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Deep Learning · Generative Models and Autoencoders

Marco Pegoraro, Evan Atherton, Bruno Roy, Aliasghar Khani, Arianna Rampini

Learning natural body motion remains challenging due to the strong coupling between spatial geometry and temporal dynamics. Embedding motion in phase manifolds, latent spaces that capture local periodicity, has proven effective for motion prediction; however, existing approaches lack scalability and remain confined to specific settings. We introduce FunPhase, a functional periodic autoencoder that learns a phase manifold for motion and replaces discrete temporal decoding with a function-space formulation, enabling smooth trajectories that can be sampled at arbitrary temporal resolutions. FunPhase unifies motion prediction and generation within a single interpretable phase manifold, enabling motion generation via latent diffusion, generalizes across skeletons and datasets, and supports downstream tasks such as motion super-resolution and partial-body completion. Our model achieves substantially lower reconstruction error than prior periodic autoencoder baselines, achieving uniform improvements of at least 45% across all metrics, while enabling a broader range of applications and performing on par with state-of-the-art motion generation methods.

Deep Learning · Generative Models and Autoencoders

Yida Xiong, Jiameng Chen, Xiuwen Gong, Jia Wu, Shirui Pan, wenbin Hu

Graph generation aims to sample discrete node and edge attributes while satisfying coupled structural constraints. Diffusion models for graphs often adopt largely factorized forward-noising, and many flow-matching methods start from factorized reference noise and coordinate-wise interpolation, so node–edge coupling is not encoded by the generative geometry and must be recovered implicitly by the core network, which can be brittle after discrete decoding. Bayesian Flow Networks (BFNs) evolve distribution parameters and naturally support discrete generation. But classical BFNs typically rely on factorized beliefs and independent channels, which limit geometric evidence fusion. We propose Variational Bayesian Flow Network (VBFN), which performs a variational lifting to a tractable joint Gaussian variational belief family governed by structured precisions. Each Bayesian update reduces to solving a symmetric positive definite linear system, enabling coupled node and edge updates within a single fusion step. We construct sample-agnostic sparse precisions from a representation-induced dependency graph, thereby avoiding label leakage while enforcing node–edge consistency. On synthetic and molecular graph datasets, VBFN improves fidelity and diversity, and surpasses baseline methods. The reproducible code is available at https://anonymous.4open.science/r/VBFN-D6B0/.

Deep Learning · Generative Models and Autoencoders

Vamshi Sunku Mohan, Kaustubh Gupta, Aneesha Das, Chandan Singh

State-space models (SSMs) have emerged as an efficient strategy for building powerful language models, avoiding the quadratic complexity of computing attention in transformers. Despite their promise, the interpretability and steerability of modern SSMs remain relatively underexplored. We take a major step in this direction by identifying *activation subspace bottlenecks* in the Mamba family of SSM models using tools from mechanistic interpretability. We then introduce a test-time steering intervention that simply multiplies the activations of the identified bottlenecks by a scalar. Across 5 SSMs and 6 diverse benchmarks, this intervention improves performance by an average of 8.27%, without requiring any task-specific tuning. Finally, we validate that the identified bottlenecks are indeed hindering performance by modifying them to yield an architecture we call Stable-Mamba, which achieves long-context performance gains when retrained from scratch.

Deep Learning · Generative Models and Autoencoders

Dengsheng Chen, Yangming Shi, Enhua Wu

Conventional autoregressive models achieve causality through next-token prediction, but suffer from prohibitive latency and typically under-perform non-causal alternatives such as masked prediction and diffusion. We propose self-token prediction, which enables predicting a flexible number of tokens per step, and introduce AGARIC, the first spatially causal image generator built on this paradigm. AGARIC delivers markedly faster inference and consistently outperforms prior autoregressive baselines, matching the performance of state-of-the-art non-causal models. Our findings point to self-token prediction as a key step toward unified and efficient multimodal autoregressive modeling.

