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Applications · Chemistry, Physics, and Earth Sciences

Urszula Julia Komorowska, Francisco Vargas, Alessandro Rondina, Pietro Lió, Mateja Jamnik

Protein's backbone flexibility is a crucial property that heavily influences its functionality. Recent work in the field of protein diffusion probabilistic modelling has leveraged Normal Mode Analysis (NMA) and, for the first time, introduced information about large scale protein motion into the generative process. However, obtaining molecules with both the desired dynamics and designable quality has proven challenging. In this work, we present NMA-tune, a new method that introduces the dynamics information to the protein design stage. NMA-tune uses a trainable component to condition the backbone generation on the lowest normal mode of oscillation. We implement NMA-tune as a plug-and-play extension to RFdiffusion, show that the proportion of samples with high quality structure and the desired dynamics is improved as compared to other methods without the trainable component, and we show the presence of the targeted modes in the Molecular Dynamics simulations.

Reinforcement Learning · Deep RL

Mingyang Sun, Pengxiang Ding, Weinan Zhang, Donglin Wang

Diffusion policies have shown promise in learning complex behaviors from demonstrations, particularly for tasks requiring precise control and long-term planning. However, they face challenges in robustness when encountering distribution shifts. This paper explores improving diffusion-based imitation learning models through online interactions with the environment. We propose OTPR (Optimal Transport-guided score-based diffusion Policy for Reinforcement learning fine-tuning), a novel method that integrates diffusion policies with RL using optimal transport theory. OTPR leverages the Q-function as a transport cost and views the policy as an optimal transport map, enabling efficient and stable fine-tuning. Moreover, we introduce masked optimal transport to guide state-action matching using expert keypoints and a compatibility-based resampling strategy to enhance training stability. Experiments on three simulation tasks demonstrate OTPR's superior performance and robustness compared to existing methods, especially in complex and sparse-reward environments. In sum, OTPR provides an effective framework for combining IL and RL, achieving versatile and reliable policy learning.

Deep Learning · Generative Models and Autoencoders

Shuangfei Zhai, Ruixiang Zhang, Preetum Nakkiran, David Berthelot, Jiatao Gu, Huangjie Zheng, Tianrong Chen, Miguel Angel Bautista Martin, Navdeep Jaitly, Joshua M Susskind

Normalizing Flows (NFs) are likelihood-based models for continuous inputs. They have demonstrated promising results on both density estimation and generative modeling tasks, but have received relatively little attention in recent years. In this work, we demonstrate that NFs are more powerful than previously believed. We present TarFlow: a simple and scalable architecture that enables highly performant NF models. TarFlow can be thought of as a Transformer-based variant of Masked Autoregressive Flows (MAFs): it consists of a stack of autoregressive Transformer blocks on image patches, alternating the autoregression direction between layers. TarFlow is straightforward to train end-to-end, and capable of directly modeling and generating pixels. We also propose three key techniques to improve sample quality: Gaussian noise augmentation during training, a post training denoising procedure, and an effective guidance method for both class-conditional and unconditional settings. Putting these together, TarFlow sets new state-of-the-art results on likelihood estimation for images, beating the previous best methods by a large margin, and generates samples with quality and diversity comparable to diffusion models, for the first time with a stand-alone NF model. We make our code available at https://github.com/apple/ml-tarflow.

Applications · Chemistry, Physics, and Earth Sciences

Benjamin Holzschuh, Qiang Liu, Georg Kohl, Nils Thuerey

We introduce PDE-Transformer, an improved transformer-based architecture for surrogate modeling of physics simulations on regular grids. We combine recent architectural improvements of diffusion transformers with adjustments specific for large-scale simulations to yield a more scalable and versatile general-purpose transformer architecture, which can be used as the backbone for building large-scale foundation models in physical sciences. We demonstrate that our proposed architecture outperforms state-of-the-art transformer architectures for computer vision on a large dataset of 16 different types of PDEs. We propose to embed different physical channels individually as spatio-temporal tokens, which interact via channel-wise self-attention. This helps to maintain a consistent information density of tokens when learning multiple types of PDEs simultaneously. We demonstrate that our pre-trained models achieve improved performance on several challenging downstream tasks compared to training from scratch and also beat other foundation model architectures for physics simulations.Our source code is available at https://github.com/tum-pbs/pde-transformer.

