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Diffusion language models promise parallel generation, yet still lag behind autoregressive (AR) models in quality. We stem this gap to a failure of introspective consistency: AR models agree with their own generations, while DLMs often do…

Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. However, traditional protein language models lack explicit structural supervision, despite its…

Biomolecules · Quantitative Biology 2024-02-09 Zuobai Zhang , Jiarui Lu , Vijil Chenthamarakshan , Aurélie Lozano , Payel Das , Jian Tang

The impact of Transformer-based language models has been unprecedented in Natural Language Processing (NLP). The success of such models has also led to their adoption in other fields including bioinformatics. Taking this into account, this…

Machine Learning · Computer Science 2025-07-21 Nimisha Ghosh , Daniele Santoni , Debaleena Nawn , Eleonora Ottaviani , Giovanni Felici

In this paper we introduce Hierarchical Diffusion Language Models (HDLM) -- a novel family of discrete diffusion models for language modeling. HDLM builds on a hierarchical vocabulary where low-level tokens with detailed semantics are…

Computation and Language · Computer Science 2025-10-13 Cai Zhou , Chenyu Wang , Dinghuai Zhang , Shangyuan Tong , Yifei Wang , Stephen Bates , Tommi Jaakkola

Diffusion language models have emerged as a promising approach for text generation. One would naturally expect this method to be an efficient replacement for autoregressive models since multiple tokens can be sampled in parallel during each…

Machine Learning · Computer Science 2025-06-10 Guhao Feng , Yihan Geng , Jian Guan , Wei Wu , Liwei Wang , Di He

Recent advances in large language models (LLMs) have shown remarkable capabilities across textual and multimodal domains. In parallel, diffusion-based language models have emerged as a promising alternative to the autoregressive paradigm,…

Prompt learning is an effective way to exploit the potential of large-scale pre-trained foundational models. Continuous prompts parameterize context tokens in prompts by turning them into differentiable vectors. Deep continuous prompts…

Machine Learning · Computer Science 2025-01-03 Zhenhan Huang , Tejaswini Pedapati , Pin-Yu Chen , Jianxi Gao

Offline reinforcement learning (RL) methods harness previous experiences to derive an optimal policy, forming the foundation for pre-trained large-scale models (PLMs). When encountering tasks not seen before, PLMs often utilize several…

Machine Learning · Computer Science 2024-11-05 Shengchao Hu , Wanru Zhao , Weixiong Lin , Li Shen , Ya Zhang , Dacheng Tao

Recent masked diffusion language models (MDLMs), such as LLaDA and Dream, have achieved performance comparable to autoregressive large language models. Unlike autoregressive models, which generate text sequentially, MDLMs generate text by…

Computation and Language · Computer Science 2026-05-19 Georu Lee , Seungwon Jeong , Hoki Kim , Jinseong Park , Woojin Lee

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based…

Quantitative Methods · Quantitative Biology 2023-10-19 Zuobai Zhang , Chuanrui Wang , Minghao Xu , Vijil Chenthamarakshan , Aurélie Lozano , Payel Das , Jian Tang

The development of large language models and multi-modal models has enabled the appealing idea of generating novel molecules from text descriptions. Generative modeling would shift the paradigm from relying on large-scale chemical screening…

Machine Learning · Computer Science 2025-08-25 Yifan Deng , Spencer S. Ericksen , Anthony Gitter

Language diffusion models aim to improve sampling speed and coherence over autoregressive LLMs. We introduce Neural Flow Diffusion Models for language generation, an extension of NFDM that enables the straightforward application of…

Computation and Language · Computer Science 2026-01-26 Nesta Midavaine , Christian A. Naesseth , Grigory Bartosh

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

We present LLaDA2.0-Uni, a unified discrete diffusion large language model (dLLM) that supports multimodal understanding and generation within a natively integrated framework. Its architecture combines a fully semantic discrete tokenizer, a…

Computer Vision and Pattern Recognition · Computer Science 2026-04-23 Inclusion AI , Tiwei Bie , Haoxing Chen , Tieyuan Chen , Zhenglin Cheng , Long Cui , Kai Gan , Zhicheng Huang , Zhenzhong Lan , Haoquan Li , Jianguo Li , Tao Lin , Qi Qin , Hongjun Wang , Xiaomei Wang , Haoyuan Wu , Yi Xin , Junbo Zhao

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

Proteins, as essential biomolecules, play a central role in biological processes, including metabolic reactions and DNA replication. Accurate prediction of their properties and functions is crucial in biological applications. Recent…

Computation and Language · Computer Science 2025-05-30 Wei Wu , Chao Wang , Liyi Chen , Mingze Yin , Yiheng Zhu , Kun Fu , Jieping Ye , Hui Xiong , Zheng Wang

Autoregressive language models decode left-to-right with irreversible commitments, limiting revision during multi-step reasoning. We propose \textbf{VDLM}, a modular variable diffusion language model that separates semantic planning from…

Computation and Language · Computer Science 2026-02-19 Shuhui Qu

We present FlowLM, a flow matching language model transformed from pre-trained diffusion language models via efficient fine-tuning. By re-aligning the curved sampling trajectories of diffusion models into straight-line flows, FlowLM enables…

Computation and Language · Computer Science 2026-05-21 Runzhe Zhang , Letian Chen , Wenpeng Zhang , Zhouhan Lin , Peilin Zhao

This paper presents a novel training method, Conditional Masked Language Modeling (CMLM), to effectively learn sentence representations on large scale unlabeled corpora. CMLM integrates sentence representation learning into MLM training by…

Computation and Language · Computer Science 2021-09-13 Ziyi Yang , Yinfei Yang , Daniel Cer , Jax Law , Eric Darve

This survey paper provides a comprehensive review of the use of diffusion models in natural language processing (NLP). Diffusion models are a class of mathematical models that aim to capture the diffusion of information or signals across a…

Computation and Language · Computer Science 2023-06-16 Hao Zou , Zae Myung Kim , Dongyeop Kang
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