Daily Papers

Convolutional Neural Networks (CNN) have been regarded as a powerful class of models for image recognition problems. Nevertheless, it is not trivial when utilizing a CNN for learning spatio-temporal video representation. A few studies have shown that performing 3D convolutions is a rewarding approach to capture both spatial and temporal dimensions in videos. However, the development of a very deep 3D CNN from scratch results in expensive computational cost and memory demand. A valid question is why not recycle off-the-shelf 2D networks for a 3D CNN. In this paper, we devise multiple variants of bottleneck building blocks in a residual learning framework by simulating 3times3times3 convolutions with 1times3times3 convolutional filters on spatial domain (equivalent to 2D CNN) plus 3times1times1 convolutions to construct temporal connections on adjacent feature maps in time. Furthermore, we propose a new architecture, named Pseudo-3D Residual Net (P3D ResNet), that exploits all the variants of blocks but composes each in different placement of ResNet, following the philosophy that enhancing structural diversity with going deep could improve the power of neural networks. Our P3D ResNet achieves clear improvements on Sports-1M video classification dataset against 3D CNN and frame-based 2D CNN by 5.3% and 1.8%, respectively. We further examine the generalization performance of video representation produced by our pre-trained P3D ResNet on five different benchmarks and three different tasks, demonstrating superior performances over several state-of-the-art techniques.

A promising direction for pre-training 3D point clouds is to leverage the massive amount of data in 2D, whereas the domain gap between 2D and 3D creates a fundamental challenge. This paper proposes a novel approach to point-cloud pre-training that learns 3D representations by leveraging pre-trained 2D networks. Different from the popular practice of predicting 2D features first and then obtaining 3D features through dimensionality lifting, our approach directly uses a 3D network for feature extraction. We train the 3D feature extraction network with the help of the novel 2D knowledge transfer loss, which enforces the 2D projections of the 3D feature to be consistent with the output of pre-trained 2D networks. To prevent the feature from discarding 3D signals, we introduce the multi-view consistency loss that additionally encourages the projected 2D feature representations to capture pixel-wise correspondences across different views. Such correspondences induce 3D geometry and effectively retain 3D features in the projected 2D features. Experimental results demonstrate that our pre-trained model can be successfully transferred to various downstream tasks, including 3D shape classification, part segmentation, 3D object detection, and semantic segmentation, achieving state-of-the-art performance.

Traditional fluorescence staining is phototoxic to live cells, slow, and expensive; thus, the subcellular structure prediction (SSP) from transmitted light (TL) images is emerging as a label-free, faster, low-cost alternative. However, existing approaches utilize 3D networks for one-to-one voxel level dense prediction, which necessitates a frequent and time-consuming Z-axis imaging process. Moreover, 3D convolutions inevitably lead to significant computation and GPU memory overhead. Therefore, we propose an efficient framework, SparseSSP, predicting fluorescent intensities within the target voxel grid in an efficient paradigm instead of relying entirely on 3D topologies. In particular, SparseSSP makes two pivotal improvements to prior works. First, SparseSSP introduces a one-to-many voxel mapping paradigm, which permits the sparse TL slices to reconstruct the subcellular structure. Secondly, we propose a hybrid dimensions topology, which folds the Z-axis information into channel features, enabling the 2D network layers to tackle SSP under low computational cost. We conduct extensive experiments to validate the effectiveness and advantages of SparseSSP on diverse sparse imaging ratios, and our approach achieves a leading performance compared to pure 3D topologies. SparseSSP reduces imaging frequencies compared to previous dense-view SSP (i.e., the number of imaging is reduced up to 87.5% at most), which is significant in visualizing rapid biological dynamics on low-cost devices and samples.

Reconstructing photo-realistic drivable human avatars from multi-view image sequences has been a popular and challenging topic in the field of computer vision and graphics. While existing NeRF-based methods can achieve high-quality novel view rendering of human models, both training and inference processes are time-consuming. Recent approaches have utilized 3D Gaussians to represent the human body, enabling faster training and rendering. However, they undermine the importance of the mesh guidance and directly predict Gaussians in 3D space with coarse mesh guidance. This hinders the learning procedure of the Gaussians and tends to produce blurry textures. Therefore, we propose UV Gaussians, which models the 3D human body by jointly learning mesh deformations and 2D UV-space Gaussian textures. We utilize the embedding of UV map to learn Gaussian textures in 2D space, leveraging the capabilities of powerful 2D networks to extract features. Additionally, through an independent Mesh network, we optimize pose-dependent geometric deformations, thereby guiding Gaussian rendering and significantly enhancing rendering quality. We collect and process a new dataset of human motion, which includes multi-view images, scanned models, parametric model registration, and corresponding texture maps. Experimental results demonstrate that our method achieves state-of-the-art synthesis of novel view and novel pose. The code and data will be made available on the homepage https://alex-jyj.github.io/UV-Gaussians/ once the paper is accepted.