Deep Learning · Algorithms

Quan Xiao, Hui Yuan, A F M Saif, Gaowen Liu, Ramana Kompella, Mengdi Wang, Tianyi Chen

Diffusion models, which iteratively denoise data samples to synthesize high-quality outputs, have achieved empirical success across domains. However, optimizing these models for downstream tasks often involves nested bilevel structures, such as tuning hyperparameters for fine-tuning tasks or noise schedules in training dynamics, where traditional bilevel methods fail due to the infinite-dimensional probability space and prohibitive sampling costs. We formalize this challenge as a generative bilevel optimization problem and address two key scenarios: (1) fine-tuning pre-trained models via an inference-only lower-level solver paired with a sample-efficient gradient estimator for the upper level, and (2) training diffusion model from scratch with noise schedule optimization by reparameterizing the lower-level problem and designing a computationally tractable gradient estimator. Our first-order bilevel framework overcomes the incompatibility of conventional bilevel methods with diffusion processes, offering theoretical grounding and computational practicality. Experiments demonstrate that our method outperforms existing fine-tuning and hyperparameter search baselines.

Applications · Computer Vision

Wenhao Wang, Yifan Sun, Zongxin Yang, Zhentao Tan, Zhengdong Hu, Yi Yang

Text-guided image-to-image diffusion models excel in translating images based on textual prompts, allowing for precise and creative visual modifications. However, such a powerful technique can be misused for *spreading misinformation*, *infringing on copyrights*, and *evading content tracing*. This motivates us to introduce the task of origin **ID**entification for text-guided **I**mage-to-image **D**iffusion models (**ID$\mathbf{^2}$**), aiming to retrieve the original image of a given translated query. A straightforward solution to ID$^2$ involves training a specialized deep embedding model to extract and compare features from both query and reference images. However, due to *visual discrepancy* across generations produced by different diffusion models, this similarity-based approach fails when training on images from one model and testing on those from another, limiting its effectiveness in real-world applications. To solve this challenge of the proposed ID$^2$ task, we contribute the first dataset and a theoretically guaranteed method, both emphasizing generalizability. The curated dataset, **OriPID**, contains abundant **Ori**gins and guided **P**rompts, which can be used to train and test potential **ID**entification models across various diffusion models. In the method section, we first prove the *existence* of a linear transformation that minimizes the distance between the pre-trained Variational Autoencoder embeddings of generated samples and their origins. Subsequently, it is demonstrated that such a simple linear transformation can be *generalized* across different diffusion models. Experimental results show that the proposed method achieves satisfying generalization performance, significantly surpassing similarity-based methods (+31.6% mAP), even those with generalization designs. The project is available at https://id2icml.github.io.

Applications · Computer Vision

Jue Gong, Jingkai Wang, Zheng Chen, Xing Liu, Hong Gu, Yulun Zhang, Xiaokang Yang

Human body restoration, as a specific application of image restoration, is widely applied in practice and plays a vital role across diverse fields. However, thorough research remains difficult, particularly due to the lack of benchmark datasets. In this study, we propose a high-quality dataset automated cropping and filtering (HQ-ACF) pipeline. This pipeline leverages existing object detection datasets and other unlabeled images to automatically crop and filter high-quality human images. Using this pipeline, we constructed a person-based restoration with sophisticated objects and natural activities (*PERSONA*) dataset, which includes training, validation, and test sets. The dataset significantly surpasses other human-related datasets in both quality and content richness. Finally, we propose *OSDHuman*, a novel one-step diffusion model for human body restoration. Specifically, we propose a high-fidelity image embedder (HFIE) as the prompt generator to better guide the model with low-quality human image information, effectively avoiding misleading prompts. Experimental results show that OSDHuman outperforms existing methods in both visual quality and quantitative metrics. The dataset and code are available at: https://github.com/gobunu/OSDHuman.

Deep Learning · Generative Models and Autoencoders

Wenhao SUN, Rong-Cheng Tu, Jingyi Liao, Zhao Jin, Dacheng Tao

Diffusion Transformers (DiTs) have proven effective in generating high-quality videos but are hindered by high computational costs. Existing video diffusion sampling acceleration methods often rely on costly fine-tuning or exhibit limited generalization capabilities. We propose Asymmetric Reduction and Restoration (**AsymRnR**), **a training-free and model-agnostic method to accelerate video DiTs**. It builds on the observation that redundancies of feature tokens in DiTs vary significantly across different model blocks, denoising steps, and feature types. Our AsymRnR asymmetrically reduces redundant tokens in the attention operation, achieving acceleration with negligible degradation in output quality and, in some cases, even improving it. We also tailored a reduction schedule to distribute the reduction across components adaptively. To further accelerate this process, we introduce a matching cache for more efficient reduction. Backed by theoretical foundations and extensive experimental validation, AsymRnR integrates into state-of-the-art video DiTs and offers substantial speedup.

