Daily Papers

Conformational ensembles of protein structures are immensely important both for understanding protein function and drug discovery in novel modalities such as cryptic pockets. Current techniques for sampling ensembles such as molecular dynamics (MD) are computationally inefficient, while many recent machine learning methods do not transfer to systems outside their training data. We propose JAMUN which performs MD in a smoothed, noised space of all-atom 3D conformations of molecules by utilizing the framework of walk-jump sampling. JAMUN enables ensemble generation for small peptides at rates of an order of magnitude faster than traditional molecular dynamics. The physical priors in JAMUN enables transferability to systems outside of its training data, even to peptides that are longer than those originally trained on. Our model, code and weights are available at https://github.com/prescient-design/jamun.

Recent advances in generative modeling have enabled significant progress in structure-based drug design (SBDD). Existing methods typically condition molecule generation on empty binding pockets from holo complexes, overlooking informative components such as the filler (ligands and solvent). Here, we leverage low-resolution electron density (ED) derived from the filler as a physically grounded condition for de novo drug design. We consider two types of ED, calculated and cryo-EM/X-ray, obtainable from computational or experimental sources, supporting unified pre-training and experimental integration. Compared with rigid pocket representations, experimental ED naturally captures conformational flexibility and provides a more faithful description of the binding environment. Based on this, we introduce EDMolGPT, a decoder-only autoregressive framework that generates molecules from low-resolution ED point clouds. By grounding generation in physically meaningful density signals, EDMolGPT mitigates structural bias and produces molecules with 3D conformations. Evaluations on 101 biological targets verify the effectiveness. Our project page: https://jiahaochen1.github.io/EDMolGPT_Page/.

Recent advances in fast sampling methods for diffusion models have demonstrated significant potential to accelerate generation on image modalities. We apply these methods to 3-dimensional molecular conformations by building on the recently introduced GeoLDM equivariant latent diffusion model (Xu et al., 2023). We evaluate trade-offs between speed gains and quality loss, as measured by molecular conformation structural stability. We introduce Equivariant Latent Progressive Distillation, a fast sampling algorithm that preserves geometric equivariance and accelerates generation from latent diffusion models. Our experiments demonstrate up to 7.5x gains in sampling speed with limited degradation in molecular stability. These results suggest this accelerated sampling method has strong potential for high-throughput in silico molecular conformations screening in computational biochemistry, drug discovery, and life sciences applications.

Recent developments in deep learning have made remarkable progress in speeding up the prediction of quantum chemical (QC) properties by removing the need for expensive electronic structure calculations like density functional theory. However, previous methods learned from 1D SMILES sequences or 2D molecular graphs failed to achieve high accuracy as QC properties primarily depend on the 3D equilibrium conformations optimized by electronic structure methods, far different from the sequence-type and graph-type data. In this paper, we propose a novel approach called Uni-Mol+ to tackle this challenge. Uni-Mol+ first generates a raw 3D molecule conformation from inexpensive methods such as RDKit. Then, the raw conformation is iteratively updated to its target DFT equilibrium conformation using neural networks, and the learned conformation will be used to predict the QC properties. To effectively learn this update process towards the equilibrium conformation, we introduce a two-track Transformer model backbone and train it with the QC property prediction task. We also design a novel approach to guide the model's training process. Our extensive benchmarking results demonstrate that the proposed Uni-Mol+ significantly improves the accuracy of QC property prediction in various datasets. We have made the code and model publicly available at https://github.com/dptech-corp/Uni-Mol.

Generating novel active molecules for a given protein is an extremely challenging task for generative models that requires an understanding of the complex physical interactions between the molecule and its environment. In this paper, we present a novel generative model, BindGPT which uses a conceptually simple but powerful approach to create 3D molecules within the protein's binding site. Our model produces molecular graphs and conformations jointly, eliminating the need for an extra graph reconstruction step. We pretrain BindGPT on a large-scale dataset and fine-tune it with reinforcement learning using scores from external simulation software. We demonstrate how a single pretrained language model can serve at the same time as a 3D molecular generative model, conformer generator conditioned on the molecular graph, and a pocket-conditioned 3D molecule generator. Notably, the model does not make any representational equivariance assumptions about the domain of generation. We show how such simple conceptual approach combined with pretraining and scaling can perform on par or better than the current best specialized diffusion models, language models, and graph neural networks while being two orders of magnitude cheaper to sample.

Deep generative models are rapidly advancing structure-based drug design, offering substantial promise for generating small molecule ligands that bind to specific protein targets. However, most current approaches assume a rigid protein binding pocket, neglecting the intrinsic flexibility of proteins and the conformational rearrangements induced by ligand binding, limiting their applicability in practical drug discovery. Here, we propose Apo2Mol, a diffusion-based generative framework for 3D molecule design that explicitly accounts for conformational flexibility in protein binding pockets. To support this, we curate a dataset of over 24,000 experimentally resolved apo-holo structure pairs from the Protein Data Bank, enabling the characterization of protein structure changes associated with ligand binding. Apo2Mol employs a full-atom hierarchical graph-based diffusion model that simultaneously generates 3D ligand molecules and their corresponding holo pocket conformations from input apo states. Empirical studies demonstrate that Apo2Mol can achieve state-of-the-art performance in generating high-affinity ligands and accurately capture realistic protein pocket conformational changes.

Denoising diffusion models have shown great potential in multiple research areas. Existing diffusion-based generative methods on de novo 3D molecule generation face two major challenges. Since majority heavy atoms in molecules allow connections to multiple atoms through single bonds, solely using pair-wise distance to model molecule geometries is insufficient. Therefore, the first one involves proposing an effective neural network as the denoising kernel that is capable to capture complex multi-body interatomic relationships and learn high-quality features. Due to the discrete nature of graphs, mainstream diffusion-based methods for molecules heavily rely on predefined rules and generate edges in an indirect manner. The second challenge involves accommodating molecule generation to diffusion and accurately predicting the existence of bonds. In our research, we view the iterative way of updating molecule conformations in diffusion process is consistent with molecular dynamics and introduce a novel molecule generation method named Geometric-Facilitated Molecular Diffusion (GFMDiff). For the first challenge, we introduce a Dual-Track Transformer Network (DTN) to fully excevate global spatial relationships and learn high quality representations which contribute to accurate predictions of features and geometries. As for the second challenge, we design Geometric-Facilitated Loss (GFLoss) which intervenes the formation of bonds during the training period, instead of directly embedding edges into the latent space. Comprehensive experiments on current benchmarks demonstrate the superiority of GFMDiff.

Molecular Representation Learning (MRL) has proven impactful in numerous biochemical applications such as drug discovery and enzyme design. While Graph Neural Networks (GNNs) are effective at learning molecular representations from a 2D molecular graph or a single 3D structure, existing works often overlook the flexible nature of molecules, which continuously interconvert across conformations via chemical bond rotations and minor vibrational perturbations. To better account for molecular flexibility, some recent works formulate MRL as an ensemble learning problem, focusing on explicitly learning from a set of conformer structures. However, most of these studies have limited datasets, tasks, and models. In this work, we introduce the first MoleculAR Conformer Ensemble Learning (MARCEL) benchmark to thoroughly evaluate the potential of learning on conformer ensembles and suggest promising research directions. MARCEL includes four datasets covering diverse molecule- and reaction-level properties of chemically diverse molecules including organocatalysts and transition-metal catalysts, extending beyond the scope of common GNN benchmarks that are confined to drug-like molecules. In addition, we conduct a comprehensive empirical study, which benchmarks representative 1D, 2D, and 3D molecular representation learning models, along with two strategies that explicitly incorporate conformer ensembles into 3D MRL models. Our findings reveal that direct learning from an accessible conformer space can improve performance on a variety of tasks and models.

Molecular pretrained representations (MPR) has emerged as a powerful approach for addressing the challenge of limited supervised data in applications such as drug discovery and material design. While early MPR methods relied on 1D sequences and 2D graphs, recent advancements have incorporated 3D conformational information to capture rich atomic interactions. However, these prior models treat molecules merely as discrete atom sets, overlooking the space surrounding them. We argue from a physical perspective that only modeling these discrete points is insufficient. We first present a simple yet insightful observation: naively adding randomly sampled virtual points beyond atoms can surprisingly enhance MPR performance. In light of this, we propose a principled framework that incorporates the entire 3D space spanned by molecules. We implement the framework via a novel Transformer-based architecture, dubbed SpaceFormer, with three key components: (1) grid-based space discretization; (2) grid sampling/merging; and (3) efficient 3D positional encoding. Extensive experiments show that SpaceFormer significantly outperforms previous 3D MPR models across various downstream tasks with limited data, validating the benefit of leveraging the additional 3D space beyond atoms in MPR models.

In this paper we tackle the problem of generating conformers of a molecule in 3D space given its molecular graph. We parameterize these conformers as continuous functions that map elements from the molecular graph to points in 3D space. We then formulate the problem of learning to generate conformers as learning a distribution over these functions using a diffusion generative model, called Molecular Conformer Fields (MCF). Our approach is simple and scalable, and achieves state-of-the-art performance on challenging molecular conformer generation benchmarks while making no assumptions about the explicit structure of molecules (e.g. modeling torsional angles). MCF represents an advance in extending diffusion models to handle complex scientific problems in a conceptually simple, scalable and effective manner.

We introduce Suiren-1.0, a family of molecular foundation models for the accurate modeling of diverse organic systems. Suiren-1.0 comprising three specialized variants (Suiren-Base, Suiren-Dimer, and Suiren-ConfAvg) is integrated within an algorithmic framework that bridges the gap between 3D conformational geometry and 2D statistical ensemble spaces. We first pre-train Suiren-Base (1.8B parameters) on a 70M-sample Density Functional Theory dataset using spatial self-supervision and SE(3)-equivariant architectures, achieving robust performance in quantum property prediction. Suiren-Dimer extends this capability through continued pre-training on 13.5M intermolecular interaction samples. To enable efficient downstream application, we propose Conformation Compression Distillation (CCD), a diffusion-based framework that distills complex 3D structural representations into 2D conformation-averaged representations. This yields the lightweight Suiren-ConfAvg, which generates high-fidelity representations from SMILES or molecular graphs. Our extensive evaluations demonstrate that Suiren-1.0 establishes state-of-the-art results across a range of tasks. All models and benchmarks are open-sourced.

Graph neural networks are emerging as promising methods for modeling molecular graphs, in which nodes and edges correspond to atoms and chemical bonds, respectively. Recent studies show that when 3D molecular geometries, such as bond lengths and angles, are available, molecular property prediction tasks can be made more accurate. However, computing of 3D molecular geometries requires quantum calculations that are computationally prohibitive. For example, accurate calculation of 3D geometries of a small molecule requires hours of computing time using density functional theory (DFT). Here, we propose to predict the ground-state 3D geometries from molecular graphs using machine learning methods. To make this feasible, we develop a benchmark, known as Molecule3D, that includes a dataset with precise ground-state geometries of approximately 4 million molecules derived from DFT. We also provide a set of software tools for data processing, splitting, training, and evaluation, etc. Specifically, we propose to assess the error and validity of predicted geometries using four metrics. We implement two baseline methods that either predict the pairwise distance between atoms or atom coordinates in 3D space. Experimental results show that, compared with generating 3D geometries with RDKit, our method can achieve comparable prediction accuracy but with much smaller computational costs. Our Molecule3D is available as a module of the MoleculeX software library (https://github.com/divelab/MoleculeX).

High-quality molecular representations are essential for property prediction and molecular design, yet large labeled datasets remain scarce. While self-supervised pretraining on molecular graphs has shown promise, many existing approaches either depend on hand-crafted augmentations or complex generative objectives, and often rely solely on 2D topology, leaving valuable 3D structural information underutilized. To address this gap, we introduce C-FREE (Contrast-Free Representation learning on Ego-nets), a simple framework that integrates 2D graphs with ensembles of 3D conformers. C-FREE learns molecular representations by predicting subgraph embeddings from their complementary neighborhoods in the latent space, using fixed-radius ego-nets as modeling units across different conformers. This design allows us to integrate both geometric and topological information within a hybrid Graph Neural Network (GNN)-Transformer backbone, without negatives, positional encodings, or expensive pre-processing. Pretraining on the GEOM dataset, which provides rich 3D conformational diversity, C-FREE achieves state-of-the-art results on MoleculeNet, surpassing contrastive, generative, and other multimodal self-supervised methods. Fine-tuning across datasets with diverse sizes and molecule types further demonstrates that pretraining transfers effectively to new chemical domains, highlighting the importance of 3D-informed molecular representations.

Molecules are frequently represented as graphs, but the underlying 3D molecular geometry (the locations of the atoms) ultimately determines most molecular properties. However, most molecules are not static and at room temperature adopt a wide variety of geometries or conformations. The resulting distribution on geometries p(x) is known as the Boltzmann distribution, and many molecular properties are expectations computed under this distribution. Generating accurate samples from the Boltzmann distribution is therefore essential for computing these expectations accurately. Traditional sampling-based methods are computationally expensive, and most recent machine learning-based methods have focused on identifying modes in this distribution rather than generating true samples. Generating such samples requires capturing conformational variability, and it has been widely recognized that the majority of conformational variability in molecules arises from rotatable bonds. In this work, we present VonMisesNet, a new graph neural network that captures conformational variability via a variational approximation of rotatable bond torsion angles as a mixture of von Mises distributions. We demonstrate that VonMisesNet can generate conformations for arbitrary molecules in a way that is both physically accurate with respect to the Boltzmann distribution and orders of magnitude faster than existing sampling methods.

Multimodal molecular models often suffer from 3D conformer unreliability and modality collapse, limiting their robustness and generalization. We propose MuMo, a structured multimodal fusion framework that addresses these challenges in molecular representation through two key strategies. To reduce the instability of conformer-dependent fusion, we design a Structured Fusion Pipeline (SFP) that combines 2D topology and 3D geometry into a unified and stable structural prior. To mitigate modality collapse caused by naive fusion, we introduce a Progressive Injection (PI) mechanism that asymmetrically integrates this prior into the sequence stream, preserving modality-specific modeling while enabling cross-modal enrichment. Built on a state space backbone, MuMo supports long-range dependency modeling and robust information propagation. Across 29 benchmark tasks from Therapeutics Data Commons (TDC) and MoleculeNet, MuMo achieves an average improvement of 2.7% over the best-performing baseline on each task, ranking first on 22 of them, including a 27% improvement on the LD50 task. These results validate its robustness to 3D conformer noise and the effectiveness of multimodal fusion in molecular representation. The code is available at: github.com/selmiss/MuMo.

We present a computational framework that transforms single images into 3D physical objects. The visual geometry of a physical object in an image is determined by three orthogonal attributes: mechanical properties, external forces, and rest-shape geometry. Existing single-view 3D reconstruction methods often overlook this underlying composition, presuming rigidity or neglecting external forces. Consequently, the reconstructed objects fail to withstand real-world physical forces, resulting in instability or undesirable deformation -- diverging from their intended designs as depicted in the image. Our optimization framework addresses this by embedding physical compatibility into the reconstruction process. We explicitly decompose the three physical attributes and link them through static equilibrium, which serves as a hard constraint, ensuring that the optimized physical shapes exhibit desired physical behaviors. Evaluations on a dataset collected from Objaverse demonstrate that our framework consistently enhances the physical realism of 3D models over existing methods. The utility of our framework extends to practical applications in dynamic simulations and 3D printing, where adherence to physical compatibility is paramount.

