Probing and steering biology across Boltz-1s trunk-diffusion boundary
AlphaFold3-class structure predictors pair a representational trunk, which processes sequence and context, with a diffusion module, which generates atomic coordinates. How biological information changes as it crosses this architectural boundary remains poorly understood. We analyze per-residue activations from the Pairformer trunk and diffusion module of Boltz-1 using linear probes, sparse autoencoders (SAEs), and causal interventions. From the trunk, both geometry (secondary structure, disorder) and sequence chemistry (amino-acid identity, signal peptides, disulfide-bond annotations) are linearly decodable. In the diffusion module, the two diverge. Secondary structure transfers essential...
| Authors | Piotr Jedryszek, Tongmeng Xie, Adam Winnifrith et al. |
|---|---|
| Primary category | q-bio.QM |
| Published | 11 August 2026 |
| Last updated at source | 11 August 2026 |
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