Deep Learning · Everything Else

Jingrong Xie, Han Ji, Yanan Sun

Automated architecture design methods, especially neural architecture search, have attracted increasing attention. However, these methods naturally need to evaluate numerous candidate architectures during the search process, thus computationally extensive and time-consuming. In this paper, we propose a prior knowledge guided neural architecture generation method to generate high-performance architectures without any search and evaluation process. Specifically, in order to identify valuable prior knowledge for architecture generation, we first quantify the contribution of each component within an architecture to its overall performance. Subsequently, a diffusion model guided by prior knowledge is presented, which can easily generate high-performance architectures for different computation tasks. Extensive experiments on new search spaces demonstrate that our method achieves superior accuracy over state-of-the-art methods. For example, we only need $0.004$ GPU Days to generate architecture with $76.1\%$ top-1 accuracy on ImageNet and $97.56\%$ on CIFAR-10. Furthermore, we can find competitive architecture for more unseen search spaces, such as TransNAS-Bench-101 and NATS-Bench, which demonstrates the broad applicability of the proposed method.

Deep Learning · Robustness

Sen Peng, Mingyue Wang, Jianfei He, Jijia Yang, Xiaohua Jia

Latent diffusion models have recently demonstrated superior capabilities in many downstream image synthesis tasks. However, customization of latent diffusion models using unauthorized data can severely compromise the privacy and intellectual property rights of data owners.Adversarial examples as protective perturbations have been developed to defend against unauthorized data usage by introducing imperceptible noise to customization samples, preventing diffusion models from effectively learning them.In this paper, we first reveal that the primary reason adversarial examples are effective as protective perturbations in latent diffusion models is the distortion of their latent representations, as demonstrated through qualitative and quantitative experiments.We then propose the Contrastive Adversarial Training (CAT) utilizing lightweight adapters as an adaptive attack against these protection methods, highlighting their lack of robustness. Extensive experiments demonstrate that our CAT method significantly reduces the effectiveness of protective perturbations in customization, urging the community to reconsider and improve the robustness of existing protective perturbations. The code is available at \url{https://github.com/senp98/CAT}.

Probabilistic Methods · Monte Carlo and Sampling Methods

Aaron Havens, Benjamin Kurt Miller, Bing Yan, Carles Domingo i Enrich, Anuroop Sriram, Daniel S. Levine, Brandon Wood, Bin Hu, Brandon Amos, Brian Karrer 等

We introduce Adjoint Sampling, a highly scalable and efficient algorithm for learning diffusion processes that sample from unnormalized densities, or energy functions. It is the first on-policy approach that allows significantly more gradient updates than the number of energy evaluations and model samples, allowing us to scale to much larger problem settings than previously explored by similar methods.Our framework is theoretically grounded in stochastic optimal control and shares the same theoretical guarantees as Adjoint Matching, being able to train without the need for corrective measures that push samples towards the target distribution.We show how to incorporate key symmetries, as well as periodic boundary conditions, for modeling molecules in both cartesian and torsional coordinates.We demonstrate the effectiveness of our approach through extensive experiments on classical energy functions, and further scale up to neural network-based energy models where we perform amortized conformer generation across many molecular systems.To encourage further research in developing highly scalable sampling methods, we plan to open source these challenging benchmarks, where successful methods can directly impact progress in computational chemistry. Code \& and benchmarks provided at https://github.com/facebookresearch/adjoint_sampling.

Applications · Chemistry, Physics, and Earth Sciences

Chris Pedersen, Laure Zanna, Joan Bruna

Autoregressive surrogate models (or *emulators*) of spatiotemporal systems provide an avenue for fast, approximate predictions, with broad applications across science and engineering. At inference time however, these models are generally unable to provide predictions over long time rollouts due to accumulation of errors leading to diverging trajectories. In essence, emulators operate out of distribution, and controlling the online distribution quickly becomes intractable in large-scale settings. To address this fundamental issue, and focusing on time-stationary systems admitting an invariant measure, we leverage diffusion models to obtain an implicit estimator of the score of this invariant measure. We show that this model of the score function can be used to stabilize autoregressive emulator rollouts by applying on-the-fly denoising during inference, a process we call *thermalization*. Thermalizing an emulator rollout is shown to extend the time horizon of stable predictions by two orders of magnitude in complex systems exhibiting turbulent and chaotic behavior, opening up a novel application of diffusion models in the context of neural emulation.

