Emyx: Fast and efficient all-atom protein generation

arXiv:2606.19377 · cs.LG, cs.AI · Submitted 2026-06-12 · Read on arXiv

cs.LG, cs.AI

Submitted: 2026-06-12

Updated: 2026-08-26

Terminology

• Flow Matching — 39× in this paper · explained in 7 episodes
• Transformer — 37× in this paper · explained in 2 episodes
• Benchmark — 28× in this paper · explained in 2 episodes
• Embeddings — 14× in this paper · explained in 2 episodes
• Alignment — 13× in this paper · explained in 1 episode
• Accuracy — 8× in this paper · explained in 1 episode
• Consistency — 8× in this paper · explained in 3 episodes
• Scaffolding — 8× in this paper · explained in 3 episodes
• Self-consistency — 8× in this paper · explained in 2 episodes
• Diffusion Model — 7× in this paper · explained in 8 episodes
• Diffusion Models — 6× in this paper · explained in 6 episodes
• Generative Model — 6× in this paper · explained in 2 episodes
• Ablation — 5× in this paper · explained in 1 episode
• Generative Models — 5× in this paper · explained in 2 episodes
• Model-Agnostic — 5× in this paper · explained in 2 episodes
• Clustering — 3× in this paper · explained in 2 episodes
• Data Augmentation — 3× in this paper · explained in 7 episodes
• AdaLN-Zero Modulation — 2× in this paper · explained in 1 episode
• Core — 2× in this paper · explained in 2 episodes
• Failure Modes — 2× in this paper · explained in 3 episodes
• Latent Representation — 2× in this paper · explained in 2 episodes
• Loss Function — 2× in this paper · explained in 2 episodes
• Sparse Attention — 2× in this paper · explained in 5 episodes
• Ablation Studies — 1× in this paper · explained in 1 episode
• Decoupling — 1× in this paper · explained in 2 episodes
• Distillation — 1× in this paper · explained in 2 episodes
• Enzyme Commission — 1× in this paper
• Fidelity — 1× in this paper · explained in 2 episodes
• Geometric Distribution — 1× in this paper · explained in 2 episodes
• Graph Construction — 1× in this paper · explained in 3 episodes
• Latent Space — 1× in this paper · explained in 7 episodes
• Normalizing Flow — 1× in this paper · explained in 3 episodes
• Normalizing Flows — 1× in this paper · explained in 4 episodes
• Regularization — 1× in this paper · explained in 3 episodes
• Score Function — 1× in this paper · explained in 4 episodes
• Two-Stage Architecture — 1× in this paper · explained in 2 episodes

Sources

• La-Proteina: Atomistic Protein Generation via Partially Latent Flow Matching
• GLU Variants Improve Transformer
• Stochastic Sampling from Deterministic Flow Models

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