ICML 2025 论文列表

The goal of protein fitness optimization is to discover new protein variants with enhanced fitness for a given use. The vast search space and the sparsely populated fitness landscape, along with the discrete nature of protein sequences, pose significant challenges when trying to determine the gradient towards configurations with higher fitness. We introduce *Variational Latent Generative Protein Optimization* (VLGPO), a variational perspective on fitness optimization. Our method embeds protein sequences in a continuous latent space to enable efficient sampling from the fitness distribution and combines a (learned) flow matching prior over sequence mutations with a fitness predictor to guide optimization towards sequences with high fitness. VLGPO achieves state-of-the-art results on two different protein benchmarks of varying complexity. Moreover, the variational design with explicit prior and likelihood functions offers a flexible plug-and-play framework that can be easily customized to suit various protein design tasks.

This paper provides a comprehensive analysis of variational inference in latent variable models for survival analysis, emphasizing the distinctive challenges associated with applying variational methods to survival data. We identify a critical weakness in the existing methodology, demonstrating how a poorly designed variational distribution may hinder the objective of survival analysis tasks—modeling time-to-event distributions. We prove that the optimal variational distribution, which perfectly bounds the log-likelihood, may depend on the censoring mechanism. To address this issue, we propose censor-dependent variational inference (CDVI), tailored for latent variable models in survival analysis. More practically, we introduce CD-CVAE, a V-structure Variational Autoencoder (VAE) designed for the scalable implementation of CDVI. Further discussion extends some existing theories and training techniques to survival analysis. Extensive experiments validate our analysis and demonstrate significant improvements in the estimation of individual survival distributions.

We introduce ResGen, an efficient Residual Vector Quantization (RVQ)-based generative model for high-fidelity generation with fast sampling. RVQ improves data fidelity by increasing the number of quantization steps, referred to as depth, but deeper quantization typically increases inference steps in generative models. To address this, ResGen directly predicts the vector embedding of collective tokens rather than individual ones, ensuring that inference steps remain independent of RVQ depth. Additionally, we formulate token masking and multi-token prediction within a probabilistic framework using discrete diffusion and variational inference. We validate the efficacy and generalizability of the proposed method on two challenging tasks across different modalities: conditional image generation on ImageNet 256×256 and zero-shot text-to-speech synthesis. Experimental results demonstrate that ResGen outperforms autoregressive counterparts in both tasks, delivering superior performance without compromising sampling speed. Furthermore, as we scale the depth of RVQ, our generative models exhibit enhanced generation fidelity or faster sampling speeds compared to similarly sized baseline models.

Flow matching (FM) models extend ODE sampler based diffusion models into a general framework, significantly reducing sampling steps through learned vector fields. However, the theoretical understanding of FM models, particularly how their sample trajectories interact with underlying data geometry, remains underexplored. A rigorous theoretical analysis of FM ODE is essential for sample quality, stability, and broader applicability. In this paper, we advance the theory of FM models through a comprehensive analysis of sample trajectories. Central to our theory is the discovery that the denoiser, a key component of FM models, guides ODE dynamics through attracting and absorbing behaviors that adapt to the data geometry. We identify and analyze the three stages of ODE evolution: in the initial and intermediate stages, trajectories move toward the mean and local clusters of the data. At the terminal stage, we rigorously establish the convergence of FM ODE under weak assumptions, addressing scenarios where the data lie on a low-dimensional submanifold---cases that previous results could not handle. Our terminal stage analysis offers insights into the memorization phenomenon and establishes equivariance properties of FM ODEs. These findings bridge critical gaps in understanding flow matching models, with practical implications for optimizing sampling strategies and architectures guided by the intrinsic geometry of data.

We study the problem of distributional reinforcement learning using categorical parametrisations and a KL divergence loss. Previous work analyzing categorical distributional RL has done so using a Cramér distance-based loss, simplifying the analysis but creating a theory-practice gap. We introduce a preconditioned version of the algorithm, and prove that it is guaranteed to converge. We further derive the asymptotic variance of the categorical estimates under different learning rate regimes, and compare to that of classical reinforcement learning. We finally empirically validate our theoretical results and perform an empirical investigation into the relative strengths of using KL losses, and derive a number of actionable insights for practitioners.

Crystal symmetry plays a fundamental role in determining its physical, chemical, and electronic properties such as electrical and thermal conductivity, optical and polarization behavior, and mechanical strength. Almost all known crystalline materials have internal symmetry. However, this is often inadequately addressed by existing generative models, making the consistent generation of stable and symmetrically valid crystal structures a significant challenge. We introduce WyFormer, a generative model that directly tackles this by formally conditioning on space group symmetry. It achieves this by using Wyckoff positions as the basis for an elegant, compressed, and discrete structure representation. To model the distribution, we develop a permutation-invariant autoregressive model based on the Transformer encoder and an absence of positional encoding. Extensive experimentation demonstrates WyFormer's compelling combination of attributes: it achieves best-in-class symmetry-conditioned generation, incorporates a physics-motivated inductive bias, produces structures with competitive stability, predicts material properties with competitive accuracy even without atomic coordinates, and exhibits unparalleled inference speed.

