ICLR 2026 Papers

Protein structure tokenizers enable the creation of multimodal models of protein structure, sequence, and function. Current approaches to protein structure tokenization rely on bespoke components that are invariant to spatial symmetries, but that are challenging to optimize and scale. We present Kanzi, a flow-based tokenizer for tokenization and generation of protein structures. Kanzi consists of a diffusion autoencoder trained with a flow matching loss. We show that this approach simplifies several aspects of protein structure tokenizers: frame-based representations can be replaced with global coordinates, complex losses are replaced with a single flow matching loss, and SE(3)-invariant attention operations can be replaced with standard attention. We find that these changes stabilize the training of parameter-efficient models that outperform existing tokenizers on reconstruction metrics at a fraction of the model size and training cost. An autoregressive model trained with Kanzi outperforms similar generative models that operate over tokens, although it does not yet match the performance of state-of-the-art continuous diffusion models.

High-resolution image synthesis remains a core challenge in generative modeling, particularly in balancing computational efficiency with the preservation of fine-grained visual detail. We present $\textit{Latent Wavelet Diffusion (LWD)}$, a lightweight training framework that significantly improves detail and texture fidelity in ultra-high-resolution (2K-4K) image synthesis. LWD introduces a novel, frequency-aware masking strategy derived from wavelet energy maps, which dynamically focuses the training process on detail-rich regions of the latent space. This is complemented by a scale-consistent VAE objective to ensure high spectral fidelity. The primary advantage of our approach is its efficiency: LWD requires no architectural modifications and adds zero additional cost during inference, making it a practical solution for scaling existing models. Across multiple strong baselines, LWD consistently improves perceptual quality and FID scores, demonstrating the power of signal-driven supervision as a principled and efficient path toward high-resolution generative modeling.

This paper introduces a novel watermarking method for diffusion models. It is based on guiding the diffusion process using the gradient computed from any off-the-shelf watermark decoder. The gradient is guided further using different image augmentations, increasing robustness to attacks against which the decoder was not originally robust, without retraining or fine-tuning. The methodology effectively allows to convert any post-hoc watermarking scheme into a scheme embedding the signal during the diffusion process. We show that this approach is complementary to watermarking techniques modifying the variational autoencoder at the end of the diffusion process. We validate the methods on different diffusion models and detectors. The watermarking guidance does not significantly alter the generated image for a given seed and prompt, preserving both the diversity and quality of generation.

Dynamic Text-Attributed Graphs (DyTAGs), which intricately integrate structural, temporal, and textual attributes, are crucial for modeling complex real-world systems. However, most existing DyTAG datasets exhibit poor textual quality, which severely limits their utility for generative DyTAG tasks requiring semantically rich inputs. Additionally, prior work mainly focuses on discriminative tasks on DyTAGs, resulting in a lack of standardized task formulations and evaluation protocols tailored for DyTAG generation. To address these critical issues, we propose \underline{G}enerative \underline{D}yTA\underline{G} \underline{B}enchmark (GDGB), which comprises eight meticulously curated DyTAG datasets with high-quality textual features for both nodes and edges, overcoming limitations of prior datasets. Building on GDGB, we define two novel DyTAG generation tasks: Transductive Dynamic Graph Generation (TDGG) and Inductive Dynamic Graph Generation (IDGG). TDGG transductively generates a target DyTAG based on the given source and destination node sets, while the more challenging IDGG introduces new node generation to inductively model the dynamic expansion of real-world graph data. To enable holistic evaluation, we design multifaceted metrics that assess the structural, temporal, and textual quality of the generated DyTAGs. We further propose GAG-General, an LLM-based multi-agent generative framework tailored for reproducible and robust benchmarking of DyTAG generation. Experimental results demonstrate that GDGB enables rigorous evaluation of TDGG and IDGG, with key insights revealing the critical interplay of structural and textual features in DyTAG generation. These findings establish GDGB as a foundational resource for advancing generative DyTAG research and unlocking further practical applications in DyTAG generation. The dataset and source code are available at \url{https://github.com/Lucas-PJ/GDGB-ALGO}.

We study how generative world models trained on video games can go beyond mere reproduction of gameplay visuals to learning game mechanics—the modular rules that causally govern gameplay. We introduce a formalization of the concept of game mechanics that operationalizes mechanic-learning as a causal counterfactual inference task and uses the causal consistency principle to address the challenge of generating gameplay with world models that do not violate game rules. We present Multiverse Mechanica, a playable video game testbed that implements a set of ground truth game mechanics based on our causal formalism. The game natively emits training data, where each training example is paired with a set of causal DAGs that encode causality, consistency, and counterfactual dependence specific to the mechanic that is in play—these provide additional artifacts that could be leveraged in mechanic-learning experiments. We provide a proof-of-concept that demonstrates fine-tuning a pre-trained model that targets mechanic learning. Multiverse Mechanica is a testbed that provides a reproducible, low-cost path for studying and comparing methods that aim to learn game mechanics—not just pixels.