Deep Learning · Generative Models and Autoencoders

Zian Li, Cai Zhou, Xiyuan Wang, Xingang Peng, Muhan Zhang

Recent advances in molecular generative models have demonstrated great promise for accelerating scientific discovery, particularly in drug design. However, these models often struggle to generate high-quality molecules, especially in conditional scenarios where specific molecular properties must be satisfied. In this work, we introduce GeoRCG, a general framework to improve molecular generative models by integrating geometric representation conditions with provable theoretical guarantees. We decompose the generation process into two stages: first, generating an informative geometric representation; second, generating a molecule conditioned on the representation. Compared with single-stage generation, the easy-to-generate representation in the first stage guides the second stage generation toward a high-quality molecule in a goal-oriented way. Leveraging EDM and SemlaFlow as base generators, we observe significant quality improvements in unconditional molecule generation on the widely used QM9 and GEOM-DRUG datasets. More notably, in the challenging conditional molecular generation task, our framework achieves an average 50\% performance improvement over state-of-the-art approaches, highlighting the superiority of conditioning on semantically rich geometric representations. Furthermore, with such representation guidance, the number of diffusion steps can be reduced to as small as 100 while largely preserving the generation quality achieved with 1,000 steps, thereby significantly reducing the generation iterations needed.

Deep Learning · Generative Models and Autoencoders

François Cornet, Federico Bergamin, Arghya Bhowmik, Juan Garcia-Lastra, Jes Frellsen, Mikkel Schmidt

Generative modeling of crystalline materials using diffusion models presents a series of challenges: the data distribution is characterized by inherent symmetries and involves multiple modalities, with some defined on specific manifolds. Notably, the treatment of fractional coordinates representing atomic positions in the unit cell requires careful consideration, as they lie on a hypertorus. In this work, we introduce Kinetic Langevin Diffusion for Materials (KLDM), a novel diffusion model for crystalline materials generation, where the key innovation resides in the modeling of the coordinates. Instead of resorting to Riemannian diffusion on the hypertorus directly, we generalize Trivialized Diffusion Model (TDM) to account for the symmetries inherent to crystals. By coupling coordinates with auxiliary Euclidean variables representing velocities, the diffusion process is now offset to a flat space. This allows us to effectively perform diffusion on the hypertorus while providing a training objective that accounts for the periodic translation symmetry of the true data distribution. We evaluate KLDM on both Crystal Structure Prediction (CSP) and De-novo Generation (DNG) tasks, demonstrating its competitive performance with current state-of-the-art models.

Deep Learning · Generative Models and Autoencoders

Dongya Jia, Zhuo Chen, Jiawei Chen, Chenpeng Du, Jian Wu, Jian Cong, Xiaobin Zhuang, Chumin Li, Zhen Wei, Yuping Wang 等

Several recent studies have attempted to autoregressively generate continuous speech representations without discrete speech tokens by combining diffusion and autoregressive models, yet they often face challenges with excessive computational loads or suboptimal outcomes.In this work, we propose Diffusion Transformer Autoregressive Modeling (DiTAR), a patch-based autoregressive framework combining a language model with a diffusion transformer. This approach significantly enhances the efficacy of autoregressive models for continuous tokens and reduces computational demands.DiTAR utilizes a divide-and-conquer strategy for patch generation, where the language model processes aggregated patch embeddings, and the diffusion transformer subsequently generates the next patch based on the output of the language model.For inference, we propose defining temperature as the time point of introducing noise during the reverse diffusion ODE to balance diversity and determinism. We also show in the extensive scaling analysis that DiTAR has superb scalability. In zero-shot speech generation, DiTAR achieves state-of-the-art performance in robustness, speaker similarity, and naturalness.

