ICML 2025 Papers

Continuous Normalizing Flows (CNFs) have proven to be a highly efficient technique for generative modeling of complex data since the introduction of Flow Matching (FM). The core of FM is to learn the constructed velocity fields of CNFs through deep least squares regression. Despite its empirical effectiveness, theoretical investigations of FM remain limited. In this paper, we present the first end-to-end error analysis of CNFs built upon FM. Our analysis shows that for general target distributions with bounded support, the generated distribution of FM is guaranteed to converge to the target distribution in the sense of the Wasserstein-2 distance. Furthermore, the convergence rate is significantly improved under an additional mild Lipschitz condition of the target score function.

Vector-Quantized Generative Models (VQGMs) have emerged as powerful tools for image generation. However, the key component of VQGMs---the codebook of discrete tokens---is still not well understood, e.g., which tokens are critical to generate an image of a certain concept? This paper introduces Concept-Oriented Token Explanation (CORTEX), a novel approach for interpreting VQGMs by identifying concept-specific token combinations. Our framework employs two methods: (1) a sample-level explanation method that analyzes token importance scores in individual images, and (2) a codebook-level explanation method that explores the entire codebook to find globally relevant tokens. Experimental results demonstrate CORTEX's efficacy in providing clear explanations of token usage in the generative process, outperforming baselines across multiple pretrained VQGMs. Besides enhancing VQGMs transparency, CORTEX is useful in applications such as targeted image editing and shortcut feature detection. Our code is available at https://github.com/YangTianze009/CORTEX.

Flow matching (FM) is a family of training algorithms for fitting continuous normalizing flows (CNFs). Conditional flow matching (CFM) exploits the fact that the marginal vector field of a CNF can be learned by fitting least-squares regression to the conditional vector field specified given one or both ends of the flow path. In this paper, we extend the CFM algorithm by defining conditional probability paths along "streams'', instances of latent stochastic paths that connect data pairs of source and target, which are modeled with Gaussian process (GP) distributions. The unique distributional properties of GPs help preserve the ``simulation-free'' nature of CFM training. We show that this generalization of the CFM can effectively reduce the variance in the estimated marginal vector field at a moderate computational cost, thereby improving the quality of the generated samples under common metrics. Additionally, adopting the GP on the streams allows for flexibly linking multiple correlated training data points (e.g., time series). We empirically validate our claim through both simulations and applications to image and neural time series data.

Diffusion models and Flow Matching generate high-quality samples but are slow at inference, and distilling them into few-step models often leads to instability and extensive tuning. To resolve these trade-offs, we propose Moment Matching Self-Distillation (MMSD), a new class of generative models for one- or few-step sampling with a single-stage training procedure. Unlike distillation, MMSD does not require pre-training initialization and optimization of two networks; and unlike Consistency Models, MMSD guarantees distribution-level convergence and remains stable under various hyperparameters and standard model architectures. MMSD surpasses diffusion models on ImageNet-256x256 with 2.13 FID using only 8 inference steps and achieves state-of-the-art 2-step FID of 2.05 on CIFAR-10 for a model trained from scratch.

It is widely believed that noise conditioning is indispensable for denoising diffusion models to work successfully. This work challenges this belief. Motivated by research on blind image denoising, we investigate a variety of denoising-based generative models in the absence of noise conditioning. To our surprise, most models exhibit graceful degradation, and in some cases, they even perform better without noise conditioning. We provide a mathematical analysis of the error introduced by removing noise conditioning and demonstrate that our analysis aligns with empirical observations. We further introduce a noise-*unconditional* model that achieves a competitive FID of 2.23 on CIFAR-10, significantly narrowing the gap to leading noise-conditional models. We hope our findings will inspire the community to revisit the foundations and formulations of denoising generative models.