3D molecule generation is crucial for drug discovery and material science, requiring models to process complex multi-modalities, including atom types, chemical bonds, and 3D coordinates. A key challenge is integrating these modalities of different shapes while maintaining SE(3) equivariance for 3D coordinates. To achieve this, existing approaches typically maintain separate latent spaces for invariant and equivariant modalities, reducing efficiency in both training and sampling. In this work, we propose Unified Variational Auto-Encoder for 3D Molecular Latent Diffusion Modeling (UAE-3D), a multi-modal VAE that compresses 3D molecules into latent sequences from a unified latent space, while maintaining near-zero reconstruction error. This unified latent space eliminates the complexities of handling multi-modality and equivariance when performing latent diffusion modeling. We demonstrate this by employing the Diffusion Transformer--a general-purpose diffusion model without any molecular inductive bias--for latent generation. Extensive experiments on GEOM-Drugs and QM9 datasets demonstrate that our method significantly establishes new benchmarks in both de novo and conditional 3D molecule generation, achieving leading efficiency and quality.

Processing information on 3D objects requires methods stable to rigid-body transformations, in particular rotations, of the input data. In image processing tasks, convolutional neural networks achieve this property using rotation-equivariant operations. However, contrary to images, graphs generally have irregular topology. This makes it challenging to define a rotation-equivariant convolution operation on these structures. In this work, we propose Spherical Graph Convolutional Network (S-GCN) that processes 3D models of proteins represented as molecular graphs. In a protein molecule, individual amino acids have common topological elements. This allows us to unambiguously associate each amino acid with a local coordinate system and construct rotation-equivariant spherical filters that operate on angular information between graph nodes. Within the framework of the protein model quality assessment problem, we demonstrate that the proposed spherical convolution method significantly improves the quality of model assessment compared to the standard message-passing approach. It is also comparable to state-of-the-art methods, as we demonstrate on Critical Assessment of Structure Prediction (CASP) benchmarks. The proposed technique operates only on geometric features of protein 3D models. This makes it universal and applicable to any other geometric-learning task where the graph structure allows constructing local coordinate systems.

Computational methods that operate on three-dimensional molecular structure have the potential to solve important questions in biology and chemistry. In particular, deep neural networks have gained significant attention, but their widespread adoption in the biomolecular domain has been limited by a lack of either systematic performance benchmarks or a unified toolkit for interacting with molecular data. To address this, we present ATOM3D, a collection of both novel and existing benchmark datasets spanning several key classes of biomolecules. We implement several classes of three-dimensional molecular learning methods for each of these tasks and show that they consistently improve performance relative to methods based on one- and two-dimensional representations. The specific choice of architecture proves to be critical for performance, with three-dimensional convolutional networks excelling at tasks involving complex geometries, graph networks performing well on systems requiring detailed positional information, and the more recently developed equivariant networks showing significant promise. Our results indicate that many molecular problems stand to gain from three-dimensional molecular learning, and that there is potential for improvement on many tasks which remain underexplored. To lower the barrier to entry and facilitate further developments in the field, we also provide a comprehensive suite of tools for dataset processing, model training, and evaluation in our open-source atom3d Python package. All datasets are available for download from https://www.atom3d.ai .

We consider the problem of antibody sequence design given 3D structural information. Building on previous work, we propose a fine-tuned inverse folding model that is specifically optimised for antibody structures and outperforms generic protein models on sequence recovery and structure robustness when applied on antibodies, with notable improvement on the hypervariable CDR-H3 loop. We study the canonical conformations of complementarity-determining regions and find improved encoding of these loops into known clusters. Finally, we consider the applications of our model to drug discovery and binder design and evaluate the quality of proposed sequences using physics-based methods.

Although recent 3D-native generators have made great progress in synthesizing reliable geometry, they still fall short in achieving realistic appearances. A key obstacle lies in the lack of diverse and high-quality real-world 3D assets with rich texture details, since capturing such data is intrinsically difficult due to the diverse scales of scenes, non-rigid motions of objects, and the limited precision of 3D scanners. We introduce Photo3D, a framework for advancing photorealistic 3D generation, which is driven by the image data generated by the GPT-4o-Image model. Considering that the generated images can distort 3D structures due to their lack of multi-view consistency, we design a structure-aligned multi-view synthesis pipeline and construct a detail-enhanced multi-view dataset paired with 3D geometry. Building on it, we present a realistic detail enhancement scheme that leverages perceptual feature adaptation and semantic structure matching to enforce appearance consistency with realistic details while preserving the structural consistency with the 3D-native geometry. Our scheme is general to different 3D-native generators, and we present dedicated training strategies to facilitate the optimization of geometry-texture coupled and decoupled 3D-native generation paradigms. Experiments demonstrate that Photo3D generalizes well across diverse 3D-native generation paradigms and achieves state-of-the-art photorealistic 3D generation performance.

The application of language models (LMs) to molecular structure generation using line notations such as SMILES and SELFIES has been well-established in the field of cheminformatics. However, extending these models to generate 3D molecular structures presents significant challenges. Two primary obstacles emerge: (1) the difficulty in designing a 3D line notation that ensures SE(3)-invariant atomic coordinates, and (2) the non-trivial task of tokenizing continuous coordinates for use in LMs, which inherently require discrete inputs. To address these challenges, we propose Mol-StrucTok, a novel method for tokenizing 3D molecular structures. Our approach comprises two key innovations: (1) We design a line notation for 3D molecules by extracting local atomic coordinates in a spherical coordinate system. This notation builds upon existing 2D line notations and remains agnostic to their specific forms, ensuring compatibility with various molecular representation schemes. (2) We employ a Vector Quantized Variational Autoencoder (VQ-VAE) to tokenize these coordinates, treating them as generation descriptors. To further enhance the representation, we incorporate neighborhood bond lengths and bond angles as understanding descriptors. Leveraging this tokenization framework, we train a GPT-2 style model for 3D molecular generation tasks. Results demonstrate strong performance with significantly faster generation speeds and competitive chemical stability compared to previous methods. Further, by integrating our learned discrete representations into Graphormer model for property prediction on QM9 dataset, Mol-StrucTok reveals consistent improvements across various molecular properties, underscoring the versatility and robustness of our approach.

Accurately modeling protein 3D structure is essential for the design of functional proteins. An important sub-task of structure modeling is protein side-chain packing: predicting the conformation of side-chains (rotamers) given the protein's backbone structure and amino-acid sequence. Conventional approaches for this task rely on expensive sampling procedures over hand-crafted energy functions and rotamer libraries. Recently, several deep learning methods have been developed to tackle the problem in a data-driven way, albeit with vastly different formulations (from image-to-image translation to directly predicting atomic coordinates). Here, we frame the problem as a joint regression over the side-chains' true degrees of freedom: the dihedral chi angles. We carefully study possible objective functions for this task, while accounting for the underlying symmetries of the task. We propose Holographic Packer (H-Packer), a novel two-stage algorithm for side-chain packing built on top of two light-weight rotationally equivariant neural networks. We evaluate our method on CASP13 and CASP14 targets. H-Packer is computationally efficient and shows favorable performance against conventional physics-based algorithms and is competitive against alternative deep learning solutions.

Obtaining the desired effect of drugs is highly dependent on their molecular geometries. Thus, the current prevailing paradigm focuses on 3D point-cloud atom representations, utilizing graph neural network (GNN) parametrizations, with rotational symmetries baked in via E(3) invariant layers. We prove that such models must necessarily disregard chirality, a geometric property of the molecules that cannot be superimposed on their mirror image by rotation and translation. Chirality plays a key role in determining drug safety and potency. To address this glaring issue, we introduce a novel field-based representation, proposing reference rotations that replace rotational symmetry constraints. The proposed model captures all molecular geometries including chirality, while still achieving highly competitive performance with E(3)-based methods across standard benchmarking metrics.

Generative models, especially diffusion models (DMs), have achieved promising results for generating feature-rich geometries and advancing foundational science problems such as molecule design. Inspired by the recent huge success of Stable (latent) Diffusion models, we propose a novel and principled method for 3D molecule generation named Geometric Latent Diffusion Models (GeoLDM). GeoLDM is the first latent DM model for the molecular geometry domain, composed of autoencoders encoding structures into continuous latent codes and DMs operating in the latent space. Our key innovation is that for modeling the 3D molecular geometries, we capture its critical roto-translational equivariance constraints by building a point-structured latent space with both invariant scalars and equivariant tensors. Extensive experiments demonstrate that GeoLDM can consistently achieve better performance on multiple molecule generation benchmarks, with up to 7\% improvement for the valid percentage of large biomolecules. Results also demonstrate GeoLDM's higher capacity for controllable generation thanks to the latent modeling. Code is provided at https://github.com/MinkaiXu/GeoLDM.

It is inherently ambiguous to lift 2D results from pre-trained diffusion models to a 3D world for text-to-3D generation. 2D diffusion models solely learn view-agnostic priors and thus lack 3D knowledge during the lifting, leading to the multi-view inconsistency problem. We find that this problem primarily stems from geometric inconsistency, and avoiding misplaced geometric structures substantially mitigates the problem in the final outputs. Therefore, we improve the consistency by aligning the 2D geometric priors in diffusion models with well-defined 3D shapes during the lifting, addressing the vast majority of the problem. This is achieved by fine-tuning the 2D diffusion model to be viewpoint-aware and to produce view-specific coordinate maps of canonically oriented 3D objects. In our process, only coarse 3D information is used for aligning. This "coarse" alignment not only resolves the multi-view inconsistency in geometries but also retains the ability in 2D diffusion models to generate detailed and diversified high-quality objects unseen in the 3D datasets. Furthermore, our aligned geometric priors (AGP) are generic and can be seamlessly integrated into various state-of-the-art pipelines, obtaining high generalizability in terms of unseen shapes and visual appearance while greatly alleviating the multi-view inconsistency problem. Our method represents a new state-of-the-art performance with an 85+% consistency rate by human evaluation, while many previous methods are around 30%. Our project page is https://sweetdreamer3d.github.io/

3D shape generation aims to produce innovative 3D content adhering to specific conditions and constraints. Existing methods often decompose 3D shapes into a sequence of localized components, treating each element in isolation without considering spatial consistency. As a result, these approaches exhibit limited versatility in 3D data representation and shape generation, hindering their ability to generate highly diverse 3D shapes that comply with the specified constraints. In this paper, we introduce a novel spatial-aware 3D shape generation framework that leverages 2D plane representations for enhanced 3D shape modeling. To ensure spatial coherence and reduce memory usage, we incorporate a hybrid shape representation technique that directly learns a continuous signed distance field representation of the 3D shape using orthogonal 2D planes. Additionally, we meticulously enforce spatial correspondences across distinct planes using a transformer-based autoencoder structure, promoting the preservation of spatial relationships in the generated 3D shapes. This yields an algorithm that consistently outperforms state-of-the-art 3D shape generation methods on various tasks, including unconditional shape generation, multi-modal shape completion, single-view reconstruction, and text-to-shape synthesis.

3D vector graphics play a crucial role in various applications including 3D shape retrieval, conceptual design, and virtual reality interactions due to their ability to capture essential structural information with minimal representation. While recent approaches have shown promise in generating 3D vector graphics, they often suffer from lengthy processing times and struggle to maintain view consistency. To address these limitations, we propose ViewCraft3D (VC3D), an efficient method that leverages 3D priors to generate 3D vector graphics. Specifically, our approach begins with 3D object analysis, employs a geometric extraction algorithm to fit 3D vector graphics to the underlying structure, and applies view-consistent refinement process to enhance visual quality. Our comprehensive experiments demonstrate that VC3D outperforms previous methods in both qualitative and quantitative evaluations, while significantly reducing computational overhead. The resulting 3D sketches maintain view consistency and effectively capture the essential characteristics of the original objects.

Topological data analysis (TDA) is an area of data science that focuses on using invariants from algebraic topology to provide multiscale shape descriptors for geometric data sets such as point clouds. One of the most important such descriptors is {\em persistent homology}, which encodes the change in shape as a filtration parameter changes; a typical parameter is the feature scale. For many data sets, it is useful to simultaneously vary multiple filtration parameters, for example feature scale and density. While the theoretical properties of single parameter persistent homology are well understood, less is known about the multiparameter case. In particular, a central question is the problem of representing multiparameter persistent homology by elements of a vector space for integration with standard machine learning algorithms. Existing approaches to this problem either ignore most of the multiparameter information to reduce to the one-parameter case or are heuristic and potentially unstable in the face of noise. In this article, we introduce a new general representation framework that leverages recent results on {\em decompositions} of multiparameter persistent homology. This framework is rich in information, fast to compute, and encompasses previous approaches. Moreover, we establish theoretical stability guarantees under this framework as well as efficient algorithms for practical computation, making this framework an applicable and versatile tool for analyzing geometric and point cloud data. We validate our stability results and algorithms with numerical experiments that demonstrate statistical convergence, prediction accuracy, and fast running times on several real data sets.

We introduce a new generative model that combines latent diffusion with persistent homology to create 3D shapes with high diversity, with a special emphasis on their topological characteristics. Our method involves representing 3D shapes as implicit fields, then employing persistent homology to extract topological features, including Betti numbers and persistence diagrams. The shape generation process consists of two steps. Initially, we employ a transformer-based autoencoding module to embed the implicit representation of each 3D shape into a set of latent vectors. Subsequently, we navigate through the learned latent space via a diffusion model. By strategically incorporating topological features into the diffusion process, our generative module is able to produce a richer variety of 3D shapes with different topological structures. Furthermore, our framework is flexible, supporting generation tasks constrained by a variety of inputs, including sparse and partial point clouds, as well as sketches. By modifying the persistence diagrams, we can alter the topology of the shapes generated from these input modalities.

The design of novel protein structures remains a challenge in protein engineering for applications across biomedicine and chemistry. In this line of work, a diffusion model over rigid bodies in 3D (referred to as frames) has shown success in generating novel, functional protein backbones that have not been observed in nature. However, there exists no principled methodological framework for diffusion on SE(3), the space of orientation preserving rigid motions in R3, that operates on frames and confers the group invariance. We address these shortcomings by developing theoretical foundations of SE(3) invariant diffusion models on multiple frames followed by a novel framework, FrameDiff, for learning the SE(3) equivariant score over multiple frames. We apply FrameDiff on monomer backbone generation and find it can generate designable monomers up to 500 amino acids without relying on a pretrained protein structure prediction network that has been integral to previous methods. We find our samples are capable of generalizing beyond any known protein structure.

