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Dequan Kong, Honghua Chen, Zhe Zhu, Mingqiang Wei

Existing diffusion-based 3D shape completion methods typically use a conditional paradigm, injecting incomplete shape information into the denoising network via deep feature interactions (e.g., concatenation, cross-attention) to guide sampling toward complete shapes, often represented by voxel-based distance functions. However, these approaches fail to explicitly model the optimal global transport path, leading to suboptimal completions. Moreover, performing diffusion directly in voxel space imposes resolution constraints, limiting the generation of fine-grained geometric details. To address these challenges, we propose BridgeShape, a novel framework for 3D shape completion via latent diffusion Schrödinger bridge. The key innovations lie in two aspects: (i) BridgeShape formulates shape completion as an optimal transport problem, explicitly modeling the transition between incomplete and complete shapes to ensure a globally coherent transformation. (ii) We introduce a Depth-Enhanced Vector Quantized Variational Autoencoder (VQ-VAE) to encode 3D shapes into a compact latent space, leveraging self-projected multi-view depth information enriched with strong DINOv2 features to enhance geometric structural perception. By operating in a compact yet structurally informative latent space, BridgeShape effectively mitigates resolution constraints and enables more efficient and high-fidelity 3D shape completion. BridgeShape achieves state-of-the-art performance on 3D shape completion benchmarks, demonstrating superior fidelity at higher resolutions and for unseen object classes.

Xianglong Jin, Zheng Wang, Rong Wang, Feiping Nie

Self-supervised 3D point cloud understanding is crucial for scene understanding, where Masked Autoencoders (MAE) have achieved excellent performance in point cloud representation learning. However, existing MAE-style methods fail to consider spatial-semantic variations in masking strategies, and joint learning with multi-view images often overlooks view redundancy. To address these challenges, we propose an MAE framework enhanced with reliable multi-view 2D-3D Key-part alignment and Reinforced masking, named as KR-MAE. Our approach comprises three key innovations: Reinforced Masking (RM) strategically samples visible tokens based on semantic saliency to enhance reconstruction fidelity; Reliable Multi-View Selector (RVS) dynamically refines the most informative image subset by filtering occluded or low-texture views, mitigating detrimental redundancy; Reliable-view 2D-3D Key-part Aligned Transformer (KAT) establishes semantic-aligned correspondence between salient 3D point cloud parts and reliable multi-view 2D image patches, leveraging rich texture cues from 2D images to compensate for sparse geometry in point cloud. Extensive experiments on 3D classification and segmentation benchmarks demonstrate that KR-MAE achieves state-of-the-art performance, surpassing prior multi-modal methods.

Yijia Guo, Wenkai Huang, Yang Li, Gaolei Li, Hang Zhang, Liwen Hu, Jianhua Li, Tiejun Huang, Lei Ma

3D Gaussian splatting (3DGS) has demonstrated impressive 3D reconstruction performance with explicit scene representations. Given the widespread application of 3DGS in 3D reconstruction and generation tasks, there is an urgent need to protect the copyright of 3DGS assets. However, existing copyright protection techniques for 3DGS overlook the usability of 3D assets, posing challenges for practical deployment. Here we describe splats in splats, the first 3DGS steganography framework that embeds 3D content in 3DGS itself without modifying any attributes. To achieve this, we take a deep insight into spherical harmonics (SH) and devise an importance-graded SH coefficient encryption strategy to embed the hidden SH coefficients. Furthermore, we employ a convolutional autoencoder to establish a mapping between the original Gaussian primitives' opacity and the hidden Gaussian primitives' opacity. Extensive experiments indicate that our method significantly outperforms existing 3D steganography techniques, with 5.31% higher scene fidelity and 3x faster rendering speed, while ensuring security, robustness, and user experience.

