Related papers: Diffusion Sequence Models for Enhanced Protein Rep…

This paper shows how diffusion language models (DLMs) can be used as effective and efficient retrievers. Existing DLM-based retrievers (e.g., DiffEmbed) follow BERT-style encoding, representing each query or passage as a single mean-pooled…

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,…

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…

A long-standing goal of machine-learning-based protein engineering is to accelerate the discovery of novel mutations that improve the function of a known protein. We introduce a sampling framework for evolving proteins in silico that…

Diffusion Language models (DLMs) are a promising avenue for text generation due to their practical properties on tractable controllable generation. They also have the advantage of not having to predict text autoregressively. However,…

In this work, we provide a systematic survey of Discrete Diffusion Language Models (dLLMs) and Discrete Diffusion Multimodal Language Models (dMLLMs). Unlike autoregressive (AR) models, dLLMs and dMLLMs adopt a multi-token, parallel…

Denoising language models (DLMs) have been proposed as a powerful alternative to traditional language models (LMs) for automatic speech recognition (ASR), motivated by their ability to use bidirectional context and adapt to a specific ASR…

Protein language models have excelled in a variety of tasks, ranging from structure prediction to protein engineering. However, proteins are highly diverse in functions and structures, and current state-of-the-art models including the…

Recently, there has been a significant upsurge of interest in leveraging large language models (LLMs) to assist scientific discovery. However, most LLMs only focus on general science, while they lack domain-specific knowledge, such as…

Diffusion language models (DLMs) have emerged as a promising alternative to autoregressive models for faster inference via parallel token generation. We provide a rigorous foundation for this advantage by formalizing a model of parallel…

Diffusion Probabilistic Models (DPMs) have recently demonstrated impressive results on various generative tasks.Despite its promises, the learned representations of pre-trained DPMs, however, have not been fully understood. In this paper,…

Protein language models (PLMs) encode rich biological information, yet their internal neuron representations are poorly understood. We introduce the first automated framework for labeling every neuron in a PLM with biologically grounded…

Masked Diffusion Models (MDMs) have emerged as a promising approach for generative modeling in discrete spaces. By generating sequences in any order and allowing for parallel decoding, they enable fast inference and strong performance on…

The prediction of amyloidogenicity in peptides and proteins remains a focal point of ongoing bioinformatics. The crucial step in this field is to apply advanced computational methodologies. Many recent approaches to predicting…

Diffusion language models (DLMs) have recently demonstrated capabilities that complement standard autoregressive (AR) models, particularly in non-sequential generation and bidirectional editing. Although recent work has shown that…

Any order generation of discrete data using masked diffusion models (MDMs) offers a compelling alternative to traditional autoregressive models, especially in domains that lack a natural causal ordering of data. However, current popular…

Latent diffusion models offer an attractive alternative to discrete diffusion for non-autoregressive text generation by operating on continuous text representations and denoising entire sequences in parallel. The major challenge in latent…

Diffusion Language Models (DLMs) promise parallel generation and bidirectional context, yet they underperform autoregressive (AR) models in both likelihood modeling and generated text quality. We identify that this performance gap arises…

The capabilities of large language models (LLMs) are widely regarded as relying on autoregressive models (ARMs). We challenge this notion by introducing LLaDA, a diffusion model trained from scratch under the pre-training and supervised…

Deep Generative Models (DGMs), including Energy-Based Models (EBMs) and Score-based Generative Models (SGMs), have advanced high-fidelity data generation and complex continuous distribution approximation. However, their application in…