ADNI
Abstract:Discrete Masked diffusion language models generate text by iterative parallel decoding, but few-step decoding suffers from a tradeoff between length and quality: with a fixed step budget, standard methods can generate a short, high-quality output, or they can produce long but repetitive text. Continuous denoising can sidestep this tradeoff by evolving all positions jointly in embedding space, but building such a model from scratch at scale remains an open problem. We show that a pretrained masked DLM can instead be lightly adapted to support continuous embedding-space denoising. Starting from LLaDA-8B-Instruct, we continue-pretrain for only 1,000 steps with Discrete Stochastic Localization (DSL), replacing binary masking with continuous per-token Gaussian noise as a soft mask. The adapted model supports continuous inference that evolves all positions jointly in embedding space and defers hard token commitment to the final step. On zero-shot summarization at low step budgets (<=16 forward passes), DSL-LLaDA-SDE achieves the best ROUGE-1 on all four benchmarks and largely avoids the premature-termination / repetition tradeoff of iterative unmasking. The same adaptation also yields selective noisy-state robustness: the model corrects corrupted tokens while preserving clean ones. Control experiments using standard masked diffusion training with the same compute demonstrate neither behavior.
Abstract:Masked diffusion language models (MDLMs) re-predict every position at each denoising step, but standard samplers commit tokens once revealed, leaving this revision capability unused. Existing approaches either add heuristic or learned mechanisms to revise committed tokens, or remask them back to [MASK] before re-predicting; a principled sampler that directly revises visible tokens without auxiliary modules remains underexplored. We introduce D3IM, a parameter-free sampler derived as a corrector-style reverse update that permits direct visible-to-visible revision without additional modules or auxiliary passes. D3IM also reveals a model-side obstacle we term preservation bias: the model tends to reproduce its own wrong committed tokens rather than correct them. We address this with SCOPE (Self-Conditioned On Prediction Errors), a lightweight post-training procedure that simulates D3IM's sampling process. On LLaDA-8B at 64 denoising steps, SCOPE+D3IM improves over the original LLaDA-8B with standard unmasking by +13.0 on GSM8K (68.3%), +4.8 on MATH-500 (23.6%), +15.3 on HumanEval (29.3%), and +10.4 on MBPP (30.8%), with gains that increase as more denoising steps are used on math and HumanEval.
Abstract:Diffusion models are typically trained using pointwise reconstruction objectives that are agnostic to the spectral and multi-scale structure of natural signals. We propose a loss-level spectral regularization framework that augments standard diffusion training with differentiable Fourier- and wavelet-domain losses, without modifying the diffusion process, model architecture, or sampling procedure. The proposed regularizers act as soft inductive biases that encourage appropriate frequency balance and coherent multi-scale structure in generated samples. Our approach is compatible with DDPM, DDIM, and EDM formulations and introduces negligible computational overhead. Experiments on image and audio generation demonstrate consistent improvements in sample quality, with the largest gains observed on higher-resolution, unconditional datasets where fine-scale structure is most challenging to model.
Abstract:Discrete diffusion language models (dLLMs) provide a fast and flexible alternative to autoregressive models (ARMs) via iterative denoising with parallel updates. However, their evaluation is challenging: existing metrics conflate denoiser approximation error with sampler-induced error from the sampling dynamics, a problem that does not arise for ARMs whose autoregressive sampling exactly reflects the learned probability model. We introduce a sampler-centric oracle framework that replaces learned denoisers with an exact Hidden Markov Model posterior derived from a ground-truth Markov chain, isolating sampler-induced error in a controlled setting. We show that few-step discrete diffusion samplers are not distributionally correct even under an oracle denoiser, with transition-level mismatch that vanishes only as the number of steps approaches the sequence length. Moreover, improvements in negative log-likelihood, generative perplexity, or MAUVE do not imply correct sampling. Code is available at https://luhantang.github.io/dllm_sampler
Abstract:Non-autoregressive (NAR) generation reduces decoding latency by predicting many tokens in parallel, but iterative refinement often suffers from error accumulation and distribution shift under self-generated drafts. Masked diffusion language models (MDLMs) and their remasking samplers (e.g., ReMDM) can be viewed as modern NAR iterative refinement, where generation repeatedly revises a partially observed draft. In this work we show that \emph{training alone} can substantially improve the step-efficiency of MDLM/ReMDM sampling. We propose \textsc{DSL} (Discrete Stochastic Localization), which trains a single SNR-invariant denoiser across a continuum of corruption levels, bridging intermediate draft noise and mask-style endpoint corruption within one Diffusion Transformer. On OpenWebText, \textsc{DSL} fine-tuning yields large MAUVE gains at low step budgets, surpassing the MDLM+ReMDM baseline with \(\sim\)4$\times$ fewer denoiser evaluations, and matches autoregressive quality at high budgets. Analyses show improved self-correction and uncertainty calibration, making remasking markedly more compute-efficient.