Dasith De Silva Edirimuni, Ajmal Saeed Mian

Most 3D scene generation methods are limited to only generating object bounding box parameters while newer diffusion methods also generate class labels and latent features. Using object size or latent feature, they then retrieve objects from a predefined database. For complex scenes of varied, multi-categorical objects, diffusion-based latents cannot be effectively decoded by current autoencoders into the correct point cloud objects which agree with target classes. We introduce a Class-Partitioned Vector Quantized Variational Autoencoder (CPVQ-VAE) that is trained to effectively decode object latent features, by employing a pioneering class-partitioned codebook where codevectors are labeled by class. To address the problem of codebook collapse, we propose a class-aware running average update which reinitializes dead codevectors within each partition. During inference, object features and class labels, both generated by a Latent-space Flow Matching Model (LFMM) designed specifically for scene generation, are consumed by the CPVQ-VAE. The CPVQ-VAE's class-aware inverse look-up then maps generated latents to codebook entries that are decoded to class-specific point cloud shapes. Thereby, we achieve pure point cloud generation without relying on an external objects database for retrieval. Extensive experiments reveal that our method reliably recovers plausible point cloud scenes, with up to 70.4% and 72.3% reduction in Chamfer and Point2Mesh errors on complex living room scenes.

Linrui Dai, Rongzhao Zhang, Yongrui Yu, Xiaofan Zhang

The recently emerging conditional diffusion models seem promising for mitigating the labor and expenses in building large 3D medical imaging datasets. However, previous studies on 3D CT generation primarily focus on specific organs characterized by a local structure and fixed contrast and have yet to fully capitalize on the benefits of both semantic and textual conditions. In this paper, we present GuideGen, a controllable framework based on easily-acquired text prompts to generate anatomical masks and corresponding CT volumes for the entire torso—from chest to pelvis. Our approach includes three core components: a text-conditional semantic synthesizer for creating realistic full-torso anatomies; an anatomy-aware high-dynamic-range (HDR) autoencoder for high-fidelity feature extraction across varying intensity levels; and a latent feature generator that ensures alignment between CT images, anatomical semantics and input prompts. Combined, these components enable data synthesis for segmentation tasks from only textual instructions. To train and evaluate GuideGen, we compile a multi-modality cancer imaging dataset with paired CT and clinical descriptions from 12 public TCIA datasets and one private real-world dataset. Comprehensive evaluations across generation quality, cross-modality alignment, and data usability on multi-organ and tumor segmentation tasks demonstrate GuideGen's superiority over existing CT generation methods.

Yarui Chen, Lehan Hong, Jianlin Shao, Jianning Yang, Tingting Zhao, Yun Liao, Yancui Shi

Variational autoencoder (VAE)-based frameworks possess a natural advantage in modeling the shared and private information inherent in multimodal data. However, current models focus on improving the quality of shared representations from the reconstruction perspective, lacking explicit mechanisms to model their underlying semantic structure. In this paper, we propose the multimodal Gaussian mixture variational autoencoder with consistency regularizations, which introduces a Gaussian mixture prior over the shared latent space to enhance its semantic structure and encourage the formation of cluster-aware latent representations. To address the cross-modal inconsistency problem under missing modality conditions, we propose a cluster-guided regularization strategy that enforces the cross-modal consistency using the pseudo-category labels from unsupervised clustering. Additionally, we design a self-supervised contrastive regularization strategy to align semantically similar representations across modalities. Extensive experiments on MNIST-SVHN and MNIST-CDCB datasets demonstrate that our method significantly outperforms prior state-of-the-art models in generation, classification, and retrieval tasks.

