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.
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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.
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.
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.
Latent Knowledge-Guided Video Diffusion for Scientific Phenomena Generation from a Single Initial Frame
PDF ↗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.
ProtSAE: Disentangling and Interpreting Protein Language Models via Semantically-Guided Sparse Autoencoders
PDF ↗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.
TIDE: Temporal-Aware Sparse Autoencoders for Interpretable Diffusion Transformers in Image Generation
PDF ↗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.
Physical-regularized Hierarchical Generative Model for Metallic Glass Structural Generation and Energy Prediction
PDF ↗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.
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.
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.
Reasoning Palette: Modulating Reasoning via Latent Contextualization for Controllable Exploration for (V)LMs
PDF ↗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.
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.
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.
This paper introduces a novel architecture for trajectory-conditioned forecasting of future 3D scene occupancy. In contrast to methods that rely on variational autoencoders (VAEs) to generate discrete occupancy tokens, which inherently limit representational capacity, our approach predicts multi-frame future occupancy in an end-to-end manner directly from raw image features. Inspired by the success of attention-based transformer architectures in foundational vision and language models such as GPT and VGGT, we employ a sparse occupancy representation that bypasses the intermediate bird's eye view (BEV) projection and its explicit geometric priors. This design allows the transformer to capture spatiotemporal dependencies more effectively. By avoiding both the finite-capacity constraint of discrete tokenization and the structural limitations of BEV representations, our method achieves state-of-the-art performance on the nuScenes benchmark for 1-3 second occupancy forecasting, outperforming existing approaches by a significant margin. Furthermore, it demonstrates robust scene dynamics understanding, consistently delivering high accuracy under arbitrary future trajectory conditioning.
Existing generative models for 3D shapes can synthesize high-fidelity and visually plausible shapes. For certain classes of shapes that have undergone an engineering design process, the realism of the shape is tightly coupled with the underlying physical properties, e.g., aerodynamic efficiency for automobiles. Since existing methods lack knowledge of such physics, they are unable to use this knowledge to enhance the realism of shape generation. Motivated by this, we propose a unified physics-based 3D shape generation pipeline, with a focus on industrial design applications. Specifically, we introduce a new flow matching model with explicit physical guidance, consisting of an alternating update process. We iteratively perform a velocity-based update and a physics-based refinement, progressively adjusting the latent code to align with the desired 3D shapes and physical properties. We further strengthen physical validity by incorporating a physics-aware regularization term into the velocity-based update step. To support such physics-guided updates, we build a shape-and-physics variational autoencoder (SP-VAE) that jointly encodes shape and physics information into a unified latent space. The experiments on three benchmarks show that this synergistic formulation improves shape realism beyond mere visual plausibility. Our code and model weights are available at https://github.com/kasvii/PhysGen.
Video comprises the vast majority of bits that are generated daily, and is the primary signal driving current innovations in robotics, remote sensing, and wearable technology. Yet, the most powerful video understanding models are too expensive for the resource-constrained platforms used in these applications. One approach is to offload inference to the cloud; this gives access to GPUs capable of processing high-resolution videos in real time. But even with reliable, high-bandwidth communication channels, the combined latency of video encoding, model inference, and round-trip communication prohibits use for certain real-time applications. The alternative is to use fully local inference; but this places extreme constraints on computational and power costs, requiring smaller models and lower resolution, leading to degraded accuracy. To address these challenges, we propose DeDelayed, a real-time inference system that divides computation between a remote model operating on delayed video frames and a local model with access to the current frame. The remote model is trained to make predictions on anticipated future frames, which the local model incorporates into its prediction for the current frame. The local and remote models are jointly optimized with an autoencoder that limits the transmission bitrate required by the available downlink communication channel. We evaluate DeDelayed on the task of real-time streaming video segmentation using the BDD100k driving dataset. For a round trip delay of 100 ms, DeDelayed improves performance by 6.4 mIoU compared to fully local inference and 9.8 mIoU compared to remote inference---an equivalent improvement to using a model ten times larger. We release our training code, pretrained models, and python library at https://github.com/InterDigitalInc/dedelayed .
