluation_score` | Native evaluation target from the explicitly named, independently checked reconstruction | | |
| Engine order in the original wide matrices: `surfdock`, `unimol`, `diffdock`, `diffdock_l`, `gnina`, `autodock`, `smina`. | |
| ## 🧬 Download and use the structural inputs | |
| ```python | |
| from huggingface_hub import snapshot_download | |
| folder = snapshot_download( | |
| repo_id="SeanWan05/MolAS-Active-Learning", | |
| repo_type="dataset", | |
| local_dir="MolAS_HF", | |
| ) | |
| ``` | |
| For a versioned analysis, pass the actual published dataset commit to `revision=`. The graph index provides each graph's relative path, size, and SHA-256 for selective downloading. Original graph files are under `data/external/protein_graphs_esmc_600m/`; ligand and projected features are under `data/features/`. Graphs are serialized molecular data, not trained selector weights. Use the preserved MolAS loader and its PyTorch/PyG dependencies rather than treating these binary files as ordinary Dataset Viewer rows. | |
| ## 🔎 Local verification and archive access | |
| From the downloaded folder, Python 3.11+ can validate all file hashes and data consistency without executing scientific experiments: | |
| ```bash | |
| python3 scripts/verify_hf_package.py | |
| python3 scripts/validate_data.py --require-complete | |
| python3 code/downstream/verify_saved_outputs.py --require-complete --original-archive-manifest provenance/downstream_original_archive_recovery.json | |
| ``` | |
| `SHA256SUMS` and `provenance/repository_files.json` cover the upload payloads, including all protein graphs. The self-generated manifests and final report are excluded from their own recursive hashes. Verification checks available bytes and recorded provenance; it does not establish a fresh end-to-end reproduction of the historical scientific experiments. | |
| Use `scripts/read_acquisition_artifact.py` to inspect one original acquisition CSV. Use `scripts/materialize_acquisition.py --destination /path/to/new/folder` to estimate expansion; add `--write` to extract. Seed 0 requires about 3.22 GB expanded, and all three acquisition seeds can be selected explicitly. Original downstream CSVs are in the six ZIPs under `results/downstream/`. | |
| ## 📁 Dataset layout | |
| ```text | |
| MolAS_HF/ | |
| ├── data/ # raw outcomes, targets, folds, descriptors, and features | |
| │ ├── external/protein_graphs_esmc_600m/ # all 3,179 original graphs | |
| │ └── viewer/ # deterministic cellwise table and graph index | |
| ├── results/ # original acquisition and downstream archives/summaries | |
| ├── code/ # pinned source mirror; GitHub remains the code reference | |
| ├── paper/ # unchanged paper, source, bibliography, and figures | |
| ├── docs/ # data dictionary, interpretation, and source attribution | |
| ├── provenance/ # source identities, component checks, and HF manifest | |
| ├── scripts/ # inspection, validation, and explicit upload helper | |
| ├── LICENSE # component-specific bundle terms | |
| ├── LICENSE_DATA.md # CC BY 4.0 grant for author-owned data contributions | |
| ├── LICENSE_CODE # MIT license for original software | |
| └── UPLOAD.md # instructions for publishing this prepared folder | |
| ``` | |
| ## ⚖️ Licensing and attribution | |
| Author-owned data contributions, original result outputs, and curation metadata are provided under **CC BY 4.0**, to the extent the authors hold the relevant rights. Original software is **MIT**. Supplied third-party data, model-derived features/graphs, software, and manuscript assets retain their separately applicable terms. The Hub metadata therefore uses `license: other` and points to the explicit [component-specific LICENSE](LICENSE), rather than assigning a blanket CC BY or MIT license to every bundled artifact. See [LICENSE_DATA.md](LICENSE_DATA.md), [LICENSE_CODE](LICENSE_CODE), and [third-party provenance](docs/third_party.md). | |
| Upstream sources include [MolAS](https://github.com/BradWangW/MolAS), its [processed-data record](https://zenodo.org/records/17760688), MOAD/PDB-derived complexes, ESM-C protein features, and the recovered ChemBERTa ligand-feature workflow. The author confirmed redistribution terms and delegated selection of the dataset's author-owned-content license; the release record is in `provenance/hf_release_authorization.json`. | |
| ## 📌 Intended use and interpretation limits | |
| - This is a retrospective reference benchmark. The full tables are offline oracles; acquisition policies may access only previously acquired training-pool outcomes/runtimes. Preserve original held-out folds and warm-start cost accounting. | |
| - **Do not randomly split the cellwise rows.** The seven rows of one complex share the same original outer-test fold. Derive each training pool from the original complex-level memberships. No protein-family/scaffold-disjoint split is newly asserted. | |
| - Acquisition and native evaluation targets are distinct. Native MolAS evaluation zeroes RMSD >5 Å or <0; the continuous acquisition target does not use that truncation. The original server-side native-target CSV bytes were not recovered; the clearly named reconstruction matches all 22,253 saved engine scores within 1.11e-16. | |
| - Extreme finite RMSD values are preserved, including 211 above 1,000 Å. Their failure/sentinel semantics are not established. They are not evidence of valid physical poses. | |
| - Runtime is hardware/workflow dependent; exact historical timing boundaries and all engine-version details are not established by the numeric tables alone. | |
| - The projected feature cache uses the original fixed full-set normalization/projection. It is not a newly fitted fold-local representation. Runtime-surrogate fitting remains a separate observed-data operation. | |
| - Acquisition artifacts cover three seeds; downstream saved results use acquisition seed 0. Recovered launcher defaults do not establish every historical selector RNG/configuration. | |
| - Per-run training configurations and some final figure-export details remain unpinned. No new experiments, significance tests, generalization studies, or prospective docking validations are claimed by this data release. | |
| ## 📚 Citation | |
| Please cite the active-learning paper and the upstream MolAS/data/feature sources when using their respective components. The manuscript remains the supplied camera-ready PDF; its original availability statement is preserved in this frozen copy. | |
| ```bibtex | |
| @inproceedings{wan2026molas_active_learning, | |
| title = {Active Learning for Molecular-Docking Algorithm Selection under Heterogeneous Runtime}, | |
| author = {Wan, Sean and Wang, Jiabao Brad and Misir, Mustafa}, | |
| booktitle = {NeurIPS Workshop on AI for Drug Discovery}, | |
| year = {2026}, | |
| url = {https://openreview.net/forum?id=tSz3wBLABm} | |
| } | |
| ``` | |
| Code: https://github.com/SeanWan514/MolAS_Active_Learning · Data snapshot version: **1.0.0**. When citing or reusing the data, record the actual dataset identifier and immutable Hub commit alongside the code version. | |