Information tasks such as writing surveys or analytical reports require complex search and reasoning, and have recently been grouped under the umbrella of _deep research_ --- a term also adopted by recent models targeting these capabilities. Despite growing interest, the scope of the deep research task remains underdefined and its distinction from other reasoning-intensive problems is poorly understood. In this paper, we propose a formal characterization of the deep research (DR) task and introduce a benchmark to evaluate the performance of DR systems. We argue that the core defining feature of deep research is not the production of lengthy report-style outputs, but rather the high fan-out over concepts required during the search process, i.e., broad and reasoning-intensive exploration.To enable objective evaluation, we define DR using an intermediate output representation that encodes key claims uncovered during search—separating the reasoning challenge from surface-level report generation. Based on this formulation, we propose a benchmark LiveDRBench with 100 challenging tasks over scientific topics (e.g., datasets, materials discovery, prior art search) and public interest events (e.g., flight incidents, movie awards). Across state-of-the-art DR systems, F1 score ranges between 0.02 and 0.72 for any sub-category. OpenAI's model performs the best with an overall F1 score of 0.55. Analysis of the reasoning traces reveals that systems cover only about half of the necessary search queries, with proprietary models issuing broader and and deeper queries than open source models, highlighting gaps in both coverage and reasoning depth.

Flow matching is a powerful generative modeling framework, valued for its simplicity and strong empirical performance. However, its standard formulation treats signals on structured spaces---such as fMRI data on brain graphs---as points in Euclidean space, overlooking the rich topological features of their domains. To address this, we introduce \emph{topological flow matching}, a topology-aware generalization of flow matching. We interpret flow matching as a framework for solving a degenerate Schrödinger bridge problem and inject topological information by augmenting the reference process with a Laplacian-derived drift. This principled modification captures the structure of the underlying domain while preserving the desirable properties of flow matching: a stable, simulation-free objective and deterministic sample paths. As a result, our framework serves as a plug-and-play replacement for standard flow matching. We demonstrate its effectiveness on diverse structured datasets, including brain fMRIs, ocean currents, seismic events, and traffic flows.

Diffusion models generate high-quality, diverse images with great generalizability, yet when overfit to the training objective, they may memorize training samples. We analyze memorization and generalization of diffusion models through the lens of representation learning. Using a two-layer ReLU denoising autoencoder (DAE) parameterization, we show that memorization corresponds to the model learning the raw data matrix for encoding and decoding, yielding spiky representations; in contrast, generalization arises when the model captures local data statistics, producing balanced representations. We validate these insights by investigating representation spaces in real-world unconditional and text-to-image diffusion models, where the same distinctions emerge. Practically, we propose a representation-based memorization detection method and a simple representation-steering method that enables controllable editing of generalized samples. Together, our results underscore that *learning good representations is central to novel and meaningful generation*.

Generating graphs with hierarchical structures remains a fundamental challenge due to the limitations of Euclidean geometry in capturing exponential complexity. Here we introduce GGBall, a novel hyperbolic framework for graph generation that integrates geometric inductive biases with modern generative paradigms. GGBall combines a Hyperbolic Vector-Quantized Autoencoder (HVQVAE) with a Riemannian flow matching prior defined via closed-form geodesics. This design enables flow-based priors to model complex latent distributions, while vector quantization helps preserve the curvature-aware structure of the hyperbolic space. We further develop a suite of hyperbolic GNN and Transformer layers that operate entirely within the manifold, ensuring stability and scalability. Empirically, GGBall establishes a new state-of-the-art across diverse benchmarks. On hierarchical graph datasets, it reduces the average generation error by up to 18% compared to the strongest baselines. These results highlight the potential of hyperbolic geometry as a powerful foundation for the generative modeling of complex, structured, and hierarchical data domains.

We introduce the Information-Estimation Metric (IEM), a novel form of distance function derived from an underlying continuous probability density over a domain of signals. The IEM is rooted in a fundamental relationship between information theory and estimation theory, which links the log-probability of a signal with the errors of an optimal denoiser, applied to noisy observations of the signal. In particular, the IEM between a pair of signals is obtained by comparing their denoising error vectors over a range of noise amplitudes. Geometrically, this amounts to comparing the score vector fields of the *blurred* density around the signals over a range of blur levels. We prove that the IEM is a valid global distance metric and derive a closed-form expression for its local second-order approximation, which yields a Riemannian metric. For Gaussian-distributed signals, the IEM coincides with the Mahalanobis distance. But for more complex distributions, it adapts, both locally and globally, to the geometry of the distribution. In practice, the IEM can be computed using a learned denoiser (analogous to generative diffusion models) and solving a one-dimensional integral. To demonstrate the value of our framework, we learn an IEM on the ImageNet database. Experiments show that this IEM is competitive with or outperforms state-of-the-art supervised image quality metrics in predicting human perceptual judgments.

