Daily Papers

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.

Accurate subsurface scattering solutions require the integration of optical material properties along many complicated light paths. We present a method that learns a simple geometric approximation of random paths in a homogeneous volume of translucent material. The generated representation allows determining the absorption along the path as well as a direct lighting contribution, which is representative of all scattering events along the path. A sequence of conditional variational auto-encoders (CVAEs) is trained to model the statistical distribution of the photon paths inside a spherical region in presence of multiple scattering events. A first CVAE learns to sample the number of scattering events, occurring on a ray path inside the sphere, which effectively determines the probability of the ray being absorbed. Conditioned on this, a second model predicts the exit position and direction of the light particle. Finally, a third model generates a representative sample of photon position and direction along the path, which is used to approximate the contribution of direct illumination due to in-scattering. To accelerate the tracing of the light path through the volumetric medium toward the solid boundary, we employ a sphere-tracing strategy that considers the light absorption and is able to perform statistically accurate next-event estimation. We demonstrate efficient learning using shallow networks of only three layers and no more than 16 nodes. In combination with a GPU shader that evaluates the CVAEs' predictions, performance gains can be demonstrated for a variety of different scenarios. A quality evaluation analyzes the approximation error that is introduced by the data-driven scattering simulation and sheds light on the major sources of error in the accelerated path tracing process.

This paper introduces a new interpretation of the Variational Autoencoder framework by taking a fully geometric point of view. We argue that vanilla VAE models unveil naturally a Riemannian structure in their latent space and that taking into consideration those geometrical aspects can lead to better interpolations and an improved generation procedure. This new proposed sampling method consists in sampling from the uniform distribution deriving intrinsically from the learned Riemannian latent space and we show that using this scheme can make a vanilla VAE competitive and even better than more advanced versions on several benchmark datasets. Since generative models are known to be sensitive to the number of training samples we also stress the method's robustness in the low data regime.

We investigate the problem of training generative models on a very sparse collection of 3D models. We use geometrically motivated energies to augment and thus boost a sparse collection of example (training) models. We analyze the Hessian of the as-rigid-as-possible (ARAP) energy to sample from and project to the underlying (local) shape space, and use the augmented dataset to train a variational autoencoder (VAE). We iterate the process of building latent spaces of VAE and augmenting the associated dataset, to progressively reveal a richer and more expressive generative space for creating geometrically and semantically valid samples. Our framework allows us to train generative 3D models even with a small set of good quality 3D models, which are typically hard to curate. We extensively evaluate our method against a set of strong baselines, provide ablation studies and demonstrate application towards establishing shape correspondences. We present multiple examples of interesting and meaningful shape variations even when starting from as few as 3-10 training shapes.

Deep neural networks are prone to adversarial examples that maliciously alter the network's outcome. Due to the increasing popularity of 3D sensors in safety-critical systems and the vast deployment of deep learning models for 3D point sets, there is a growing interest in adversarial attacks and defenses for such models. So far, the research has focused on the semantic level, namely, deep point cloud classifiers. However, point clouds are also widely used in a geometric-related form that includes encoding and reconstructing the geometry. In this work, we are the first to consider the problem of adversarial examples at a geometric level. In this setting, the question is how to craft a small change to a clean source point cloud that leads, after passing through an autoencoder model, to the reconstruction of a different target shape. Our attack is in sharp contrast to existing semantic attacks on 3D point clouds. While such works aim to modify the predicted label by a classifier, we alter the entire reconstructed geometry. Additionally, we demonstrate the robustness of our attack in the case of defense, where we show that remnant characteristics of the target shape are still present at the output after applying the defense to the adversarial input. Our code is publicly available at https://github.com/itailang/geometric_adv.

Graph neural networks (GNNs) have been used extensively for addressing problems in drug design and discovery. Both ligand and target molecules are represented as graphs with node and edge features encoding information about atomic elements and bonds respectively. Although existing deep learning models perform remarkably well at predicting physicochemical properties and binding affinities, the generation of new molecules with optimized properties remains challenging. Inherently, most GNNs perform poorly in whole-graph representation due to the limitations of the message-passing paradigm. Furthermore, step-by-step graph generation frameworks that use reinforcement learning or other sequential processing can be slow and result in a high proportion of invalid molecules with substantial post-processing needed in order to satisfy the principles of stoichiometry. To address these issues, we propose a representation-first approach to molecular graph generation. We guide the latent representation of an autoencoder by capturing graph structure information with the geometric scattering transform and apply penalties that structure the representation also by molecular properties. We show that this highly structured latent space can be directly used for molecular graph generation by the use of a GAN. We demonstrate that our architecture learns meaningful representations of drug datasets and provides a platform for goal-directed drug synthesis.

