Stop the Flip-Flop: Context-Preserving Verification for Fast Revocable Diffusion Decoding

Parallel diffusion decoding can accelerate diffusion language model inference by unmasking multiple tokens per step, but aggressive parallelism often harms quality. Revocable decoding mitigates this by rechecking earlier tokens, yet we observe that existing verification schemes frequently trigger flip-flop oscillations, where tokens are remasked and later restored unchanged. This behaviour slows inference in two ways: remasking verified positions weakens the conditioning context for parallel drafting, and repeated remask cycles consume the revision budget with little net progress. We propose COVER (Cache Override Verification for Efficient Revision), which performs leave-one-out verification and stable drafting within a single forward pass. COVER constructs two attention views via KV cache override: selected seeds are masked for verification, while their cached key value states are injected for all other queries to preserve contextual information, with a closed form diagonal correction preventing self leakage at the seed positions. COVER further prioritises seeds using a stability aware score that balances uncertainty, downstream influence, and cache drift, and it adapts the number of verified seeds per step. Across benchmarks, COVER markedly reduces unnecessary revisions and yields faster decoding while preserving output quality.

Protein generation with embedding learning for motif diversification

A fundamental challenge in protein design is the trade-off between generating structural diversity while preserving motif biological function. Current state-of-the-art methods, such as partial diffusion in RFdiffusion, often fail to resolve this trade-off: small perturbations yield motifs nearly identical to the native structure, whereas larger perturbations violate the geometric constraints necessary for biological function. We introduce Protein Generation with Embedding Learning (PGEL), a general framework that learns high-dimensional embeddings encoding sequence and structural features of a target motif in the representation space of a diffusion model's frozen denoiser, and then enhances motif diversity by introducing controlled perturbations in the embedding space. PGEL is thus able to loosen geometric constraints while satisfying typical design metrics, leading to more diverse yet viable structures. We demonstrate PGEL on three representative cases: a monomer, a protein-protein interface, and a cancer-related transcription factor complex. In all cases, PGEL achieves greater structural diversity, better designability, and improved self-consistency, as compared to partial diffusion. Our results establish PGEL as a general strategy for embedding-driven protein generation allowing for systematic, viable diversification of functional motifs.