AtomSurf : Surface Representation for Learning on Protein Structures

Recent advancements in Cryo-EM and protein structure prediction algorithms have made large-scale protein structures accessible, paving the way for machine learning-based functional annotations.The field of geometric deep learning focuses on creating methods working on geometric data. An essential aspect of learning from protein structures is representing these structures as a geometric object (be it a grid, graph, or surface) and applying a learning method tailored to this representation. The performance of a given approach will then depend on both the representation and its corresponding learning method. In this paper, we investigate representing proteins as $\textit{3D mesh surfaces}$ and incorporate them into an established representation benchmark. Our first finding is that despite promising preliminary results, the surface representation alone does not seem competitive with 3D grids. Building on this, we introduce a synergistic approach, combining surface representations with graph-based methods, resulting in a general framework that incorporates both representations in learning. We show that using this combination, we are able to obtain state-of-the-art results across $\textit{all tested tasks}$. Our code and data can be found online: https://github.com/Vincentx15/atom2D .

Spatially and Spectrally Consistent Deep Functional Maps

Cycle consistency has long been exploited as a powerful prior for jointly optimizing maps within a collection of shapes. In this paper, we investigate its utility in the approaches of Deep Functional Maps, which are considered state-of-the-art in non-rigid shape matching. We first justify that under certain conditions, the learned maps, when represented in the spectral domain, are already cycle consistent. Furthermore, we identify the discrepancy that spectrally consistent maps are not necessarily spatially, or point-wise, consistent. In light of this, we present a novel design of unsupervised Deep Functional Maps, which effectively enforces the harmony of learned maps under the spectral and the point-wise representation. By taking advantage of cycle consistency, our framework produces state-of-the-art results in mapping shapes even under significant distortions. Beyond that, by independently estimating maps in both spectral and spatial domains, our method naturally alleviates over-fitting in network training, yielding superior generalization performance and accuracy within an array of challenging tests for both near-isometric and non-isometric datasets. Codes are available at https://github.com/rqhuang88/Spatiallyand-Spectrally-Consistent-Deep-Functional-Maps.

VoroMesh: Learning Watertight Surface Meshes with Voronoi Diagrams

In stark contrast to the case of images, finding a concise, learnable discrete representation of 3D surfaces remains a challenge. In particular, while polygon meshes are arguably the most common surface representation used in geometry processing, their irregular and combinatorial structure often make them unsuitable for learning-based applications. In this work, we present VoroMesh, a novel and differentiable Voronoi-based representation of watertight 3D shape surfaces. From a set of 3D points (called generators) and their associated occupancy, we define our boundary representation through the Voronoi diagram of the generators as the subset of Voronoi faces whose two associated (equidistant) generators are of opposite occupancy: the resulting polygon mesh forms a watertight approximation of the target shape's boundary. To learn the position of the generators, we propose a novel loss function, dubbed VoroLoss, that minimizes the distance from ground truth surface samples to the closest faces of the Voronoi diagram which does not require an explicit construction of the entire Voronoi diagram. A direct optimization of the Voroloss to obtain generators on the Thingi32 dataset demonstrates the geometric efficiency of our representation compared to axiomatic meshing algorithms and recent learning-based mesh representations. We further use VoroMesh in a learning-based mesh prediction task from input SDF grids on the ABC dataset, and show comparable performance to state-of-the-art methods while guaranteeing closed output surfaces free of self-intersections.

Zero-Shot 3D Shape Correspondence

We propose a novel zero-shot approach to computing correspondences between 3D shapes. Existing approaches mainly focus on isometric and near-isometric shape pairs (e.g., human vs. human), but less attention has been given to strongly non-isometric and inter-class shape matching (e.g., human vs. cow). To this end, we introduce a fully automatic method that exploits the exceptional reasoning capabilities of recent foundation models in language and vision to tackle difficult shape correspondence problems. Our approach comprises multiple stages. First, we classify the 3D shapes in a zero-shot manner by feeding rendered shape views to a language-vision model (e.g., BLIP2) to generate a list of class proposals per shape. These proposals are unified into a single class per shape by employing the reasoning capabilities of ChatGPT. Second, we attempt to segment the two shapes in a zero-shot manner, but in contrast to the co-segmentation problem, we do not require a mutual set of semantic regions. Instead, we propose to exploit the in-context learning capabilities of ChatGPT to generate two different sets of semantic regions for each shape and a semantic mapping between them. This enables our approach to match strongly non-isometric shapes with significant differences in geometric structure. Finally, we employ the generated semantic mapping to produce coarse correspondences that can further be refined by the functional maps framework to produce dense point-to-point maps. Our approach, despite its simplicity, produces highly plausible results in a zero-shot manner, especially between strongly non-isometric shapes.

SATR: Zero-Shot Semantic Segmentation of 3D Shapes

We explore the task of zero-shot semantic segmentation of 3D shapes by using large-scale off-the-shelf 2D image recognition models. Surprisingly, we find that modern zero-shot 2D object detectors are better suited for this task than contemporary text/image similarity predictors or even zero-shot 2D segmentation networks. Our key finding is that it is possible to extract accurate 3D segmentation maps from multi-view bounding box predictions by using the topological properties of the underlying surface. For this, we develop the Segmentation Assignment with Topological Reweighting (SATR) algorithm and evaluate it on two challenging benchmarks: FAUST and ShapeNetPart. On these datasets, SATR achieves state-of-the-art performance and outperforms prior work by at least 22\% on average in terms of mIoU. Our source code and data will be publicly released. Project webpage: https://samir55.github.io/SATR/

