NeurIPS 2025 论文列表

This paper investigates low-rank structure in the gradients of the training loss for two-layer neural networks while relaxing the usual isotropy assumptions on the training data and parameters. We consider a spiked data model in which the bulk can be anisotropic and ill-conditioned, we do not require independent data and weight matrices and we also analyze both the mean-field and neural-tangent-kernel scalings. We show that the gradient with respect to the input weights is approximately low rank and is dominated by two rank-one terms: one aligned with the bulk data–residue, and another aligned with the rank one spike in the input data. We characterize how properties of the training data, the scaling regime and the activation function govern the balance between these two components. Additionally, we also demonstrate that standard regularizers, such as weight decay, input noise and Jacobian penalties, also selectively modulate these components. Experiments on synthetic and real data corroborate our theoretical predictions.

Diffusion models have shown remarkable abilities in generating realistic and high-quality images from text prompts. However, a trained model remains largely black-box; little do we know about the roles of its components in exhibiting a concept such as objects or styles. Recent works employ causal tracing to localize knowledge-storing layers in generative models without showing how other layers contribute to the target concept. In this work, we approach diffusion models' interpretability problem from a more general perspective and pose a question: \textit{``How do model components work jointly to demonstrate knowledge?''}. To answer this question, we decompose diffusion models using component attribution, systematically unveiling the importance of each component (specifically the model parameter) in generating a concept. The proposed framework, called \textbf{C}omponent \textbf{A}ttribution for \textbf{D}iffusion Model (CAD), discovers the localization of concept-inducing (positive) components, while interestingly uncovers another type of components that contribute negatively to generating a concept, which is missing in the previous knowledge localization work. Based on this holistic understanding of diffusion models, we present and empirically evaluate one utility of component attribution in controlling the generation process. Specifically, we introduce two fast, inference-time model editing algorithms, CAD-Erase and CAD-Amplify; in particular, CAD-Erase enables erasure and CAD-Amplify allows amplification of a generated concept by ablating the positive and negative components, respectively, while retaining knowledge of other concepts. Extensive experimental results validate the significance of both positive and negative components pinpointed by our framework, demonstrating the potential of providing a complete view of interpreting generative models.

Understanding how Transformers work and how they process information is key to the theoretical and empirical advancement of these machines. In this work, we demonstrate the existence of two phenomena in Transformers, namely _isolation_ and _continuity_. Both of these phenomena hinder Transformers to learn even simple pattern sequences. Isolation expresses that any learnable sequence must be isolated from another learnable sequence, and hence some sequences cannot be learned by a single Transformer at the same time. Continuity entails that an attractor basin forms around a learned sequence, such that any sequence falling in that basin will collapse towards the learned sequence. Here, we mathematically prove these phenomena emerge in all Transformers that use compact positional encoding, and design rigorous experiments, demonstrating that the theoretical limitations we shed light on occur on the practical scale.

Reinforcement learning (RL) typically assumes repetitive resets to provide an agent with diverse and unbiased experiences. These resets require significant human intervention and result in poor training efficiency in real-world settings. Autonomous RL (ARL) addresses this challenge by jointly training forward and reset policies. While recent ARL algorithms have shown promise in reducing human intervention, they assume narrow support over the distributions of initial or goal states and rely on task-specific knowledge to identify irreversible states. In this paper, we propose a robust and scalable ARL algorithm, called RSA, that enables an agent to handle diverse initial and goal states and to avoid irreversible states without task-specific knowledge. RSA generates a curriculum by identifying informative states based on the learning progress of an agent. We hypothesize that informative states are neither overly difficult nor trivially easy for the agent being trained. To detect and avoid irreversible states without task-specific knowledge, RSA encodes the behaviors exhibited in those states rather than the states themselves. Experimental results demonstrate that RSA outperforms existing ARL algorithms with fewer manual resets in both reversible and irreversible environments.

In this work, we introduce TreeGen, a novel generative framework modeling distributions over hierarchies. We extend Bayesian Flow Networks (BFNs) to enable transitions between probabilistic and discrete hierarchies parametrized via categorical distributions. Our proposed scheduler provides smooth and consistent entropy decay across varying numbers of categories. We empirically evaluate TreeGen on the jet-clustering task in high-energy physics, demonstrating that it consistently generates valid trees that adhere to physical constraints and closely align with ground-truth log-likelihoods. Finally, by comparing TreeGen’s samples to the exact posterior distribution and performing likelihood maximization via rejection sampling, we demonstrate that TreeGen outperforms various baselines.