When manipulating three-dimensional data, it is possible to ensure that rotational and translational symmetries are respected by applying so-called SE(3)-equivariant models. Protein structure prediction is a prominent example of a task which displays these symmetries. Recent work in this area has successfully made use of an SE(3)-equivariant model, applying an iterative SE(3)-equivariant attention mechanism. Motivated by this application, we implement an iterative version of the SE(3)-Transformer, an SE(3)-equivariant attention-based model for graph data. We address the additional complications which arise when applying the SE(3)-Transformer in an iterative fashion, compare the iterative and single-pass versions on a toy problem, and consider why an iterative model may be beneficial in some problem settings. We make the code for our implementation available to the community.

Textured 3D morphing seeks to generate smooth and plausible transitions between two 3D assets, preserving both structural coherence and fine-grained appearance. This ability is crucial not only for advancing 3D generation research but also for practical applications in animation, editing, and digital content creation. Existing approaches either operate directly on geometry, limiting them to shape-only morphing while neglecting textures, or extend 2D interpolation strategies into 3D, which often causes semantic ambiguity, structural misalignment, and texture blurring. These challenges underscore the necessity to jointly preserve geometric consistency, texture alignment, and robustness throughout the transition process. To address this, we propose Interp3D, a novel training-free framework for textured 3D morphing. It harnesses generative priors and adopts a progressive alignment principle to ensure both geometric fidelity and texture coherence. Starting from semantically aligned interpolation in condition space, Interp3D enforces structural consistency via SLAT (Structured Latent)-guided structure interpolation, and finally transfers appearance details through fine-grained texture fusion. For comprehensive evaluations, we construct a dedicated dataset, Interp3DData, with graded difficulty levels and assess generation results from fidelity, transition smoothness, and plausibility. Both quantitative metrics and human studies demonstrate the significant advantages of our proposed approach over previous methods. Source code is available at https://github.com/xiaolul2/Interp3D.

Ligand molecule conformation generation is a critical challenge in drug discovery. Deep learning models have been developed to tackle this problem, particularly through the use of generative models in recent years. However, these models often generate conformations that lack meaningful structure and randomness due to the absence of essential side information. Examples of such side information include the chemical and geometric features of the target protein, ligand-target compound interactions, and ligand chemical properties. Without these constraints, the generated conformations may not be suitable for further selection and design of new drugs. To address this limitation, we propose a novel method for generating ligand conformations that leverage side information and incorporate flexible constraints into standard diffusion models. Drawing inspiration from the concept of message passing, we introduce ligand-target massage passing block, a mechanism that facilitates the exchange of information between target nodes and ligand nodes, thereby incorporating target node features. To capture non-covalent interactions, we introduce ligand-target compound inter and intra edges. To further improve the biological relevance of the generated conformations, we train energy models using scalar chemical features. These models guide the progress of the standard Denoising Diffusion Probabilistic Models, resulting in more biologically meaningful conformations. We evaluate the performance of SIDEGEN using the PDBBind-2020 dataset, comparing it against other methods. The results demonstrate improvements in both Aligned RMSD and Ligand RMSD evaluations. Specifically, our model outperforms GeoDiff (trained on PDBBind-2020) by 20% in terms of the median aligned RMSD metric.

Deep generative models have shown significant promise in generating valid 3D molecular structures, with the GEOM-Drugs dataset serving as a key benchmark. However, current evaluation protocols suffer from critical flaws, including incorrect valency definitions, bugs in bond order calculations, and reliance on force fields inconsistent with the reference data. In this work, we revisit GEOM-Drugs and propose a corrected evaluation framework: we identify and fix issues in data preprocessing, construct chemically accurate valency tables, and introduce a GFN2-xTB-based geometry and energy benchmark. We retrain and re-evaluate several leading models under this framework, providing updated performance metrics and practical recommendations for future benchmarking. Our results underscore the need for chemically rigorous evaluation practices in 3D molecular generation. Our recommended evaluation methods and GEOM-Drugs processing scripts are available at https://github.com/isayevlab/geom-drugs-3dgen-evaluation.

We present a novel task: text-to-3D sketch animation, which aims to bring freeform sketches to life in dynamic 3D space. Unlike prior works focused on photorealistic content generation, we target sparse, stylized, and view-consistent 3D vector sketches, a lightweight and interpretable medium well-suited for visual communication and prototyping. However, this task is very challenging: (i) no paired dataset exists for text and 3D (or 4D) sketches; (ii) sketches require structural abstraction that is difficult to model with conventional 3D representations like NeRFs or point clouds; and (iii) animating such sketches demands temporal coherence and multi-view consistency, which current pipelines do not address. Therefore, we propose 4-Doodle, the first training-free framework for generating dynamic 3D sketches from text. It leverages pretrained image and video diffusion models through a dual-space distillation scheme: one space captures multi-view-consistent geometry using differentiable Bézier curves, while the other encodes motion dynamics via temporally-aware priors. Unlike prior work (e.g., DreamFusion), which optimizes from a single view per step, our multi-view optimization ensures structural alignment and avoids view ambiguity, critical for sparse sketches. Furthermore, we introduce a structure-aware motion module that separates shape-preserving trajectories from deformation-aware changes, enabling expressive motion such as flipping, rotation, and articulated movement. Extensive experiments show that our method produces temporally realistic and structurally stable 3D sketch animations, outperforming existing baselines in both fidelity and controllability. We hope this work serves as a step toward more intuitive and accessible 4D content creation.

We consider molecule generation in 3D space using language models (LMs), which requires discrete tokenization of 3D molecular geometries. Although tokenization of molecular graphs exists, that for 3D geometries is largely unexplored. Here, we attempt to bridge this gap by proposing the Geo2Seq, which converts molecular geometries into SE(3)-invariant 1D discrete sequences. Geo2Seq consists of canonical labeling and invariant spherical representation steps, which together maintain geometric and atomic fidelity in a format conducive to LMs. Our experiments show that, when coupled with Geo2Seq, various LMs excel in molecular geometry generation, especially in controlled generation tasks.

3D molecule generation is crucial for drug discovery and material design. While prior efforts focus on 3D diffusion models for their benefits in modeling continuous 3D conformers, they overlook the advantages of 1D SELFIES-based Language Models (LMs), which can generate 100% valid molecules and leverage the billion-scale 1D molecule datasets. To combine these advantages for 3D molecule generation, we propose a foundation model -- NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation. NExT-Mol uses an extensively pretrained molecule LM for 1D molecule generation, and subsequently predicts the generated molecule's 3D conformers with a 3D diffusion model. We enhance NExT-Mol's performance by scaling up the LM's model size, refining the diffusion neural architecture, and applying 1D to 3D transfer learning. Notably, our 1D molecule LM significantly outperforms baselines in distributional similarity while ensuring validity, and our 3D diffusion model achieves leading performances in conformer prediction. Given these improvements in 1D and 3D modeling, NExT-Mol achieves a 26% relative improvement in 3D FCD for de novo 3D generation on GEOM-DRUGS, and a 13% average relative gain for conditional 3D generation on QM9-2014. Our codes and pretrained checkpoints are available at https://github.com/acharkq/NExT-Mol.

Generative models for structure-based drug design (SBDD) have shown promising results in recent years. Existing works mainly focus on how to generate molecules with higher binding affinity, ignoring the feasibility prerequisites for generated 3D poses and resulting in false positives. We conduct thorough studies on key factors of ill-conformational problems when applying autoregressive methods and diffusion to SBDD, including mode collapse and hybrid continuous-discrete space. In this paper, we introduce MolCRAFT, the first SBDD model that operates in the continuous parameter space, together with a novel noise reduced sampling strategy. Empirical results show that our model consistently achieves superior performance in binding affinity with more stable 3D structure, demonstrating our ability to accurately model interatomic interactions. To our best knowledge, MolCRAFT is the first to achieve reference-level Vina Scores (-6.59 kcal/mol) with comparable molecular size, outperforming other strong baselines by a wide margin (-0.84 kcal/mol). Code is available at https://github.com/AlgoMole/MolCRAFT.

Text-to-3D generation from a single-view image is a popular but challenging task in 3D vision. Although numerous methods have been proposed, existing works still suffer from the inconsistency issues, including 1) semantic inconsistency, 2) geometric inconsistency, and 3) saturation inconsistency, resulting in distorted, overfitted, and over-saturated generations. In light of the above issues, we present Consist3D, a three-stage framework Chasing for semantic-, geometric-, and saturation-Consistent Text-to-3D generation from a single image, in which the first two stages aim to learn parameterized consistency tokens, and the last stage is for optimization. Specifically, the semantic encoding stage learns a token independent of views and estimations, promoting semantic consistency and robustness. Meanwhile, the geometric encoding stage learns another token with comprehensive geometry and reconstruction constraints under novel-view estimations, reducing overfitting and encouraging geometric consistency. Finally, the optimization stage benefits from the semantic and geometric tokens, allowing a low classifier-free guidance scale and therefore preventing oversaturation. Experimental results demonstrate that Consist3D produces more consistent, faithful, and photo-realistic 3D assets compared to previous state-of-the-art methods. Furthermore, Consist3D also allows background and object editing through text prompts.

Structure-based drug discovery, encompassing the tasks of protein-ligand docking and pocket-aware 3D drug design, represents a core challenge in drug discovery. However, no existing work can deal with both tasks to effectively leverage the duality between them, and current methods for each task are hindered by challenges in modeling 3D information and the limitations of available data. To address these issues, we propose 3DMolFormer, a unified dual-channel transformer-based framework applicable to both docking and 3D drug design tasks, which exploits their duality by utilizing docking functionalities within the drug design process. Specifically, we represent 3D pocket-ligand complexes using parallel sequences of discrete tokens and continuous numbers, and we design a corresponding dual-channel transformer model to handle this format, thereby overcoming the challenges of 3D information modeling. Additionally, we alleviate data limitations through large-scale pre-training on a mixed dataset, followed by supervised and reinforcement learning fine-tuning techniques respectively tailored for the two tasks. Experimental results demonstrate that 3DMolFormer outperforms previous approaches in both protein-ligand docking and pocket-aware 3D drug design, highlighting its promising application in structure-based drug discovery. The code is available at: https://github.com/HXYfighter/3DMolFormer .

We present a novel video generation framework that integrates 3-dimensional geometry and dynamic awareness. To achieve this, we augment 2D videos with 3D point trajectories and align them in pixel space. The resulting 3D-aware video dataset, PointVid, is then used to fine-tune a latent diffusion model, enabling it to track 2D objects with 3D Cartesian coordinates. Building on this, we regularize the shape and motion of objects in the video to eliminate undesired artifacts, \eg, nonphysical deformation. Consequently, we enhance the quality of generated RGB videos and alleviate common issues like object morphing, which are prevalent in current video models due to a lack of shape awareness. With our 3D augmentation and regularization, our model is capable of handling contact-rich scenarios such as task-oriented videos. These videos involve complex interactions of solids, where 3D information is essential for perceiving deformation and contact. Furthermore, our model improves the overall quality of video generation by promoting the 3D consistency of moving objects and reducing abrupt changes in shape and motion.

3D shape is a crucial but heavily underutilized cue in today's computer vision systems, mostly due to the lack of a good generic shape representation. With the recent availability of inexpensive 2.5D depth sensors (e.g. Microsoft Kinect), it is becoming increasingly important to have a powerful 3D shape representation in the loop. Apart from category recognition, recovering full 3D shapes from view-based 2.5D depth maps is also a critical part of visual understanding. To this end, we propose to represent a geometric 3D shape as a probability distribution of binary variables on a 3D voxel grid, using a Convolutional Deep Belief Network. Our model, 3D ShapeNets, learns the distribution of complex 3D shapes across different object categories and arbitrary poses from raw CAD data, and discovers hierarchical compositional part representations automatically. It naturally supports joint object recognition and shape completion from 2.5D depth maps, and it enables active object recognition through view planning. To train our 3D deep learning model, we construct ModelNet -- a large-scale 3D CAD model dataset. Extensive experiments show that our 3D deep representation enables significant performance improvement over the-state-of-the-arts in a variety of tasks.

Recent advances in video generation have enabled the synthesis of high-quality and visually realistic clips using diffusion transformer models. However, most existing approaches operate purely in the 2D pixel space and lack explicit mechanisms for modeling 3D structures, often resulting in temporally inconsistent geometries, implausible motions, and structural artifacts. In this work, we introduce geometric regularization losses into video generation by augmenting latent diffusion models with per-frame depth prediction. We adopted depth as the geometric representation because of the great progress in depth prediction and its compatibility with image-based latent encoders. Specifically, to enforce structural consistency over time, we propose a multi-view geometric loss that aligns the predicted depth maps across frames within a shared 3D coordinate system. Our method bridges the gap between appearance generation and 3D structure modeling, leading to improved spatio-temporal coherence, shape consistency, and physical plausibility. Experiments across multiple datasets show that our approach produces significantly more stable and geometrically consistent results than existing baselines.

The integration of molecule and language has garnered increasing attention in molecular science. Recent advancements in Language Models (LMs) have demonstrated potential for the comprehensive modeling of molecule and language. However, existing works exhibit notable limitations. Most existing works overlook the modeling of 3D information, which is crucial for understanding molecular structures and also functions. While some attempts have been made to leverage external structure encoding modules to inject the 3D molecular information into LMs, there exist obvious difficulties that hinder the integration of molecular structure and language text, such as modality alignment and separate tuning. To bridge this gap, we propose 3D-MolT5, a unified framework designed to model both 1D molecular sequence and 3D molecular structure. The key innovation lies in our methodology for mapping fine-grained 3D substructure representations (based on 3D molecular fingerprints) to a specialized 3D token vocabulary for 3D-MolT5. This 3D structure token vocabulary enables the seamless combination of 1D sequence and 3D structure representations in a tokenized format, allowing 3D-MolT5 to encode molecular sequence (SELFIES), molecular structure, and text sequences within a unified architecture. Alongside, we further introduce 1D and 3D joint pre-training to enhance the model's comprehension of these diverse modalities in a joint representation space and better generalize to various tasks for our foundation model. Through instruction tuning on multiple downstream datasets, our proposed 3D-MolT5 shows superior performance than existing methods in molecular property prediction, molecule captioning, and text-based molecule generation tasks. Our code will be available on GitHub soon.

Establishing the relationship between 3D structures and the energy states of molecular systems has proven to be a promising approach for learning 3D molecular representations. However, existing methods are limited to modeling the molecular energy states from classical mechanics. This limitation results in a significant oversight of quantum mechanical effects, such as quantized (discrete) energy level structures, which offer a more accurate estimation of molecular energy and can be experimentally measured through energy spectra. In this paper, we propose to utilize the energy spectra to enhance the pre-training of 3D molecular representations (MolSpectra), thereby infusing the knowledge of quantum mechanics into the molecular representations. Specifically, we propose SpecFormer, a multi-spectrum encoder for encoding molecular spectra via masked patch reconstruction. By further aligning outputs from the 3D encoder and spectrum encoder using a contrastive objective, we enhance the 3D encoder's understanding of molecules. Evaluations on public benchmarks reveal that our pre-trained representations surpass existing methods in predicting molecular properties and modeling dynamics.

