LINCS L1000 level-5 releases should not be assumed interchangeable: cross-release instability in virtual perturbation screening and a four-layer diagnostic framework

Frozen archive for the manuscript. Contains the cache-reconstruction scripts, four model checkpoints, ESM caches, the LayerDiag diagnostic toolkit, and every result table and figure reported in the paper. The preprocessed LINCS L1000 level-5 matrices (~7.5 GB) are NOT distributed with the archive; they are regenerated from public sources (GSE92742, the LINCS level-5 beta release, and the DCIC 2021 distribution) by the cache-reconstruction scripts included here. zenodo_archive_index_20260926.csv lists all 101 files with their SHA-256 (including the matrices, which are reconstructed rather than downloaded).