A major challenge of the long measurement times in magnetic resonance imaging (MRI), an important medical imaging technology, is that patients may move during data acquisition. This leads to severe motion artifacts in the reconstructed images and volumes. In this paper, we propose a deep learning-based test-time-training method for accurate motion estimation. The key idea is that a neural network trained for motion-free reconstruction has a small loss if there is no motion, thus optimizing over motion parameters passed through the reconstruction network enables accurate estimation of motion. The estimated motion parameters enable to correct for the motion and to reconstruct accurate motion-corrected images. Our method uses 2D reconstruction networks to estimate rigid motion in 3D, and constitutes the first deep learning based method for 3D rigid motion estimation towards 3D-motion-corrected MRI. We show that our method can provably reconstruct motion parameters for a simple signal and neural network model. We demonstrate the effectiveness of our method for both retrospectively simulated motion and prospectively collected real motion-corrupted data.

In recent years, the neural radiance field (NeRF) model has gained popularity due to its ability to recover complex 3D scenes. Following its success, many approaches proposed different NeRF representations in order to further improve both runtime and performance. One such example is Triplane, in which NeRF is represented using three 2D feature planes. This enables easily using existing 2D neural networks in this framework, e.g., to generate the three planes. Despite its advantage, the triplane representation lagged behind in its 3D recovery quality compared to NeRF solutions. In this work, we propose TriNeRFLet, a 2D wavelet-based multiscale triplane representation for NeRF, which closes the 3D recovery performance gap and is competitive with current state-of-the-art methods. Building upon the triplane framework, we also propose a novel super-resolution (SR) technique that combines a diffusion model with TriNeRFLet for improving NeRF resolution.

Access to high-quality and diverse 3D articulated digital human assets is crucial in various applications, ranging from virtual reality to social platforms. Generative approaches, such as 3D generative adversarial networks (GANs), are rapidly replacing laborious manual content creation tools. However, existing 3D GAN frameworks typically rely on scene representations that leverage either template meshes, which are fast but offer limited quality, or volumes, which offer high capacity but are slow to render, thereby limiting the 3D fidelity in GAN settings. In this work, we introduce layered surface volumes (LSVs) as a new 3D object representation for articulated digital humans. LSVs represent a human body using multiple textured mesh layers around a conventional template. These layers are rendered using alpha compositing with fast differentiable rasterization, and they can be interpreted as a volumetric representation that allocates its capacity to a manifold of finite thickness around the template. Unlike conventional single-layer templates that struggle with representing fine off-surface details like hair or accessories, our surface volumes naturally capture such details. LSVs can be articulated, and they exhibit exceptional efficiency in GAN settings, where a 2D generator learns to synthesize the RGBA textures for the individual layers. Trained on unstructured, single-view 2D image datasets, our LSV-GAN generates high-quality and view-consistent 3D articulated digital humans without the need for view-inconsistent 2D upsampling networks.

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 ShapeNetPart and our proposed FAUST benchmarks. SATR achieves state-of-the-art performance and outperforms a baseline algorithm by 1.3% and 4% average mIoU on the FAUST coarse and fine-grained benchmarks, respectively, and by 5.2% average mIoU on the ShapeNetPart benchmark. Our source code and data will be publicly released. Project webpage: https://samir55.github.io/SATR/.

Accurately perceiving instances and predicting their future motion are key tasks for autonomous vehicles, enabling them to navigate safely in complex urban traffic. While bird's-eye view (BEV) representations are commonplace in perception for autonomous driving, their potential in a motion prediction setting is less explored. Existing approaches for BEV instance prediction from surround cameras rely on a multi-task auto-regressive setup coupled with complex post-processing to predict future instances in a spatio-temporally consistent manner. In this paper, we depart from this paradigm and propose an efficient novel end-to-end framework named POWERBEV, which differs in several design choices aimed at reducing the inherent redundancy in previous methods. First, rather than predicting the future in an auto-regressive fashion, POWERBEV uses a parallel, multi-scale module built from lightweight 2D convolutional networks. Second, we show that segmentation and centripetal backward flow are sufficient for prediction, simplifying previous multi-task objectives by eliminating redundant output modalities. Building on this output representation, we propose a simple, flow warping-based post-processing approach which produces more stable instance associations across time. Through this lightweight yet powerful design, POWERBEV outperforms state-of-the-art baselines on the NuScenes Dataset and poses an alternative paradigm for BEV instance prediction. We made our code publicly available at: https://github.com/EdwardLeeLPZ/PowerBEV.