In this work, we recover the underlying 3D structure of non-geometrically consistent scenes. We focus our analysis on hand-drawn images from cartoons and anime. Many cartoons are created by artists without a 3D rendering engine, which means that any new image of a scene is hand-drawn. The hand-drawn images are usually faithful representations of the world, but only in a qualitative sense, since it is difficult for humans to draw multiple perspectives of an object or scene 3D consistently. Nevertheless, people can easily perceive 3D scenes from inconsistent inputs! In this work, we correct for 2D drawing inconsistencies to recover a plausible 3D structure such that the newly warped drawings are consistent with each other. Our pipeline consists of a user-friendly annotation tool, camera pose estimation, and image deformation to recover a dense structure. Our method warps images to obey a perspective camera model, enabling our aligned results to be plugged into novel-view synthesis reconstruction methods to experience cartoons from viewpoints never drawn before. Our project page is https://toon3d.studio/.

Current diffusion or flow-based generative models for 3D shapes divide to two: distilling pre-trained 2D image diffusion models, and training directly on 3D shapes. When training a diffusion or flow models on 3D shapes a crucial design choice is the shape representation. An effective shape representation needs to adhere three design principles: it should allow an efficient conversion of large 3D datasets to the representation form; it should provide a good tradeoff of approximation power versus number of parameters; and it should have a simple tensorial form that is compatible with existing powerful neural architectures. While standard 3D shape representations such as volumetric grids and point clouds do not adhere to all these principles simultaneously, we advocate in this paper a new representation that does. We introduce Mosaic-SDF (M-SDF): a simple 3D shape representation that approximates the Signed Distance Function (SDF) of a given shape by using a set of local grids spread near the shape's boundary. The M-SDF representation is fast to compute for each shape individually making it readily parallelizable; it is parameter efficient as it only covers the space around the shape's boundary; and it has a simple matrix form, compatible with Transformer-based architectures. We demonstrate the efficacy of the M-SDF representation by using it to train a 3D generative flow model including class-conditioned generation with the 3D Warehouse dataset, and text-to-3D generation using a dataset of about 600k caption-shape pairs.

We introduce DrugFlow, a generative model for structure-based drug design that integrates continuous flow matching with discrete Markov bridges, demonstrating state-of-the-art performance in learning chemical, geometric, and physical aspects of three-dimensional protein-ligand data. We endow DrugFlow with an uncertainty estimate that is able to detect out-of-distribution samples. To further enhance the sampling process towards distribution regions with desirable metric values, we propose a joint preference alignment scheme applicable to both flow matching and Markov bridge frameworks. Furthermore, we extend our model to also explore the conformational landscape of the protein by jointly sampling side chain angles and molecules.

Molecular conformation optimization is crucial to computer-aided drug discovery and materials design. Traditional energy minimization techniques rely on iterative optimization methods that use molecular forces calculated by a physical simulator (oracle) as anti-gradients. However, this is a computationally expensive approach that requires many interactions with a physical simulator. One way to accelerate this procedure is to replace the physical simulator with a neural network. Despite recent progress in neural networks for molecular conformation energy prediction, such models are prone to distribution shift, leading to inaccurate energy minimization. We find that the quality of energy minimization with neural networks can be improved by providing optimization trajectories as additional training data. Still, it takes around 5 times 10^5 additional conformations to match the physical simulator's optimization quality. In this work, we present the Gradual Optimization Learning Framework (GOLF) for energy minimization with neural networks that significantly reduces the required additional data. The framework consists of an efficient data-collecting scheme and an external optimizer. The external optimizer utilizes gradients from the energy prediction model to generate optimization trajectories, and the data-collecting scheme selects additional training data to be processed by the physical simulator. Our results demonstrate that the neural network trained with GOLF performs on par with the oracle on a benchmark of diverse drug-like molecules using 50x less additional data.

In the literature, it has been shown that the evolution of the known explicit 3D surface to the target one can be learned from 2D images using the instantaneous flow field, where the known and target 3D surfaces may largely differ in topology. We are interested in capturing 4D shapes whose topology changes largely over time. We encounter that the straightforward extension of the existing 3D-based method to the desired 4D case performs poorly. In this work, we address the challenges in extending 3D neural evolution to 4D under large topological changes by proposing two novel modifications. More precisely, we introduce (i) a new architecture to discretize and encode the deformation and learn the SDF and (ii) a technique to impose the temporal consistency. (iii) Also, we propose a rendering scheme for color prediction based on Gaussian splatting. Furthermore, to facilitate learning directly from 2D images, we propose a learning framework that can disentangle the geometry and appearance from RGB images. This method of disentanglement, while also useful for the 4D evolution problem that we are concentrating on, is also novel and valid for static scenes. Our extensive experiments on various data provide awesome results and, most importantly, open a new approach toward reconstructing challenging scenes with significant topological changes and deformations. Our source code and the dataset are publicly available at https://github.com/insait-institute/N4DE.

Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and the expanded availability of experimental 3D protein structures have accelerated structure prediction, the dynamic nature of protein structures has received limited attention. This study introduces an innovative 4D diffusion model incorporating molecular dynamics (MD) simulation data to learn dynamic protein structures. Our approach is distinguished by the following components: (1) a unified diffusion model capable of generating dynamic protein structures, including both the backbone and side chains, utilizing atomic grouping and side-chain dihedral angle predictions; (2) a reference network that enhances structural consistency by integrating the latent embeddings of the initial 3D protein structures; and (3) a motion alignment module aimed at improving temporal structural coherence across multiple time steps. To our knowledge, this is the first diffusion-based model aimed at predicting protein trajectories across multiple time steps simultaneously. Validation on benchmark datasets demonstrates that our model exhibits high accuracy in predicting dynamic 3D structures of proteins containing up to 256 amino acids over 32 time steps, effectively capturing both local flexibility in stable states and significant conformational changes.

In this paper, we tackle a new task of 3D object synthesis, where a 3D model is composited with another object category to create a novel 3D model. However, most existing text/image/3D-to-3D methods struggle to effectively integrate multiple content sources, often resulting in inconsistent textures and inaccurate shapes. To overcome these challenges, we propose a straightforward yet powerful approach, category+3D-to-3D (C33D), for generating novel and structurally coherent 3D models. Our method begins by rendering multi-view images and normal maps from the input 3D model, then generating a novel 2D object using adaptive text-image harmony (ATIH) with the front-view image and a text description from another object category as inputs. To ensure texture consistency, we introduce texture multi-view diffusion, which refines the textures of the remaining multi-view RGB images based on the novel 2D object. For enhanced shape accuracy, we propose shape multi-view diffusion to improve the 2D shapes of both the multi-view RGB images and the normal maps, also conditioned on the novel 2D object. Finally, these outputs are used to reconstruct a complete and novel 3D model. Extensive experiments demonstrate the effectiveness of our method, yielding impressive 3D creations, such as shark(3D)-crocodile(text) in the first row of Fig. 1. A project page is available at: https://xzr52.github.io/C33D/

Structure-Based Drug Design (SBDD) is crucial for identifying bioactive molecules. Recent deep generative models are faced with challenges in geometric structure modeling. A major bottleneck lies in the twisted probability path of multi-modalities -- continuous 3D positions and discrete 2D topologies -- which jointly determine molecular geometries. By establishing the fact that noise schedules decide the Variational Lower Bound (VLB) for the twisted probability path, we propose VLB-Optimal Scheduling (VOS) strategy in this under-explored area, which optimizes VLB as a path integral for SBDD. Our model effectively enhances molecular geometries and interaction modeling, achieving state-of-the-art PoseBusters passing rate of 95.9% on CrossDock, more than 10% improvement upon strong baselines, while maintaining high affinities and robust intramolecular validity evaluated on held-out test set. Code is available at https://github.com/AlgoMole/MolCRAFT.

Self-supervised learning has recently gained growing interest in molecular modeling for scientific tasks such as AI-assisted drug discovery. Current studies consider leveraging both 2D and 3D molecular structures for representation learning. However, relying on straightforward alignment strategies that treat each modality separately, these methods fail to exploit the intrinsic correlation between 2D and 3D representations that reflect the underlying structural characteristics of molecules, and only perform coarse-grained molecule-level alignment. To derive fine-grained alignment and promote structural molecule understanding, we introduce an atomic-relation level "blend-then-predict" self-supervised learning approach, MoleBLEND, which first blends atom relations represented by different modalities into one unified relation matrix for joint encoding, then recovers modality-specific information for 2D and 3D structures individually. By treating atom relationships as anchors, MoleBLEND organically aligns and integrates visually dissimilar 2D and 3D modalities of the same molecule at fine-grained atomic level, painting a more comprehensive depiction of each molecule. Extensive experiments show that MoleBLEND achieves state-of-the-art performance across major 2D/3D molecular benchmarks. We further provide theoretical insights from the perspective of mutual-information maximization, demonstrating that our method unifies contrastive, generative (cross-modality prediction) and mask-then-predict (single-modality prediction) objectives into one single cohesive framework.

Recent advancements in implicit 3D representations and generative models have markedly propelled the field of 3D object generation forward. However, it remains a significant challenge to accurately model geometries with defined sharp features under parametric controls, which is crucial in fields like industrial design and manufacturing. To bridge this gap, we introduce a framework that employs Large Language Models (LLMs) to generate text-driven 3D shapes, manipulating 3D software via program synthesis. We present 3D-PreMise, a dataset specifically tailored for 3D parametric modeling of industrial shapes, designed to explore state-of-the-art LLMs within our proposed pipeline. Our work reveals effective generation strategies and delves into the self-correction capabilities of LLMs using a visual interface. Our work highlights both the potential and limitations of LLMs in 3D parametric modeling for industrial applications.

We present Stable Video 3D (SV3D) -- a latent video diffusion model for high-resolution, image-to-multi-view generation of orbital videos around a 3D object. Recent work on 3D generation propose techniques to adapt 2D generative models for novel view synthesis (NVS) and 3D optimization. However, these methods have several disadvantages due to either limited views or inconsistent NVS, thereby affecting the performance of 3D object generation. In this work, we propose SV3D that adapts image-to-video diffusion model for novel multi-view synthesis and 3D generation, thereby leveraging the generalization and multi-view consistency of the video models, while further adding explicit camera control for NVS. We also propose improved 3D optimization techniques to use SV3D and its NVS outputs for image-to-3D generation. Extensive experimental results on multiple datasets with 2D and 3D metrics as well as user study demonstrate SV3D's state-of-the-art performance on NVS as well as 3D reconstruction compared to prior works.

Advances in 3D reconstruction have enabled high-quality 3D capture, but require a user to collect hundreds to thousands of images to create a 3D scene. We present CAT3D, a method for creating anything in 3D by simulating this real-world capture process with a multi-view diffusion model. Given any number of input images and a set of target novel viewpoints, our model generates highly consistent novel views of a scene. These generated views can be used as input to robust 3D reconstruction techniques to produce 3D representations that can be rendered from any viewpoint in real-time. CAT3D can create entire 3D scenes in as little as one minute, and outperforms existing methods for single image and few-view 3D scene creation. See our project page for results and interactive demos at https://cat3d.github.io .

3D foundation models (3DFMs) have recently transformed 3D vision, enabling joint prediction of depths, poses, and point maps directly from images. Yet their ability to reason under extreme, non-overlapping views remains largely unexplored. In this work, we study their internal representations and find that 3DFMs exhibit an emergent understanding of extreme-view geometry, despite never being trained for such conditions. To further enhance these capabilities, we introduce a lightweight alignment scheme that refines their internal 3D representation by tuning only a small subset of backbone bias terms, leaving all decoder heads frozen. This targeted adaptation substantially improves relative pose estimation under extreme viewpoints without degrading per-image depth or point quality. Additionally, we contribute MegaUnScene, a new benchmark of Internet scenes unseen by existing 3DFMs, with dedicated test splits for both relative pose estimation and dense 3D reconstruction. All code and data will be released.

Recent advances in dense 3D reconstruction have led to significant progress, yet achieving accurate unified geometric prediction remains a major challenge. Most existing methods are limited to predicting a single geometry quantity from input images. However, geometric quantities such as depth, surface normals, and point maps are inherently correlated, and estimating them in isolation often fails to ensure consistency, thereby limiting both accuracy and practical applicability. This motivates us to explore a unified framework that explicitly models the structural coupling among different geometric properties to enable joint regression. In this paper, we present Dens3R, a 3D foundation model designed for joint geometric dense prediction and adaptable to a wide range of downstream tasks. Dens3R adopts a two-stage training framework to progressively build a pointmap representation that is both generalizable and intrinsically invariant. Specifically, we design a lightweight shared encoder-decoder backbone and introduce position-interpolated rotary positional encoding to maintain expressive power while enhancing robustness to high-resolution inputs. By integrating image-pair matching features with intrinsic invariance modeling, Dens3R accurately regresses multiple geometric quantities such as surface normals and depth, achieving consistent geometry perception from single-view to multi-view inputs. Additionally, we propose a post-processing pipeline that supports geometrically consistent multi-view inference. Extensive experiments demonstrate the superior performance of Dens3R across various dense 3D prediction tasks and highlight its potential for broader applications.

We present Motion 3-to-4, a feed-forward framework for synthesising high-quality 4D dynamic objects from a single monocular video and an optional 3D reference mesh. While recent advances have significantly improved 2D, video, and 3D content generation, 4D synthesis remains difficult due to limited training data and the inherent ambiguity of recovering geometry and motion from a monocular viewpoint. Motion 3-to-4 addresses these challenges by decomposing 4D synthesis into static 3D shape generation and motion reconstruction. Using a canonical reference mesh, our model learns a compact motion latent representation and predicts per-frame vertex trajectories to recover complete, temporally coherent geometry. A scalable frame-wise transformer further enables robustness to varying sequence lengths. Evaluations on both standard benchmarks and a new dataset with accurate ground-truth geometry show that Motion 3-to-4 delivers superior fidelity and spatial consistency compared to prior work. Project page is available at https://motion3-to-4.github.io/.

This report presents a comprehensive framework for generating high-quality 3D shapes and textures from diverse input prompts, including single images, multi-view images, and text descriptions. The framework consists of 3D shape generation and texture generation. (1). The 3D shape generation pipeline employs a Variational Autoencoder (VAE) to encode implicit 3D geometries into a latent space and a diffusion network to generate latents conditioned on input prompts, with modifications to enhance model capacity. An alternative Artist-Created Mesh (AM) generation approach is also explored, yielding promising results for simpler geometries. (2). Texture generation involves a multi-stage process starting with frontal images generation followed by multi-view images generation, RGB-to-PBR texture conversion, and high-resolution multi-view texture refinement. A consistency scheduler is plugged into every stage, to enforce pixel-wise consistency among multi-view textures during inference, ensuring seamless integration. The pipeline demonstrates effective handling of diverse input formats, leveraging advanced neural architectures and novel methodologies to produce high-quality 3D content. This report details the system architecture, experimental results, and potential future directions to improve and expand the framework. The source code and pretrained weights are released at: https://github.com/Tencent/Tencent-XR-3DGen.