Deep Learning · Generative Models and Autoencoders

Bin Zang, Rengan Xie, Xiaoliang Luo, Zhiyuan Fang, Shi Li, Lvchun Wang, Wei Yu, Yi Zhao, Yuchi Huo, Tian Xie 等

Recently, a line of works can generate impressive 3D objects from a single image, but they are limited by restricted representation resolution, making them unsuitable for 3D scene generation. In this work, we introduce \name, a novel method for high-quality 3D scene generation based on hierarchical voxel enhancement framework. Specifically, given a single scene image as input, we first produce a coarse initial scene, then introduce image segmentation and attention-based retrieval to align 2D image components with 3D scene components. Subsequently, we organize these scene relations into a hierarchical component tree, where nodes closer to the leaves denote finer-grained components. Finally, we propose a voxel super-resolution model that generates refined voxels for the target instance while maintaining strong consistency with the coarse voxels. Equipped with this model, we perform coarse-to-fine hierarchical super-resolution on images and voxels for each component, producing a high-resolution and high-quality 3D scene. Extensive experiments demonstrate that our method significantly outperforms previous approaches, achieving state-of-the-art performance.

Deep Learning · Generative Models and Autoencoders

Henry Smith, Nathaniel Diamant, Brian Trippe

Generative models frequently suffer miscalibration, wherein statistics of the sampling distribution such as class probabilities deviate from desired values. We frame calibration as a constrained optimization problem and seek the closest model in Kullback-Leibler divergence satisfying calibration constraints. To address the intractability of imposing these constraints exactly, we introduce two surrogate objectives for fine-tuning: (1) the relax loss, which replaces the constraint with a miscalibration penalty, and (2) the reward loss, which converts calibration into a reward fine-tuning problem. We demonstrate that these approaches substantially reduce calibration error across hundreds of simultaneous constraints and models with up to nine billion parameters, spanning applications in protein design, image generation, and language modeling.

Deep Learning · Generative Models and Autoencoders

Andreas Grivas, Lorenzo Loconte, Emile van Krieken, Piotr Nawrot, Yu Zhao, Euan Wielewski, Pasquale Minervini, Edoardo Ponti, Antonio Vergari

Multi-token prediction (MTP) is a prominent strategy to significantly speed up generation in large language models (LLMs), especially in byte-level LLMs, which are tokeniser-free but prohibitively slow. However, existing MTP methods often sacrifice expressiveness by assuming independence between future tokens. In this work, we investigate the trade-off between expressiveness and latency in MTP within the framework of probabilistic circuits (PCs). Our framework, named MTPC, allows one to explore different ways to encode the joint distributions over future tokens by selecting different circuit architectures, generalising classical models such as (hierarchical) mixture models, hidden Markov models, and tensor networks. We show the efficacy of MTPC by retrofitting existing byte-level LLMs, such as EvaByte, and byte-fied subword models, such as Llama3.2 3B. Our experiments show that, when combined with speculative decoding, MTPC substantially speeds up generation compared to MTP with independence assumptions, while guaranteeing to retain the performance of the original verifier LLM. We also rigorously study the optimal trade-off between expressiveness and latency when exploring the possible parameterisations of MTPC, such as PC architectures and partial layer sharing between the verifier and draft LLMs.

Deep Learning · Generative Models and Autoencoders

Sangwon Jang, Taekyung Ki, Jaehyeong Jo, Saining Xie, Jaehong Yoon, Sung Ju Hwang

Modern video generators still struggle with complex physical dynamics, often falling short of physical realism. Existing approaches address this using external verifiers or additional training on augmented data, which is computationally expensive and still limited in capturing fine-grained motion. In this work, we present self-refining video sampling, a simple method that uses a pre-trained video generator trained on large-scale datasets as its own self-refiner. By interpreting the generator as a denoising autoencoder, we enable iterative inner-loop refinement at inference time without any external verifier or additional training. We further introduce an uncertainty-aware refinement strategy that selectively refines regions based on self-consistency, which prevents artifacts caused by over-refinement. Experiments on state-of-the-art video generators demonstrate significant improvements in motion coherence and physics alignment, achieving over 70% human preference compared to the default sampler and guidance-based sampler.