Abstract:Masked Diffusion Models (MDMs) significantly accelerate inference by trading off sequential determinism. However, the theoretical mechanisms governing generation order and the risks inherent in parallelization remain under-explored. In this work, we provide a unified information-theoretic framework to decouple and analyze two fundamental sources of failure: order sensitivity and parallelization bias. Our analysis yields three key insights: (1) The benefits of Easy-First decoding (prioritizing low-entropy tokens) are magnified as model error increases; (2) factorized parallel decoding introduces intrinsic sampling errors that can lead to arbitrary large Reverse KL divergence, capturing "incoherence" failures that standard Forward KL metrics overlook; and (3) while verification can eliminate sampling error, it incurs an exponential cost governed by the total correlation within a block. Conversely, heuristics like remasking, though computationally efficient, cannot guarantee distributional correctness. Experiments on a controlled Block-HMM and large-scale MDMs (LLaDA) for arithmetic reasoning validate our theoretical framework.
Abstract:Autoregressive (AR) language models enforce a fixed left-to-right generation order, creating a fundamental limitation when the required output structure conflicts with natural reasoning (e.g., producing answers before explanations due to presentation or schema constraints). In such cases, AR models must commit to answers before generating intermediate reasoning, and this rigid constraint forces premature commitment. Masked diffusion language models (MDLMs), which iteratively refine all tokens in parallel, offer a way to decouple computation order from output structure. We validate this capability on GSM8K, Math500, and ReasonOrderQA, a benchmark we introduce with controlled difficulty and order-level evaluation. When prompts request answers before reasoning, AR models exhibit large accuracy gaps compared to standard chain-of-thought ordering (up to 67% relative drop), while MDLMs remain stable ($\leq$14% relative drop), a property we term "order robustness". Using ReasonOrderQA, we present evidence that MDLMs achieve order robustness by stabilizing simpler tokens (e.g., reasoning steps) earlier in the diffusion process than complex ones (e.g., final answers), enabling reasoning tokens to stabilize before answer commitment. Finally, we identify failure conditions where this advantage weakens, outlining the limits required for order robustness.
Abstract:Deep learning has been successful in predicting neurodegenerative disorders, such as Alzheimer's disease, from magnetic resonance imaging (MRI). Combining multiple imaging modalities, such as T1-weighted (T1) and diffusion-weighted imaging (DWI) scans, can increase diagnostic performance. However, complete multimodal datasets are not always available. We use a conditional denoising diffusion probabilistic model to impute missing DWI scans from T1 scans. We perform extensive experiments to evaluate whether such imputation improves the accuracy of uni-modal and bi-modal deep learning models for 3-way Alzheimer's disease classification-cognitively normal, mild cognitive impairment, and Alzheimer's disease. We observe improvements in several metrics, particularly those sensitive to minority classes, for several imputation configurations.
Abstract:Diffusion models provide a powerful way to incorporate complex prior information for solving inverse problems. However, existing methods struggle to correctly incorporate guidance from conflicting signals in the prior and measurement, especially in the challenging setting of non-Gaussian or unknown noise. To bridge these gaps, we propose Measurement-Aligned Sampling (MAS), a novel framework for linear inverse problem solving that can more flexibly balance prior and measurement information. MAS unifies and extends existing approaches like DDNM and DAPS, and offers a new optimization perspective. MAS can generalize to handle known Gaussian noise, unknown or non-Gaussian noise types. Extensive experiments show that MAS consistently outperforms state-of-the-art methods across a range of tasks.
Abstract:Complementarity Determining Regions (CDRs) are critical segments of an antibody that facilitate binding to specific antigens. Current computational methods for CDR design utilize reconstruction losses and do not jointly optimize binding energy, a crucial metric for antibody efficacy. Rather, binding energy optimization is done through computationally expensive Online Reinforcement Learning (RL) pipelines rely heavily on unreliable binding energy estimators. In this paper, we propose AbFlowNet, a novel generative framework that integrates GFlowNet with Diffusion models. By framing each diffusion step as a state in the GFlowNet framework, AbFlowNet jointly optimizes standard diffusion losses and binding energy by directly incorporating energy signals into the training process, thereby unifying diffusion and reward optimization in a single procedure. Experimental results show that AbFlowNet outperforms the base diffusion model by 3.06% in amino acid recovery, 20.40% in geometric reconstruction (RMSD), and 3.60% in binding energy improvement ratio. ABFlowNet also decreases Top-1 total energy and binding energy errors by 24.8% and 38.1% without pseudo-labeling the test dataset or using computationally expensive online RL regimes.