In this report, we introduce UltraShape 1.0, a scalable 3D diffusion framework for high-fidelity 3D geometry generation. The proposed approach adopts a two-stage generation pipeline: a coarse global structure is first synthesized and then refined to produce detailed, high-quality geometry. To support reliable 3D generation, we develop a comprehensive data processing pipeline that includes a novel watertight processing method and high-quality data filtering. This pipeline improves the geometric quality of publicly available 3D datasets by removing low-quality samples, filling holes, and thickening thin structures, while preserving fine-grained geometric details. To enable fine-grained geometry refinement, we decouple spatial localization from geometric detail synthesis in the diffusion process. We achieve this by performing voxel-based refinement at fixed spatial locations, where voxel queries derived from coarse geometry provide explicit positional anchors encoded via RoPE, allowing the diffusion model to focus on synthesizing local geometric details within a reduced, structured solution space. Our model is trained exclusively on publicly available 3D datasets, achieving strong geometric quality despite limited training resources. Extensive evaluations demonstrate that UltraShape 1.0 performs competitively with existing open-source methods in both data processing quality and geometry generation. All code and trained models will be released to support future research.

In neural networks, it is often desirable to work with various representations of the same space. For example, 3D rotations can be represented with quaternions or Euler angles. In this paper, we advance a definition of a continuous representation, which can be helpful for training deep neural networks. We relate this to topological concepts such as homeomorphism and embedding. We then investigate what are continuous and discontinuous representations for 2D, 3D, and n-dimensional rotations. We demonstrate that for 3D rotations, all representations are discontinuous in the real Euclidean spaces of four or fewer dimensions. Thus, widely used representations such as quaternions and Euler angles are discontinuous and difficult for neural networks to learn. We show that the 3D rotations have continuous representations in 5D and 6D, which are more suitable for learning. We also present continuous representations for the general case of the n-dimensional rotation group SO(n). While our main focus is on rotations, we also show that our constructions apply to other groups such as the orthogonal group and similarity transforms. We finally present empirical results, which show that our continuous rotation representations outperform discontinuous ones for several practical problems in graphics and vision, including a simple autoencoder sanity test, a rotation estimator for 3D point clouds, and an inverse kinematics solver for 3D human poses.

Accurate prediction of protein-ligand binding poses is crucial for structure-based drug design, yet existing methods struggle to balance speed, accuracy, and physical plausibility. We introduce Matcha, a novel molecular docking pipeline that combines multi-stage flow matching with learned scoring and physical validity filtering. Our approach consists of three sequential stages applied consecutively to refine docking predictions, each implemented as a flow matching model operating on appropriate geometric spaces (R^3, SO(3), and SO(2)). We enhance the prediction quality through a dedicated scoring model and apply unsupervised physical validity filters to eliminate unrealistic poses. Compared to various approaches, Matcha demonstrates superior performance on Astex and PDBbind test sets in terms of docking success rate and physical plausibility. Moreover, our method works approximately 25 times faster than modern large-scale co-folding models. The model weights and inference code to reproduce our results are available at https://github.com/LigandPro/Matcha.

Given that visual foundation models (VFMs) are trained on extensive datasets but often limited to 2D images, a natural question arises: how well do they understand the 3D world? With the differences in architecture and training protocols (i.e., objectives, proxy tasks), a unified framework to fairly and comprehensively probe their 3D awareness is urgently needed. Existing works on 3D probing suggest single-view 2.5D estimation (e.g., depth and normal) or two-view sparse 2D correspondence (e.g., matching and tracking). Unfortunately, these tasks ignore texture awareness, and require 3D data as ground-truth, which limits the scale and diversity of their evaluation set. To address these issues, we introduce Feat2GS, which readout 3D Gaussians attributes from VFM features extracted from unposed images. This allows us to probe 3D awareness for geometry and texture via novel view synthesis, without requiring 3D data. Additionally, the disentanglement of 3DGS parameters - geometry (x, alpha, Sigma) and texture (c) - enables separate analysis of texture and geometry awareness. Under Feat2GS, we conduct extensive experiments to probe the 3D awareness of several VFMs, and investigate the ingredients that lead to a 3D aware VFM. Building on these findings, we develop several variants that achieve state-of-the-art across diverse datasets. This makes Feat2GS useful for probing VFMs, and as a simple-yet-effective baseline for novel-view synthesis. Code and data will be made available at https://fanegg.github.io/Feat2GS/.

Molecule pretraining has quickly become the go-to schema to boost the performance of AI-based drug discovery. Naturally, molecules can be represented as 2D topological graphs or 3D geometric point clouds. Although most existing pertaining methods focus on merely the single modality, recent research has shown that maximizing the mutual information (MI) between such two modalities enhances the molecule representation ability. Meanwhile, existing molecule multi-modal pretraining approaches approximate MI based on the representation space encoded from the topology and geometry, thus resulting in the loss of critical structural information of molecules. To address this issue, we propose MoleculeSDE. MoleculeSDE leverages group symmetric (e.g., SE(3)-equivariant and reflection-antisymmetric) stochastic differential equation models to generate the 3D geometries from 2D topologies, and vice versa, directly in the input space. It not only obtains tighter MI bound but also enables prosperous downstream tasks than the previous work. By comparing with 17 pretraining baselines, we empirically verify that MoleculeSDE can learn an expressive representation with state-of-the-art performance on 26 out of 32 downstream tasks.

Recently, significant advances have been made in 3D object generation. Building upon the generated geometry, current pipelines typically employ image diffusion models to generate multi-view RGB images, followed by UV texture reconstruction through texture baking. While 3D geometry generation has improved significantly, supported by multiple open-source frameworks, 3D texture generation remains underexplored. In this work, we systematically investigate 3D texture generation through the lens of three core dimensions: reference-texture alignment, geometry-texture consistency, and local texture quality. To tackle these issues, we propose MVPainter, which employs data filtering and augmentation strategies to enhance texture fidelity and detail, and introduces ControlNet-based geometric conditioning to improve texture-geometry alignment. Furthermore, we extract physically-based rendering (PBR) attributes from the generated views to produce PBR meshes suitable for real-world rendering applications. MVPainter achieves state-of-the-art results across all three dimensions, as demonstrated by human-aligned evaluations. To facilitate further research and reproducibility, we also release our full pipeline as an open-source system, including data construction, model architecture, and evaluation tools.

Text-to-3D generation represents an exciting field that has seen rapid advancements, facilitating the transformation of textual descriptions into detailed 3D models. However, current progress often neglects the intricate high-order correlation of geometry and texture within 3D objects, leading to challenges such as over-smoothness, over-saturation and the Janus problem. In this work, we propose a method named ``3D Gaussian Generation via Hypergraph (Hyper-3DG)'', designed to capture the sophisticated high-order correlations present within 3D objects. Our framework is anchored by a well-established mainflow and an essential module, named ``Geometry and Texture Hypergraph Refiner (HGRefiner)''. This module not only refines the representation of 3D Gaussians but also accelerates the update process of these 3D Gaussians by conducting the Patch-3DGS Hypergraph Learning on both explicit attributes and latent visual features. Our framework allows for the production of finely generated 3D objects within a cohesive optimization, effectively circumventing degradation. Extensive experimentation has shown that our proposed method significantly enhances the quality of 3D generation while incurring no additional computational overhead for the underlying framework. (Project code: https://github.com/yjhboy/Hyper3DG)

The 3D CAD shapes in current 3D benchmarks are mostly collected from online model repositories. Thus, they typically have insufficient geometric details and less informative textures, making them less attractive for comprehensive and subtle research in areas such as high-quality 3D mesh and texture recovery. This paper presents 3D Furniture shape with TextURE (3D-FUTURE): a richly-annotated and large-scale repository of 3D furniture shapes in the household scenario. At the time of this technical report, 3D-FUTURE contains 20,240 clean and realistic synthetic images of 5,000 different rooms. There are 9,992 unique detailed 3D instances of furniture with high-resolution textures. Experienced designers developed the room scenes, and the 3D CAD shapes in the scene are used for industrial production. Given the well-organized 3D-FUTURE, we provide baseline experiments on several widely studied tasks, such as joint 2D instance segmentation and 3D object pose estimation, image-based 3D shape retrieval, 3D object reconstruction from a single image, and texture recovery for 3D shapes, to facilitate related future researches on our database.

Despite the availability of large-scale 3D datasets and advancements in 3D generative models, the complexity and uneven quality of 3D geometry and texture data continue to hinder the performance of 3D generation techniques. In most existing approaches, 3D geometry and texture are generated in separate stages using different models and non-unified representations, frequently leading to unsatisfactory coherence between geometry and texture. To address these challenges, we propose a novel framework for joint generation of 3D geometry and texture. Specifically, we focus in generate a versatile 2.5D representations that can be seamlessly transformed between 2D and 3D. Our approach begins by integrating multiview RGB, normal, and coordinate images into a unified representation, termed as 2.5D latents. Next, we adapt pre-trained 2D foundation models for high-fidelity 2.5D generation, utilizing both text and image conditions. Finally, we introduce a lightweight 2.5D-to-3D refiner-decoder framework that efficiently generates detailed 3D representations from 2.5D images. Extensive experiments demonstrate that our model not only excels in generating high-quality 3D objects with coherent structure and color from text and image inputs but also significantly outperforms existing methods in geometry-conditioned texture generation.

Recent advancements in diffusion techniques have propelled image and video generation to unprece- dented levels of quality, significantly accelerating the deployment and application of generative AI. However, 3D shape generation technology has so far lagged behind, constrained by limitations in 3D data scale, complexity of 3D data process- ing, and insufficient exploration of advanced tech- niques in the 3D domain. Current approaches to 3D shape generation face substantial challenges in terms of output quality, generalization capa- bility, and alignment with input conditions. We present TripoSG, a new streamlined shape diffu- sion paradigm capable of generating high-fidelity 3D meshes with precise correspondence to input images. Specifically, we propose: 1) A large-scale rectified flow transformer for 3D shape generation, achieving state-of-the-art fidelity through training on extensive, high-quality data. 2) A hybrid supervised training strategy combining SDF, normal, and eikonal losses for 3D VAE, achieving high- quality 3D reconstruction performance. 3) A data processing pipeline to generate 2 million high- quality 3D samples, highlighting the crucial rules for data quality and quantity in training 3D gen- erative models. Through comprehensive experi- ments, we have validated the effectiveness of each component in our new framework. The seamless integration of these parts has enabled TripoSG to achieve state-of-the-art performance in 3D shape generation. The resulting 3D shapes exhibit en- hanced detail due to high-resolution capabilities and demonstrate exceptional fidelity to input im- ages. Moreover, TripoSG demonstrates improved versatility in generating 3D models from diverse image styles and contents, showcasing strong gen- eralization capabilities. To foster progress and innovation in the field of 3D generation, we will make our model publicly available.

To address the data scarcity associated with 3D assets, 2D-lifting techniques such as Score Distillation Sampling (SDS) have become a widely adopted practice in text-to-3D generation pipelines. However, the diffusion models used in these techniques are prone to viewpoint bias and thus lead to geometric inconsistencies such as the Janus problem. To counter this, we introduce MT3D, a text-to-3D generative model that leverages a high-fidelity 3D object to overcome viewpoint bias and explicitly infuse geometric understanding into the generation pipeline. Firstly, we employ depth maps derived from a high-quality 3D model as control signals to guarantee that the generated 2D images preserve the fundamental shape and structure, thereby reducing the inherent viewpoint bias. Next, we utilize deep geometric moments to ensure geometric consistency in the 3D representation explicitly. By incorporating geometric details from a 3D asset, MT3D enables the creation of diverse and geometrically consistent objects, thereby improving the quality and usability of our 3D representations.

We present a novel alignment-before-generation approach to tackle the challenging task of generating general 3D shapes based on 2D images or texts. Directly learning a conditional generative model from images or texts to 3D shapes is prone to producing inconsistent results with the conditions because 3D shapes have an additional dimension whose distribution significantly differs from that of 2D images and texts. To bridge the domain gap among the three modalities and facilitate multi-modal-conditioned 3D shape generation, we explore representing 3D shapes in a shape-image-text-aligned space. Our framework comprises two models: a Shape-Image-Text-Aligned Variational Auto-Encoder (SITA-VAE) and a conditional Aligned Shape Latent Diffusion Model (ASLDM). The former model encodes the 3D shapes into the shape latent space aligned to the image and text and reconstructs the fine-grained 3D neural fields corresponding to given shape embeddings via the transformer-based decoder. The latter model learns a probabilistic mapping function from the image or text space to the latent shape space. Our extensive experiments demonstrate that our proposed approach can generate higher-quality and more diverse 3D shapes that better semantically conform to the visual or textural conditional inputs, validating the effectiveness of the shape-image-text-aligned space for cross-modality 3D shape generation.

Text-to-3D synthesis has recently seen intriguing advances by combining the text-to-image models with 3D representation methods, e.g., Gaussian Splatting (GS), via Score Distillation Sampling (SDS). However, a hurdle of existing methods is the low efficiency, per-prompt optimization for a single 3D object. Therefore, it is imperative for a paradigm shift from per-prompt optimization to one-stage generation for any unseen text prompts, which yet remains challenging. A hurdle is how to directly generate a set of millions of 3D Gaussians to represent a 3D object. This paper presents BrightDreamer, an end-to-end single-stage approach that can achieve generalizable and fast (77 ms) text-to-3D generation. Our key idea is to formulate the generation process as estimating the 3D deformation from an anchor shape with predefined positions. For this, we first propose a Text-guided Shape Deformation (TSD) network to predict the deformed shape and its new positions, used as the centers (one attribute) of 3D Gaussians. To estimate the other four attributes (i.e., scaling, rotation, opacity, and SH coefficient), we then design a novel Text-guided Triplane Generator (TTG) to generate a triplane representation for a 3D object. The center of each Gaussian enables us to transform the triplane feature into the four attributes. The generated 3D Gaussians can be finally rendered at 705 frames per second. Extensive experiments demonstrate the superiority of our method over existing methods. Also, BrightDreamer possesses a strong semantic understanding capability even for complex text prompts. The project code is available at https://vlislab22.github.io/BrightDreamer.

Recent 3D content generation pipelines often leverage Variational Autoencoders (VAEs) to encode shapes into compact latent representations, facilitating diffusion-based generation. Efficiently compressing 3D shapes while preserving intricate geometric details remains a key challenge. Existing 3D shape VAEs often employ uniform point sampling and 1D/2D latent representations, such as vector sets or triplanes, leading to significant geometric detail loss due to inadequate surface coverage and the absence of explicit 3D representations in the latent space. Although recent work explores 3D latent representations, their large scale hinders high-resolution encoding and efficient training. Given these challenges, we introduce Hyper3D, which enhances VAE reconstruction through efficient 3D representation that integrates hybrid triplane and octree features. First, we adopt an octree-based feature representation to embed mesh information into the network, mitigating the limitations of uniform point sampling in capturing geometric distributions along the mesh surface. Furthermore, we propose a hybrid latent space representation that integrates a high-resolution triplane with a low-resolution 3D grid. This design not only compensates for the lack of explicit 3D representations but also leverages a triplane to preserve high-resolution details. Experimental results demonstrate that Hyper3D outperforms traditional representations by reconstructing 3D shapes with higher fidelity and finer details, making it well-suited for 3D generation pipelines.