This paper tries to address a fundamental question in point cloud self-supervised learning: what is a good signal we should leverage to learn features from point clouds without annotations? To answer that, we introduce a point cloud representation learning framework, based on geometric feature reconstruction. In contrast to recent papers that directly adopt masked autoencoder (MAE) and only predict original coordinates or occupancy from masked point clouds, our method revisits differences between images and point clouds and identifies three self-supervised learning objectives peculiar to point clouds, namely centroid prediction, normal estimation, and curvature prediction. Combined with occupancy prediction, these four objectives yield an nontrivial self-supervised learning task and mutually facilitate models to better reason fine-grained geometry of point clouds. Our pipeline is conceptually simple and it consists of two major steps: first, it randomly masks out groups of points, followed by a Transformer-based point cloud encoder; second, a lightweight Transformer decoder predicts centroid, normal, and curvature for points in each voxel. We transfer the pre-trained Transformer encoder to a downstream peception model. On the nuScene Datset, our model achieves 3.38 mAP improvment for object detection, 2.1 mIoU gain for segmentation, and 1.7 AMOTA gain for multi-object tracking. We also conduct experiments on the Waymo Open Dataset and achieve significant performance improvements over baselines as well.

In this paper we study generative modeling via autoencoders while using the elegant geometric properties of the optimal transport (OT) problem and the Wasserstein distances. We introduce Sliced-Wasserstein Autoencoders (SWAE), which are generative models that enable one to shape the distribution of the latent space into any samplable probability distribution without the need for training an adversarial network or defining a closed-form for the distribution. In short, we regularize the autoencoder loss with the sliced-Wasserstein distance between the distribution of the encoded training samples and a predefined samplable distribution. We show that the proposed formulation has an efficient numerical solution that provides similar capabilities to Wasserstein Autoencoders (WAE) and Variational Autoencoders (VAE), while benefiting from an embarrassingly simple implementation.

A triangular mesh is one of the most popular 3D data representations. As such, the deployment of deep neural networks for mesh processing is widely spread and is increasingly attracting more attention. However, neural networks are prone to adversarial attacks, where carefully crafted inputs impair the model's functionality. The need to explore these vulnerabilities is a fundamental factor in the future development of 3D-based applications. Recently, mesh attacks were studied on the semantic level, where classifiers are misled to produce wrong predictions. Nevertheless, mesh surfaces possess complex geometric attributes beyond their semantic meaning, and their analysis often includes the need to encode and reconstruct the geometry of the shape. We propose a novel framework for a geometric adversarial attack on a 3D mesh autoencoder. In this setting, an adversarial input mesh deceives the autoencoder by forcing it to reconstruct a different geometric shape at its output. The malicious input is produced by perturbing a clean shape in the spectral domain. Our method leverages the spectral decomposition of the mesh along with additional mesh-related properties to obtain visually credible results that consider the delicacy of surface distortions. Our code is publicly available at https://github.com/StolikTomer/SAGA.

Hand-object pose estimation from monocular RGB images remains a significant challenge mainly due to the severe occlusions inherent in hand-object interactions. Existing methods do not sufficiently explore global structural perception and reasoning, which limits their effectiveness in handling occluded hand-object interactions. To address this challenge, we propose an occlusion-aware hand-object pose estimation method based on masked autoencoders, termed as HOMAE. Specifically, we propose a target-focused masking strategy that imposes structured occlusion on regions of hand-object interaction, encouraging the model to learn context-aware features and reason about the occluded structures. We further integrate multi-scale features extracted from the decoder to predict a signed distance field (SDF), capturing both global context and fine-grained geometry. To enhance geometric perception, we combine the implicit SDF with an explicit point cloud derived from the SDF, leveraging the complementary strengths of both representations. This fusion enables more robust handling of occluded regions by combining the global context from the SDF with the precise local geometry provided by the point cloud. Extensive experiments on challenging DexYCB and HO3Dv2 benchmarks demonstrate that HOMAE achieves state-of-the-art performance in hand-object pose estimation. We will release our code and model.

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.

