RIBOSPAN: A Long-Context RNA Foundation Model for Versatile RNA Modeling

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arXiv:2608.22849v2 Announce Type: replace Abstract: Full-length RNAs, particularly messenger RNAs, often exceed the context lengths used to pretrain existing RNA foundation models, limiting complete-transcript modeling at single-nucleotide resolution. We present RIBOSPAN, a 1.61-billion-parameter bidirectional RNA foundation model natively pretrained with context lengths up to 10,240 nt. RIBOSPAN combines dense bidirectional self-attention, single-nucleotide tokenization, and attention-isolated sequence packing to enable high-resolution modeling of complete long RNAs. Native 10K pretraining preserves strong reconstruction at 10,240 tokens and, in a controlled long-context benchmark, maintains strong contextual responsiveness and context-specific representation separation while keeping perturbation-induced changes highly localized. Inference-time YaRN scaling recovers much of the contextual organization lost by direct short-context extrapolation, but induces substantially greater distal representation diffusion. Frozen RNA-type evaluations show that RIBOSPAN learns state-of-the-art RNA representations, with a particularly clear advantage on long RNAs. Across downstream biological benchmarks, RIBOSPAN emerges as the strongest encoder-only RNA foundation model, achieving state-of-the-art performance in both full-transcript biological property prediction and zero-shot mutation-fitness modeling. Building on the same backbone, we develop a multidimensionally conditioned discrete-diffusion framework for full-length mRNA generation and redesign, including synonymous-codon …

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