Deep Learning · Generative Models and Autoencoders

Yuxuan Yao, Yuxuan Chen, Hui Li, Kaihui Cheng, Qipeng Guo, Yuwei Sun, Zilong Dong, Jingdong Wang, Siyu Zhu

Multimodal Diffusion Transformers (MMDiTs) for text-to-image generation maintain separate text and image branches, with bidirectional information flow between text tokens and visual latents throughout denoising. In this setting, we observe a prompt forgetting phenomenon: the semantics of the prompt representation in the text branch is progressively forgotten as depth increases. We further verify this effect on three representative MMDiTs—SD3, SD3.5, and FLUX.1 by probing linguistic attributes of the representations over the layers in the text branch. Motivated by these findings, we introduce a training-free approach, prompt reinjection, which reinjects prompt representations from early layers into later layers to alleviate this forgetting. Experiments on GenEval, DPG, and T2I-CompBench++ show consistent gains in instruction-following capability, along with improvements on metrics capturing preference, aesthetics, and overall text--image generation quality.

Deep Learning · Generative Models and Autoencoders

Yunhan Yang, Chunshi Wang, Junliang Ye, YANG LI, Zanxin Chen, Zehuan Huang, Yao Mu, Zhuo Chen, Chunchao Guo, Xihui Liu

Synthesizing physics-grounded 3D assets is a critical bottleneck for interactive virtual worlds and embodied AI. Existing methods predominantly focus on static geometry, overlooking the functional properties essential for interaction. We propose that interactive asset generation must be rooted in functional logic and hierarchical physics. To bridge this gap, we introduce PhysForge, a decoupled two-stage framework supported by PhysDB, a large-scale dataset of 150,000 assets with four-tier physical annotations. First, a VLM acts as a physical architect to plan a Hierarchical Physical Blueprint defining material, functional, and kinematic constraints. Second, a physics-grounded diffusion model realizes this blueprint by synthesizing high-fidelity geometry alongside precise kinematic parameters via a novel KineVoxel Injection (KVI) mechanism. Experiments demonstrate that PhysForge produces functionally plausible, simulation-ready assets, providing a robust data engine for interactive 3D content and embodied agents.

Deep Learning · Generative Models and Autoencoders

Samuel Garcin, Tom Walker, Steven McDonagh, Tim Pearce, Hakan Bilen, Tianyu He, Kaixin Wang, Jiang Bian

Interactive world models continually generate video by responding to a user's actions, enabling open-ended generation capabilities. However, existing models typically lack a 3D representation of the environment, meaning 3D consistency must be implicitly learned from data, and spatial memory is restricted to limited temporal context windows. This results in an unrealistic user experience, and presents significant obstacles to down-stream tasks such as training agents. To address this, we present PERSIST, a new paradigm of world model which simulates the evolution of a latent 3D scene: environment, camera and renderer. This allows us to synthesize new frames with persistent spatial memory and consistent geometry. Our approach achieves substantial improvements in spatial memory, 3D consistency, and long-horizon video generation quality over existing methods, producing coherent and evolving 3D worlds.

