On statistical rates and provably efficient criteria of latent diffusion transformers (dits)

JYC Hu, W Wu, Z Li, Z Song, H Liu - arXiv preprint arXiv:2407.01079, 2024 - arxiv.org
We investigate the statistical and computational limits of latent\textbf {Di} ffusion\textbf {T}
ransformers (\textbf {DiT} s) under the low-dimensional linear latent space assumption …

Differentially private kernel density estimation

E Liu, JYC Hu, A Reneau, Z Song, H Liu - arXiv preprint arXiv:2409.01688, 2024 - arxiv.org
We introduce a refined differentially private (DP) data structure for kernel density estimation
(KDE), offering not only improved privacy-utility tradeoff but also better efficiency over prior …

Toward De Novo Protein Design from Natural Language

F Dai, Y Fan, J Su, C Wang, C Han, X Zhou, J Liu… - bioRxiv, 2024 - biorxiv.org
De novo protein design (DNPD) aims to create new protein sequences from scratch, without
relying on existing protein templates. However, current deep learning-based DNPD …

Steering Masked Discrete Diffusion Models via Discrete Denoising Posterior Prediction

J Rector-Brooks, M Hasan, Z Peng, Z Quinn… - arXiv preprint arXiv …, 2024 - arxiv.org
Generative modeling of discrete data underlies important applications spanning text-based
agents like ChatGPT to the design of the very building blocks of life in protein sequences …

Towards deep learning sequence-structure co-generation for protein design

C Wang, S Alamdari, C Domingo-Enrich… - arXiv preprint arXiv …, 2024 - arxiv.org
Deep generative models that learn from the distribution of natural protein sequences and
structures may enable the design of new proteins with valuable functions. While the majority …

ProteinBench: A Holistic Evaluation of Protein Foundation Models

F Ye, Z Zheng, D Xue, Y Shen, L Wang, Y Ma… - arXiv preprint arXiv …, 2024 - arxiv.org
Recent years have witnessed a surge in the development of protein foundation models,
significantly improving performance in protein prediction and generative tasks ranging from …

Unlocking Guidance for Discrete State-Space Diffusion and Flow Models

H Nisonoff, J Xiong, S Allenspach… - arXiv preprint arXiv …, 2024 - arxiv.org
Generative models on discrete state-spaces have a wide range of potential applications,
particularly in the domain of natural sciences. In continuous state-spaces, controllable and …

CryoFM: A Flow-based Foundation Model for Cryo-EM Densities

Y Zhou, Y Li, J Yuan, Q Gu - arXiv preprint arXiv:2410.08631, 2024 - arxiv.org
Cryo-electron microscopy (cryo-EM) is a powerful technique in structural biology and drug
discovery, enabling the study of biomolecules at high resolution. Significant advancements …

An adaptive autoregressive diffusion approach to design active humanized antibody and nanobody

J Ma, F Wu, T Xu, S Xu, W Liu, D Yan, Q Bai, J Yao - bioRxiv, 2024 - biorxiv.org
Humanization is a critical process for designing efficiently specific antibodies and
nanobodies prior to clinical trials. Developing widely recognized deep learning techniques …