Triangle meshes are fundamental to 3D applications, enabling efficient modification and rasterization while maintaining compatibility with standard rendering pipelines. However, current automatic mesh generation methods typically rely on intermediate representations that lack the continuous surface quality inherent to meshes. Converting these representations into meshes produces dense, suboptimal outputs. Although recent autoregressive approaches demonstrate promise in directly modeling mesh vertices and faces, they are constrained by the limitation in face count, scalability, and structural fidelity. To address these challenges, we propose Nautilus, a locality-aware autoencoder for artist-like mesh generation that leverages the local properties of manifold meshes to achieve structural fidelity and efficient representation. Our approach introduces a novel tokenization algorithm that preserves face proximity relationships and compresses sequence length through locally shared vertices and edges, enabling the generation of meshes with an unprecedented scale of up to 5,000 faces. Furthermore, we develop a Dual-stream Point Conditioner that provides multi-scale geometric guidance, ensuring global consistency and local structural fidelity by capturing fine-grained geometric features. Extensive experiments demonstrate that Nautilus significantly outperforms state-of-the-art methods in both fidelity and scalability. The project page is at https://nautilusmeshgen.github.io.

In recent years, the field of 3D self-supervised learning has witnessed significant progress, resulting in the emergence of Multi-Modality Masked AutoEncoders (MAE) methods that leverage both 2D images and 3D point clouds for pre-training. However, a notable limitation of these approaches is that they do not fully utilize the multi-view attributes inherent in 3D point clouds, which is crucial for a deeper understanding of 3D structures. Building upon this insight, we introduce a novel approach employing a 3D to multi-view masked autoencoder to fully harness the multi-modal attributes of 3D point clouds. To be specific, our method uses the encoded tokens from 3D masked point clouds to generate original point clouds and multi-view depth images across various poses. This approach not only enriches the model's comprehension of geometric structures but also leverages the inherent multi-modal properties of point clouds. Our experiments illustrate the effectiveness of the proposed method for different tasks and under different settings. Remarkably, our method outperforms state-of-the-art counterparts by a large margin in a variety of downstream tasks, including 3D object classification, few-shot learning, part segmentation, and 3D object detection. Code will be available at: https://github.com/Zhimin-C/Multiview-MAE

Self-supervised learning (SSL) has demonstrated remarkable success in 3D point cloud analysis, particularly through masked autoencoders (MAEs). However, existing MAE-based methods lack rotation invariance, leading to significant performance degradation when processing arbitrarily rotated point clouds in real-world scenarios. To address this limitation, we introduce Handcrafted Feature-Based Rotation-Invariant Masked Autoencoder (HFBRI-MAE), a novel framework that refines the MAE design with rotation-invariant handcrafted features to ensure stable feature learning across different orientations. By leveraging both rotation-invariant local and global features for token embedding and position embedding, HFBRI-MAE effectively eliminates rotational dependencies while preserving rich geometric structures. Additionally, we redefine the reconstruction target to a canonically aligned version of the input, mitigating rotational ambiguities. Extensive experiments on ModelNet40, ScanObjectNN, and ShapeNetPart demonstrate that HFBRI-MAE consistently outperforms existing methods in object classification, segmentation, and few-shot learning, highlighting its robustness and strong generalization ability in real-world 3D applications.

This paper introduces a novel hierarchical autoencoder that maps 3D models into a highly compressed latent space. The hierarchical autoencoder is specifically designed to tackle the challenges arising from large-scale datasets and generative modeling using diffusion. Different from previous approaches that only work on a regular image or volume grid, our hierarchical autoencoder operates on unordered sets of vectors. Each level of the autoencoder controls different geometric levels of detail. We show that the model can be used to represent a wide range of 3D models while faithfully representing high-resolution geometry details. The training of the new architecture takes 0.70x time and 0.58x memory compared to the baseline. We also explore how the new representation can be used for generative modeling. Specifically, we propose a cascaded diffusion framework where each stage is conditioned on the previous stage. Our design extends existing cascaded designs for image and volume grids to vector sets.

We present a new approach for generating 3D house wireframes with semantic enrichment using an autoregressive model. Unlike conventional generative models that independently process vertices, edges, and faces, our approach employs a unified wire-based representation for improved coherence in learning 3D wireframe structures. By re-ordering wire sequences based on semantic meanings, we facilitate seamless semantic integration during sequence generation. Our two-phase technique merges a graph-based autoencoder with a transformer-based decoder to learn latent geometric tokens and generate semantic-aware wireframes. Through iterative prediction and decoding during inference, our model produces detailed wireframes that can be easily segmented into distinct components, such as walls, roofs, and rooms, reflecting the semantic essence of the shape. Empirical results on a comprehensive house dataset validate the superior accuracy, novelty, and semantic fidelity of our model compared to existing generative models. More results and details can be found on https://vcc.tech/research/2024/3DWire.

