arXiv:2605. 00182v3 Announce Type: replace Abstract: Proteins are shaped by gradual evolution under biophysical and functional constraints.
arXiv:2603. 14717v2 Announce Type: replace Abstract: Generating novel protein sequences that respect a family's statistical constraints typically requires training deep generative models on thousands to millions of examples.
arXiv:2512. 15133v3 Announce Type: replace-cross Abstract: Proteins inherently possess a consistent sequence-structure duality.
arXiv:2606. 10543v1 Announce Type: cross Abstract: Designing functional biological sequences requires navigating vast discrete spaces under strict evolutionary and biophysical constraints.
arXiv:2509. 26405v2 Announce Type: replace Abstract: We introduce InVirtuoGen, a discrete flow generative model for fragmented SMILES for de novo and fragment-constrained generation, and target-property/lead optimization of small molecules.
arXiv:2606. 02133v1 Announce Type: cross Abstract: Non-monotonic sequence generation methods, such as masked diffusion models, provide a flexible alternative to left-to-right autoregressive modeling by allowing tokens to be generated in non-fixed and prescribed orders.
arXiv:2606. 16044v1 Announce Type: new Abstract: Protein language models (pLMs) can generate novel protein sequences with properties beyond those observed in nature, yet the mechanisms underlying protein generation remain poorly understood.
arXiv:2507. 08920v4 Announce Type: replace-cross Abstract: We introduce AMix-1, a powerful protein foundation model built on Bayesian Flow Networks and empowered by a systematic training methodology, encompassing pretraining scaling laws, emergent capability analysis, in-context learning mechanism, and test-time scaling algorithm.
arXiv:2602. 18695v2 Announce Type: replace Abstract: Existing insertion-based masked diffusion models that generate sequences by interleaving token insertion with unmasking use fixed schedules that are not dependent on the data.
arXiv:2606. 08100v1 Announce Type: new Abstract: Multimodal $\Delta\Delta G$ predictors integrating protein language models with inverse-folding representations achieve strong in-distribution accuracy on the Megascale dataset but exhibit limited robustness on out-of-distribution (OOD) proteins, persistent forward-reverse bias on paired-mutation benchmarks, and under-representation of rare stabilizing mutations.
arXiv:2607. 09039v1 Announce Type: new Abstract: The ability to generate variable-length proteins is crucial in protein design, where the optimal length is often unknown and tightly coupled to designability.
arXiv:2605. 02937v2 Announce Type: replace-cross Abstract: Deep learning in de novo protein design has achieved atomic-level fidelity.
Diffusion Language Models (DLMs) have recently achieved substantial progress in natural language generation tasks. Recent research demonstrates that adaptive token generation ordering can significantly improve performance in mathematical reasoning and code synthesis applications.