Deep Learning · Generative Models and Autoencoders

Yufan Deng, Zilin Pan, Hongyu Zhang, Xiaojie Li, Huruoqing, Yufei Ding, Yiming Zou, Yan Zeng, Zhou Daquan

While video generation holds promise for embodied intelligence, current video models struggle with physical realism, and progress is hindered by the lack of standardized benchmarks. To address this gap, we introduce a comprehensive robotics benchmark, RBench, designed to evaluate robot-oriented video generation across five task domains and four distinct embodiments. By assessing task correctness and visual fidelity through reproducible metrics, our evaluation of 25 models reveals significant deficiencies in generating physically realistic robot behaviors. Furthermore, the benchmark achieves a 0.96 Spearman correlation with human judgment, validating its effectiveness. While RBench provides the necessary lens to identify these deficiencies, achieving physical realism requires moving beyond evaluation to address the critical shortage of high-quality training data. Driven by these insights, we introduce a refined four-stage data pipeline, resulting in RoVid-X, the largest open-source robotic dataset for video generation with 4 million annotated video clips, covering thousands of tasks and enriched with physical property annotations. Extensive experiments demonstrate that finetuning on RoVid-X yields consistent performance gains. Collectively, this synergistic ecosystem of evaluation and data establishes a robust foundation for rigorous assessment and scalable training of video models, accelerating the evolution of embodied AI toward physical intelligence. The code and video demos are available in the supplementary materials.

Deep Learning · Generative Models and Autoencoders

Marcel Hirt, Domenico Campolo, Victoria Leong, Juan-Pablo Ortega

Devising deep latent variable models for multi-modal data has been a long-standing theme in machine learning research. Multi-modal Variational Autoencoders (VAEs) have been a popular generative model class that learns latent representations that jointly explain multiple modalities. Various objective functions for such models have been suggested, often motivated as lower bounds on the multi-modal data log-likelihood or from information-theoretic considerations. To encode latent variables from different modality subsets, Product-of-Experts (PoE) or Mixture-of-Experts (MoE) aggregation schemes have been routinely used and shown to yield different trade-offs, for instance, regarding their generative quality or consistency across multiple modalities. In this work, we consider a variational objective that can tightly approximate the data log-likelihood. We develop more flexible aggregation schemes that avoid the inductive biases in PoE or MoE approaches by combining encoded features from different modalities based on permutation-invariant neural networks. Our numerical experiments illustrate trade-offs for multi-modal variational objectives and various aggregation schemes. We show that our variational objective and more flexible aggregation models can become beneficial when one wants to approximate the true joint distribution over observed modalities and latent variables in identifiable models.

Deep Learning · Generative Models and Autoencoders

Kaizhen Zhu, Mokai Pan, Zhechuan Yu, Jingya Wang, Jingyi Yu, Ye Shi

Diffusion Bridge and Flow Matching have both demonstrated compelling empirical performance in transformation between arbitrary distributions. However, there remains confusion about which approach is generally preferable, and the substantial discrepancies in their modeling assumptions and practical implementations have hindered a unified theoretical account of their relative merits. We have, for the first time, provided a unified theoretical and experimental validation of these two models. We recast their frameworks through the lens of Stochastic Optimal Control and prove that the cost function of the Diffusion Bridge is lower, guiding the system toward more stable and natural trajectories. Simultaneously, from the perspective of Optimal Transport, interpolation coefficients $t$ and $1-t$ of Flow Matching become increasingly ineffective when the training data size is reduced. To corroborate these theoretical claims, we propose a novel, powerful architecture for Diffusion Bridge built on a latent Transformer, and implement a Flow Matching model with the same structure to enable a fair performance comparison in various experiments. Comprehensive experiments are conducted across Image Restoration, Translation, and Style Transfer tasks, systematically varying both the distributional discrepancy (different difficulty) and the training data size. Extensive empirical results align perfectly with our theoretical predictions and allow us to delineate the respective advantages and disadvantages of these two models. Our code is available at \url{https://anonymous.4open.science/r/DBFM-3E8E/}.

