NeurIPS 2025 Papers

We show how to use low-quality, synthetic, and out-of-distribution images to improve the quality of a diffusion model. Typically, diffusion models are trained on curated datasets that emerge from highly filtered data pools from the Web and other sources. We show that there is immense value in the lower-quality images that are often discarded. We present Ambient Diffusion Omni, a simple, principled framework to train diffusion models that can extract signal from arbitrarily images during training. Our framework exploits two properties of natural images -- spectral power law decay and locality. We first validate our framework by successfully training diffusion models with images synthetically corrupted by Gaussian blur, JPEG compression, and motion blur. We use our framework to achieve state-of-the-art ImageNet FID and we show significant improvements in both image quality and diversity for text-to-image generative modeling. The core insight is that noise dampens the initial skew between the desired high-quality distribution and the mixed distribution we actually observe. We provide rigorous theoretical justification for our approach by analyzing the trade-off between learning from biased data versus limited unbiased data across diffusion times.

Autoregressive models have driven remarkable progress in language modeling. Their foundational reliance on discrete tokens, unidirectional context, and single-pass decoding, while central to their success, also inspires the exploration of a design space that could offer new axes of modeling flexibility. In this work, we explore an alternative paradigm, shifting language modeling from a discrete token space to a continuous latent space. We propose a novel framework that employs transformer-based autoregressive normalizing flows to model these continuous representations. This approach unlocks substantial flexibility, enabling the construction of models that can capture global bi-directional context through stacked, alternating-direction autoregressive transformations, support block-wise generation with flexible token patch sizes, and facilitate a hierarchical multi-pass generation process. We further propose new mixture-based coupling transformations designed to capture complex dependencies within the latent space shaped by discrete data, and demonstrate theoretical connections to conventional discrete autoregressive models. Extensive experiments on language modeling benchmarks demonstrate strong likelihood performance and highlight the flexible modeling capabilities inherent in our framework.

The expressiveness of flow-based models combined with stochastic variational inference (SVI) has expanded the application of optimization-based Bayesian inference to highly complex problems. However, despite the importance of multi-model Bayesian inference, defined over a transdimensional joint model and parameter space, flow-based SVI has been limited to problems defined over a fixed-dimensional parameter space. We introduce CoSMIC normalizing flows (COntextually-Specified Masking for Identity-mapped Components), an extension to neural autoregressive conditional normalizing flow architectures that enables use of a single amortized variational density for inference over a transdimensional (multi-model) conditional target distribution. We propose a combined stochastic variational transdimensional inference (VTI) approach to training CoSMIC flows using ideas from Bayesian optimization and Monte Carlo gradient estimation. Numerical experiments show the performance of VTI on challenging problems that scale to high-cardinality model spaces.

Uncertainty quantification (UQ) is essential for safe deployment of generative AI models such as large language models (LLMs), especially in high-stakes applications. Conformal prediction (CP) offers a principled uncertainty quantification framework, but classical methods focus on regression and classification, relying on geometric distances or softmax scores--tools that presuppose structured outputs. We depart from this paradigm by studying CP in a query-only setting, where prediction sets must be constructed solely from finite queries to a black-box generative model, introducing a new trade-off between coverage, test-time query budget, and informativeness. We introduce **Conformal Prediction with Query Oracle** (CPQ), a framework characterizing the optimal interplay between these objectives. Our finite-sample algorithm is built on two core principles: one governs the optimal query policy, and the other defines the optimal mapping from queried samples to prediction sets. Remarkably, both are rooted in the classical **missing mass problem** in statistics. Specifically, the optimal query policy depends on the rate of decay--or the derivative--of the missing mass, for which we develop a novel estimator. Meanwhile, the optimal mapping hinges on the missing mass itself, which we estimate using Good-Turing estimators. We then turn our focus to implementing our method for language models, particularly in open-ended LLM tasks involving question answering, multi-step reasoning, and structured information extraction, where outputs are vast, variable, and often under-specified. Fine-grained experiments on three real-world open-ended tasks and two LLMs, show CPQ's applicability to **any black-box LLM** and highlight: (1) individual contribution of each principle to CPQ’s performance, and (2) CPQ's ability to yield significantly more informative prediction sets than existing conformal methods for language uncertainty quantification.

