7 accepted papers
Motif scaffolding in protein design involves generating complete protein structures while preserving the 3D geometry of designated structural fragments, analogous to image outpainting in computer vision. Current benchmarks focus on functional motifs, leaving general geometric preservation capabiliti…
The performance of pre-trained masked diffusion models is often constrained by their sampling procedure, which makes decisions irreversible and struggles in low-step generation regimes. We introduce a novel sampling algorithm that works with pre-trained models and, after a lightweight fine-tuning of…
Unpaired domain translation remains a challenging task due to the need of finding a balance between faithfulness and realism. In this paper, we propose a method called Regularized Distribution Matching Distillation (RDMD) that combines the best properties of Optimal Transport (OT) and diffusion-base…
Diffusion models have achieved state-of-the-art performance in generating images, audio, and video, but their adaptation to text remains challenging due to its discrete nature. Prior approaches either apply Gaussian diffusion in continuous latent spaces, which inherits semantic structure but struggl…
Autoregressive language models dominate modern text generation, yet their sequential nature introduces fundamental limitations: decoding is slow, and maintaining global coherence remains challenging. Diffusion models offer a promising alternative by enabling parallel generation and flexible control;…
Protein *sequence* design has seen significant advances through discrete diffusion and autoregressive approaches, yet the potential of continuous diffusion remains underexplored. Here, we present *DiMA*, a latent diffusion framework that operates on protein language model representations. Through sy…
This paper presents the Text Encoding Diffusion Model (TEncDM), a novel approach to diffusion modeling that operates in the space of pre-trained language model encodings. In contrast to traditionally used embeddings, encodings integrate contextual information. In our approach, we also employ a trans…