Feed-forward 3D reconstruction models are efficient but rigid: once trained, they perform inference in a zero-shot manner and cannot adapt to the test scene. As a result, visually plausible reconstructions often contain errors, particularly under occlusions, specularities, and ambiguous cues. To address this, we introduce Free Geometry, a framework that enables feed-forward 3D reconstruction models to self-evolve at test time without any 3D ground truth. Our key insight is that, when the model receives more views, it produces more reliable and view-consistent reconstructions. Leveraging this property, given a testing sequence, we mask a subset of frames to construct a self-supervised task. Free Geometry enforces cross-view feature consistency between representations from full and partial observations, while maintaining the pairwise relations implied by the held-out frames. This self-supervision allows for fast recalibration via lightweight LoRA updates, taking less than 2 minutes per dataset on a single GPU. Our approach consistently improves state-of-the-art foundation models, including Depth Anything 3 and VGGT, across 4 benchmark datasets, yielding an average improvement of 3.73% in camera pose accuracy and 2.88% in point map prediction. Code is available at https://github.com/hiteacherIamhumble/Free-Geometry .

Knot diagrams are among the most common visual tools in topology. Computer programs now make it possible to draw, manipulate and render them digitally, which proves to be useful in knot theory teaching and research. Still, an openly available tool to manipulate knot diagrams in a real-time, interactive way is yet to be developed. We introduce a method of operating on the geometry of the knot diagram itself without any underlying three-dimensional structure that can underpin such an application. This allows us to directly interact with vector graphics knot diagrams while at the same time computing knot invariants in ways proposed by previous work. An implementation of this method is provided.

3D shape modeling is labor-intensive, time-consuming, and requires years of expertise. To facilitate 3D shape modeling, we propose a 3D shape generation network that takes a 3D VR sketch as a condition. We assume that sketches are created by novices without art training and aim to reconstruct geometrically realistic 3D shapes of a given category. To handle potential sketch ambiguity, our method creates multiple 3D shapes that align with the original sketch's structure. We carefully design our method, training the model step-by-step and leveraging multi-modal 3D shape representation to support training with limited training data. To guarantee the realism of generated 3D shapes we leverage the normalizing flow that models the distribution of the latent space of 3D shapes. To encourage the fidelity of the generated 3D shapes to an input sketch, we propose a dedicated loss that we deploy at different stages of the training process. The code is available at https://github.com/Rowl1ng/3Dsketch2shape.

We present Symphony, an E(3)-equivariant autoregressive generative model for 3D molecular geometries that iteratively builds a molecule from molecular fragments. Existing autoregressive models such as G-SchNet and G-SphereNet for molecules utilize rotationally invariant features to respect the 3D symmetries of molecules. In contrast, Symphony uses message-passing with higher-degree E(3)-equivariant features. This allows a novel representation of probability distributions via spherical harmonic signals to efficiently model the 3D geometry of molecules. We show that Symphony is able to accurately generate small molecules from the QM9 dataset, outperforming existing autoregressive models and approaching the performance of diffusion models.

Recent works on text-to-3d generation show that using only 2D diffusion supervision for 3D generation tends to produce results with inconsistent appearances (e.g., faces on the back view) and inaccurate shapes (e.g., animals with extra legs). Existing methods mainly address this issue by retraining diffusion models with images rendered from 3D data to ensure multi-view consistency while struggling to balance 2D generation quality with 3D consistency. In this paper, we present a new framework Sculpt3D that equips the current pipeline with explicit injection of 3D priors from retrieved reference objects without re-training the 2D diffusion model. Specifically, we demonstrate that high-quality and diverse 3D geometry can be guaranteed by keypoints supervision through a sparse ray sampling approach. Moreover, to ensure accurate appearances of different views, we further modulate the output of the 2D diffusion model to the correct patterns of the template views without altering the generated object's style. These two decoupled designs effectively harness 3D information from reference objects to generate 3D objects while preserving the generation quality of the 2D diffusion model. Extensive experiments show our method can largely improve the multi-view consistency while retaining fidelity and diversity. Our project page is available at: https://stellarcheng.github.io/Sculpt3D/.

This paper deals with 3D reconstruction of seabirds which recently came into focus of environmental scientists as valuable bio-indicators for environmental change. Such 3D information is beneficial for analyzing the bird's behavior and physiological shape, for example by tracking motion, shape, and appearance changes. From a computer vision perspective birds are especially challenging due to their rapid and oftentimes non-rigid motions. We propose an approach to reconstruct the 3D pose and shape from monocular videos of a specific breed of seabird - the common murre. Our approach comprises a full pipeline of detection, tracking, segmentation, and temporally consistent 3D reconstruction. Additionally, we propose a temporal loss that extends current single-image 3D bird pose estimators to the temporal domain. Moreover, we provide a real-world dataset of 10000 frames of video observations on average capture nine birds simultaneously, comprising a large variety of motions and interactions, including a smaller test set with bird-specific keypoint labels. Using our temporal optimization, we achieve state-of-the-art performance for the challenging sequences in our dataset.

Designing metal-organic frameworks (MOFs) with novel chemistries is a longstanding challenge due to their large combinatorial space and complex 3D arrangements of the building blocks. While recent deep generative models have enabled scalable MOF generation, they assume (1) a fixed set of building blocks and (2) known local 3D coordinates of building blocks. However, this limits their ability to (1) design novel MOFs and (2) generate the structure using novel building blocks. We propose a two-stage MOF generation framework that overcomes these limitations by modeling both chemical and geometric degrees of freedom. First, we train an SMILES-based autoregressive model to generate metal and organic building blocks, paired with a cheminformatics toolkit for 3D structure initialization. Second, we introduce a flow matching model that predicts translations, rotations, and torsional angles to assemble the blocks into valid 3D frameworks. Our experiments demonstrate improved reconstruction accuracy, the generation of valid, novel, and unique MOFs, and the ability to create novel building blocks. Our code is available at https://github.com/nayoung10/MOFFlow-2.

With the rising industrial attention to 3D virtual modeling technology, generating novel 3D content based on specified conditions (e.g. text) has become a hot issue. In this paper, we propose a new generative 3D modeling framework called Diffusion-SDF for the challenging task of text-to-shape synthesis. Previous approaches lack flexibility in both 3D data representation and shape generation, thereby failing to generate highly diversified 3D shapes conforming to the given text descriptions. To address this, we propose a SDF autoencoder together with the Voxelized Diffusion model to learn and generate representations for voxelized signed distance fields (SDFs) of 3D shapes. Specifically, we design a novel UinU-Net architecture that implants a local-focused inner network inside the standard U-Net architecture, which enables better reconstruction of patch-independent SDF representations. We extend our approach to further text-to-shape tasks including text-conditioned shape completion and manipulation. Experimental results show that Diffusion-SDF generates both higher quality and more diversified 3D shapes that conform well to given text descriptions when compared to previous approaches. Code is available at: https://github.com/ttlmh/Diffusion-SDF

The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction, directly generating diverse, novel protein structures from neural networks remains difficult. In this work, we present a new diffusion-based generative model that designs protein backbone structures via a procedure that mirrors the native folding process. We describe protein backbone structure as a series of consecutive angles capturing the relative orientation of the constituent amino acid residues, and generate new structures by denoising from a random, unfolded state towards a stable folded structure. Not only does this mirror how proteins biologically twist into energetically favorable conformations, the inherent shift and rotational invariance of this representation crucially alleviates the need for complex equivariant networks. We train a denoising diffusion probabilistic model with a simple transformer backbone and demonstrate that our resulting model unconditionally generates highly realistic protein structures with complexity and structural patterns akin to those of naturally-occurring proteins. As a useful resource, we release the first open-source codebase and trained models for protein structure diffusion.

Crystal structures are characterized by atomic bases within a primitive unit cell that repeats along a regular lattice throughout 3D space. The periodic and infinite nature of crystals poses unique challenges for geometric graph representation learning. Specifically, constructing graphs that effectively capture the complete geometric information of crystals and handle chiral crystals remains an unsolved and challenging problem. In this paper, we introduce a novel approach that utilizes the periodic patterns of unit cells to establish the lattice-based representation for each atom, enabling efficient and expressive graph representations of crystals. Furthermore, we propose ComFormer, a SE(3) transformer designed specifically for crystalline materials. ComFormer includes two variants; namely, iComFormer that employs invariant geometric descriptors of Euclidean distances and angles, and eComFormer that utilizes equivariant vector representations. Experimental results demonstrate the state-of-the-art predictive accuracy of ComFormer variants on various tasks across three widely-used crystal benchmarks. Our code is publicly available as part of the AIRS library (https://github.com/divelab/AIRS).

Despite having tremendous progress in image-to-3D generation, existing methods still struggle to produce multi-view consistent images with high-resolution textures in detail, especially in the paradigm of 2D diffusion that lacks 3D awareness. In this work, we present High-resolution Image-to-3D model (Hi3D), a new video diffusion based paradigm that redefines a single image to multi-view images as 3D-aware sequential image generation (i.e., orbital video generation). This methodology delves into the underlying temporal consistency knowledge in video diffusion model that generalizes well to geometry consistency across multiple views in 3D generation. Technically, Hi3D first empowers the pre-trained video diffusion model with 3D-aware prior (camera pose condition), yielding multi-view images with low-resolution texture details. A 3D-aware video-to-video refiner is learnt to further scale up the multi-view images with high-resolution texture details. Such high-resolution multi-view images are further augmented with novel views through 3D Gaussian Splatting, which are finally leveraged to obtain high-fidelity meshes via 3D reconstruction. Extensive experiments on both novel view synthesis and single view reconstruction demonstrate that our Hi3D manages to produce superior multi-view consistency images with highly-detailed textures. Source code and data are available at https://github.com/yanghb22-fdu/Hi3D-Official.

While generative artificial intelligence has advanced significantly across text, image, audio, and video domains, 3D generation remains comparatively underdeveloped due to fundamental challenges such as data scarcity, algorithmic limitations, and ecosystem fragmentation. To this end, we present Step1X-3D, an open framework addressing these challenges through: (1) a rigorous data curation pipeline processing >5M assets to create a 2M high-quality dataset with standardized geometric and textural properties; (2) a two-stage 3D-native architecture combining a hybrid VAE-DiT geometry generator with an diffusion-based texture synthesis module; and (3) the full open-source release of models, training code, and adaptation modules. For geometry generation, the hybrid VAE-DiT component produces TSDF representations by employing perceiver-based latent encoding with sharp edge sampling for detail preservation. The diffusion-based texture synthesis module then ensures cross-view consistency through geometric conditioning and latent-space synchronization. Benchmark results demonstrate state-of-the-art performance that exceeds existing open-source methods, while also achieving competitive quality with proprietary solutions. Notably, the framework uniquely bridges the 2D and 3D generation paradigms by supporting direct transfer of 2D control techniques~(e.g., LoRA) to 3D synthesis. By simultaneously advancing data quality, algorithmic fidelity, and reproducibility, Step1X-3D aims to establish new standards for open research in controllable 3D asset generation.

We introduce Garment3DGen a new method to synthesize 3D garment assets from a base mesh given a single input image as guidance. Our proposed approach allows users to generate 3D textured clothes based on both real and synthetic images, such as those generated by text prompts. The generated assets can be directly draped and simulated on human bodies. First, we leverage the recent progress of image to 3D diffusion methods to generate 3D garment geometries. However, since these geometries cannot be utilized directly for downstream tasks, we propose to use them as pseudo ground-truth and set up a mesh deformation optimization procedure that deforms a base template mesh to match the generated 3D target. Second, we introduce carefully designed losses that allow the input base mesh to freely deform towards the desired target, yet preserve mesh quality and topology such that they can be simulated. Finally, a texture estimation module generates high-fidelity texture maps that are globally and locally consistent and faithfully capture the input guidance, allowing us to render the generated 3D assets. With Garment3DGen users can generate the textured 3D garment of their choice without the need of artist intervention. One can provide a textual prompt describing the garment they desire to generate a simulation-ready 3D asset. We present a plethora of quantitative and qualitative comparisons on various assets both real and generated and provide use-cases of how one can generate simulation-ready 3D garments.

In this work, we introduce Unique3D, a novel image-to-3D framework for efficiently generating high-quality 3D meshes from single-view images, featuring state-of-the-art generation fidelity and strong generalizability. Previous methods based on Score Distillation Sampling (SDS) can produce diversified 3D results by distilling 3D knowledge from large 2D diffusion models, but they usually suffer from long per-case optimization time with inconsistent issues. Recent works address the problem and generate better 3D results either by finetuning a multi-view diffusion model or training a fast feed-forward model. However, they still lack intricate textures and complex geometries due to inconsistency and limited generated resolution. To simultaneously achieve high fidelity, consistency, and efficiency in single image-to-3D, we propose a novel framework Unique3D that includes a multi-view diffusion model with a corresponding normal diffusion model to generate multi-view images with their normal maps, a multi-level upscale process to progressively improve the resolution of generated orthographic multi-views, as well as an instant and consistent mesh reconstruction algorithm called ISOMER, which fully integrates the color and geometric priors into mesh results. Extensive experiments demonstrate that our Unique3D significantly outperforms other image-to-3D baselines in terms of geometric and textural details.

The D4D Dataset provides paired endoscopic video and high-quality structured-light geometry for evaluating 3D reconstruction of deforming abdominal soft tissue in realistic surgical conditions. Data were acquired from six porcine cadaver sessions using a da Vinci Xi stereo endoscope and a Zivid structured-light camera, registered via optical tracking and manually curated iterative alignment methods. Three sequence types - whole deformations, incremental deformations, and moved-camera clips - probe algorithm robustness to non-rigid motion, deformation magnitude, and out-of-view updates. Each clip provides rectified stereo images, per-frame instrument masks, stereo depth, start/end structured-light point clouds, curated camera poses and camera intrinsics. In postprocessing, ICP and semi-automatic registration techniques are used to register data, and instrument masks are created. The dataset enables quantitative geometric evaluation in both visible and occluded regions, alongside photometric view-synthesis baselines. Comprising over 300,000 frames and 369 point clouds across 98 curated recordings, this resource can serve as a comprehensive benchmark for developing and evaluating non-rigid SLAM, 4D reconstruction, and depth estimation methods.

Proteins move and deform to ensure their biological functions. Despite significant progress in protein structure prediction, approximating conformational ensembles at physiological conditions remains a fundamental open problem. This paper presents a novel perspective on the problem by directly targeting continuous compact representations of protein motions inferred from sparse experimental observations. We develop a task-specific loss function enforcing data symmetries, including scaling and permutation operations. Our method PETIMOT (Protein sEquence and sTructure-based Inference of MOTions) leverages transfer learning from pre-trained protein language models through an SE(3)-equivariant graph neural network. When trained and evaluated on the Protein Data Bank, PETIMOT shows superior performance in time and accuracy, capturing protein dynamics, particularly large/slow conformational changes, compared to state-of-the-art flow-matching approaches and traditional physics-based models.