Efficient equilibrium sampling of molecular conformations remains a core challenge in computational chemistry and statistical inference. Classical approaches such as molecular dynamics or Markov chain Monte Carlo inherently lack amortization; the computational cost of sampling must be paid in-full for each system of interest. The widespread success of generative models has inspired interest into overcoming this limitation through learning sampling algorithms. Despite performing on par with conventional methods when trained on a single system, learned samplers have so far demonstrated limited ability to transfer across systems. We prove that deep learning enables the design of scalable and transferable samplers by introducing Ensemble, a 200 million parameter all-atom transferable normalizing flow trained on a corpus of peptide molecular dynamics trajectories up to 8 residues in length. Ensemble draws zero-shot uncorrelated proposal samples for arbitrary peptide systems, achieving the previously intractable transferability across sequence length, whilst retaining the efficient likelihood evaluation of normalizing flows. Through extensive empirical evaluation we demonstrate the efficacy of Ensemble as a proposal for a variety of sampling algorithms, finding a simple importance sampling-based finetuning procedure to achieve superior performance to established methods such as sequential Monte Carlo. We open-source the Ensemble codebase, model weights, and training dataset, to further stimulate research into amortized sampling methods and finetuning objectives.

Pre-trained diffusion models are commonly used to generate clean data (e.g., images) from random noises, effectively forming pairs of noises and corresponding clean images. Distillation on these pre-trained models can be viewed as the process of constructing advanced trajectories within the pair to accelerate sampling. For instance, consistency model distillation develops consistent projection functions to regulate trajectories, although sampling efficiency remains a concern. Rectified flow method enforces straight trajectories to enable faster sampling, yet relies on numerical ODE solvers, which may introduce approximation errors. In this work, we bridge the gap between the consistency model and the rectified flow method by proposing a Straight-Consistent Trajectories~(SCoT) model. SCoT enjoys the benefits of both approaches for fast sampling, producing trajectories with consistent and straight properties simultaneously. These dual properties are strategically balanced by targeting two critical objectives: (1) regulating the gradient of SCoT's mapping function to a constant and (2) ensuring trajectory consistency. Extensive experimental results demonstrate the effectiveness and efficiency of SCoT.

Autoregressive generative models naturally generate variable-length sequences, while non-autoregressive models struggle, often imposing rigid, token-wise structures. We propose Edit Flows, a non-autoregressive model that overcomes these limitations by defining a discrete flow over sequences through edit operations---insertions, deletions, and substitutions. By modeling these operations within a Continuous-time Markov Chain over the sequence space, Edit Flows enable flexible, position-relative generation that aligns more closely with the structure of sequence data. Our training method leverages an expanded state space with auxiliary variables, making the learning process efficient and tractable. Empirical results show that Edit Flows outperforms both autoregressive and mask models on image captioning and significantly outperforms the mask construction in text and code generation.

Flow-based generative models have gained popularity for image generation and editing. For instruction-based image editing, it is critical to ensure that modifications are confined to the targeted regions. Yet existing methods often fail to maintain consistency in non-targeted regions between the original / edited images. Our primary contribution is to identify the cause of this limitation as the error accumulation across individual editing steps and to address it by incorporating the historical editing trajectory. Specifically, we formulate image editing as a control problem and leverage the Kalman filter to integrate the historical editing trajectory. Our proposed algorithm, dubbed Kalman-Edit, reuses early-stage details from the historical trajectory to enhance the structural consistency of the editing results. To speed up editing, we introduce a shortcut technique based on approximate vector field velocity estimation. Extensive experiments on several datasets demonstrate its superior performance compared to previous state-of-the-art methods.