Current state-of-the-art machine translation systems are based on encoder-decoder architectures, that first encode the input sequence, and then generate an output sequence based on the input encoding. Both are interfaced with an attention mechanism that recombines a fixed encoding of the source tokens based on the decoder state. We propose an alternative approach which instead relies on a single 2D convolutional neural network across both sequences. Each layer of our network re-codes source tokens on the basis of the output sequence produced so far. Attention-like properties are therefore pervasive throughout the network. Our model yields excellent results, outperforming state-of-the-art encoder-decoder systems, while being conceptually simpler and having fewer parameters.

We present a content-based automatic music tagging algorithm using fully convolutional neural networks (FCNs). We evaluate different architectures consisting of 2D convolutional layers and subsampling layers only. In the experiments, we measure the AUC-ROC scores of the architectures with different complexities and input types using the MagnaTagATune dataset, where a 4-layer architecture shows state-of-the-art performance with mel-spectrogram input. Furthermore, we evaluated the performances of the architectures with varying the number of layers on a larger dataset (Million Song Dataset), and found that deeper models outperformed the 4-layer architecture. The experiments show that mel-spectrogram is an effective time-frequency representation for automatic tagging and that more complex models benefit from more training data.

The integration of artificial intelligence in image-guided interventions holds transformative potential, promising to extract 3D geometric and quantitative information from conventional 2D imaging modalities during complex procedures. Achieving this requires the rapid and precise alignment of 2D intraoperative images (e.g., X-ray) with 3D preoperative volumes (e.g., CT, MRI). However, current 2D/3D registration methods fail across the broad spectrum of procedures dependent on X-ray guidance: traditional optimization techniques require custom parameter tuning for each subject, whereas neural networks trained on small datasets do not generalize to new patients or require labor-intensive manual annotations, increasing clinical burden and precluding application to new anatomical targets. To address these challenges, we present xvr, a fully automated framework for training patient-specific neural networks for 2D/3D registration. xvr uses physics-based simulation to generate abundant high-quality training data from a patient's own preoperative volumetric imaging, thereby overcoming the inherently limited ability of supervised models to generalize to new patients and procedures. Furthermore, xvr requires only 5 minutes of training per patient, making it suitable for emergency interventions as well as planned procedures. We perform the largest evaluation of a 2D/3D registration algorithm on real X-ray data to date and find that xvr robustly generalizes across a diverse dataset comprising multiple anatomical structures, imaging modalities, and hospitals. Across surgical tasks, xvr achieves submillimeter-accurate registration at intraoperative speeds, improving upon existing methods by an order of magnitude. xvr is released as open-source software freely available at https://github.com/eigenvivek/xvr.

We introduce MedMNIST v2, a large-scale MNIST-like dataset collection of standardized biomedical images, including 12 datasets for 2D and 6 datasets for 3D. All images are pre-processed into a small size of 28x28 (2D) or 28x28x28 (3D) with the corresponding classification labels so that no background knowledge is required for users. Covering primary data modalities in biomedical images, MedMNIST v2 is designed to perform classification on lightweight 2D and 3D images with various dataset scales (from 100 to 100,000) and diverse tasks (binary/multi-class, ordinal regression, and multi-label). The resulting dataset, consisting of 708,069 2D images and 10,214 3D images in total, could support numerous research / educational purposes in biomedical image analysis, computer vision, and machine learning. We benchmark several baseline methods on MedMNIST v2, including 2D / 3D neural networks and open-source / commercial AutoML tools. The data and code are publicly available at https://medmnist.com/.