Deep Learning · Generative Models and Autoencoders

Bo Yin, Xiaobin Hu, Xingyu Zhou, Yu HE, Peng-Tao Jiang, Yue Liao, Junwei Zhu, Jiangning Zhang, Ying Tai, Shuicheng YAN

Diffusion models have achieved remarkable success in generative modeling, yet how to effectively adapting large pretrained models to new tasks remains challenging. We revisit the reconstruction behavior of diffusion models during denoising to unveil the underlying frequency–energy mechanism governing this process. Building upon this observation, we propose \textbf{FeRA}, a frequency-driven fine-tuning framework that aligns parameter updates with the intrinsic frequency–energy progression of diffusion. FeRA establishes a comprehensive frequency–energy framework for effective diffusion adaptation fine-tuning, comprising three synergistic components: \textit{(i)} a compact frequency–energy indicator that characterizes the latent’s bandwise energy distribution, \textit{(ii)} a soft frequency router that adaptively fuses multiple frequency-specific adapter experts, and \textit{(iii)} a frequency–energy consistency regularization that stabilizes diffusion optimization and ensures coherent adaptation across bands. Routing operates in both training and inference, with inference-time routing dynamically determined by the latent frequency energy. It integrates seamlessly with adapter-based tuning schemes and generalizes well across diffusion backbones and resolutions. By aligning adaptation with the frequency–energy mechanism, \textbf{FeRA} provides a simple, stable, and compatible paradigm for effective and robust diffusion model adaptation. Codes will be made publicly available.

Deep Learning · Generative Models and Autoencoders

Hongkun Dou, Zike Chen, fengji Li, Hongjue Li, Yue Deng

Controllable generation with discrete diffusion models is often hindered by high computational overhead or the need for retraining. In this paper, we present Gradient-Informed Logit Correction (GILC), a plug-and-play framework that efficiently estimates guidance signals by repurposing the pretrained denoising network as a variational proxy. To circumvent the gradient instability inherent in high-dimensional discrete spaces, we introduce a Jacobian-free mechanism that directly corrects the clean prediction logits, facilitating stable and effective guidance. Our method accommodates both differentiable and non-differentiable reward functions. Extensive experiments across DNA, protein sequence, and molecular generation tasks demonstrate that GILC achieves state-of-the-art performance without additional training, frequently outperforming fine-tuning approaches.

Namjoon Suh, Yuning Yang, Din-Yin Hsieh, Qitong Luan, Shirong Xu, Shixiang Zhu, Guang Cheng

We present \texttt{TimeAutoDiff}, a unified latent-diffusion framework that addresses four fundamental time-series tasks—unconditional generation, missing-data imputation, forecasting, and time-varying-metadata conditional generation—within a single model that natively handles heterogeneous features (continuous, binary, and categorical). We unify these tasks through a simple masked-modeling strategy: a binary mask specifies which time feature cells are observed and which must be generated. To make this work on mixed data types, we pair a lightweight variational autoencoder (i.e., VAE)—which maps continuous, categorical, and binary variables into a continuous latent sequence—with a diffusion model that learns dynamics in that latent space, avoiding separate likelihoods for each data type while still capturing temporal and cross-feature structure.Two design choices give \texttt{TimeAutoDiff} clear speed and scalability advantages. First, the diffusion process samples a single latent trajectory for the full time horizon rather than denoising one timestep at a time; this whole-sequence sampling drastically reduces reverse-diffusion calls and yields an order-of-magnitude throughput gain. Second, the VAE compresses along the feature axis, so very wide tables are modeled in a lower-dimensional latent space, further reducing computational load. Empirical evaluation demonstrates that \texttt{TimeAutoDiff} matches or surpasses strong baselines in synthetic sequence fidelity (discriminative, temporal-correlation, and predictive metrics) and consistently lowers MAE/MSE for imputation and forecasting tasks. Time-varying metadata conditioning unlocks real-world scenario exploration: by editing metadata sequences, practitioners can generate coherent families of counterfactual trajectories that track intended directional changes, preserve cross-feature dependencies, and remain conditionally calibrated—making "what-if" analysis practical. Our ablation studies confirm that performance is impacted by key architectural choices, such as the VAE's continuous feature encoding and specific components of the DDPM denoiser. Furthermore, a distance-to-closest-record (DCR) audit demonstrates that the model achieves generalization with limited memorization given enough dataset. Code implementations of \texttt{TimeAutoDiff} are provided in https://github.com/namjoonsuh/TimeAutoDiff.