Synthesizability remains a critical bottleneck in generative molecular design. While recent advances have addressed synthesizability in 2D graphs, extending these constraints to 3D for geometry-based conditional generation remains largely unexplored. In this work, we present SynCoGen (Synthesizable Co-Generation), a single framework that combines simultaneous masked graph diffusion and flow matching for synthesizable 3D molecule generation. SynCoGen samples from the joint distribution of molecular building blocks, chemical reactions, and atomic coordinates. To train the model, we curated SynSpace, a dataset family containing over 1.2M synthesis-aware building block graphs and 7.5M conformers. SynCoGen achieves state-of-the-art performance in unconditional small molecule graph and conformer co-generation. For protein ligand generation in drug discovery, the amortized model delivers superior performance in both molecular linker design and pharmacophore-conditioned generation across diverse targets without relying on any scoring functions. Overall, this multimodal non-autoregressive formulation represents a foundation for a range of molecular design applications, including analog expansion, lead optimization, and direct de novo design.

We address the problem of aligning real-world 3D data of garments, which benefits many applications such as texture learning, physical parameter estimation, generative modeling of garments, etc. Existing extrinsic methods typically perform non-rigid iterative closest point and struggle to align details due to incorrect closest matches and rigidity constraints. While intrinsic methods based on functional maps can produce high-quality correspondences, they work under isometric assumptions and become unreliable for garment deformations which are highly non-isometric. To achieve wrinkle-level as well as texture-level alignment, we present a novel coarse-to-fine two-stage method that leverages intrinsic manifold properties with two neural deformation fields, in the 3D space and the intrinsic space, respectively. The coarse stage performs a 3D fitting, where we leverage intrinsic manifold properties to define a manifold deformation field. The coarse fitting then induces a functional map that produces an alignment of intrinsic embeddings. We further refine the intrinsic alignment with a second neural deformation field for higher accuracy. We evaluate our method with our captured garment dataset, GarmCap. The method achieves accurate wrinkle-level and texture-level alignment and works for difficult garment types such as long coats. Our project page is https://jsnln.github.io/iccv2023_intrinsic/index.html.

Animating a newly designed character using motion capture (mocap) data is a long standing problem in computer animation. A key consideration is the skeletal structure that should correspond to the available mocap data, and the shape deformation in the joint regions, which often requires a tailored, pose-specific refinement. In this work, we develop a neural technique for articulating 3D characters using enveloping with a pre-defined skeletal structure which produces high quality pose dependent deformations. Our framework learns to rig and skin characters with the same articulation structure (e.g., bipeds or quadrupeds), and builds the desired skeleton hierarchy into the network architecture. Furthermore, we propose neural blend shapes--a set of corrective pose-dependent shapes which improve the deformation quality in the joint regions in order to address the notorious artifacts resulting from standard rigging and skinning. Our system estimates neural blend shapes for input meshes with arbitrary connectivity, as well as weighting coefficients which are conditioned on the input joint rotations. Unlike recent deep learning techniques which supervise the network with ground-truth rigging and skinning parameters, our approach does not assume that the training data has a specific underlying deformation model. Instead, during training, the network observes deformed shapes and learns to infer the corresponding rig, skin and blend shapes using indirect supervision. During inference, we demonstrate that our network generalizes to unseen characters with arbitrary mesh connectivity, including unrigged characters built by 3D artists. Conforming to standard skeletal animation models enables direct plug-and-play in standard animation software, as well as game engines.

With their meaningful geometry and their omnipresence in the 3D world, edges are extremely useful primitives in computer vision. 3D edges comprise of lines and curves, and methods to reconstruct them use either multi-view images or point clouds as input. State-of-the-art image-based methods first learn a 3D edge point cloud then fit 3D edges to it. The edge point cloud is obtained by learning a 3D neural implicit edge field from which the 3D edge points are sampled on a specific level set (0 or 1). However, such methods present two important drawbacks: i) it is not realistic to sample points on exact level sets due to float imprecision and training inaccuracies. Instead, they are sampled within a range of levels so the points do not lie accurately on the 3D edges and require further processing. ii) Such implicit representations are computationally expensive and require long training times. In this paper, we address these two limitations and propose a 3D edge mapping that is simpler, more efficient, and preserves accuracy. Our method learns explicitly the 3D edge points and their edge direction hence bypassing the need for point sampling. It casts a 3D edge point as the center of a 3D Gaussian and the edge direction as the principal axis of the Gaussian. Such a representation has the advantage of being not only geometrically meaningful but also compatible with the efficient training optimization defined in Gaussian Splatting. Results show that the proposed method produces edges as accurate and complete as the state-of-the-art while being an order of magnitude faster. Code is released at https://github.com/kunalchelani/EdgeGaussians.

Generating 3D models lies at the core of computer graphics and has been the focus of decades of research. With the emergence of advanced neural representations and generative models, the field of 3D content generation is developing rapidly, enabling the creation of increasingly high-quality and diverse 3D models. The rapid growth of this field makes it difficult to stay abreast of all recent developments. In this survey, we aim to introduce the fundamental methodologies of 3D generation methods and establish a structured roadmap, encompassing 3D representation, generation methods, datasets, and corresponding applications. Specifically, we introduce the 3D representations that serve as the backbone for 3D generation. Furthermore, we provide a comprehensive overview of the rapidly growing literature on generation methods, categorized by the type of algorithmic paradigms, including feedforward generation, optimization-based generation, procedural generation, and generative novel view synthesis. Lastly, we discuss available datasets, applications, and open challenges. We hope this survey will help readers explore this exciting topic and foster further advancements in the field of 3D content generation.

Volumetry is one of the principal downstream applications of 3D medical image segmentation, for example, to detect abnormal tissue growth or for surgery planning. Conformal Prediction is a promising framework for uncertainty quantification, providing calibrated predictive intervals associated with automatic volume measurements. However, this methodology is based on the hypothesis that calibration and test samples are exchangeable, an assumption that is in practice often violated in medical image applications. A weighted formulation of Conformal Prediction can be framed to mitigate this issue, but its empirical investigation in the medical domain is still lacking. A potential reason is that it relies on the estimation of the density ratio between the calibration and test distributions, which is likely to be intractable in scenarios involving high-dimensional data. To circumvent this, we propose an efficient approach for density ratio estimation relying on the compressed latent representations generated by the segmentation model. Our experiments demonstrate the efficiency of our approach to reduce the coverage error in the presence of covariate shifts, in both synthetic and real-world settings. Our implementation is available at https://github.com/benolmbrt/wcp_miccai

Unsupervised learning of 3D-aware generative adversarial networks has lately made much progress. Some recent work demonstrates promising results of learning human generative models using neural articulated radiance fields, yet their generalization ability and controllability lag behind parametric human models, i.e., they do not perform well when generalizing to novel pose/shape and are not part controllable. To solve these problems, we propose VeRi3D, a generative human vertex-based radiance field parameterized by vertices of the parametric human template, SMPL. We map each 3D point to the local coordinate system defined on its neighboring vertices, and use the corresponding vertex feature and local coordinates for mapping it to color and density values. We demonstrate that our simple approach allows for generating photorealistic human images with free control over camera pose, human pose, shape, as well as enabling part-level editing.

Large Reconstruction Models have made significant strides in the realm of automated 3D content generation from single or multiple input images. Despite their success, these models often produce 3D meshes with geometric inaccuracies, stemming from the inherent challenges of deducing 3D shapes solely from image data. In this work, we introduce a novel framework, the Large Image and Point Cloud Alignment Model (LAM3D), which utilizes 3D point cloud data to enhance the fidelity of generated 3D meshes. Our methodology begins with the development of a point-cloud-based network that effectively generates precise and meaningful latent tri-planes, laying the groundwork for accurate 3D mesh reconstruction. Building upon this, our Image-Point-Cloud Feature Alignment technique processes a single input image, aligning to the latent tri-planes to imbue image features with robust 3D information. This process not only enriches the image features but also facilitates the production of high-fidelity 3D meshes without the need for multi-view input, significantly reducing geometric distortions. Our approach achieves state-of-the-art high-fidelity 3D mesh reconstruction from a single image in just 6 seconds, and experiments on various datasets demonstrate its effectiveness.

Autoregressive models have achieved remarkable success across various domains, yet their performance in 3D shape generation lags significantly behind that of diffusion models. In this paper, we introduce OctGPT, a novel multiscale autoregressive model for 3D shape generation that dramatically improves the efficiency and performance of prior 3D autoregressive approaches, while rivaling or surpassing state-of-the-art diffusion models. Our method employs a serialized octree representation to efficiently capture the hierarchical and spatial structures of 3D shapes. Coarse geometry is encoded via octree structures, while fine-grained details are represented by binary tokens generated using a vector quantized variational autoencoder (VQVAE), transforming 3D shapes into compact multiscale binary sequences suitable for autoregressive prediction. To address the computational challenges of handling long sequences, we incorporate octree-based transformers enhanced with 3D rotary positional encodings, scale-specific embeddings, and token-parallel generation schemes. These innovations reduce training time by 13 folds and generation time by 69 folds, enabling the efficient training of high-resolution 3D shapes, e.g.,1024^3, on just four NVIDIA 4090 GPUs only within days. OctGPT showcases exceptional versatility across various tasks, including text-, sketch-, and image-conditioned generation, as well as scene-level synthesis involving multiple objects. Extensive experiments demonstrate that OctGPT accelerates convergence and improves generation quality over prior autoregressive methods, offering a new paradigm for high-quality, scalable 3D content creation.

From an image of a person, we can easily infer the natural 3D pose and shape of the person even if ambiguity exists. This is because we have a mental model that allows us to imagine a person's appearance at different viewing directions from a given image and utilize the consistency between them for inference. However, existing human mesh recovery methods only consider the direction in which the image was taken due to their structural limitations. Hence, we propose "Implicit 3D Human Mesh Recovery (ImpHMR)" that can implicitly imagine a person in 3D space at the feature-level via Neural Feature Fields. In ImpHMR, feature fields are generated by CNN-based image encoder for a given image. Then, the 2D feature map is volume-rendered from the feature field for a given viewing direction, and the pose and shape parameters are regressed from the feature. To utilize consistency with pose and shape from unseen-view, if there are 3D labels, the model predicts results including the silhouette from an arbitrary direction and makes it equal to the rotated ground-truth. In the case of only 2D labels, we perform self-supervised learning through the constraint that the pose and shape parameters inferred from different directions should be the same. Extensive evaluations show the efficacy of the proposed method.

3D reconstruction, which aims to recover the dense three-dimensional structure of a scene, is a cornerstone technology for numerous applications, including augmented/virtual reality, autonomous driving, and robotics. While traditional pipelines like Structure from Motion (SfM) and Multi-View Stereo (MVS) achieve high precision through iterative optimization, they are limited by complex workflows, high computational cost, and poor robustness in challenging scenarios like texture-less regions. Recently, deep learning has catalyzed a paradigm shift in 3D reconstruction. A new family of models, exemplified by DUSt3R, has pioneered a feed-forward approach. These models employ a unified deep network to jointly infer camera poses and dense geometry directly from an Unconstrained set of images in a single forward pass. This survey provides a systematic review of this emerging domain. We begin by dissecting the technical framework of these feed-forward models, including their Transformer-based correspondence modeling, joint pose and geometry regression mechanisms, and strategies for scaling from two-view to multi-view scenarios. To highlight the disruptive nature of this new paradigm, we contrast it with both traditional pipelines and earlier learning-based methods like MVSNet. Furthermore, we provide an overview of relevant datasets and evaluation metrics. Finally, we discuss the technology's broad application prospects and identify key future challenges and opportunities, such as model accuracy and scalability, and handling dynamic scenes.

Text-to-3D generation has achieved significant success by incorporating powerful 2D diffusion models, but insufficient 3D prior knowledge also leads to the inconsistency of 3D geometry. Recently, since large-scale multi-view datasets have been released, fine-tuning the diffusion model on the multi-view datasets becomes a mainstream to solve the 3D inconsistency problem. However, it has confronted with fundamental difficulties regarding the limited quality and diversity of 3D data, compared with 2D data. To sidestep these trade-offs, we explore a retrieval-augmented approach tailored for score distillation, dubbed RetDream. We postulate that both expressiveness of 2D diffusion models and geometric consistency of 3D assets can be fully leveraged by employing the semantically relevant assets directly within the optimization process. To this end, we introduce novel framework for retrieval-based quality enhancement in text-to-3D generation. We leverage the retrieved asset to incorporate its geometric prior in the variational objective and adapt the diffusion model's 2D prior toward view consistency, achieving drastic improvements in both geometry and fidelity of generated scenes. We conduct extensive experiments to demonstrate that RetDream exhibits superior quality with increased geometric consistency. Project page is available at https://ku-cvlab.github.io/RetDream/.

Recent multimodal large language models have achieved strong performance in unified text and image understanding and generation, yet extending such native capability to 3D remains challenging due to limited data. Compared to abundant 2D imagery, high-quality 3D assets are scarce, making 3D synthesis under-constrained. Existing methods often rely on indirect pipelines that edit in 2D and lift results into 3D via optimization, sacrificing geometric consistency. We present Omni123, a 3D-native foundation model that unifies text-to-2D and text-to-3D generation within a single autoregressive framework. Our key insight is that cross-modal consistency between images and 3D can serve as an implicit structural constraint. By representing text, images, and 3D as discrete tokens in a shared sequence space, the model leverages abundant 2D data as a geometric prior to improve 3D representations. We introduce an interleaved X-to-X training paradigm that coordinates diverse cross-modal tasks over heterogeneous paired datasets without requiring fully aligned text-image-3D triplets. By traversing semantic-visual-geometric cycles (e.g., text to image to 3D to image) within autoregressive sequences, the model jointly enforces semantic alignment, appearance fidelity, and multi-view geometric consistency. Experiments show that Omni123 significantly improves text-guided 3D generation and editing, demonstrating a scalable path toward multimodal 3D world models.

We introduce CLR-Wire, a novel framework for 3D curve-based wireframe generation that integrates geometry and topology into a unified Continuous Latent Representation. Unlike conventional methods that decouple vertices, edges, and faces, CLR-Wire encodes curves as Neural Parametric Curves along with their topological connectivity into a continuous and fixed-length latent space using an attention-driven variational autoencoder (VAE). This unified approach facilitates joint learning and generation of both geometry and topology. To generate wireframes, we employ a flow matching model to progressively map Gaussian noise to these latents, which are subsequently decoded into complete 3D wireframes. Our method provides fine-grained modeling of complex shapes and irregular topologies, and supports both unconditional generation and generation conditioned on point cloud or image inputs. Experimental results demonstrate that, compared with state-of-the-art generative approaches, our method achieves substantial improvements in accuracy, novelty, and diversity, offering an efficient and comprehensive solution for CAD design, geometric reconstruction, and 3D content creation.