Human pose estimation (HPE) in the top-view using fisheye cameras presents a promising and innovative application domain. However, the availability of datasets capturing this viewpoint is extremely limited, especially those with high-quality 2D and 3D keypoint annotations. Addressing this gap, we leverage the capabilities of Neural Radiance Fields (NeRF) technique to establish a comprehensive pipeline for generating human pose datasets from existing 2D and 3D datasets, specifically tailored for the top-view fisheye perspective. Through this pipeline, we create a novel dataset NToP570K (NeRF-powered Top-view human Pose dataset for fisheye cameras with over 570 thousand images), and conduct an extensive evaluation of its efficacy in enhancing neural networks for 2D and 3D top-view human pose estimation. A pretrained ViTPose-B model achieves an improvement in AP of 33.3 % on our validation set for 2D HPE after finetuning on our training set. A similarly finetuned HybrIK-Transformer model gains 53.7 mm reduction in PA-MPJPE for 3D HPE on the validation set.

While 2D generative adversarial networks have enabled high-resolution image synthesis, they largely lack an understanding of the 3D world and the image formation process. Thus, they do not provide precise control over camera viewpoint or object pose. To address this problem, several recent approaches leverage intermediate voxel-based representations in combination with differentiable rendering. However, existing methods either produce low image resolution or fall short in disentangling camera and scene properties, e.g., the object identity may vary with the viewpoint. In this paper, we propose a generative model for radiance fields which have recently proven successful for novel view synthesis of a single scene. In contrast to voxel-based representations, radiance fields are not confined to a coarse discretization of the 3D space, yet allow for disentangling camera and scene properties while degrading gracefully in the presence of reconstruction ambiguity. By introducing a multi-scale patch-based discriminator, we demonstrate synthesis of high-resolution images while training our model from unposed 2D images alone. We systematically analyze our approach on several challenging synthetic and real-world datasets. Our experiments reveal that radiance fields are a powerful representation for generative image synthesis, leading to 3D consistent models that render with high fidelity.

Developing blind video deflickering (BVD) algorithms to enhance video temporal consistency, is gaining importance amid the flourish of image processing and video generation. However, the intricate nature of video data complicates the training of deep learning methods, leading to high resource consumption and instability, notably under severe lighting flicker. This underscores the critical need for a compact representation beyond pixel values to advance BVD research and applications. Inspired by the classic scale-time equalization (STE), our work introduces the histogram-assisted solution, called BlazeBVD, for high-fidelity and rapid BVD. Compared with STE, which directly corrects pixel values by temporally smoothing color histograms, BlazeBVD leverages smoothed illumination histograms within STE filtering to ease the challenge of learning temporal data using neural networks. In technique, BlazeBVD begins by condensing pixel values into illumination histograms that precisely capture flickering and local exposure variations. These histograms are then smoothed to produce singular frames set, filtered illumination maps, and exposure maps. Resorting to these deflickering priors, BlazeBVD utilizes a 2D network to restore faithful and consistent texture impacted by lighting changes or localized exposure issues. BlazeBVD also incorporates a lightweight 3D network to amend slight temporal inconsistencies, avoiding the resource consumption issue. Comprehensive experiments on synthetic, real-world and generated videos, showcase the superior qualitative and quantitative results of BlazeBVD, achieving inference speeds up to 10x faster than state-of-the-arts.

We propose a novel feed-forward 3D editing framework called Shap-Editor. Prior research on editing 3D objects primarily concentrated on editing individual objects by leveraging off-the-shelf 2D image editing networks. This is achieved via a process called distillation, which transfers knowledge from the 2D network to 3D assets. Distillation necessitates at least tens of minutes per asset to attain satisfactory editing results, and is thus not very practical. In contrast, we ask whether 3D editing can be carried out directly by a feed-forward network, eschewing test-time optimisation. In particular, we hypothesise that editing can be greatly simplified by first encoding 3D objects in a suitable latent space. We validate this hypothesis by building upon the latent space of Shap-E. We demonstrate that direct 3D editing in this space is possible and efficient by building a feed-forward editor network that only requires approximately one second per edit. Our experiments show that Shap-Editor generalises well to both in-distribution and out-of-distribution 3D assets with different prompts, exhibiting comparable performance with methods that carry out test-time optimisation for each edited instance.

Spatial reasoning is an important component of human intelligence. We can imagine the shapes of 3D objects and reason about their spatial relations by merely looking at their three-view line drawings in 2D, with different levels of competence. Can deep networks be trained to perform spatial reasoning tasks? How can we measure their "spatial intelligence"? To answer these questions, we present the SPARE3D dataset. Based on cognitive science and psychometrics, SPARE3D contains three types of 2D-3D reasoning tasks on view consistency, camera pose, and shape generation, with increasing difficulty. We then design a method to automatically generate a large number of challenging questions with ground truth answers for each task. They are used to provide supervision for training our baseline models using state-of-the-art architectures like ResNet. Our experiments show that although convolutional networks have achieved superhuman performance in many visual learning tasks, their spatial reasoning performance on SPARE3D tasks is either lower than average human performance or even close to random guesses. We hope SPARE3D can stimulate new problem formulations and network designs for spatial reasoning to empower intelligent robots to operate effectively in the 3D world via 2D sensors. The dataset and code are available at https://ai4ce.github.io/SPARE3D.