Social Aspects · Accountability, Transparency, and Interpretability

Michal Moshkovitz, Suraj Srinivas, Lesia Semenova, Nave Frost, Cyrus Rashtchian, Valentyn Boreiko, Shichang Zhang, Himabindu Lakkaraju, Cynthia Rudin, Jennifer Wortman Vaughan

Despite the proliferation of Explainable AI (XAI) techniques—from feature attributions to sparse autoencoders—explanations rarely influence real-world workflows. In practice, they are often generated and discarded without guiding meaningful action. This gap reflects foundational shortcomings: research has not yet established methodologies for integrating explanations into end-to-end, human-in-the-loop systems. This position paper argues that the machine learning community must pivot from ad-hoc XAI methods toward addressing foundational \& structural challenges, including unclear problem formulations, underspecified evaluation objectives, and the absence of pipelines for explanation-driven feedback. We support this claim through an analysis of recent ICML, NeurIPS, and ICLR papers and a survey of XAI practitioners, revealing recurring issues that limit cumulative progress. We conclude by outlining a practical checklist designed to shift XAI toward a more human-centered, action-oriented paradigm. By emphasizing foundational clarity over the development of ad-hoc methods, we hope to provide a roadmap for integrating explanations into actionable, feedback-driven AI systems.

Deep Learning · Generative Models and Autoencoders

Dongjiang Niu, Xiaofeng Wang, Zhiqiang Wei, Zhen Li

Although peptides are well suited for flexible and shallow binding interfaces, their intrinsic flexibility induces a strongly coupled sequence–structure relationship that current fixed-geometry latent models cannot simultaneously model with conformational diversity and physical feasibility, ultimately limiting design quality. To overcome this bottleneck, PepFGLD is proposed as a receptor-conditioned, flexibility-aware framework for full-atom peptide design. The framework is motivated by a systematic analysis of existing limitations: geometry shifts driven by interfacial flexibility are not well captured by standard equivariant encoders; the static combination of sequence information and 3D geometry cannot represent their dynamic interactions; and diffusion models without timely geometric feedback tend to drift away from physically reasonable energy landscapes. In PepFGLD, FlexEGNN is used to improve the sensitivity of geometric representations to local flexibility, a coherent and adaptable latent conformational manifold is formed through bidirectional sequence–structure interaction and nonlinear latent mapping, and a time-dependent energy-guided diffusion mechanism is incorporated to balance exploration and convergence during diffusion so that sampling trajectories are continuously guided toward physically feasible full-atom structures. PepFGLD yields improved binding affinity and design success across multiple peptide design tasks.

Deep Learning · Generative Models and Autoencoders

Jeongwoo Shin, Jinhwan Sul, Joonseok Lee, Jaewoong Choi, Jaemoo Choi

Diffusion models often yield highly curved trajectories and noisy score targets due to an uninformative, memoryless forward process that induces independent data-noise coupling. We propose Adjoint Schrödinger Bridge Matching (ASBM), a generative modeling framework that recovers optimal trajectories in high dimensions via two stages. First, we view the Schrödinger Bridge (SB) forward dynamic as a coupling construction problem and learn it through a data-to-energy sampling perspective that transports data to an energy-defined prior. Then, we learn the backward generative dynamic with a simple matching loss supervised by the induced optimal coupling. By operating in a non-memoryless regime, ASBM produces significantly straighter and more efficient sampling paths. Compared to prior works, ASBM scales to high-dimensional data with notably improved stability and efficiency. Extensive experiments on image generation show that ASBM improves fidelity with fewer sampling steps. We further showcase the effectiveness of our optimal trajectory via distillation to a one-step generator.