v1.0.4 — final submission snapshot (sensitivity addendum)

Final submission snapshot for Journal of Cheminformatics, including the pre-registered sensitivity addendum (protocol/sensitivity_addendum_v1.md).

• 5-split checkpoint-selection sensitivity under fixed-final / global-vs-global / endpoint-vs-endpoint / hybrid rules (corrected MTL training; validation selection attenuates but does not reverse the absolute contrast; protocol interaction positive under every rule)
• Chemical-entity identity collision audit (L1 standardized-parent key, L2 InChIKey upper bound); Level-1 filtering leaves Gamma = +0.083 unchanged
• Unit tests for exact-key isolation and L1 determinism
• Manuscript updated: checkpoint narrative, SI Table S4 + Figures S3-S4, SI S12 identity audit

v1.0.3 — final submission snapshot

Final submission snapshot for Journal of Cheminformatics.

Round-13..16: split-level uncertainty in all figures (no pseudo-replication), corrected permutation sanity check, SI table layout fixes (all tables fit), Figure 1 redrawn (vertical evidential chain, GIN and secondary analyses as independent dashed branches), Figure 4B fixed and restyled, final wording per reviewer reports.

Contents: analysis code (b3_main_v2 / controls / STL-8x / GNN / figures), frozen split manifests, prediction tables (parquet), docs/manuscript.pdf.

v1.0.2 — submission snapshot (Zenodo trigger)

Trigger release for Zenodo archiving. Same content as v1.0.1: final submission snapshot of the leakage-controlled MTL diagnostic (J Cheminformatics), with manuscript PDF (docs/manuscript.pdf), frozen protocol, all prediction tables and split manifests.

v1.0.1 — submission snapshot (final)

Final submission snapshot for the leakage-controlled MTL diagnostic (J Cheminformatics).

• Manuscript: docs/manuscript.pdf (28 pages) + Supporting Information
• Frozen protocol: docs/PROTOCOL.md + protocol/final_confirmatory_plan.md
• All prediction tables and split manifests committed under results/ and splits/
• Environment pinned in requirements.txt (Python 3.10, PyTorch 2.13.0+cu130, RDKit 2023.09.6)

v1.0.0 — submission snapshot

Submission snapshot for the leakage-controlled MTL diagnostic (J Cheminformatics). Pinned environment in requirements.txt; frozen protocol in docs/PROTOCOL.md; split hashes in the repository.