Qinglong Cao, Xirui Li, Ding Wang, Chao Ma, Yuntian Chen, Xiaokang Yang

Video diffusion models have achieved impressive results in natural scene generation, yet they struggle to generalize to scientific phenomena such as fluid simulations and meteorological processes, where underlying dynamics are governed by scientific laws. These tasks pose unique challenges, including severe domain gaps, limited training data, and the lack of descriptive language annotations. To handle this dilemma, we extracted the latent scientific phenomena knowledge and further proposed a fresh framework that teaches video diffusion models to generate scientific phenomena from a single initial frame. Particularly, static knowledge is extracted via pre-trained masked autoencoders, while dynamic knowledge is derived from pre-trained optical flow prediction. Subsequently, based on the aligned spatial relations between the CLIP vision and language encoders, the visual embeddings of scientific phenomena, guided by latent scientific phenomena knowledge, are projected to generate the pseudo-language prompt embeddings in both spatial and frequency domains. By incorporating these prompts and fine-tuning the video diffusion model, we enable the generation of videos that better adhere to scientific laws. Extensive experiments on both computational fluid dynamics simulations and real-world typhoon observations demonstrate the effectiveness of our approach, achieving superior fidelity and consistency across diverse scientific scenarios.

Tianwen Zhu, Guangyu Wu, Zhiwei Cao, Ruihang Wang, Jimin Jia, Yong Luo, Yonggang Wen

Existing battery State of Health (SOH) prediction approaches often struggle to provide both accurate predictions and reliable uncertainty estimates. This paper presents a novel Multi-Task Learning (MTL) framework that jointly tackles SOH prediction and provides a proxy metric for uncertainty through a unified architecture. The framework combines a Physics-Informed Neural Network (PINN) for SOH prediction with a deep autoencoding Gaussian mixture model for uncertainty modeling. Particularly, the energy score from the Gaussian mixture model serves as a proxy metric for uncertainty, where a higher score indicates potential prediction unreliability. Moreover, to enhance task-specific learning, we employ a multi-head attention mechanism that adaptively captures distinct feature relationships. Our experiments show improvements in prediction performance compared to the state-of-the-art baseline. A comprehensive evaluation on six XJTU battery benchmark datasets demonstrates that our framework achieves a prediction accuracy of 99.50% (MAPE: 0.0050) while providing reliable uncertainty quantification through the proxy metric.

Xiangyu Liu, Haodi Lei, Yi Liu, Yang Liu, Wei Hu

Sparse Autoencoder (SAE) has emerged as a powerful tool for mechanistic interpretability of large language models. Recent works apply SAE to protein language models (PLMs), aiming to extract and analyze biologically meaningful features from their latent spaces. However, SAE suffers from semantic entanglement, where individual neurons often mix multiple nonlinear concepts, making it difficult to reliably interpret or manipulate model behaviors. In this paper, we propose a semantically-guided SAE, called ProtSAE. Unlike existing SAE which requires annotation datasets to filter and interpret activations, we guide semantic disentanglement during training using both annotation datasets and domain knowledge to mitigate the effects of entangled attributes. We design interpretability experiments showing that ProtSAE learns more biologically relevant and interpretable hidden features compared to previous methods. Performance analyses further demonstrate that ProtSAE maintains high reconstruction fidelity while achieving better results in interpretable probing. We also show the potential of ProtSAE in steering PLMs for downstream generation tasks.

Yue Ling, Peiqi Zhang, Zhenyi Zhang, Peijie Zhou

Single-cell RNA sequencing (scRNA-seq), especially temporally resolved datasets, enables genome-wide profiling of gene expression dynamics at single-cell resolution across discrete time points. However, current technologies provide only sparse, static snapshots of cell states and are inherently influenced by technical noise, complicating the inference and representation of continuous transcriptional dynamics. Although embedding methods can reduce dimensionality and mitigate technical noise, the majority of existing approaches typically treat trajectory inference separately from embedding construction, often neglecting temporal structure. To address this challenge, here we introduce CellStream, a novel deep learning framework that jointly learns embedding and cellular dynamics from single-cell snapshots data by integrating an autoencoder with unbalanced dynamical optimal transport. Compared to existing methods, CellStream generates dynamics-informed embeddings that robustly capture temporal developmental processes while maintaining high consistency with the underlying data manifold. We demonstrate CellStream’s effectiveness on both simulated datasets and real scRNA-seq data, including spatial transcriptomics. Our experiments indicate significant quantitative improvements over state-of-the-art methods in representing cellular trajectories with enhanced temporal coherence and reduced noise sensitivity. Overall, CellStream provides a new tool for learning and representing continuous streams from the noisy, static snapshots of single-cell gene expression.