The increasing use of generative ML foundation models for image restoration tasks such as super-resolution calls for robust and interpretable uncertainty quantification methods. We address this need by presenting a novel approach based on conformal prediction techniques to create a `confidence mask' capable of reliably and intuitively communicating where the generated image can be trusted. Our method is adaptable to any black-box generative model, including those locked behind an opaque API, requires only easily attainable data for calibration, and is highly customizable via the choice of a local image similarity metric. We prove strong theoretical guarantees for our method that span fidelity error control (according to our local image similarity metric), reconstruction quality, and robustness in the face of data leakage. Finally, we empirically evaluate these results and establish our method's solid performance.

Solving inverse problems—recovering signals from incomplete or noisy measurements—is fundamental in science and engineering. Score-based generative models (SGMs) have recently emerged as a powerful framework for this task. Two main paradigms have formed: unsupervised approaches that adapt pretrained generative models to inverse problems, and supervised bridge methods that train stochastic processes conditioned on paired clean and corrupted data. While the former typically assume knowledge of the measurement model, the latter have largely overlooked this structural information. We introduce System-embedded Diffusion Bridge Models (SDBs), a new class of supervised bridge methods that explicitly embed the known linear measurement system into the coefficients of a matrix-valued SDE. This principled integration yields consistent improvements across diverse linear inverse problems and demonstrates robust generalization under system misspecification between training and deployment, offering a promising solution to real-world applications.

Deep generative models have recently been applied to physical systems governed by partial differential equations (PDEs), offering scalable simulation and uncertainty-aware inference. However, enforcing physical constraints, such as conservation laws (linear and nonlinear) and physical consistencies, remains challenging. Existing methods often rely on soft penalties or architectural biases that fail to guarantee hard constraints. In this work, we propose Physics-Constrained Flow Matching (PCFM), a zero-shot inference framework that enforces arbitrary nonlinear constraints in pretrained flow-based generative models. PCFM continuously guides the sampling process through physics-based corrections applied to intermediate solution states, while remaining aligned with the learned flow and satisfying physical constraints. Empirically, PCFM outperforms both unconstrained and constrained baselines on a range of PDEs, including those with shocks, discontinuities, and sharp features, while ensuring exact constraint satisfaction at the final solution. Our method provides a flexible framework for enforcing hard constraints in both scientific and general-purpose generative models, especially in applications where constraint satisfaction is essential.

A fundamental challenge in organic chemistry is identifying and predicting the sequence of reactions that synthesize a desired target molecule. Due to the combinatorial nature of the chemical search space, single-step reactant prediction—i.e., single-step retrosynthesis—remains difficult, even for state-of-the-art template-free generative methods. These models often struggle to produce an accurate yet diverse set of feasible reactions in a chemically rational manner. In this paper, we propose RETRO SYNFLOW (RSF), a discrete flow-matching framework that formulates single-step retrosynthesis as a Markov bridge between a given product molecule and its corresponding reactants. Unlike prior approaches, RSF introduces a reaction center identification step to extract intermediate structures, or synthons, which serve as a more informative and structured source distribution for the discrete flow model. To further improve the diversity and chemical feasibility of generated samples, RSF incorporates Feynman-Kac (FK) steering with Sequential Monte Carlo (SMC) resampling at inference time. This approach leverages a learned forward-synthesis reward oracle to guide the generation process toward more promising reactant candidates. Empirically, RSF substantially outperforms the previous state-of-the-art methods in top-1 accuracy. In addition, FK-steering significantly improves round-trip accuracy, demonstrating stronger chemical validity and synthetic feasibility, all while maintaining competitive top-k performance. These results establish RSF as a new leading approach for single-step retrosynthesis prediction.

Diffusion models can be improved with additional guidance towards more effective representations of input. Indeed, prior empirical work has already shown that aligning internal representations of the diffusion model with those of pre-trained models improves generation quality. In this paper, we present a systematic framework for incorporating representation guidance into diffusion models. We provide alternative decompositions of denoising models along with their associated training criteria, where the decompositions determine when and how the auxiliary representations are incorporated. Guided by our theoretical insights, we introduce two new strategies for enhancing representation alignment in diffusion models. First, we pair examples with target representations either derived from themselves or arisen from different synthetic modalities, and subsequently learn a joint model over the multimodal pairs. Second, we design an optimal training curriculum that balances representation learning and data generation. Our experiments across image, protein sequence, and molecule generation tasks demonstrate superior performance as well as accelerated training. In particular, on the class-conditional ImageNet $256\times 256$ benchmark, our guidance results in $23.3$ times faster training than the original SiT-XL as well as four times speedup over the state-of-the-art method REPA.

