A-CODE presents a fully atomic one-stage multimodal diffusion model for protein co-design that claims superior unconditional generation performance over prior one- and two-stage models plus a tenfold success-rate gain on hard binder-design tasks.
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arXiv preprint arXiv:2410.13782 , year=
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LLaDA is a scalable diffusion-based language model that matches autoregressive LLMs like LLaMA3 8B on tasks and surpasses GPT-4o on reversal poem completion.
ConTact decomposes CDR design into surface fingerprint learning, contact prediction, and contact-gated sequence generation using distance-biased attention and weighted loss, reporting 7% RMSD and 10% F1 gains on CHIMERA-Bench.
ΔLPS is a gradient-guided discrete posterior sampler for inverse problems that works with masked or uniform discrete diffusion priors and outperforms prior discrete methods on image restoration tasks.
PartDiffuser is a semi-autoregressive discrete diffusion framework that generates high-fidelity 3D meshes from point clouds by combining inter-part autoregression with intra-part parallel diffusion using a part-aware DiT architecture.
AgForce improves antigen-conditioned antibody design by using framework dropout, gated bottlenecks, hyperbolic cross attention, MDN sequence head with Potts-like coupling, annealed MCL, and antigen cycle consistency to achieve 8% better amino acid recovery and superior binding metrics on CHIMERA-BEN
EvoStruct integrates evolutionary priors from a protein language model with structural priors from an E(3)-equivariant GNN to raise amino acid recovery by 16% and diversity by 2.3x on CHIMERA-Bench while cutting perplexity 43%.
Yeti is a compact tokenizer for protein structures that delivers strong codebook use, token diversity, and reconstruction while enabling from-scratch multimodal generation of plausible sequences and structures with 10x fewer parameters than ESM3.
Coupling Models enable single-step discrete sequence generation via learned couplings to Gaussian latents and outperform prior one-step baselines on text perplexity, biological FBD, and image FID metrics.
PAR is a multi-scale autoregressive transformer framework for protein backbone generation that uses coarse-to-fine prediction, noisy context learning, and flow-based decoding to achieve high-quality unconditional and zero-shot conditional outputs.
CodeFP jointly generates protein sequences and structures using functional local structures and auxiliary supervision, yielding 6.1% better functional consistency and 3.2% better foldability than prior baselines.
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Yeti: A compact protein structure tokenizer for reconstruction and multi-modal generation
Yeti is a compact tokenizer for protein structures that delivers strong codebook use, token diversity, and reconstruction while enabling from-scratch multimodal generation of plausible sequences and structures with 10x fewer parameters than ESM3.