English
Related papers

Related papers: Diffusion on language model encodings for protein …

200 papers

Attention-based models trained on protein sequences have demonstrated incredible success at classification and generation tasks relevant for artificial intelligence-driven protein design. However, we lack a sufficient understanding of how…

Machine Learning · Computer Science 2022-06-29 Erik Nijkamp , Jeffrey Ruffolo , Eli N. Weinstein , Nikhil Naik , Ali Madani

While Masked Diffusion Language Models (MDLMs) relying on token masking and unmasking have shown promise in language modeling, their computational efficiency and generation flexibility remain constrained by the masking paradigm. In this…

Computation and Language · Computer Science 2026-03-26 Fangyu Ding , Ding Ding , Sijin Chen , Kaibo Wang , Peng Xu , Zijin Feng , Haoli Bai , Kai Han , Youliang Yan , Binhang Yuan , Jiacheng Sun

In recent developments, the Mamba architecture, known for its selective state space approach, has shown potential in the efficient modeling of long sequences. However, its application in image generation remains underexplored. Traditional…

Computer Vision and Pattern Recognition · Computer Science 2024-05-28 Shentong Mo , Yapeng Tian

Fashion content generation is an emerging area at the intersection of artificial intelligence and creative design, with applications ranging from virtual try-on to culturally diverse design prototyping. Existing methods often struggle with…

Computation and Language · Computer Science 2025-01-28 Spencer Ramsey , Amina Grant , Jeffrey Lee

Goal-directed molecular generation requires satisfying heterogeneous constraints such as protein--ligand compatibility and multi-objective drug-like properties, yet existing methods often optimize these constraints in isolation, failing to…

Machine Learning · Computer Science 2026-04-14 Yanting Li , Zhuoyang Jiang , Enyan Dai , Lei Wang , Wen-Cai Ye , Li Liu

Diffusion models excel at capturing the natural design spaces of images, molecules, DNA, RNA, and protein sequences. However, rather than merely generating designs that are natural, we often aim to optimize downstream reward functions while…

In real-life conversations, the content is diverse, and there exists the one-to-many problem that requires diverse generation. Previous studies attempted to introduce discrete or Gaussian-based continuous latent variables to address the…

Computation and Language · Computer Science 2024-04-11 Jianxiang Xiang , Zhenhua Liu , Haodong Liu , Yin Bai , Jia Cheng , Wenliang Chen

Diffusion models are a new class of generative models that have shown outstanding performance in image generation literature. As a consequence, studies have attempted to apply diffusion models to other tasks, such as speech enhancement. A…

Audio and Speech Processing · Electrical Eng. & Systems 2024-10-10 Philippe Gonzalez , Zheng-Hua Tan , Jan Østergaard , Jesper Jensen , Tommy Sonne Alstrøm , Tobias May

Although diffusion language models (DLMs) are evolving quickly, many recent models converge on a set of shared components. These components, however, are distributed across ad-hoc research codebases or lack transparent implementations,…

Computation and Language · Computer Science 2026-02-27 Zhanhui Zhou , Lingjie Chen , Hanghang Tong , Dawn Song

Mass spectrometry plays a fundamental role in elucidating the structures of unknown molecules and subsequent scientific discoveries. One formulation of the structure elucidation task is the conditional de novo generation of molecular…

Machine Learning · Computer Science 2025-05-29 Montgomery Bohde , Mrunali Manjrekar , Runzhong Wang , Shuiwang Ji , Connor W. Coley

Despite remarkable progress in autoregressive language models, alternative generative paradigms beyond left-to-right generation are still being actively explored. Discrete diffusion models, with the capacity for parallel generation, have…

Computation and Language · Computer Science 2025-03-10 Minkai Xu , Tomas Geffner , Karsten Kreis , Weili Nie , Yilun Xu , Jure Leskovec , Stefano Ermon , Arash Vahdat

We introduce MMaDA, a novel class of multimodal diffusion foundation models designed to achieve superior performance across diverse domains such as textual reasoning, multimodal understanding, and text-to-image generation. The approach is…

Computer Vision and Pattern Recognition · Computer Science 2025-09-26 Ling Yang , Ye Tian , Bowen Li , Xinchen Zhang , Ke Shen , Yunhai Tong , Mengdi Wang

Diffusion language models (DLMs) have emerged as a promising alternative to autoregressive (AR) generation, yet their reliance on Transformer backbones limits inference efficiency due to quadratic attention or KV-cache overhead. We…

Machine Learning · Computer Science 2026-03-02 Vaibhav Singh , Oleksiy Ostapenko , Pierre-André Noël , Eugene Belilovsky , Torsten Scholak

We introduce Lumina-DiMOO, an open-source foundational model for seamless multi-modal generation and understanding. Lumina-DiMOO sets itself apart from prior unified models by utilizing a fully discrete diffusion modeling to handle inputs…

With the exponential increase of the protein sequence databases over time, multiple-sequence alignment (MSA) methods, like PSI-BLAST, perform exhaustive and time-consuming database search to retrieve evolutionary information. The resulting…

Quantitative Methods · Quantitative Biology 2023-08-21 Issar Arab

Diffusion generative models have emerged as a powerful framework for addressing problems in structural biology and structure-based drug design. These models operate directly on 3D molecular structures. Due to the unfavorable scaling of…

Biomolecules · Quantitative Biology 2024-05-10 Ian Dunn , David Ryan Koes

Combining discrete and continuous data is an important capability for generative models. We present Discrete Flow Models (DFMs), a new flow-based model of discrete data that provides the missing link in enabling flow-based generative models…

Machine Learning · Statistics 2024-06-07 Andrew Campbell , Jason Yim , Regina Barzilay , Tom Rainforth , Tommi Jaakkola

We present a diffusion-based framework for document-centric background generation that achieves foreground preservation and multi-page stylistic consistency through latent-space design rather than explicit constraints. Instead of…

Computer Vision and Pattern Recognition · Computer Science 2026-01-30 Taewon Kang

Designing protein-binding proteins with high affinity is critical in biomedical research and biotechnology. Despite recent advancements targeting specific proteins, the ability to create high-affinity binders for arbitrary protein targets…

Machine Learning · Computer Science 2025-11-03 Zhenqiao Song , Tiaoxiao Li , Lei Li , Martin Renqiang Min

Diffusion model, a new generative modelling paradigm, has achieved great success in image, audio, and video generation. However, considering the discrete categorical nature of text, it is not trivial to extend continuous diffusion models to…

Computation and Language · Computer Science 2023-05-23 Hongyi Yuan , Zheng Yuan , Chuanqi Tan , Fei Huang , Songfang Huang