Victor Shea-Jay Huang, Le Zhuo, Yi Xin, Zhaokai Wang, Fu-Yun Wang, Yuchi Wang, Renrui Zhang, Peng Gao, Hongsheng Li

Diffusion Transformers (DiTs) are a powerful yet underexplored class of generative models compared to U-Net-based diffusion architectures. We propose TIDE—Temporal-aware sparse autoencoders for Interpretable Diffusion transformErs—a framework designed to extract sparse, interpretable activation features across timesteps in DiTs. TIDE effectively captures temporally-varying representations and reveals that DiTs naturally learn hierarchical semantics (e.g., 3D structure, object class, and fine-grained concepts) during large-scale pretraining. Experiments show that TIDE enhances interpretability and controllability while maintaining reasonable generation quality, enabling applications such as safe image editing and style transfer.

Qiyuan Chen, Ajay Annamareddy, Ying-Fei Li, Dane Morgan, Bu Wang

Disordered materials such as glasses, unlike crystals, lack long‑range atomic order and have no periodic unit cells, yielding a high‑dimensional configuration space with widely varying properties. The complexity not only increases computational costs for atomistic simulations but also makes it difficult for generative AI models to deliver accurate property predictions and realistic structure generation. In this work, we introduce GlassVAE, a hierarchical graph variational autoencoder that uses graph representations to learn compact, translation‑, and permutation‑invariant embeddings of atomic configurations. The resulting structured latent space not only enables efficient generation of novel, physically plausible structures but also supports exploration of the glass energy landscape. To enforce structural realism and physical fidelity, we augment GlassVAE with two physics‑informed regularizers: a radial distribution function (RDF) loss that captures characteristic short‑ and medium‑range ordering and an energy regression loss that reflects the broad configurational energetics. Both theoretical analysis and experimental results highlight the critical impact of these regularizers. By encoding high‑dimensional atomistic data into a compact latent vector and decoding it into structures with accurate energy predictions, GlassVAE provides a fast, physics‑aware path for modeling and designing disordered materials.

Can Zhang, Gim Hee Lee

Existing methods for category-level object articulation from a single 3D observation often rely on dense supervision, multi-frame inputs, or CAD templates, and still struggle to disentangle geometry from articulation or to recover explicit joint parameters. We propose SCAPO , a self-supervised framework that estimates canonical geometry, rigid part segmentation, and joint pivots, axes, and articulation states from a single RGB-D observation without ground-truth labels or category-specific models. Our SCAPO first uses an SE(3)-equivariant vector-neuron autoencoder to factor out global pose and align diverse instances into a shared canonical space. On this aligned shape, a joint-aware blend-skinning module is then designed to model part motion. We learn this representation through cycle reconstruction between observed and canonical shapes and cross-space alignment with a learnable canonical template that decouples shared category geometry from instance-specific residual shape. Experiments on synthetic and real articulated-object datasets show that our SCAPO recovers consistent part structure and accurate articulation parameters and outperforms all self-supervised baselines.

Peter Yongho Kim, Juhyeon Park, Jungwoo Park, Jubin Choi, Jungwoo Seo, Jiook Cha, Taesup Moon

Modeling long-range spatiotemporal dynamics in functional Magnetic Resonance Imaging (fMRI) remains a key challenge due to the high dimensionality of the four-dimensional signals. Prior voxel-based models, although demonstrating excellent performance and interpretation capabilities, are constrained by prohibitive memory demands and thus can only capture limited temporal windows. To address this, we propose TABLeT (Two-dimensionally Autoencoded Brain Latent Transformer), a novel approach that tokenizes fMRI volumes using a pre-trained 2D natural image autoencoder. Each 3D fMRI volume is compressed into a compact set of continuous tokens, enabling long-sequence modeling with a simple Transformer encoder with limited VRAM. Across large-scale benchmarks including the UK-Biobank (UKB), Human Connectome Project (HCP), and ADHD-200 datasets, TABLeT outperforms existing models in multiple tasks, while demonstrating substantial gains in computational and memory efficiency over the state-of-the-art voxel-based method given the same input. Furthermore, we develop a self-supervised masked token modeling approach to pre-train TABLeT, which improves the model's performance for various downstream tasks. Our findings suggest a promising approach for scalable and interpretable spatiotemporal modeling of brain activity. Our code is available at https://github.com/beotborry/TABLeT.