Recently, deep convolutional neural networks have achieved great success for medical image segmentation. However, unlike segmentation of natural images, most medical images such as MRI and CT are volumetric data. In order to make full use of volumetric information, 3D CNNs are widely used. However, 3D CNNs suffer from higher inference time and computation cost, which hinders their further clinical applications. Additionally, with the increased number of parameters, the risk of overfitting is higher, especially for medical images where data and annotations are expensive to acquire. To issue this problem, many 2.5D segmentation methods have been proposed to make use of volumetric spatial information with less computation cost. Despite these works lead to improvements on a variety of segmentation tasks, to the best of our knowledge, there has not previously been a large-scale empirical comparison of these methods. In this paper, we aim to present a review of the latest developments of 2.5D methods for volumetric medical image segmentation. Additionally, to compare the performance and effectiveness of these methods, we provide an empirical study of these methods on three representative segmentation tasks involving different modalities and targets. Our experimental results highlight that 3D CNNs may not always be the best choice. Despite all these 2.5D methods can bring performance gains to 2D baseline, not all the methods hold the benefits on different datasets. We hope the results and conclusions of our study will prove useful for the community on exploring and developing efficient volumetric medical image segmentation methods.

Graphs have often been used to answer questions about the interaction between real-world entities by taking advantage of their capacity to represent complex topologies. Complex networks are known to be graphs that capture such non-trivial topologies; they are able to represent human phenomena such as epidemic processes, the dynamics of populations, and the urbanization of cities. The investigation of complex networks has been extrapolated to many fields of science, with particular emphasis on computing techniques, including artificial intelligence. In such a case, the analysis of the interaction between entities of interest is transposed to the internal learning of algorithms, a paradigm whose investigation is able to expand the state of the art in Computer Science. By exploring this paradigm, this thesis puts together complex networks and machine learning techniques to improve the understanding of the human phenomena observed in pandemics, pendular migration, and street networks. Accordingly, we contribute with: (i) a new neural network architecture capable of modeling dynamic processes observed in spatial and temporal data with applications in epidemics propagation, weather forecasting, and patient monitoring in intensive care units; (ii) a machine-learning methodology for analyzing and predicting links in the scope of human mobility between all the cities of Brazil; and, (iii) techniques for identifying inconsistencies in the urban planning of cities while tracking the most influential vertices, with applications over Brazilian and worldwide cities. We obtained results sustained by sound evidence of advances to the state of the art in artificial intelligence, rigorous formalisms, and ample experimentation. Our findings rely upon real-world applications in a range of domains, demonstrating the applicability of our methodologies.

Random walks are widely used for mining networks due to the computational efficiency of computing them. For instance, graph representation learning learns a d-dimensional embedding space, so that the nodes that tend to co-occur on random walks (a proxy of being in the same network neighborhood) are close in the embedding space. Specific local network topology (i.e., structure) influences the co-occurrence of nodes on random walks, so random walks of limited length capture only partial topological information, hence diminishing the performance of downstream methods. We explicitly capture all topological neighborhood information and improve performance by introducing orbit adjacencies that quantify the adjacencies of two nodes as co-occurring on a given pair of graphlet orbits, which are symmetric positions on graphlets (small, connected, non-isomorphic, induced subgraphs of a large network). Importantly, we mathematically prove that random walks on up to k nodes capture only a subset of all the possible orbit adjacencies for up to k-node graphlets. Furthermore, we enable orbit adjacency-based analysis of networks by developing an efficient GRaphlet-orbit ADjacency COunter (GRADCO), which exhaustively computes all 28 orbit adjacency matrices for up to four-node graphlets. Note that four-node graphlets suffice, because real networks are usually small-world. In large networks on around 20,000 nodes, GRADCOcomputesthe28matricesinminutes. Onsixrealnetworksfromvarious domains, we compare the performance of node-label predictors obtained by using the network embeddings based on our orbit adjacencies to those based on random walks. We find that orbit adjacencies, which include those unseen by random walks, outperform random walk-based adjacencies, demonstrating the importance of the inclusion of the topological neighborhood information that is unseen by random walks.