Understanding and Improving Features Learned in Deep Functional Maps

Deep functional maps have recently emerged as a successful paradigm for non-rigid 3D shape correspondence tasks. An essential step in this pipeline consists in learning feature functions that are used as constraints to solve for a functional map inside the network. However, the precise nature of the information learned and stored in these functions is not yet well understood. Specifically, a major question is whether these features can be used for any other objective, apart from their purely algebraic role in solving for functional map matrices. In this paper, we show that under some mild conditions, the features learned within deep functional map approaches can be used as point-wise descriptors and thus are directly comparable across different shapes, even without the necessity of solving for a functional map at test time. Furthermore, informed by our analysis, we propose effective modifications to the standard deep functional map pipeline, which promote structural properties of learned features, significantly improving the matching results. Finally, we demonstrate that previously unsuccessful attempts at using extrinsic architectures for deep functional map feature extraction can be remedied via simple architectural changes, which encourage the theoretical properties suggested by our analysis. We thus bridge the gap between intrinsic and extrinsic surface-based learning, suggesting the necessary and sufficient conditions for successful shape matching. Our code is available at https://github.com/pvnieo/clover.

Generalizable Local Feature Pre-training for Deformable Shape Analysis

Transfer learning is fundamental for addressing problems in settings with little training data. While several transfer learning approaches have been proposed in 3D, unfortunately, these solutions typically operate on an entire 3D object or even scene-level and thus, as we show, fail to generalize to new classes, such as deformable organic shapes. In addition, there is currently a lack of understanding of what makes pre-trained features transferable across significantly different 3D shape categories. In this paper, we make a step toward addressing these challenges. First, we analyze the link between feature locality and transferability in tasks involving deformable 3D objects, while also comparing different backbones and losses for local feature pre-training. We observe that with proper training, learned features can be useful in such tasks, but, crucially, only with an appropriate choice of the receptive field size. We then propose a differentiable method for optimizing the receptive field within 3D transfer learning. Jointly, this leads to the first learnable features that can successfully generalize to unseen classes of 3D shapes such as humans and animals. Our extensive experiments show that this approach leads to state-of-the-art results on several downstream tasks such as segmentation, shape correspondence, and classification. Our code is available at \url{https://github.com/pvnieo/vader}.

NCP: Neural Correspondence Prior for Effective Unsupervised Shape Matching

We present Neural Correspondence Prior (NCP), a new paradigm for computing correspondences between 3D shapes. Our approach is fully unsupervised and can lead to high-quality correspondences even in challenging cases such as sparse point clouds or non-isometric meshes, where current methods fail. Our first key observation is that, in line with neural priors observed in other domains, recent network architectures on 3D data, even without training, tend to produce pointwise features that induce plausible maps between rigid or non-rigid shapes. Secondly, we show that given a noisy map as input, training a feature extraction network with the input map as supervision tends to remove artifacts from the input and can act as a powerful correspondence denoising mechanism, both between individual pairs and within a collection. With these observations in hand, we propose a two-stage unsupervised paradigm for shape matching by (i) performing unsupervised training by adapting an existing approach to obtain an initial set of noisy matches, and (ii) using these matches to train a network in a supervised manner. We demonstrate that this approach significantly improves the accuracy of the maps, especially when trained within a collection. We show that NCP is data-efficient, fast, and achieves state-of-the-art results on many tasks. Our code can be found online: https://github.com/pvnieo/NCP.

TIDE: Time Derivative Diffusion for Deep Learning on Graphs

A prominent paradigm for graph neural networks is based on the message passing framework. In this framework, information communication is realized only between neighboring nodes. The challenge of approaches that use this paradigm is to ensure efficient and accurate \textit{long distance communication} between nodes, as deep convolutional networks are prone to over-smoothing. In this paper, we present a novel method based on time derivative graph diffusion (TIDE), with a learnable time parameter. Our approach allows to adapt the spatial extent of diffusion across different tasks and network channels, thus enabling medium and long-distance communication efficiently. Furthermore, we show that our architecture directly enables local message passing and thus inherits from the expressive power of local message passing approaches. We show that on widely used graph benchmarks we achieve comparable performance and on a synthetic mesh dataset we outperform state-of-the-art methods like GCN or GRAND by a significant margin.

Equivalence Between SE(3) Equivariant Networks via Steerable Kernels and Group Convolution

A wide range of techniques have been proposed in recent years for designing neural networks for 3D data that are equivariant under rotation and translation of the input. Most approaches for equivariance under the Euclidean group $\mathrm{SE}(3)$ of rotations and translations fall within one of the two major categories. The first category consists of methods that use $\mathrm{SE}(3)$-convolution which generalizes classical $\mathbb{R}^3$-convolution on signals over $\mathrm{SE}(3)$. Alternatively, it is possible to use \textit{steerable convolution} which achieves $\mathrm{SE}(3)$-equivariance by imposing constraints on $\mathbb{R}^3$-convolution of tensor fields. It is known by specialists in the field that the two approaches are equivalent, with steerable convolution being the Fourier transform of $\mathrm{SE}(3)$ convolution. Unfortunately, these results are not widely known and moreover the exact relations between deep learning architectures built upon these two approaches have not been precisely described in the literature on equivariant deep learning. In this work we provide an in-depth analysis of both methods and their equivalence and relate the two constructions to multiview convolutional networks. Furthermore, we provide theoretical justifications of separability of $\mathrm{SE}(3)$ group convolution, which explain the applicability and success of some recent approaches. Finally, we express different methods using a single coherent formalism and provide explicit formulas that relate the kernels learned by different methods. In this way, our work helps to unify different previously-proposed techniques for achieving roto-translational equivariance, and helps to shed light on both the utility and precise differences between various alternatives. We also derive new TFN non-linearities from our equivalence principle and test them on practical benchmark datasets.