Xiaojie Li, Yang Zhao, Ming Li, Yancheng Zhang, Zonglin Lyu, Yunpeng Chen, Rui Wang, Daquan Zhou

Latent generative modeling has emerged as the dominant paradigm for Diffusion Transformers (DiT), where a pretrained autoencoder compresses image pixels into a latent space to facilitate the diffusion process. Recently, the use of semantic encoders within autoencoders (AEs) has gained attention, yet their influence on image reconstruction and diffusion model training remains insufficiently explored. In this study, we perform an in-depth examination of how semantic encoders shape latent representation learning for the autoencoders. Our findings reveal a fundamental trade-off: while semantic encoders generate latent spaces enriched with visual semantics, their high level of abstraction makes it challenging to capture fine-grained geometric relationships, thereby requiring larger models and longer training for convergence. To address this issue, we build upon recent advances in representation learning that enable the joint modeling of both semantic abstraction and geometric detail. This leads to a Semantic Auto-Encoder (S-AE) that achieves state-of-the-art performance, combining superior reconstruction quality and discriminative capability. Specifically, with S-AE, we are able to provide a unified latent space that achieves 0.06 FID for image reconstruction and 81.9% classification accuracy on ImageNet, set a state-of-the-art benchmark. Codes and model weights will be made publicably available.

Nan An, Long Ma, Tengyu Ma, Zhu Liu, Yingchi Liu, Risheng Liu

The emergence of large generative models has substantially advanced learning-based scene recovery in the synthetic domain. However, these models generalize poorly to real scenarios stemming from the significant distribution gap, alongside poor adaptation to complex and unforeseen degradations. Consequently, it is imperative to develop a real scene adaptation strategy that yields faithful restorations with reliable generalizability. To this end, we propose Bilevel Prompt LoRA, a novel learning paradigm designed to effectively adapt pre-trained generative models for real scene recovery. First, we introduce a self-supervised distribution-fidelity learning scheme to calibrate the autoencoding pathway under task-irrelevant real distributions to improve texture fidelity. Subsequently, a bilevel joint modeling via hyperparameter optimization is further established, empowering robust synthetic-to-real adaptation for both seen and unseen scenes by exploiting the complementary advantages between LoRA and Prompts to foster mutual promotion. Extensive evaluations on diverse real adverse scenarios demonstrate our superiority, with comprehensive algorithm analyses proving our effectiveness.

Rujiao Long, Yang Li, Xingyao Zhang, Weixun Wang, Tianqianjin Lin, Xi Zhao, Yuchi Xu, Wenbo Su, Junchi Yan, Bo Zheng

Exploration capacity shapes both inference-time performance and reinforcement learning (RL) training for large (vision-) language models, as stochastic sampling often yields redundant reasoning paths with little high-level diversity. This paper proposes Reasoning Palette, a novel latent-modulation framework that endows the model with a stochastic latent variable for strategic contextualization, guiding its internal planning prior to token generation. This latent context is inferred from the mean-pooled embedding of a question-answer pair via a variational autoencoder (VAE), where each sampled latent potentially encodes a distinct reasoning context. During inference, a sampled latent is decoded into learnable token prefixes and prepended to the input prompt, modulating the model's internal reasoning trajectory. In this way, the model performs internal sampling over reasoning strategies prior to output generation, which shapes the style and structure of the entire response sequence. A brief supervised fine-tuning (SFT) warm-up phase allows the model to adapt to this latent conditioning. Within RL optimization, Reasoning Palette facilitates structured exploration by enabling on-demand injection for diverse reasoning modes, significantly enhancing exploration efficiency and sustained learning capability. Experiments across multiple reasoning benchmarks demonstrate that our method enables interpretable and controllable control over the (vision-) language model's strategic behavior, thereby achieving consistent performance gains over standard RL methods.

