Creator 1.0: phylogeny-guided stagewise pretraining for plant genome models across 1,000 species

[bioRxiv] Yang et al. present Creator 1.0, a 2-billion-parameter plant genome foundation model pretrained on 1,000 plant genomes using phylogeny-guided stagewise pretraining (PGSP), according to the preprint. Training comprised 83 consecutive stages and produced 52 cumulative checkpoints associated with distinct plant orders. According to the authors, on GENEB the stage 83 checkpoint ranked first among 46 models across 10 plant-related tasks with a mean Matthews correlation coefficient (MCC) of 0.565, and fourth across all 100 tasks. Evaluation of the 52 checkpoints on six plant lncRNA tasks identified different optimal stages under full-data, 10-shot and 1-shot settings, corresponding to stages 71, 72 and 29, respectively. The authors said checkpoint performance varied across tasks, without consistent advantages for corresponding plant orders. The preprint has not been peer-reviewed.