Triggered by limitations of graph-based deep learning methods in terms of computational expressivity and model flexibility, recent years have seen a surge of interest in computational models that operate on higher-order topological domains such as hypergraphs and simplicial complexes. While the increased expressivity of these models can indeed lead to a better classification performance and a more faithful representation of the underlying system, the computational cost of these higher-order models can increase dramatically. To this end, we here explore a simplicial complex neural network learning architecture based on random walks and fast 1D convolutions (SCRaWl), in which we can adjust the increase in computational cost by varying the length and number of random walks considered while accounting for higher-order relationships. Importantly, due to the random walk-based design, the expressivity of the proposed architecture is provably incomparable to that of existing message-passing simplicial neural networks. We empirically evaluate SCRaWl on real-world datasets and show that it outperforms other simplicial neural networks.

The execution of graph algorithms using neural networks has recently attracted significant interest due to promising empirical progress. This motivates further understanding of how neural networks can replicate reasoning steps with relational data. In this work, we study the ability of transformer networks to simulate algorithms on graphs from a theoretical perspective. The architecture that we utilize is a looped transformer with extra attention heads that interact with the graph. We prove by construction that this architecture can simulate algorithms such as Dijkstra's shortest path algorithm, Breadth- and Depth-First Search, and Kosaraju's strongly connected components algorithm. The width of the network does not increase with the size of the input graph, which implies that the network can simulate the above algorithms for any graph. Despite this property, we show that there is a limit to simulation in our solution due to finite precision. Finally, we show a Turing Completeness result with constant width when the extra attention heads are utilized.

This work studies a central extremal graph theory problem inspired by a 1975 conjecture of Erdos, which aims to find graphs with a given size (number of nodes) that maximize the number of edges without having 3- or 4-cycles. We formulate this problem as a sequential decision-making problem and compare AlphaZero, a neural network-guided tree search, with tabu search, a heuristic local search method. Using either method, by introducing a curriculum -- jump-starting the search for larger graphs using good graphs found at smaller sizes -- we improve the state-of-the-art lower bounds for several sizes. We also propose a flexible graph-generation environment and a permutation-invariant network architecture for learning to search in the space of graphs.

In recent years, Graph Neural Networks (GNNs) have made significant advances in processing structured data. However, most of them primarily adopted a model-centric approach, which simplifies graphs by converting them into undirected formats and emphasizes model designs. This approach is inherently limited in real-world applications due to the unavoidable information loss in simple undirected graphs and the model optimization challenges that arise when exceeding the upper bounds of this sub-optimal data representational capacity. As a result, there has been a shift toward data-centric methods that prioritize improving graph quality and representation. Specifically, various types of graphs can be derived from naturally structured data, including heterogeneous graphs, hypergraphs, and directed graphs. Among these, directed graphs offer distinct advantages in topological systems by modeling causal relationships, and directed GNNs have been extensively studied in recent years. However, a comprehensive survey of this emerging topic is still lacking. Therefore, we aim to provide a comprehensive review of directed graph learning, with a particular focus on a data-centric perspective. Specifically, we first introduce a novel taxonomy for existing studies. Subsequently, we re-examine these methods from the data-centric perspective, with an emphasis on understanding and improving data representation. It demonstrates that a deep understanding of directed graphs and their quality plays a crucial role in model performance. Additionally, we explore the diverse applications of directed GNNs across 10+ domains, highlighting their broad applicability. Finally, we identify key opportunities and challenges within the field, offering insights that can guide future research and development in directed graph learning.

Prediction tasks over nodes and edges in networks require careful effort in engineering features used by learning algorithms. Recent research in the broader field of representation learning has led to significant progress in automating prediction by learning the features themselves. However, present feature learning approaches are not expressive enough to capture the diversity of connectivity patterns observed in networks. Here we propose node2vec, an algorithmic framework for learning continuous feature representations for nodes in networks. In node2vec, we learn a mapping of nodes to a low-dimensional space of features that maximizes the likelihood of preserving network neighborhoods of nodes. We define a flexible notion of a node's network neighborhood and design a biased random walk procedure, which efficiently explores diverse neighborhoods. Our algorithm generalizes prior work which is based on rigid notions of network neighborhoods, and we argue that the added flexibility in exploring neighborhoods is the key to learning richer representations. We demonstrate the efficacy of node2vec over existing state-of-the-art techniques on multi-label classification and link prediction in several real-world networks from diverse domains. Taken together, our work represents a new way for efficiently learning state-of-the-art task-independent representations in complex networks.