Hao Guo, Liyuan Deng, Yongkang Dai, Ruohan Wang, Jiahao Li, Yunpeng Bai, Yilei Shi

Due to the heterogeneity of faces and edges in B-rep, conventional graph-based representations is incapable of establishing a unified formulation for faces and edges, thereby constraining the capabilities of B-rep generative models. We propose a B-rep Variational Graph Auto Encoding (BrepVGAE), the first variational graph autoencoder framework capable of holistically encoding and decoding boundary representations of B-rep models.Firstly, we novelly represent both geometry faces and edges as nodes in a graph representation. We then design a sparse graph autoencoder to aggregate the complete B-rep structure into a compact global latent vector. We then construct a decoder that employs set-based generation, which uses bilinear layers to reconstruct adjacency relationships, i.e., topology, with a single latent vector. Afterwards, the same decoder generates node features for all faces and edges through learnable query vectors and cross-attention mechanisms. Finally, a two-stage training strategy ensures effective coupling of geometry and topology throughout. Comprehensive experiments demonstrate that BrepVGAE significantly outperforms existing methods in reconstruction accuracy, topological validity, and generative diversity. This validates the feasibility and efficacy of decoding complete CAD geometric-topological distributions from a unified latent representation, while also offering novel insights for CAD part retrieval and feature recognition domains.

Manish Bhurtel, Danda B. Rawat

Semantic segmentation in unstructured environments presents unique challenges due to irregular terrain, occlusions, and complex spatial layouts. While structured settings (e.g., urban scenes) have been widely studied, segmentation in unstructured settings remains relatively underexplored, both in terms of standardized benchmarking and architectural design. In this work, we propose a encoder-decoder based semantic segmentation architecture that integrates a Reduced Masked Autoencoder (RMAE) as the encoder, a Feature-to-Pyramid (F2P) neck, and a novel decoder called ProGRess. The ProGRess decoder introduces Progressive Leapwise Fusion (PLF) for top-down multi-scale fusion of non-contiguous feature maps, a Lightweight Channel Attention gate with Residuals (LCAR) module, and a Bottleneck Feature Fusion (BFF) block for compact refinement. We establish comprehensive baselines by benchmarking state-of-the-art CNN and transformer-based models on challenging unstructured environment datasets viz. RELLIS-3D, it's coarse-grained variant, and RUGD. Our architecture achieves the state-of-the-art performance with 57.41% mIoU on RELLIS-3D, 45.63% mIoU on RUGD, 78.95% mIoU on RELLIS-3DC datasets while maintaining competitive parameter-count and vRAM usage.

Akshay Kulkarni, Tsui-Wei Weng, Vivek Narayanaswamy, Shusen Liu, Wesam A. Sakla, Kowshik Thopalli

Sparse autoencoders (SAEs) promise a unified approach for mechanistic interpretability, concept discovery, and model steering in LLMs and LVLMs. However, realizing this potential requires learned features to be both interpretable and steerable. To that end, we introduce two new computationally inexpensive interpretability and steerability metrics for a systematic analysis of LVLM SAEs. This uncovers two observations; (i) a majority of SAE neurons exhibit either low interpretability or low steerability or both, rendering them ineffective for downstream use; and (ii) user-desired concepts are often absent in the SAE, thus limiting their practical utility. To address these limitations, we propose Concept Bottleneck Sparse Autoencoders (CB-SAE)--a novel post-hoc framework that prunes low-utility neurons and augments the latent space with a lightweight concept bottleneck aligned to a user-defined concept set. The resulting CB-SAE improves interpretability by +32.1% and steerability by +14.5% across LVLMs and image generation tasks.