Sampling from high-dimensional, multi-modal distributions remains a fundamental challenge across domains such as statistical Bayesian inference and physics-based machine learning. In this paper, we propose Annealing Flow (AF), a method built on Continuous Normalizing Flows (CNFs) for sampling from high-dimensional and multi-modal distributions. AF is trained with a dynamic Optimal Transport (OT) objective incorporating Wasserstein regularization, and guided by annealing procedures, facilitating effective exploration of modes in high-dimensional spaces. Compared to recent NF methods, AF significantly improves training efficiency and stability, with minimal reliance on MC assistance. We demonstrate the superior performance of AF compared to state-of-the-art methods through extensive experiments on various challenging distributions and real-world datasets, particularly in high-dimensional and multi-modal settings. We also highlight AF’s potential for sampling the least favorable distributions.

Conditional mean independence (CMI) testing is crucial for statistical tasks including model determination and variable importance evaluation. In this work, we introduce a novel population CMI measure and a bootstrap-based testing procedure that utilizes deep generative neural networks to estimate the conditional mean functions involved in the population measure. The test statistic is thoughtfully constructed to ensure that even slowly decaying nonparametric estimation errors do not affect the asymptotic accuracy of the test. Our approach demonstrates strong empirical performance in scenarios with high-dimensional covariates and response variable, can handle multivariate responses, and maintains nontrivial power against local alternatives outside an $n^{-1/2}$ neighborhood of the null hypothesis. We also use numerical simulations and real-world imaging data applications to highlight the efficacy and versatility of our testing procedure.

Inferring Gene Regulatory Networks (GRNs) from gene expression data is crucial for understanding biological processes. While supervised models are reported to achieve high performance for this task, they rely on costly ground truth (GT) labels and risk learning gene-specific biases—such as class imbalances of GT interactions—rather than true regulatory mechanisms. To address these issues, we introduce InfoSEM, an unsupervised generative model that leverages textual gene embeddings as informative priors, improving GRN inference without GT labels. InfoSEM can also integrate GT labels as an additional prior when available, avoiding biases and further enhancing performance. Additionally, we propose a biologically motivated benchmarking framework that better reflects real-world applications such as biomarker discovery and reveals learned biases of existing supervised methods. InfoSEM outperforms existing models by 38.5% across four datasets using textual embeddings prior and further boosts performance by 11.1% when integrating labeled data as priors.

Normalizing flows are a flexible class of probability distributions, expressed as transformations of a simple base distribution. A limitation of standard normalizing flows is representing distributions with heavy tails, which arise in applications to both density estimation and variational inference. A popular current solution to this problem is to use a heavy tailed base distribution. We argue this can lead to poor performance due to the difficulty of optimising neural networks, such as normalizing flows, under heavy tailed input. We propose an alternative, "tail transform flow'' (TTF), which uses a Gaussian base distribution and a final transformation layer which can produce heavy tails. Experimental results show this approach outperforms current methods, especially when the target distribution has large dimension or tail weight.

We present a novel method for efficiently computing optimal transport maps and Wasserstein barycenters in high-dimensional spaces. Our approach uses conditional normalizing flows to approximate the input distributions as invertible pushforward transformations from a common latent space. This makes it possible to directly solve the primal problem using gradient-based minimization of the transport cost, unlike previous methods that rely on dual formulations and complex adversarial optimization. We show how this approach can be extended to compute Wasserstein barycenters by solving a conditional variance minimization problem. A key advantage of our conditional architecture is that it enables the computation of barycenters for hundreds of input distributions, which was computationally infeasible with previous methods. Our numerical experiments illustrate that our approach yields accurate results across various high-dimensional tasks and compares favorably with previous state-of-the-art methods.

Estimating Individual Treatment Effects (ITE) from observational data is challenging due to covariate shift and counterfactual absence. While existing methods attempt to balance distributions globally, they often lack fine-grained sample-level alignment, especially in scenarios with significant individual heterogeneity. To address these issues, we reconsider counterfactual as a proxy to emulate balanced randomization. Furthermore, we derive a theoretical bound that links the expected ITE estimation error to both factual prediction errors and representation distances between factuals and counterfactuals. Building on this theoretical foundation, we propose FCCL, a novel method designed to effectively capture the nuances of potential outcomes under different treatments by (i) generating diffeomorphic counterfactuals that adhere to the data manifold while maintaining high semantic similarity to their factual counterparts, and (ii) mitigating distribution shift via sample-level alignment grounded in our derived generalization-error bound, which considers factual-counterfactual similarity and category consistency. Extensive evaluations on benchmark datasets demonstrate that FCCL outperforms 13 state-of-the-art methods, particularly in capturing individual-level heterogeneity and handling sparse boundary samples.