Motivated by applications in chemistry and other sciences, we study the expressive power of message-passing neural networks for geometric graphs, whose node features correspond to 3-dimensional positions. Recent work has shown that such models can separate generic pairs of non-isomorphic geometric graphs, though they may fail to separate some rare and complicated instances. However, these results assume a fully connected graph, where each node possesses complete knowledge of all other nodes. In contrast, often, in application, every node only possesses knowledge of a small number of nearest neighbors. This paper shows that generic pairs of non-isomorphic geometric graphs can be separated by message-passing networks with rotation equivariant features as long as the underlying graph is connected. When only invariant intermediate features are allowed, generic separation is guaranteed for generically globally rigid graphs. We introduce a simple architecture, EGENNET, which achieves our theoretical guarantees and compares favorably with alternative architecture on synthetic and chemical benchmarks. Our code is available at https://github.com/yonatansverdlov/E-GenNet.

Graph Neural Networks (GNNs), especially message-passing neural networks (MPNNs), have emerged as powerful architectures for learning on graphs in diverse applications. However, MPNNs face challenges when modeling non-local interactions in graphs such as large conjugated molecules, and social networks due to oversmoothing and oversquashing. Although Spectral GNNs and traditional neural networks such as recurrent neural networks and transformers mitigate these challenges, they often lack generalizability, or fail to capture detailed structural relationships or symmetries in the data. To address these concerns, we introduce Matrix Function Neural Networks (MFNs), a novel architecture that parameterizes non-local interactions through analytic matrix equivariant functions. Employing resolvent expansions offers a straightforward implementation and the potential for linear scaling with system size. The MFN architecture achieves stateof-the-art performance in standard graph benchmarks, such as the ZINC and TU datasets, and is able to capture intricate non-local interactions in quantum systems, paving the way to new state-of-the-art force fields.

Graph neural networks (GNNs), in general, are built on the assumption of a static set of features characterizing each node in a graph. This assumption is often violated in practice. Existing methods partly address this issue through feature imputation. However, these techniques (i) assume uniformity of feature set across nodes, (ii) are transductive by nature, and (iii) fail to work when features are added or removed over time. In this work, we address these limitations through a novel GNN framework called GRAFENNE. GRAFENNE performs a novel allotropic transformation on the original graph, wherein the nodes and features are decoupled through a bipartite encoding. Through a carefully chosen message passing framework on the allotropic transformation, we make the model parameter size independent of the number of features and thereby inductive to both unseen nodes and features. We prove that GRAFENNE is at least as expressive as any of the existing message-passing GNNs in terms of Weisfeiler-Leman tests, and therefore, the additional inductivity to unseen features does not come at the cost of expressivity. In addition, as demonstrated over four real-world graphs, GRAFENNE empowers the underlying GNN with high empirical efficacy and the ability to learn in continual fashion over streaming feature sets.

Deep learning has revolutionized many machine learning tasks in recent years, ranging from image classification and video processing to speech recognition and natural language understanding. The data in these tasks are typically represented in the Euclidean space. However, there is an increasing number of applications where data are generated from non-Euclidean domains and are represented as graphs with complex relationships and interdependency between objects. The complexity of graph data has imposed significant challenges on existing machine learning algorithms. Recently, many studies on extending deep learning approaches for graph data have emerged. In this survey, we provide a comprehensive overview of graph neural networks (GNNs) in data mining and machine learning fields. We propose a new taxonomy to divide the state-of-the-art graph neural networks into four categories, namely recurrent graph neural networks, convolutional graph neural networks, graph autoencoders, and spatial-temporal graph neural networks. We further discuss the applications of graph neural networks across various domains and summarize the open source codes, benchmark data sets, and model evaluation of graph neural networks. Finally, we propose potential research directions in this rapidly growing field.

Graph Neural Networks (GNNs) have been shown to be effective models for different predictive tasks on graph-structured data. Recent work on their expressive power has focused on isomorphism tasks and countable feature spaces. We extend this theoretical framework to include continuous features - which occur regularly in real-world input domains and within the hidden layers of GNNs - and we demonstrate the requirement for multiple aggregation functions in this context. Accordingly, we propose Principal Neighbourhood Aggregation (PNA), a novel architecture combining multiple aggregators with degree-scalers (which generalize the sum aggregator). Finally, we compare the capacity of different models to capture and exploit the graph structure via a novel benchmark containing multiple tasks taken from classical graph theory, alongside existing benchmarks from real-world domains, all of which demonstrate the strength of our model. With this work, we hope to steer some of the GNN research towards new aggregation methods which we believe are essential in the search for powerful and robust models.