The Schrödinger Bridge (SB) problem has become a fundamental tool in computational optimal transport and generative modeling. To address this problem, ideal methods such as Iterative Proportional Fitting and Iterative Markovian Fitting (IMF) have been proposed—alongside practical approximations like Diffusion Schrödinger Bridge and its Matching (DSBM) variant. While previous work have established asymptotic convergence guarantees for IMF, a quantitative, non-asymptotic understanding remains unknown. In this paper, we provide the first non-asymptotic exponential convergence guarantees for IMF under mild structural assumptions on the reference measure and marginal distributions, assuming a sufficiently large time horizon. Our results encompass two key regimes: one where the marginals are log-concave, and another where they are weakly log-concave. The analysis relies on new contraction results for the Markovian projection operator and paves the way to theoretical guarantees for DSBM.

Score-based diffusion models have emerged as powerful tools in generative modeling, yet their theoretical foundations remain underexplored. In this work, we focus on the Wasserstein convergence analysis of score-based diffusion models. Specifically, we investigate the impact of various discretization schemes, including Euler discretization, exponential integrators, and midpoint randomization methods. Our analysis provides the first quantitative comparison of these discrete approximations, emphasizing their influence on convergence behavior. Furthermore, we explore scenarios where Hessian information is available and propose an accelerated sampler based on the local linearization method. We establish the first Wasserstein convergence analysis for such a Hessian-based method, showing that it achieves an improved convergence rate of order $\widetilde{\mathcal{O}}\left(\frac{\sqrt{d}}{\varepsilon}\right)$, which significantly outperforms the standard rate $\widetilde{\mathcal{O}}\left(\frac{d}{\varepsilon^2}\right)$ of vanilla diffusion models. Numerical experiments on synthetic data and the MNIST dataset validate our theoretical insights.

Transformer models have driven breakthroughs across various language tasks by their strong capability to learn rich contextual representations. Scaling them to improve representation, however, often demands substantial memory and compute costs, such as the Key-Value (KV) cache used during auto-regressive decoding. Skip connections offer a promising way to improve representation without bloating resource usage, yet most prior works either improve expressivity while leaving KV costs unchanged, or reduce memory at the cost of weaker representation. In this work, we propose SkipV1Former, a Transformer variant that uses skip connections from the first layer's Value heads to strengthen model representation and reduce KV cache. Specifically, from the second block onward, each layer reuses half of its Value heads from the very first layer, while computing the other half as usual-cutting Value projections and V cache by nearly 50 \%. Theoretically, we show that routing uncompressed first-layer Values into deeper layers restores information lost to compression and accelerates the model’s implicit mesa-optimization-a key pattern of Transformer in auto-regressive tasks. Empirically, across different model scales, SkipV1Former delivers consistent reductions of approximately 25 \% in KV cache while improving perplexity relative to standard Multi-Head Attention (MHA) Transformers and some advanced variants. Moreover, we propose a recipe for uptraining existing MHA Transformer checkpoints to SkipV1Former with only 10-15\% additional compute. Finally, SkipV1Former can seamlessly combine advanced methods like Group-Query Attention and Multi-Latent Attention to achieve further KV cache savings and performance improvement. When combined with YOCO, it cuts KV cache size by nearly 50 \% while still improving performance. The code is available at: https://github.com/Zhoutong-Wu/SkipV1Former.

Recent advances in Structure-based Drug Design (SBDD) have leveraged generative models for 3D molecular generation, predominantly evaluating model performance by binding affinity to target proteins. However, practical drug discovery necessitates high binding affinity along with synthetic feasibility and selectivity, critical properties that were largely neglected in previous evaluations. To address this gap, we identify fundamental limitations of conventional diffusion-based generative models in effectively guiding molecule generation toward these diverse pharmacological properties. We propose $\texttt{CByG}$, a novel framework extending Bayesian Flow Network into a gradient-based conditional generative model that robustly integrates property-specific guidance. Additionally, we introduce a comprehensive evaluation scheme incorporating practical benchmarks for binding affinity, synthetic feasibility, and selectivity, overcoming the limitations of conventional evaluation methods. Extensive experiments demonstrate that our proposed $\texttt{CByG}$, framework significantly outperforms baseline models across multiple essential evaluation criteria, highlighting its effectiveness and practicality for real-world drug discovery applications.