Iris-based biometric systems are vulnerable to presentation attacks (PAs), where adversaries present physical artifacts (e.g., printed iris images, textured contact lenses) to defeat the system. This has led to the development of various presentation attack detection (PAD) algorithms, which typically perform well in intra-domain settings. However, they often struggle to generalize effectively in cross-domain scenarios, where training and testing employ different sensors, PA instruments, and datasets. In this work, we use adversarial training samples of both bonafide irides and PAs to improve the cross-domain performance of a PAD classifier. The novelty of our approach lies in leveraging transformation parameters from classical data augmentation schemes (e.g., translation, rotation) to generate adversarial samples. We achieve this through a convolutional autoencoder, ADV-GEN, that inputs original training samples along with a set of geometric and photometric transformations. The transformation parameters act as regularization variables, guiding ADV-GEN to generate adversarial samples in a constrained search space. Experiments conducted on the LivDet-Iris 2017 database, comprising four datasets, and the LivDet-Iris 2020 dataset, demonstrate the efficacy of our proposed method. The code is available at https://github.com/iPRoBe-lab/ADV-GEN-IrisPAD.

This paper introduces Least Volume-a simple yet effective regularization inspired by geometric intuition-that can reduce the necessary number of latent dimensions needed by an autoencoder without requiring any prior knowledge of the intrinsic dimensionality of the dataset. We show that the Lipschitz continuity of the decoder is the key to making it work, provide a proof that PCA is just a linear special case of it, and reveal that it has a similar PCA-like importance ordering effect when applied to nonlinear models. We demonstrate the intuition behind the regularization on some pedagogical toy problems, and its effectiveness on several benchmark problems, including MNIST, CIFAR-10 and CelebA.

Geometric alignment appears in a variety of applications, ranging from domain adaptation, optimal transport, and normalizing flows in machine learning; optical flow and learned augmentation in computer vision and deformable registration within biomedical imaging. A recurring challenge is the alignment of domains whose topology is not the same; a problem that is routinely ignored, potentially introducing bias in downstream analysis. As a first step towards solving such alignment problems, we propose an unsupervised algorithm for the detection of changes in image topology. The model is based on a conditional variational auto-encoder and detects topological changes between two images during the registration step. We account for both topological changes in the image under spatial variation and unexpected transformations. Our approach is validated on two tasks and datasets: detection of topological changes in microscopy images of cells, and unsupervised anomaly detection brain imaging.

In this paper, we introduce MeshGen, an advanced image-to-3D pipeline that generates high-quality 3D meshes with detailed geometry and physically based rendering (PBR) textures. Addressing the challenges faced by existing 3D native diffusion models, such as suboptimal auto-encoder performance, limited controllability, poor generalization, and inconsistent image-based PBR texturing, MeshGen employs several key innovations to overcome these limitations. We pioneer a render-enhanced point-to-shape auto-encoder that compresses meshes into a compact latent space by designing perceptual optimization with ray-based regularization. This ensures that the 3D shapes are accurately represented and reconstructed to preserve geometric details within the latent space. To address data scarcity and image-shape misalignment, we further propose geometric augmentation and generative rendering augmentation techniques, which enhance the model's controllability and generalization ability, allowing it to perform well even with limited public datasets. For the texture generation, MeshGen employs a reference attention-based multi-view ControlNet for consistent appearance synthesis. This is further complemented by our multi-view PBR decomposer that estimates PBR components and a UV inpainter that fills invisible areas, ensuring a seamless and consistent texture across the 3D mesh. Our extensive experiments demonstrate that MeshGen largely outperforms previous methods in both shape and texture generation, setting a new standard for the quality of 3D meshes generated with PBR textures. See our code at https://github.com/heheyas/MeshGen, project page https://heheyas.github.io/MeshGen

Most image watermarking systems focus on robustness, capacity, and imperceptibility while treating the embedded payload as meaningless bits. This bit-centric view imposes a hard ceiling on capacity and prevents watermarks from carrying useful information. We propose LatentSeal, which reframes watermarking as semantic communication: a lightweight text autoencoder maps full-sentence messages into a compact 256-dimensional unit-norm latent vector, which is robustly embedded by a finetuned watermark model and secured through a secret, invertible rotation. The resulting system hides full-sentence messages, decodes in real time, and survives valuemetric and geometric attacks. It surpasses prior state of the art in BLEU-4 and Exact Match on several benchmarks, while breaking through the long-standing 256-bit payload ceiling. It also introduces a statistically calibrated score that yields a ROC AUC score of 0.97-0.99, and practical operating points for deployment. By shifting from bit payloads to semantic latent vectors, LatentSeal enables watermarking that is not only robust and high-capacity, but also secure and interpretable, providing a concrete path toward provenance, tamper explanation, and trustworthy AI governance. Models, training and inference code, and data splits will be available upon publication.