AI Research
IsoAlign: Isoform-Aware DNA-Protein Alignment via Joint-Embedding Predictive Architectures
IsoAlign targets a blind spot in genomic foundation model pretraining: alternative splicing.
Genomic foundation models (GFMs) have emerged as a powerful paradigm for learning DNA sequence representations, yet existing self-supervised pretraining strategies overlook alternative splicing and underperform compared to specialized models.
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ArXiv CS.LG
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ArXiv CS.LG
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Accounting for alternative splicing could address a blind spot in genomic foundation models’ DNA representations. Isoform-aware DNA-protein alignment offers a direction beyond pretraining strategies that overlook this biology.
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