pretty_name: Retrocomposite experiment data
tags:
- chemistry
- retrosynthesis
- synplanner
- reaction-rules
Retrocomposite datasets
Prepared data for Protolaw/retrocomposite.
The verified composite release is n1-n5-composites-inchi-v1, pinned at
e4e575d7a9e066eca65f43fc3fde5b905b0cf309. It contains both composite cohorts, unchanged single-step data and
union stock, new InChI-grouped splits, and complete selection/support audits.
All 62 payload files passed anonymous download and SHA-256 checks; all three
relocated splits loaded successfully. The full code suite passes 80 tests.
| Cohort | Rules | Product/rule pairs | Train | Validation |
|---|---|---|---|---|
| Single-step | 11,209 | 57,381 | 51,642 | 5,739 |
| Primary composites | 3,185 | 4,232 | 3,809 | 423 |
| Patent-disjoint composites | 2,322 | 2,988 | 2,689 | 299 |
Contents and protocol
The release contains native SynPlanner rule TSVs and corresponding product/rule policy-data TSVs, certified composite decomposition records, occurrence/support audits, the 20,087-molecule union leaf stock and planning targets, and all three portable grouped train/validation splits. Composite target graphs preserve every row and label. No trained weights are included.
Inputs are the cleaned standalone n1/n5 files selected on 2026-10-25: 10,000 routes
each, SHA-256 prefixes c1e396cd and 5a27be2e. The updated standalone n1
composite library uses identity v3. Only its 13,121 certified linear links enter
selection; branched and uncertified constructions are excluded.
Composite supervision uses eligible n1 root/internal motif targets from tactics
shared with n5. E1 removes n1 routes with an n5 final target; E2 removes motif
inputs present at any n5 root/internal nonterminal node; E3 removes occurrences
containing an ordered adjacent pair of InChI reaction signatures present in n5.
Each signature retains its product, complete reactant multiset and side roles;
reactant multiplicity and reaction order matter. Middle-field reagents are ignored.
Standard InChI is stereo-free and normalizes supported tautomers. Atom-map and
exact graph-state differences do not rescue E3 matches. Exact graph comparisons
are diagnostic only: {'different': 1, 'match': 7098} witness statuses.
The additional sensitivity cohort excludes n1 routes sharing a patent-document
ID with n5. Patent families are not inferred.
Primary retains 4,243 certified links supporting 2,221 tactics; patent-disjoint retains 2,996 links and 1,663 tactics. The full selection has 1 links with eligibility errors and zero n5 reference-index errors. The single error is on already-excluded n1 route 434: source and library inputs agree, but model-input canonicalization changes a tautomer that Standard InChI distinguishes. It enters neither cohort. Every retained occurrence was rechecked against the frozen indexes. Full witnesses and support losses accompany the data.
The seed-42 splits group by molecule InChI and all supporting routes. They preserve training support for every rule and have zero molecule/route/group overlap. Validation coverage is sparse: 9,236 single-step, 2,867 primary and 2,089 sensitivity rules have no validation example. Review this limitation before model selection.
Single-step supervision intentionally uses n1+n5, and n5 informs the shared-tactic vocabulary. This is a controlled action-space comparison, not an unseen-molecule or standard held-out PaRoutes benchmark. Route 9035's inferred tautomer-only step and unresolved cyclization split remain upstream step-granularity questions.
Download
python scripts/hub_artifacts.py download --kind dataset \
--release n1-n5-composites-inchi-v1 --revision e4e575d7a9e066eca65f43fc3fde5b905b0cf309 \
--output data/releases/n1-n5-composites-inchi-v1
The helper in the project verifies all checksums and records the immutable commit. The preserved source snapshots and setup script recreate the environment. See the mobility guide. Model runs will be stored separately at Protolaw/retrocomposite-models.
Correction and historical release
The source-error interpretation in audits/n1-n5-input-readiness-v1 was incorrect.
The three reported n5 precursor mismatches were false positives caused by
Retrocomposite's asymmetric extra canonicalization; stored mapped precursors
matched their route children. Stereo-free Chython InChI resolves these checks.
The new release completes indexing and cohort selection with unchanged sources.
See the versioned correction.
Historical files and immutable revisions remain available.
n1-n5-single-step-v1 at 4ba2b7f366ea881825fbebe343ccefdd7899af42 remains the
historical single-step release. Its rules, data and stock are unchanged here,
but its version-1 SMILES split is superseded by new InChI assignments. Identical
partition sizes do not mean identical assignments.
No original source dataset license is replaced by this repository; source terms and provenance remain applicable to each release.