In many machine learning tasks, it is often necessary for the relationship between input and output variables to be monotonic, including both strictly monotonic and implicitly monotonic relationships. Traditional methods for maintaining monotonicity mainly rely on construction or regularization techniques, whereas this paper shows that the issue of strict monotonic probability can be viewed as a partial order between an observable revenue variable and a latent cost variable. This perspective enables us to reformulate the monotonicity challenge into modeling the latent cost variable. To tackle this, we introduce a generative network for the latent cost variable, termed the Generative Cost Model (**GCM**), which inherently addresses the strict monotonic problem, and propose the Implicit Generative Cost Model (**IGCM**) to address the implicit monotonic problem. We further validate our approach with a numerical simulation of quantile regression and conduct multiple experiments on public datasets, showing that our method significantly outperforms existing monotonic modeling techniques. The code for our experiments can be found at [https://github.com/tyxaaron/GCM](https://github.com/tyxaaron/GCM).

Scalable sampling of molecular states in thermodynamic equilibrium is a long-standing challenge in statistical physics. Boltzmann generators tackle this problem by pairing normalizing flows with importance sampling to obtain uncorrelated samples under the target distribution. In this paper, we extend the Boltzmann generator framework with two key contributions, denoting our framework Sequential Boltzmann Generators (SBG). The first is a highly efficient Transformer-based normalizing flow operating directly on all-atom Cartesian coordinates. In contrast to the equivariant continuous flows of prior methods, we leverage exactly invertible non-equivariant architectures which are highly efficient during both sample generation and likelihood evaluation. This efficiency unlocks more sophisticated inference strategies beyond standard importance sampling. In particular, we perform inference-time scaling of flow samples using a continuous-time variant of sequential Monte Carlo, in which flow samples are transported towards the target distribution with annealed Langevin dynamics. SBG achieves state-of-the-art performance w.r.t. all metrics on peptide systems, demonstrating the first equilibrium sampling in Cartesian coordinates of tri-, tetra- and hexa-peptides that were thus far intractable for prior Boltzmann generators.

Density-based distances (DBDs) provide a principled approach to metric learning by defining distances in terms of the underlying data distribution. By employing a Riemannian metric that increases in regions of low probability density, shortest paths naturally follow the data manifold. Fermat distances, a specific type of DBD, have attractive properties, but existing estimators based on nearest neighbor graphs suffer from poor convergence due to inaccurate density estimates. Moreover, graph-based methods scale poorly to high dimensions, as the proposed geodesics are often insufficiently smooth. We address these challenges in two key ways. First, we learn densities using normalizing flows. Second, we refine geodesics through relaxation, guided by a learned score model. Additionally, we introduce a dimension-adapted Fermat distance that scales intuitively to high dimensions and improves numerical stability. Our work paves the way for the practical use of density-based distances, especially in high-dimensional spaces.

Efficient sampling of unnormalized probability densities such as the Boltzmann distribution of molecular systems is a longstanding challenge. Next to conventional approaches like molecular dynamics or Markov chain Monte Carlo, variational approaches, such as training normalizing flows with the reverse Kullback-Leibler divergence, have been introduced. However, such methods are prone to mode collapse and often do not learn to sample the full configurational space. Here, we present temperature-annealed Boltzmann generators (TA-BG) to address this challenge. First, we demonstrate that training a normalizing flow with the reverse Kullback-Leibler divergence at high temperatures is possible without mode collapse. Furthermore, we introduce a reweighting-based training objective to anneal the distribution to lower target temperatures. We apply this methodology to three molecular systems of increasing complexity and, compared to the baseline, achieve better results in almost all metrics while requiring up to three times fewer target energy evaluations. For the largest system, our approach is the only method that accurately resolves the metastable states of the system.