Generative models of graphs based on discrete Denoising Diffusion Probabilistic Models (DDPMs) offer a principled approach to molecular generation by systematically removing structural noise through iterative atom and bond adjustments. However, existing formulations are fundamentally limited by their inability to adapt the graph size (that is, the number of atoms) during the diffusion process, severely restricting their effectiveness in conditional generation scenarios such as property-driven molecular design, where the targeted property often correlates with the molecular size. In this paper, we reformulate the noising and denoising processes to support monotonic insertion and deletion of nodes. The resulting model, which we call GrIDDD, dynamically grows or shrinks the chemical graph during generation. GrIDDD matches or exceeds the performance of existing graph diffusion models on molecular property targeting despite being trained on a more difficult problem. Furthermore, when applied to molecular optimization, GrIDDD exhibits competitive performance compared to specialized optimization models. This work paves the way for size-adaptive molecular generation with graph diffusion.

Traditional continuous deep reinforcement learning (RL) algorithms employ deterministic or unimodal Gaussian actors, which cannot express complex multimodal decision distributions. This limitation can hinder their performance in diversity-critical scenarios. There have been some attempts to design online multimodal RL algorithms based on diffusion or amortized actors. However, these actors are intractable, making existing methods struggle with balancing performance, decision diversity, and efficiency simultaneously. To overcome this challenge, we first reformulate existing intractable multimodal actors within a unified framework, and prove that they can be directly optimized by policy gradient via reparameterization. Then, we propose a distance-based diversity regularization that does not explicitly require decision probabilities. We identify two diversity-critical domains, namely multi-goal achieving and generative RL, to demonstrate the advantages of multimodal policies and our method, particularly in terms of few-shot robustness. In conventional MuJoCo benchmarks, our algorithm also shows competitive performance. Moreover, our experiments highlight that the amortized actor is a promising policy model class with strong multimodal expressivity and high performance.

Optimal transport (OT) provides a powerful framework for comparing and transforming probability distributions, with wide applications in generative modeling, AI4Science and statistical inference. However, existing estimation theory typically requires stringent smoothness conditions on the underlying Brenier potentials and assumes bounded distribution supports, limiting practical applicability. In this paper, we introduce a unified theoretical framework for semi-dual OT map estimation that relaxes both of these restrictions. Building on sieved convex conjugate, our framework has two key contributions: (i) a new map stability bounds that holds without any second-order regularity assumptions on the true Brenier potentials, and (ii) an oracle inequality that cleanly decomposes the estimation error into statistical error, sieved bias, and approximation error. Specifically, our approximation error is measured in the $L^\infty$ norm rather than Sobolev norm in the existing results, aligning more naturally with classical approximation theory. Leveraging these tools, we provide statistical error of semi-dual estimators with mild and verifiable conditions on the true OT map. Moreover, we establish the first theoretical guarantee for deep neural network OT map estimator between general distributions, with Tanh network function class as an example.

Score-based Generative Models (SGMs) have achieved impressive performance in data generation across a wide range of applications and benefit from strong theoretical guarantees. Recently, methods inspired by statistical mechanics, in particular, Hamiltonian dynamics, have introduced Critically-damped Langevin Diffusions (CLDs), which define diffusion processes on extended spaces by coupling the data with auxiliary variables. These approaches, along with their associated score-matching and sampling procedures, have been shown to outperform standard diffusion-based samplers numerically. In this paper, we analyze a generalized dynamic that extends classical CLDs by introducing an additional hyperparameter controlling the noise applied to the data coordinate, thereby better exploiting the extended space. We further derive a novel upper bound on the sampling error of CLD-based generative models in the Wasserstein metric. This additional hyperparameter influences the smoothness of sample paths, and our discretization error analysis provides practical guidance for its tuning, leading to improved sampling performance.

Diffusion models have achieved significant progress in image generation and the pre-trained Stable Diffusion (SD) models are helpful for image deblurring by providing clear image priors. However, directly using a blurry image or a pre-deblurred one as a conditional control for SD will either hinder accurate structure extraction or make the results overly dependent on the deblurring network. In this work, we propose a Latent Kernel Prediction Network (LKPN) to achieve robust real-world image deblurring. Specifically, we co-train the LKPN in the latent space with conditional diffusion. The LKPN learns a spatially variant kernel to guide the restoration of sharp images in the latent space. By applying element-wise adaptive convolution (EAC), the learned kernel is utilized to adaptively process the blurry feature, effectively preserving the information of the blurry input. This process thereby more effectively guides the generative process of SD, enhancing both the deblurring efficacy and the quality of detail reconstruction. Moreover, the results at each diffusion step are utilized to iteratively estimate the kernels in LKPN to better restore the sharp latent by EAC in the subsequent step. This iterative refinement enhances the accuracy and robustness of the deblurring process. Extensive experimental results demonstrate that the proposed method outperforms state-of-the-art image deblurring methods on both benchmark and real-world images.