Diffusion models transform random noise into images of remarkable fidelity, yet the structure of this noise-to-image map remains largely unexplored. We investigate this relationship using patch-wise Principal Component Analysis (PCA) and empirically demonstrate that low-frequency components of the initial noise predominantly influence the compositional structure of generated images. Our analyses reveal that noise seeds inherently contain universal compositional cues, evident when identical seeds produce images with similar structural attributes across different datasets and model architectures. Leveraging these insights, we develop and theoretically justify a simple yet effective Patch PCA denoiser that extracts underlying structure from noise using only generic natural image statistics. The robustness of these structural cues is observed to persist across both pixel-space models and latent diffusion models, highlighting their fundamental nature. Finally, we introduce a zero-shot editing method that enables injecting compositional control over generated images, providing an intuitive approach to guided generation without requiring model fine-tuning or additional training.

Many real-world problems require reasoning across multiple scales, demanding models which operate not on single data points, but on entire distributions. We introduce generative distribution embeddings (GDE), a framework that lifts autoencoders to the space of distributions. In GDEs, an encoder acts on sets of samples, and the decoder is replaced by a generator which aims to match the input distribution. This framework enables learning representations of distributions by coupling conditional generative models with encoder networks which satisfy a criterion we call distributional invariance. We show that GDEs learn predictive sufficient statistics embedded in the Wasserstein space, such that latent GDE distances approximately recover the $W_2$ distance, and latent interpolation approximately recovers optimal transport trajectories for Gaussian and Gaussian mixture distributions. We systematically benchmark GDEs against existing approaches on synthetic datasets, demonstrating consistently stronger performance. We then apply GDEs to six key problems in computational biology: learning donor-level representations from single-nuclei RNA sequencing data (6M cells), capturing clonal dynamics in lineage-traced RNA sequencing data (150K cells), predicting perturbation effects on transcriptomes (1M cells), predicting perturbation effects on cellular phenotypes (20M single-cell images), designing synthetic yeast promoters (34M sequences), and spatiotemporal modeling of viral protein sequences (1M sequences).

Modern reinforcement learning (RL) algorithms have found success by using powerful probabilistic models, such as transformers, energy-based models, and diffusion/flow-based models. To this end, RL researchers often choose to pay the price of accommodating these models into their algorithms -- diffusion models are expressive, but are computationally intensive due to their reliance on solving differential equations, while autoregressive transformer models are scalable but typically require learning discrete representations. Normalizing flows (NFs), by contrast, seem to provide an appealing alternative, as they enable likelihoods and sampling without solving differential equations or autoregressive architectures. However, their potential in RL has received limited attention, partly due to the prevailing belief that normalizing flows lack sufficient expressivity. We show that this is not the case. Building on recent work in NFs, we propose a single NF architecture which integrates seamlessly into RL algorithms, serving as a policy, Q-function, and occupancy measure. Our approach leads to much simpler algorithms, and achieves higher performance in imitation learning, offline, goal conditioned RL and unsupervised RL.

The widespread use of generative models has created a feedback loop in which each generation of models is trained on data partially produced by its predecessors. This process has raised concerns about model collapse: A critical degradation in performance caused by repeated training on synthetic data. However, different analyses in the literature have reached different conclusions as to the severity of model collapse. As such, it remains unclear how concerning this phenomenon is, and under which assumptions it can be avoided. To address this, we theoretically study model collapse for maximum likelihood estimation (MLE), in a natural setting where synthetic data is gradually added to the original training set. Under standard assumptions (similar to those long used for proving asymptotic consistency and normality of MLE), we establish non-asymptotic bounds showing that collapse can be avoided even as the fraction of real data vanishes. On the other hand, we prove that some assumptions (beyond MLE consistency) are indeed necessary: Without them, model collapse can occur arbitrarily quickly, even when the original data is still present in the training set. To the best of our knowledge, these are the first rigorous examples of iterative generative modeling with accumulating data that rapidly leads to model collapse.

