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. 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. 10543v1 Announce Type: cross Abstract: Designing functional biological sequences requires navigating vast discrete spaces under strict evolutionary and biophysical constraints.
arXiv:2607. 09277v1 Announce Type: new Abstract: Three-dimensional (3D) molecule generation has been dominated by diffusion models, which achieve strong generation quality but typically require the molecular size to be specified a priori.
arXiv:2605. 15354v2 Announce Type: replace Abstract: Despite the success of foundation models in language and vision, molecular graph generation still lacks a unified framework for heterogeneous design tasks with reliable controllability.
arXiv:2606. 01220v1 Announce Type: cross Abstract: Generating molecules that simultaneously satisfy drug-like properties and conform to the 3D structure of a target protein is a core challenge in structure-based drug design (SBDD).
arXiv:2605. 00182v3 Announce Type: replace Abstract: Proteins are shaped by gradual evolution under biophysical and functional 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. 00295v1 Announce Type: new Abstract: Masked diffusion models have seen great success in capturing data distributions over discrete sequences in domains such as text and proteins.
arXiv:2602. 13136v2 Announce Type: replace Abstract: Template-free retrosynthesis methods treat the task as black-box sequence generation, limiting learning efficiency, while semi-template approaches rely on rigid reaction libraries that constrain generalization.
arXiv:2607. 19686v1 Announce Type: cross Abstract: Masked diffusion models (MDMs) are a promising family of language generators, but achieving high-quality few-step generation remains challenging.
arXiv:2603. 23398v3 Announce Type: replace-cross Abstract: Generative modeling of discrete data, such as graphs, underpins many scientific and industrial applications, including molecular discovery and materials design.
arXiv:2603. 14504v2 Announce Type: replace-cross Abstract: Optimizing the noise samples of diffusion and flow models is an increasingly popular approach to align these models to target rewards at inference time.