Recent advances in latent diffusion models have demonstrated their effectiveness for high-resolution image synthesis. However, the properties of the latent space from tokenizer for better learning and generation of diffusion models remain under-explored. Theoretically and empirically, we find that improved generation quality is closely tied to the latent distributions with better structure, such as the ones with fewer Gaussian Mixture modes and more discriminative features. Motivated by these insights, we propose MAETok, an autoencoder (AE) leveraging mask modeling to learn semantically rich latent space while maintaining reconstruction fidelity. Extensive experiments validate our analysis, demonstrating that the variational form of autoencoders is not necessary, and a discriminative latent space from AE alone enables state-of-the-art performance on ImageNet generation using only 128 tokens. MAETok achieves significant practical improvements, enabling a gFID of 1.69 with 76× faster training and 31× higher inference throughput for 512×512 generation. Our findings show that the structure of the latent space, rather than variational constraints, is crucial for effective diffusion models. Code and trained models will be released.

Modular object-centric representations are essential for *human-like reasoning* but are challenging to obtain under spatial ambiguities, *e.g. due to occlusions and view ambiguities*. However, addressing challenges presents both theoretical and practical difficulties. We introduce a novel multi-view probabilistic approach that aggregates view-specific slots to capture *invariant content* information while simultaneously learning disentangled global *viewpoint-level* information. Unlike prior single-view methods, our approach resolves spatial ambiguities, provides theoretical guarantees for identifiability, and requires *no viewpoint annotations*. Extensive experiments on standard benchmarks and novel complex datasets validate our method's robustness and scalability.

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.

High-dimensional time-series datasets are common in domains such as healthcare and economics. Variational autoencoder (VAE) models, where latent variables are modeled with a Gaussian process (GP) prior, have become a prominent model class to analyze such correlated datasets. However, their applications are challenged by the inherent cubic time complexity that requires specific GP approximation techniques, as well as the general challenge of modeling both shared and individual-specific correlations across time. Though inducing points enhance GP prior VAE scalability, optimizing them remains challenging, especially since discrete covariates resist gradient‑based methods. In this work, we propose a scalable basis function approximation technique for GP prior VAEs that mitigates these challenges and results in linear time complexity, with a global parametrization that eliminates the need for amortized variational inference and the associated amortization gap, making it well-suited for conditional generation tasks where accuracy and efficiency are crucial. Empirical evaluations on synthetic and real-world benchmark datasets demonstrate that our approach not only improves scalability and interpretability but also drastically enhances predictive performance.

We introduce Spatial Reasoning Models (SRMs), a framework to perform reasoning over sets of continuous variables via denoising generative models. SRMs infer continuous representations on a set of unobserved variables, given observations on observed variables. Current generative models on spatial domains, such as diffusion and flow matching models, often collapse to hallucination in case of complex distributions. To measure this, we introduce a set of benchmark tasks that test the quality of complex reasoning in generative models and can quantify hallucination. The SRM framework allows to report key findings about importance of sequentialization in generation, the associated order, as well as the sampling strategies during training. It demonstrates, for the first time, that order of generation can successfully be predicted by the denoising network itself. Using these findings, we can increase the accuracy of specific reasoning tasks from <1% to >50%. Our [project website](https://geometric-rl.mpi-inf.mpg.de/srm/) provides additional videos, code, and the benchmark datasets.

Diffusion distillation is a widely used technique to reduce the sampling cost of diffusion models, yet it often requires extensive training, and the student performance tends to be degraded. Recent studies show that incorporating a GAN objective may alleviate these issues, yet the underlying mechanism remains unclear. In this work, we first identify a key limitation of distillation: mismatched step sizes and parameter numbers between the teacher and the student model lead them to converge to different local minima, rendering direct imitation suboptimal. We further demonstrate that a standalone GAN objective, without relying a distillation loss, overcomes this limitation and is sufficient to convert diffusion models into efficient one-step generators. Based on this finding, we propose that diffusion training may be viewed as a form of generative pre-training, equipping models with capabilities that can be unlocked through lightweight GAN fine-tuning. Supporting this view, we create a one-step generation model by fine-tuning a pre-trained model with 85% of parameters frozen, achieving strong performance with only 0.2M images and near-SOTA results with 5M images. We further present a frequency-domain analysis that may explain the one-step generative capability gained in diffusion training. Overall, our work provides a new perspective for diffusion training, highlighting its role as a powerful generative pre-training process, which can be the basis for building efficient one-step generation models.

Generative Flow Networks (GFlowNets) are a family of generative models that learn to sample objects from a given probability distribution, potentially known up to a normalizing constant. Instead of working in the object space, GFlowNets proceed by sampling trajectories in an appropriately constructed directed acyclic graph environment, greatly relying on the acyclicity of the graph. In our paper, we revisit the theory that relaxes the acyclicity assumption and present a simpler theoretical framework for non-acyclic GFlowNets in discrete environments. Moreover, we provide various novel theoretical insights related to training with fixed backward policies, the nature of flow functions, and connections between entropy-regularized RL and non-acyclic GFlowNets, which naturally generalize the respective concepts and theoretical results from the acyclic setting. In addition, we experimentally re-examine the concept of loss stability in non-acyclic GFlowNet training, as well as validate our own theoretical findings.