Deep Learning · Generative Models and Autoencoders

Subham Sekhar Sahoo, Justin Deschenaux, Aaron Gokaslan, Guanghan Wang, Justin Chiu, Volodymyr Kuleshov

Uniform-state discrete diffusion models hold the promise of fast text generation due to their inherent ability to self-correct. However, they are typically outperformed by autoregressive models and masked diffusion models. In this work, we narrow this performance gap by leveraging a key insight: Uniform-state diffusion processes naturally emerge from an underlying Gaussian diffusion. Our method, Duo, transfers powerful techniques from Gaussian diffusion to improve both training and sampling. First, we introduce a curriculum learning strategy guided by the Gaussian process, **doubling training speed** by reducing variance. Models trained with curriculum learning surpass autoregressive models in zero-shot perplexity on 3 of 7 benchmarks.Second, we present Discrete Consistency Distillation, which adapts consistency distillation from the continuous to the discrete setting. This algorithm **unlocks few-step generation in diffusion language models** by accelerating sampling by two orders of magnitude. We provide the code and model checkpoints on the project page: http://s-sahoo.github.io/duo

General Machine Learning · Clustering

Roy Uziel, Irit Chelly, Oren Freifeld, Ari Pakman

Diffusion models, widely recognized for their success in generative tasks, have not yet been applied to clustering. We introduce Clustering via Diffusion (CLUDI), a self-supervised framework that combines the generative power of diffusion models with pre-trained Vision Transformer features to achieve robust and accurate clustering. CLUDI is trained via a teacher–student paradigm: the teacher uses stochastic diffusion-based sampling to produce diverse cluster assignments, which the student refines into stable predictions. This stochasticity acts as a novel data augmentation strategy, enabling CLUDI to uncover intricate structures in high-dimensional data. Extensive evaluations on challenging datasets demonstrate that CLUDI achieves state-of-the-art performance in unsupervised classification, setting new benchmarks in clustering robustness and adaptability to complex data distributions.

Deep Learning · Generative Models and Autoencoders

Kevin Rojas, Yuchen Zhu, Sichen Zhu, Felix Ye, Molei Tao

Diffusion models have demonstrated remarkable performance in generating unimodal data across various tasks, including image, video, and text generation. On the contrary, the joint generation of multimodal data through diffusion models is still in the early stages of exploration. Existing approaches heavily rely on external preprocessing protocols, such as tokenizers and variational autoencoders, to harmonize varied data representations into a unified, unimodal format. This process heavily demands the high accuracy of encoders and decoders, which can be problematic for applications with limited data. To lift this restriction, we propose a novel framework for building multimodal diffusion models on arbitrary state spaces, enabling native generation of coupled data across different modalities. By introducing an innovative decoupled noise schedule for each modality, we enable both unconditional and modality-conditioned generation within a single model simultaneously. We empirically validate our approach for text-image generation and mixed-type tabular data synthesis, demonstrating that it achieves competitive performance.

Deep Learning · Generative Models and Autoencoders

Valentin De Bortoli, Alexandre Galashov, Arthur Gretton, Arnaud Doucet

Speculative sampling is a popular technique for accelerating inference in Large Language Models by generating candidate tokens using a fast draft model and then accepting or rejecting them based on the target model's distribution. While speculative sampling was previously limited to discrete sequences, we extend it to diffusion models, which generate samples via continuous, vector-valued Markov chains. In this context, the target model is a high-quality but computationally expensive diffusion model. We propose various drafting strategies, including a simple and effective approach that does not require training a draft model and is applicable out-of-the-box to any diffusion model. We demonstrate significant generation speedup on various diffusion models, halving the number of function evaluations while generating exact samples from the target model. Finally, we also show how this procedure can be used to accelerate Langevin diffusions to sample unnormalized distributions.

Deep Learning · Generative Models and Autoencoders

Rafał Karczewski, Markus Heinonen, Vikas Garg

Diffusion models have emerged as a powerful class of generative models, capable of producing high-quality images by mapping noise to a data distribution. However, recent findings suggest that image likelihood does not align with perceptual quality: high-likelihood samples tend to be smooth, while lower-likelihood ones are more detailed. Controlling sample density is thus crucial for balancing realism and detail. In this paper, we analyze an existing technique, Prior Guidance, which scales the latent code to influence image detail. We introduce score alignment, a condition that explains why this method works and show that it can be tractably checked for any continuous normalizing flow model. We then propose Density Guidance, a principled modification of the generative ODE that enables exact log-density control during sampling. Finally, we extend Density Guidance to stochastic sampling, ensuring precise log-density control while allowing controlled variation in structure or fine details. Our experiments demonstrate that these techniques provide fine-grained control over image detail without compromising sample quality. Code is available at https://github.com/Aalto-QuML/density-guidance.