VenusGenome: Genome-Aware Masked Autoencoding for Microbial Genome Representation Learning

arXiv:2611.05405v1 Announce Type: cross Abstract: Genomic-context models have shown that contextualizing protein embeddings can improve predictions of microbial function. We observe that a gene's protein embedding is partially predictable from the embeddings of neighboring genes in the genome, motivating high-ratio masking that requires reconstruction from sparser genomic context. Genomic modeling must also distinguish biological relationships from assembly conventions, since the ordering of separate contigs does not imply adjacency and strand labels depend on the reference orientation. We the

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