Generating high-fidelity, seamless textures directly on 3D surfaces, a process we term 3D-native texturing, is a fundamental open challenge, promising to overcome the limitations of traditional UV-based and multi-view projection methods. While promising, existing native approaches are bottlenecked by the lack of a powerful and versatile latent representation, severely limiting the fidelity of generated results. In this work, we identify this representation gap as the central roadblock to progress. We introduce Lafite, a framework that resolves this challenge by learning to generate textures as a 3D generative sparse latent color field. At its core, Lafite leverages a variational autoencoder (VAE) to encode complex surface appearance into a sparse, structured latent space and then decoded into a continuous color field. This novel representation achieves unprecedented fidelity, i.e., yielding a >10 dB PSNR improvement in reconstruction over state-of-the-art methods, by effectively disentangling texture from mesh topology and UV parameterizations. Building on this superior representation, a conditional rectified flow model synthesizes textures with state-of-the-art quality and coherence. Extensive experiments show that Lafite not only sets a new standard for native texturing but also enables flexible downstream applications like editing and material synthesis, paving the way for the next generation of 3D content creation workflows.
Nestwork: Conditional 3D Furnished House Layout Generation through Latent Heterogeneous Graph Diffusion
PDF ↗This paper introduces Nestwork, a unified latent-diffusion framework for conditional 3D furnished house layout generation using a heterogeneous graph of rooms and furniture. Designing reasonable and controllable 3D layouts that reflect the underlying semantic structure of a house is a key challenge in AI-assisted architectural design. Existing graph-based methods either produce unfurnished multi-room layouts or generate furnished scenes one room at a time, preventing joint reasoning over room structure and furniture placement. Nestwork represents an entire house as a heterogeneous graph with typed room and furniture nodes and multiple spatial relations. A single unconditional autoencoder based on a heterogeneous graph attention network embeds this graph into a compact latent space, and a low-rank relational field compensates for missing geometric edge information at test time. A diffusion denoiser is trained once using random masking, enabling the same model to operate under different conditioning strengths, from topology-only to fully annotated graphs. Multi-level conditioning combines masked node-level attention with graph-level embeddings to support flexible user control, including layouts specified through natural-language descriptions. Experiments on the 3D-FRONT dataset show that Nestwork achieves high fidelity, structural consistency, and diversity. Controlled ablations further validate the contributions of each component.
Dual-Level Hypergraph Generation for Addressing Feature Scarcity in Whole-Slide Image Classification
PDF ↗Lymph node metastasis diagnosis in pathological images is a highly challenging four-class classification task, comprising macrometastasis, micrometastasis, isolated tumor cells (ITC), and negative lesions.Unlike conventional classification settings, this four-class scenario simultaneously suffers from inter-class and intra-slide scarcity of minority information.Existing approaches based on CNNs or GNNs primarily emphasize node-level feature learning, making it difficult to capture high-order feature interactions and topological dependencies among cells, while also overlooking the representational insufficiency induced by class scarcity.To address these challenges, we propose a dual-level generative framework that integrates class-prompt priors with high-order structural modeling to enhance the representation capacity of minority classes.At the hypergraph level, we develop a prompt-guided hierarchical hypergraph variational autoencoder (HGVAE) capable of generating diverse and topologically consistent hypergraph representations for minority classes.At the hypernode level, we introduce an anchor-diffusion mixup strategy to enrich the minority node features of high-attention positive anchor nodes.Extensive experiments on the four-class NIMM dataset, as well as TCGA datasets, demonstrate that the proposed framework effectively alleviates feature scarcity and significantly boosts the classification performance of minority classes.
Latent-space modeling has been the standard for Diffusion Transformers (DiTs). However, it relies on a two-stage pipeline where the pretrained autoencoder introduces lossy reconstruction, leading to error accumulation while hindering joint optimization. To address these issues, we propose PixelDiT, a single-stage, end-to-end model that eliminates the need for the autoencoder and learns the diffusion process directly in the pixel space. PixelDiT adopts a fully transformer-based architecture shaped by a dual-level design: a patch-level DiT that captures global semantics and a pixel-level DiT that refines texture details, enabling efficient training of a pixel-space diffusion model while preserving fine details. PixelDiT achieves 1.61 FID on ImageNet 256 and 1.81 FID on ImageNet 512, surpassing existing pixel generative models by a large margin. We further extend PixelDiT to text-to-image generation and pretrain it at the 1024^ 2 resolution in pixel space. It achieves 0.74 on GenEval and 83.5 on DPG-bench, approaching the best latent diffusion models.