TomatoPGFM: A graph-conditioned foundation model for tomato pangenomes
Jinlei Han, Tuerhong Yushan, Juan Wang, Haitao Yang, Jiantao Zhao, Fangling Jiang, Chunping Jia, Tao Yang, Baike Wang, Changwei Zhang, Qinghui Yu
TomatoPGFM is a graph-conditioned foundation model for tomato pangenomes that improves sequence representation using graph context, achieving higher classification performance than DNABERT-2.
bioRxiv · Sep 1, 2026 · PreprintBioinformatics