Flagship multimodal, multi-task model: the full repertoire of non-B conformations, conditioned on open chromatin.
Sequence and accessibility signal (ATAC-seq / DNase-seq) are encoded in parallel and fused by cross-attention, with a cell-type embedding conditioning the shared representation; separate heads output Z-DNA, G-quadruplex, H-DNA and cruciform probabilities at base resolution.
Because accessibility supplies the torsional and structural context in which flipons actually form, AlphaFlipon produces cell-type-specific flipon maps rather than a single static motif annotation, and an attribution module separates sequence-intrinsic from chromatin-driven contributions to each call.