DNA pretraining suffers from inappropriate evaluation datasets, flawed neighbor-masking, and neglected vocabulary design; the authors supply guidelines and a reproducible testbed to fix them.
Nucleotide trans- former: building and evaluating robust foundation models for human genomics.Nature Methods, 22(2):287–297, 2025
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In Search of Lost DNA Sequence Pretraining
DNA pretraining suffers from inappropriate evaluation datasets, flawed neighbor-masking, and neglected vocabulary design; the authors supply guidelines and a reproducible testbed to fix them.