We propose a framework for learning maps between probability distributions that broadly generalizes the time dynamics of flow and diffusion models. To enable this, we generalize stochastic interpolants by replacing the scalar time variable with vectors, matrices, or linear operators, allowing us to bridge probability distributions across multiple dimensional spaces. This approach enables the construction of versatile generative models capable of fulfilling multiple tasks without task-specific training. Our operator-based interpolants not only provide a unifying theoretical perspective for existing generative models but also extend their capabilities. Through numerical experiments, we demonstrate the zero-shot efficacy of our method on conditional generation and inpainting, fine-tuning and posterior sampling, and multiscale modeling, suggesting its potential as a generic task-agnostic alternative to specialized models.

Many natural systems, including neural circuits involved in decision making, are modeled as high-dimensional dynamical systems with multiple stable states. While existing analytical tools primarily describe behavior near stable equilibria, characterizing separatrices -- the manifolds that delineate boundaries between different basins of attraction -- remains challenging, particularly in high-dimensional settings. Here, we introduce a numerical framework leveraging Koopman Theory combined with Deep Neural Networks to effectively characterize separatrices. Specifically, we approximate Koopman Eigenfunctions (KEFs) associated with real positive eigenvalues, which vanish precisely at the separatrices. Utilizing these scalar KEFs, optimization methods efficiently locate separatrices even in complex systems. We demonstrate our approach on synthetic benchmarks, ecological network models, and high-dimensional recurrent neural networks trained on either neuroscience-inspired tasks or fit to real neural data. Moreover, we illustrate the practical utility of our method by designing optimal perturbations that can shift systems across separatrices, enabling predictions relevant to optogenetic stimulation experiments in neuroscience.

Time series data is ubiquitous, with forecasting applications spanning from finance to healthcare. Beyond popular deterministic methods, generative models are gaining attention due to advancements in areas like image synthesis and video generation, as well as their inherent ability to provide probabilistic predictions. However, existing generative approaches mostly involve recurrent generative operations or repeated denoising steps, making the prediction laborious, particularly for long-term forecasting. Most of them only conduct experiments for relatively short-term forecasting, with limited comparison to deterministic methods in long-term forecasting, leaving their practical advantages unclear. This paper presents TARFVAE, a novel generative framework that combines the Transformer-based autoregressive flow (TARFLOW) and variational autoencoder (VAE) for efficient one-step generative time series forecasting. Inspired by the rethinking that complex architectures for extracting time series representations might not be necessary, we add a flow module, TARFLOW, to VAE to promote spontaneous learning of latent variables that benefit predictions. TARFLOW enhances VAE's posterior estimation by breaking the Gaussian assumption, thereby enabling a more informative latent space. TARFVAE uses only the forward process of TARFLOW, avoiding autoregressive inverse operations and thus ensuring fast generation. During generation, it samples from the prior latent space and directly generates full-horizon forecasts via the VAE decoder. With simple MLP modules, TARFVAE achieves superior performance over state-of-the-art deterministic and generative models across different forecast horizons on benchmark datasets while maintaining efficient prediction speed, demonstrating its effectiveness as an efficient and powerful solution for generative time series forecasting. Our code is available at https://github.com/Gavine77/TARFVAE.

We present STARFlow, a scalable generative model based on normalizing flows that achieves strong performance on high-resolution image synthesis. STARFlow's main building block is Transformer Autoregressive Flow (TARFlow), which combines normalizing flows with Autoregressive Transformer architectures and has recently achieved impressive results in image modeling. In this work, we first establish the theoretical universality of TARFlow for modeling continuous distributions. Building on this foundation, we introduce a set of architectural and algorithmic innovations that significantly enhance the scalability: (1) a deep-shallow design where a deep Transformer block captures most of the model’s capacity, followed by a few shallow Transformer blocks that are computationally cheap yet contribute non-negligibly, (2) learning in the latent space of pretrained autoencoders, which proves far more effective than modeling pixels directly, and (3) a novel guidance algorithm that substantially improves sample quality. Crucially, our model remains a single, end-to-end normalizing flow, allowing exact maximum likelihood training in continuous space without discretization. STARFlow achieves competitive results in both class- and text-conditional image generation, with sample quality approaching that of state-of-the-art diffusion models. To our knowledge, this is the **first** successful demonstration of normalizing flows at this scale and resolution. Code and weights available at https://github.com/apple/ml-starflow.