We propose LayerSync, a domain-agnostic approach for improving the generation quality and the training efficiency of diffusion models. Prior studies have highlighted the connection between the quality of generation and the representations learned by diffusion models, showing that external guidance on model intermediate representations accelerates training. We reconceptualize this paradigm by regularizing diffusion models with their own intermediate representations. Building on the observation that representation quality varies across diffusion model layers, we show that the most semantically rich representations can act as an intrinsic guidance for weaker ones, reducing the need for external supervision. Our approach, LayerSync, is a self-sufficient, plug-and-play regularizer term with no overhead on diffusion model training and generalizes beyond the visual domain to other modalities. LayerSync requires no pretrained models nor additional data. We extensively evaluate the method on image generation and demonstrate its applicability to other domains such as audio, video, and motion generation. We show that it consistently improves the generation quality and the training efficiency. For example, we speed up the training of flow-based transformer by over 8.75$\times$ on ImageNet dataset and improve the generation quality by 23.6\%.

A central aim of interpretability tools applied to language models is to recover meaningful concepts from model activations. Existing feature extraction methods focus on single activations regardless of the context, implicitly assuming independence (and therefore stationarity). This leaves open whether they can capture the rich temporal and context-sensitive structure in the activations of language models (LMs). Adopting a Bayesian view, we demonstrate that standard Sparse Autoencoders (SAEs) impose priors that assume independence of concepts across time. We then show that LM representations exhibit rich temporal dynamics, including systematic growth in conceptual dimensionality, context-dependent correlations, and pronounced non-stationarity, in direct conflict with the priors of SAEs. This mismatch casts doubt on existing SAEs' ability to reflect temporal structures of interest in the data. We introduce a novel SAE architecture---Temporal SAE---with a temporal inductive bias that decomposes representations at a given time into two parts: a predictable component, which can be inferred from the context, and a residual component, which captures novel information that cannot be captured by the context. Experiments on LLM activations with Temporal SAE demonstrate its ability to correctly parse garden path sentences, identify event boundaries, and more broadly delineate abstract, slow-moving information from novel, fast-moving information, while existing SAEs show significant pitfalls in all the above tasks. Our results underscore the need for inductive biases that match the data in designing robust interpretability tools.

Time-series forecasting increasingly demands not only accurate observational predictions but also causal forecasting under interventional and counterfactual queries in multivariate systems. We present DoFlow, a flow-based generative model defined over a causal Directed Acyclic Graph (DAG) that delivers coherent observational and interventional predictions, as well as counterfactuals through the natural encoding–decoding mechanism of continuous normalizing flows (CNFs). We also provide a supporting counterfactual recovery theory under certain assumptions. Beyond forecasting, DoFlow provides explicit likelihoods of future trajectories, enabling principled anomaly detection. Experiments on synthetic datasets with various causal DAG structures and real-world hydropower and cancer-treatment time series show that DoFlow achieves accurate system-wide observational forecasting, enables causal forecasting over interventional and counterfactual queries, and effectively detects anomalies. This work contributes to the broader goal of unifying causal reasoning and generative modeling for complex dynamical systems.

Flow models parameterized as time-dependent velocity fields can generate data from noise by integrating an ODE. These models are often trained using flow matching, i.e. by sampling random pairs of noise and target points $(x_0,x_1)$ and ensuring that the velocity field is aligned, on average, with $x_1-x_0$ when evaluated along a time-indexed segment linking $x_0$ to $x_1$. While these noise/data pairs are sampled independently by default, they can also be selected more carefully by matching batches of $n$ noise to $n$ target points using an optimal transport (OT) solver. Although promising in theory, the OT flow matching (OT-FM) approach (Pooladian et al., 2023, Tong et al., 2024) is not widely used in practice. Zhang et al. (2025), pointed out recently that OT-FM truly starts paying off when the batch size $n$ grows significantly, which only a multi-GPU implementation of the Sinkhorn algorithm can handle. Unfortunately, the pre-compute costs of running Sinkhorn can quickly balloon, requiring $O(n^2/\varepsilon^2)$ operations for every $n$ pairs used to fit the velocity field, where $\varepsilon$ is a regularization parameter that should be typically small to yield better results. To fulfill the theoretical promises of OT-FM, we propose to move away from batch-OT and rely instead on a semidiscrete formulation that can leverage the fact that the target dataset distribution is usually of finite size $N$. The SD-OT problem is solved by estimating a dual potential vector of size $N$ using SGD; using that vector, freshly sampled noise vectors at train time can then be matched with data points at the cost of a maximum inner product search (MIPS) over the dataset. Semidiscrete FM (SD-FM) removes the quadratic dependency on $n/\varepsilon$ that bottlenecks OT-FM. SD-FM beats both FM and OT-FM on all training metrics and inference budget constraints, across multiple datasets, on unconditional/conditional generation, or when using mean-flow models.