Diffusion-based generative models (diffusion models) often require a large amount of data to train a score-based model that learns the score function of the data distribution through denoising score matching. However, collecting and cleaning such data can be expensive, time-consuming, and even infeasible. In this paper, we present a novel theoretical insight for diffusion models that two factors, i.e., the denoiser function hypothesis space and the number of training samples, can affect the denoising score matching error of all training samples. Based on this theoretical insight, it is evident that minimizing the total denoising score matching error is challenging within the denoiser function hypothesis space in existing methods, when training diffusion models with limited data. To address this, we propose a new diffusion model called Limited Data Diffusion (LD-Diffusion), which consists of two main components: a compressing model and a novel mixed augmentation with fixed probability (MAFP) strategy. Specifically, the compressing model can constrain the complexity of the denoiser function hypothesis space and MAFP can effectively increase the training samples by providing more informative guidance than existing data augmentation methods in the compressed hypothesis space. Extensive experiments on several datasets demonstrate that LD-Diffusion can achieve better performance compared to other diffusion models. Codes are available at https://github.com/zzhang05/LD-Diffusion.

Antibodies are widely used as therapeutics, but their development requires costly affinity maturation, involving iterative mutations to enhance binding affinity. This paper explores a sequence-only scenario for affinity maturation, using solely antibody and antigen sequences. Recently AlphaFlow wraps AlphaFold within flow matching to generate diverse protein structures, enabling a sequence-conditioned generative model of structure. Building on this, we propose an \textit{alternating optimization} framework that (1) fixes the sequence to guide structure generation toward high binding affinity using a structure-based predictor, then (2) applies inverse folding to create sequence mutations, refined by a sequence-based predictor. A key challenge is the lack of labeled data for training both predictors. To address this, we develop a \textit{co-teaching} module that incorporates valuable information from noisy biophysical energies into predictor refinement. The sequence-based predictor selects consensus samples to teach the structure-based predictor, and vice versa. Our method, \textit{AffinityFlow}, achieves state-of-the-art performance in proof-of-concept affinity maturation experiments.

Many applications in machine learning involve data represented as probability distributions. The emergence of such data requires radically novel techniques to design tractable gradient flows on probability distributions over this type of (infinite-dimensional) objects. For instance, being able to flow labeled datasets is a core task for applications ranging from domain adaptation to transfer learning or dataset distillation. In this setting, we propose to represent each class by the associated conditional distribution of features, and to model the dataset as a mixture distribution supported on these classes (which are themselves probability distributions), meaning that labeled datasets can be seen as probability distributions over probability distributions. We endow this space with a metric structure from optimal transport, namely the Wasserstein over Wasserstein (WoW) distance, derive a differential structure on this space, and define WoW gradient flows. The latter enables to design dynamics over this space that decrease a given objective functional. We apply our framework to transfer learning and dataset distillation tasks, leveraging our gradient flow construction as well as novel tractable functionals that take the form of Maximum Mean Discrepancies with Sliced-Wasserstein based kernels between probability distributions.

This paper presents a novel method for analyzing the latent space geometry of generative models, including statistical physics models and diffusion models, by reconstructing the Fisher information metric. The method approximates the posterior distribution of latent variables given generated samples and uses this to learn the log-partition function, which defines the Fisher metric for exponential families. Theoretical convergence guarantees are provided, and the method is validated on the Ising and TASEP models, outperforming existing baselines in reconstructing thermodynamic quantities. Applied to diffusion models, the method reveals a fractal structure of phase transitions in the latent space, characterized by abrupt changes in the Fisher metric. We demonstrate that while geodesic interpolations are approximately linear within individual phases, this linearity breaks down at phase boundaries, where the diffusion model exhibits a divergent Lipschitz constant with respect to the latent space. These findings provide new insights into the complex structure of diffusion model latent spaces and their connection to phenomena like phase transitions. Our source code is available at \url{https://github.com/alobashev/hessian-geometry-of-diffusion-models}.