We present a novel generative approach based on Denoising Diffusion Models (DDMs), which produces high-quality image samples *along* with their losslessly compressed bit-stream representations. This is obtained by replacing the standard Gaussian noise sampling in the reverse diffusion with a selection of noise samples from pre-defined codebooks of fixed iid Gaussian vectors. Surprisingly, we find that our method, termed *Denoising Diffusion Codebook Model* (DDCM), retains sample quality and diversity of standard DDMs, even for extremely small codebooks. We leverage DDCM and pick the noises from the codebooks that best match a given image, converting our generative model into a highly effective lossy image codec achieving state-of-the-art perceptual image compression results. More generally, by setting other noise selections rules, we extend our compression method to any conditional image generation task (e.g., image restoration), where the generated images are produced jointly with their condensed bit-stream representations. Our work is accompanied by a mathematical interpretation of the proposed compressed conditional generation schemes, establishing a connection with score-based approximations of posterior samplers for the tasks considered. Code and demo are available on our project's [website](https://ddcm-2025.github.io/).

What happens when generative machine learning models are pretrained on web-scale datasets containing data generated by earlier models? Some prior work warns of “model collapse” as the web is overwhelmed by synthetic data; other work suggests the problem can be contained (i.e. collapse can be avoided) by managing how available data are used in pretraining. In this paper, we report experiments on three ways of using data (training-workflows), across three generative model task-settings (multivariate Gaussian estimation, kernel density estimation, and language-model fine-tuning) to further confirm the possibility of containment: (a) we confirm that the training-workflow of {\it replacing} all real data by successive generations of purely synthetic data indeed suffers model collapse in all task-settings studied; (b) we consider the training-workflow of {\it accumulating} synthetic data alongside real data and training on all data combined and confirming that, although the proportion of real data eventually becomes zero, models remain stable and their test losses do not diverge under this training-workflow; (c) we consider a training-workflow where real and synthetic data accumulate together but successive generations of pretraining are constrained to use fixed-size data subsets each generation. In this workflow, we observe slow and gradual rather than explosive degradation of test loss performance across generations. Our insights are particularly important when forecasting whether future frontier generative models will collapse or thrive, and our results open avenues for empirically and mathematically studying the context-dependent value of synthetic data.

This paper introduces the Discrete Markov Probabilistic Model (DMPM), a novel algorithm for discrete data generation. The algorithm operates in discrete space, where the noising process is a continuous-time Markov chain that can be sampled exactly via a Poissonian clock that flips labels uniformly at random. The time-reversal process, like the forward noise process, is a jump process, with its intensity governed by a discrete analogue of the classical score function. Crucially, this intensity is proven to be the conditional expectation of a function of the forward process, strengthening its theoretical alignment with score-based generative models while ensuring robustness and efficiency. We further establish convergence bounds for the algorithm under minimal assumptions and demonstrate its effectiveness through experiments on low-dimensional Bernoulli-distributed datasets and high-dimensional binary MNIST data. The results highlight its strong performance in generating discrete structures. This work bridges theoretical foundations and practical applications, advancing the development of effective and theoretically grounded discrete generative modeling.

As AI systems become increasingly capable and influential, ensuring their alignment with human values, preferences, and goals has become a critical research focus. Current alignment methods primarily focus on designing algorithms and loss functions but often underestimate the crucial role of data. This paper advocates for a shift towards data-centric AI alignment, emphasizing the need to enhance the quality and representativeness of data used in aligning AI systems. In this position paper, we highlight key challenges associated with both human-based and AI-based feedback within the data-centric alignment framework. Through qualitative analysis, we identify multiple sources of unreliability in human feedback, as well as problems related to temporal drift, context dependence, and AI-based feedback failing to capture human values due to inherent model limitations. We propose future research directions, including improved feedback collection practices, robust data-cleaning methodologies, and rigorous feedback verification processes. We call for future research into these critical directions to ensure, addressing gaps that persist in understanding and improving data-centric alignment practices.

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.

Recent Diffusion models (DMs) advancements have explored incorporating the second-order diffusion Fisher information (DF), defined as the negative Hessian of log density, into various downstream tasks and theoretical analysis. However, current practices typically approximate the diffusion Fisher by applying auto-differentiation to the learned score network. This black-box method, though straightforward, lacks any accuracy guarantee and is time-consuming. In this paper, we show that the diffusion Fisher actually resides within a space spanned by the outer products of score and initial data. Based on the outer-product structure, we develop two efficient approximation algorithms to access the trace and matrix-vector multiplication of DF, respectively. These algorithms bypass the auto-differentiation operations with time-efficient vector-product calculations. Furthermore, we establish the approximation error bounds for the proposed algorithms. Experiments in likelihood evaluation and adjoint optimization demonstrate the superior accuracy and reduced computational cost of our proposed algorithms. Additionally, based on the novel outer-product formulation of DF, we design the first numerical verification experiment for the optimal transport property of the general PF-ODE deduced map.