Discrete diffusion models are a powerful class of generative models that demonstrate strong performance across many domains. However, for efficiency, discrete diffusion typically parameterizes the generative (reverse) process with factorized distributions, which makes it difficult for the model to learn a target process in a small number of steps and necessitates a long, computationally expensive sampling procedure. To reduce the gap between the target and model distributions and enable few-step generation, we introduce a learnable noising (forward) process for discrete diffusion. Instead of fixing a Markovian forward chain, we adopt a non-Markovian formulation and introduce learnable marginal and posterior distributions. This allows the generative process to remain factorized while matching the target defined by the noising process. We train all parameters end-to-end under the standard variational objective.

Diffusion models have achieved remarkable success across diverse domains, but they remain vulnerable to memorization---reproducing training data rather than generating novel outputs. This not only limits their creative potential but also raises concerns about privacy and safety. While empirical studies have explored mitigation strategies, theoretical understanding of memorization remains limited. We address this gap through developing a dual-separation result via two complementary perspectives: statistical estimation and network approximation. From the estimation side, we show that the ground-truth score function does not minimize the empirical denoising loss, creating a separation that drives memorization. From the approximation side, we prove that implementing the empirical score function requires network size to scale with sample size, spelling a separation compared to the more compact network representation of the ground-truth score function. Guided by these insights, we develop a pruning-based method that reduces memorization while maintaining generation quality in diffusion transformers.

High-quality 3D world models are pivotal for embodied intelligence and Artificial General Intelligence (AGI), underpinning applications such as AR/VR content creation and robotic navigation. Despite the established strong imaginative priors, current video foundation models lack explicit 3D grounding capabilities, thus being limited in both spatial consistency and their utility for downstream 3D reasoning tasks. In this work, we present FantasyWorld, a geometry-enhanced framework that augments frozen video foundation models with a trainable geometric branch, enabling joint modeling of video latents and an implicit 3D field in a single forward pass. Our approach introduces cross-branch supervision, where geometry cues guide video generation and video priors regularize 3D prediction, thus yielding consistent and generalizable 3D-aware video representations. Notably, the resulting latents from the geometric branch can potentially serve as versatile representations for downstream 3D tasks such as novel view synthesis and navigation, without requiring per-scene optimization or fine-tuning. Extensive experiments show that FantasyWorld effectively bridges video imagination and 3D perception, outperforming recent geometry-consistent baselines in multi-view coherence and style consistency. Ablation studies further confirm that these gains stem from the unified backbone and cross-branch information exchange.

The success of denoising diffusion models raises important questions regarding their generalisation behaviour, particularly in high-dimensional settings. Notably, it has been shown that when training and sampling are performed perfectly, these models memorise training data—implying that some form of regularisation is essential for generalisation. Existing theoretical analyses primarily rely on algorithm-independent techniques such as uniform convergence, heavily utilising model structure to obtain generalisation bounds. In this work, we instead leverage the algorithmic aspects that promote generalisation in diffusion models, developing a general theory of algorithm-dependent generalisation for this setting. Borrowing from the framework of algorithmic stability, we introduce the notion of score stability, which quantifies the sensitivity of score-matching algorithms to dataset perturbations. We derive generalisation bounds in terms of score stability, and apply our framework to several fundamental learning settings, identifying sources of regularisation. In particular, we consider denoising score matching with early stopping (denoising regularisation), sampler-wide coarse discretisation (sampler regularisation), and optimising with SGD (optimisation regularisation). By grounding our analysis in algorithmic properties rather than model structure, we identify multiple sources of implicit regularisation unique to diffusion models that have so far been overlooked in the literature.

Diffusion-based generative models have reformed generative AI, and have enabled new capabilities in the science domain, for example, generating 3D structures of molecules. Due to the intrinsic problem structure of certain tasks, there is often a symmetry in the system, which identifies objects that can be converted by a group action as equivalent, hence the target distribution is essentially defined on the quotient space with respect to the group. In this work, we establish a formal framework for diffusion modeling on a general quotient space, and apply it to molecular structure generation which follows the special Euclidean group SE(3) symmetry. The framework reduces the necessity of learning the component corresponding to the group action, hence simplifies learning difficulty over conventional group-equivariant diffusion models, and the sampler guarantees recovering the target distribution, while heuristic alignment strategies lack proper samplers. The arguments are empirically validated on structure generation for small molecules and proteins, indicating that the principled quotient-space diffusion model provides a new framework that outperforms previous symmetry treatments.