Learning 3D shape representation with dense correspondence for deformable objects is a fundamental problem in computer vision. Existing approaches often need additional annotations of specific semantic domain, e.g., skeleton poses for human bodies or animals, which require extra annotation effort and suffer from error accumulation, and they are limited to specific domain. In this paper, we propose a novel self-supervised approach to learn neural implicit shape representation for deformable objects, which can represent shapes with a template shape and dense correspondence in 3D. Our method does not require the priors of skeleton and skinning weight, and only requires a collection of shapes represented in signed distance fields. To handle the large deformation, we constrain the learned template shape in the same latent space with the training shapes, design a new formulation of local rigid constraint that enforces rigid transformation in local region and addresses local reflection issue, and present a new hierarchical rigid constraint to reduce the ambiguity due to the joint learning of template shape and correspondences. Extensive experiments show that our model can represent shapes with large deformations. We also show that our shape representation can support two typical applications, such as texture transfer and shape editing, with competitive performance. The code and models are available at https://iscas3dv.github.io/deformshape

In this paper, we study the problem of continuous 3D shape representations. The majority of existing successful methods are coordinate-based implicit neural representations. However, they are inefficient to render novel views or recover explicit surface points. A few works start to formulate 3D shapes as ray-based neural functions, but the learned structures are inferior due to the lack of multi-view geometry consistency. To tackle these challenges, we propose a new framework called RayDF. It consists of three major components: 1) the simple ray-surface distance field, 2) the novel dual-ray visibility classifier, and 3) a multi-view consistency optimization module to drive the learned ray-surface distances to be multi-view geometry consistent. We extensively evaluate our method on three public datasets, demonstrating remarkable performance in 3D surface point reconstruction on both synthetic and challenging real-world 3D scenes, clearly surpassing existing coordinate-based and ray-based baselines. Most notably, our method achieves a 1000x faster speed than coordinate-based methods to render an 800x800 depth image, showing the superiority of our method for 3D shape representation. Our code and data are available at https://github.com/vLAR-group/RayDF

Powerful priors allow us to perform inference with insufficient information. In this paper, we propose an autoregressive prior for 3D shapes to solve multimodal 3D tasks such as shape completion, reconstruction, and generation. We model the distribution over 3D shapes as a non-sequential autoregressive distribution over a discretized, low-dimensional, symbolic grid-like latent representation of 3D shapes. This enables us to represent distributions over 3D shapes conditioned on information from an arbitrary set of spatially anchored query locations and thus perform shape completion in such arbitrary settings (e.g., generating a complete chair given only a view of the back leg). We also show that the learned autoregressive prior can be leveraged for conditional tasks such as single-view reconstruction and language-based generation. This is achieved by learning task-specific naive conditionals which can be approximated by light-weight models trained on minimal paired data. We validate the effectiveness of the proposed method using both quantitative and qualitative evaluation and show that the proposed method outperforms the specialized state-of-the-art methods trained for individual tasks. The project page with code and video visualizations can be found at https://yccyenchicheng.github.io/AutoSDF/.

Recent approaches for predicting layouts from 360 panoramas produce excellent results. These approaches build on a common framework consisting of three steps: a pre-processing step based on edge-based alignment, prediction of layout elements, and a post-processing step by fitting a 3D layout to the layout elements. Until now, it has been difficult to compare the methods due to multiple different design decisions, such as the encoding network (e.g. SegNet or ResNet), type of elements predicted (e.g. corners, wall/floor boundaries, or semantic segmentation), or method of fitting the 3D layout. To address this challenge, we summarize and describe the common framework, the variants, and the impact of the design decisions. For a complete evaluation, we also propose extended annotations for the Matterport3D dataset [3], and introduce two depth-based evaluation metrics.

Human perception of 3D shapes goes beyond reconstructing them as a set of points or a composition of geometric primitives: we also effortlessly understand higher-level shape structure such as the repetition and reflective symmetry of object parts. In contrast, recent advances in 3D shape sensing focus more on low-level geometry but less on these higher-level relationships. In this paper, we propose 3D shape programs, integrating bottom-up recognition systems with top-down, symbolic program structure to capture both low-level geometry and high-level structural priors for 3D shapes. Because there are no annotations of shape programs for real shapes, we develop neural modules that not only learn to infer 3D shape programs from raw, unannotated shapes, but also to execute these programs for shape reconstruction. After initial bootstrapping, our end-to-end differentiable model learns 3D shape programs by reconstructing shapes in a self-supervised manner. Experiments demonstrate that our model accurately infers and executes 3D shape programs for highly complex shapes from various categories. It can also be integrated with an image-to-shape module to infer 3D shape programs directly from an RGB image, leading to 3D shape reconstructions that are both more accurate and more physically plausible.

Generating high-quality 3D assets from text and images has long been challenging, primarily due to the absence of scalable 3D representations capable of capturing intricate geometry distributions. In this work, we introduce Direct3D, a native 3D generative model scalable to in-the-wild input images, without requiring a multiview diffusion model or SDS optimization. Our approach comprises two primary components: a Direct 3D Variational Auto-Encoder (D3D-VAE) and a Direct 3D Diffusion Transformer (D3D-DiT). D3D-VAE efficiently encodes high-resolution 3D shapes into a compact and continuous latent triplane space. Notably, our method directly supervises the decoded geometry using a semi-continuous surface sampling strategy, diverging from previous methods relying on rendered images as supervision signals. D3D-DiT models the distribution of encoded 3D latents and is specifically designed to fuse positional information from the three feature maps of the triplane latent, enabling a native 3D generative model scalable to large-scale 3D datasets. Additionally, we introduce an innovative image-to-3D generation pipeline incorporating semantic and pixel-level image conditions, allowing the model to produce 3D shapes consistent with the provided conditional image input. Extensive experiments demonstrate the superiority of our large-scale pre-trained Direct3D over previous image-to-3D approaches, achieving significantly better generation quality and generalization ability, thus establishing a new state-of-the-art for 3D content creation. Project page: https://nju-3dv.github.io/projects/Direct3D/.

Recently, image-to-3D approaches have achieved significant results with a natural image as input. However, it is not always possible to access these enriched color input samples in practical applications, where only sketches are available. Existing sketch-to-3D researches suffer from limitations in broad applications due to the challenges of lacking color information and multi-view content. To overcome them, this paper proposes a novel generation paradigm Sketch3D to generate realistic 3D assets with shape aligned with the input sketch and color matching the textual description. Concretely, Sketch3D first instantiates the given sketch in the reference image through the shape-preserving generation process. Second, the reference image is leveraged to deduce a coarse 3D Gaussian prior, and multi-view style-consistent guidance images are generated based on the renderings of the 3D Gaussians. Finally, three strategies are designed to optimize 3D Gaussians, i.e., structural optimization via a distribution transfer mechanism, color optimization with a straightforward MSE loss and sketch similarity optimization with a CLIP-based geometric similarity loss. Extensive visual comparisons and quantitative analysis illustrate the advantage of our Sketch3D in generating realistic 3D assets while preserving consistency with the input.

Diffusion models have emerged as a powerful generative method, capable of producing stunning photo-realistic images from natural language descriptions. However, these models lack explicit control over the 3D structure in the generated images. Consequently, this hinders our ability to obtain detailed 3D annotations for the generated images or to craft instances with specific poses and distances. In this paper, we propose 3D Diffusion Style Transfer (3D-DST), which incorporates 3D geometry control into diffusion models. Our method exploits ControlNet, which extends diffusion models by using visual prompts in addition to text prompts. We generate images of the 3D objects taken from 3D shape repositories (e.g., ShapeNet and Objaverse), render them from a variety of poses and viewing directions, compute the edge maps of the rendered images, and use these edge maps as visual prompts to generate realistic images. With explicit 3D geometry control, we can easily change the 3D structures of the objects in the generated images and obtain ground-truth 3D annotations automatically. This allows us to improve a wide range of vision tasks, e.g., classification and 3D pose estimation, in both in-distribution (ID) and out-of-distribution (OOD) settings. We demonstrate the effectiveness of our method through extensive experiments on ImageNet-100/200, ImageNet-R, PASCAL3D+, ObjectNet3D, and OOD-CV. The results show that our method significantly outperforms existing methods, e.g., 3.8 percentage points on ImageNet-100 using DeiT-B.

Accurately estimating the 3D pose and shape is an essential step towards understanding animal behavior, and can potentially benefit many downstream applications, such as wildlife conservation. However, research in this area is held back by the lack of a comprehensive and diverse dataset with high-quality 3D pose and shape annotations. In this paper, we propose Animal3D, the first comprehensive dataset for mammal animal 3D pose and shape estimation. Animal3D consists of 3379 images collected from 40 mammal species, high-quality annotations of 26 keypoints, and importantly the pose and shape parameters of the SMAL model. All annotations were labeled and checked manually in a multi-stage process to ensure highest quality results. Based on the Animal3D dataset, we benchmark representative shape and pose estimation models at: (1) supervised learning from only the Animal3D data, (2) synthetic to real transfer from synthetically generated images, and (3) fine-tuning human pose and shape estimation models. Our experimental results demonstrate that predicting the 3D shape and pose of animals across species remains a very challenging task, despite significant advances in human pose estimation. Our results further demonstrate that synthetic pre-training is a viable strategy to boost the model performance. Overall, Animal3D opens new directions for facilitating future research in animal 3D pose and shape estimation, and is publicly available.

Recent advancements in large language models and their multi-modal extensions have demonstrated the effectiveness of unifying generation and understanding through autoregressive next-token prediction. However, despite the critical role of 3D structural generation and understanding ({3D GU}) in AI for science, these tasks have largely evolved independently, with autoregressive methods remaining underexplored. To bridge this gap, we introduce Uni-3DAR, a unified framework that seamlessly integrates {3D GU} tasks via autoregressive prediction. At its core, Uni-3DAR employs a novel hierarchical tokenization that compresses 3D space using an octree, leveraging the inherent sparsity of 3D structures. It then applies an additional tokenization for fine-grained structural details, capturing key attributes such as atom types and precise spatial coordinates in microscopic 3D structures. We further propose two optimizations to enhance efficiency and effectiveness. The first is a two-level subtree compression strategy, which reduces the octree token sequence by up to 8x. The second is a masked next-token prediction mechanism tailored for dynamically varying token positions, significantly boosting model performance. By combining these strategies, Uni-3DAR successfully unifies diverse {3D GU} tasks within a single autoregressive framework. Extensive experiments across multiple microscopic {3D GU} tasks, including molecules, proteins, polymers, and crystals, validate its effectiveness and versatility. Notably, Uni-3DAR surpasses previous state-of-the-art diffusion models by a substantial margin, achieving up to 256\% relative improvement while delivering inference speeds up to 21.8x faster. The code is publicly available at https://github.com/dptech-corp/Uni-3DAR.

With the growing demand for high-fidelity 3D models from 2D images, existing methods still face significant challenges in accurately reproducing fine-grained geometric details due to limitations in domain gaps and inherent ambiguities in RGB images. To address these issues, we propose Hi3DGen, a novel framework for generating high-fidelity 3D geometry from images via normal bridging. Hi3DGen consists of three key components: (1) an image-to-normal estimator that decouples the low-high frequency image pattern with noise injection and dual-stream training to achieve generalizable, stable, and sharp estimation; (2) a normal-to-geometry learning approach that uses normal-regularized latent diffusion learning to enhance 3D geometry generation fidelity; and (3) a 3D data synthesis pipeline that constructs a high-quality dataset to support training. Extensive experiments demonstrate the effectiveness and superiority of our framework in generating rich geometric details, outperforming state-of-the-art methods in terms of fidelity. Our work provides a new direction for high-fidelity 3D geometry generation from images by leveraging normal maps as an intermediate representation.

Graph neural networks that model 3D data, such as point clouds or atoms, are typically desired to be SO(3) equivariant, i.e., equivariant to 3D rotations. Unfortunately equivariant convolutions, which are a fundamental operation for equivariant networks, increase significantly in computational complexity as higher-order tensors are used. In this paper, we address this issue by reducing the SO(3) convolutions or tensor products to mathematically equivalent convolutions in SO(2) . This is accomplished by aligning the node embeddings' primary axis with the edge vectors, which sparsifies the tensor product and reduces the computational complexity from O(L^6) to O(L^3), where L is the degree of the representation. We demonstrate the potential implications of this improvement by proposing the Equivariant Spherical Channel Network (eSCN), a graph neural network utilizing our novel approach to equivariant convolutions, which achieves state-of-the-art results on the large-scale OC-20 and OC-22 datasets.

3D fragment reassembly aims to recover the rigid poses of unordered fragment point clouds or meshes in a common object coordinate system to reconstruct the complete shape. The problem becomes particularly challenging as the number of fragments grows, since the target shape is unknown and fragments provide weak semantic cues. Existing end-to-end approaches are prone to cascading failures due to unreliable contact reasoning, most notably inaccurate fragment adjacencies. To address this, we propose Structure-Aware Reassembly (SARe), a generative framework with SARe-Gen for Euclidean-space assembly generation and SARe-Refine for inference-time refinement, with explicit contact modeling. SARe-Gen jointly predicts fracture-surface token probabilities and an inter-fragment contact graph to localize contact regions and infer candidate adjacencies. It adopts a query-point-based conditioning scheme and extracts aligned local geometric tokens at query locations from a frozen geometry encoder, yielding queryable structural representations without additional structural pretraining. We further introduce an inference-time refinement stage, SARe-Refine. By verifying candidate contact edges with geometric-consistency checks, it selects reliable substructures and resamples the remaining uncertain regions while keeping verified parts fixed, leading to more stable and consistent assemblies in the many-fragment regime. We evaluate SARe across three settings, including synthetic fractures, simulated fractures from scanned real objects, and real physically fractured scans. The results demonstrate state-of-the-art performance, with more graceful degradation and higher success rates as the fragment count increases in challenging large-scale reassembly.

Massive molecular simulations of drug-target proteins have been used as a tool to understand disease mechanism and develop therapeutics. This work focuses on learning a generative neural network on a structural ensemble of a drug-target protein, e.g. SARS-CoV-2 Spike protein, obtained from computationally expensive molecular simulations. Model tasks involve characterizing the distinct structural fluctuations of the protein bound to various drug molecules, as well as efficient generation of protein conformations that can serve as an complement of a molecular simulation engine. Specifically, we present a geometric autoencoder framework to learn separate latent space encodings of the intrinsic and extrinsic geometries of the protein structure. For this purpose, the proposed Protein Geometric AutoEncoder (ProGAE) model is trained on the protein contact map and the orientation of the backbone bonds of the protein. Using ProGAE latent embeddings, we reconstruct and generate the conformational ensemble of a protein at or near the experimental resolution, while gaining better interpretability and controllability in term of protein structure generation from the learned latent space. Additionally, ProGAE models are transferable to a different state of the same protein or to a new protein of different size, where only the dense layer decoding from the latent representation needs to be retrained. Results show that our geometric learning-based method enjoys both accuracy and efficiency for generating complex structural variations, charting the path toward scalable and improved approaches for analyzing and enhancing high-cost simulations of drug-target proteins.