We present a unified representation for actionable spatial perception: 3D Dynamic Scene Graphs. Scene graphs are directed graphs where nodes represent entities in the scene (e.g. objects, walls, rooms), and edges represent relations (e.g. inclusion, adjacency) among nodes. Dynamic scene graphs (DSGs) extend this notion to represent dynamic scenes with moving agents (e.g. humans, robots), and to include actionable information that supports planning and decision-making (e.g. spatio-temporal relations, topology at different levels of abstraction). Our second contribution is to provide the first fully automatic Spatial PerceptIon eNgine(SPIN) to build a DSG from visual-inertial data. We integrate state-of-the-art techniques for object and human detection and pose estimation, and we describe how to robustly infer object, robot, and human nodes in crowded scenes. To the best of our knowledge, this is the first paper that reconciles visual-inertial SLAM and dense human mesh tracking. Moreover, we provide algorithms to obtain hierarchical representations of indoor environments (e.g. places, structures, rooms) and their relations. Our third contribution is to demonstrate the proposed spatial perception engine in a photo-realistic Unity-based simulator, where we assess its robustness and expressiveness. Finally, we discuss the implications of our proposal on modern robotics applications. 3D Dynamic Scene Graphs can have a profound impact on planning and decision-making, human-robot interaction, long-term autonomy, and scene prediction. A video abstract is available at https://youtu.be/SWbofjhyPzI

Mesh-based simulations are central to modeling complex physical systems in many disciplines across science and engineering. Mesh representations support powerful numerical integration methods and their resolution can be adapted to strike favorable trade-offs between accuracy and efficiency. However, high-dimensional scientific simulations are very expensive to run, and solvers and parameters must often be tuned individually to each system studied. Here we introduce MeshGraphNets, a framework for learning mesh-based simulations using graph neural networks. Our model can be trained to pass messages on a mesh graph and to adapt the mesh discretization during forward simulation. Our results show it can accurately predict the dynamics of a wide range of physical systems, including aerodynamics, structural mechanics, and cloth. The model's adaptivity supports learning resolution-independent dynamics and can scale to more complex state spaces at test time. Our method is also highly efficient, running 1-2 orders of magnitude faster than the simulation on which it is trained. Our approach broadens the range of problems on which neural network simulators can operate and promises to improve the efficiency of complex, scientific modeling tasks.

Graph neural networks have shown significant success in the field of graph representation learning. Graph convolutions perform neighborhood aggregation and represent one of the most important graph operations. Nevertheless, one layer of these neighborhood aggregation methods only consider immediate neighbors, and the performance decreases when going deeper to enable larger receptive fields. Several recent studies attribute this performance deterioration to the over-smoothing issue, which states that repeated propagation makes node representations of different classes indistinguishable. In this work, we study this observation systematically and develop new insights towards deeper graph neural networks. First, we provide a systematical analysis on this issue and argue that the key factor compromising the performance significantly is the entanglement of representation transformation and propagation in current graph convolution operations. After decoupling these two operations, deeper graph neural networks can be used to learn graph node representations from larger receptive fields. We further provide a theoretical analysis of the above observation when building very deep models, which can serve as a rigorous and gentle description of the over-smoothing issue. Based on our theoretical and empirical analysis, we propose Deep Adaptive Graph Neural Network (DAGNN) to adaptively incorporate information from large receptive fields. A set of experiments on citation, co-authorship, and co-purchase datasets have confirmed our analysis and insights and demonstrated the superiority of our proposed methods.

Graph Neural Networks operate through bottom-up message-passing, fundamentally differing from human visual perception, which intuitively captures global structures first. We investigate the underappreciated potential of vision models for graph understanding, finding they achieve performance comparable to GNNs on established benchmarks while exhibiting distinctly different learning patterns. These divergent behaviors, combined with limitations of existing benchmarks that conflate domain features with topological understanding, motivate our introduction of GraphAbstract. This benchmark evaluates models' ability to perceive global graph properties as humans do: recognizing organizational archetypes, detecting symmetry, sensing connectivity strength, and identifying critical elements. Our results reveal that vision models significantly outperform GNNs on tasks requiring holistic structural understanding and maintain generalizability across varying graph scales, while GNNs struggle with global pattern abstraction and degrade with increasing graph size. This work demonstrates that vision models possess remarkable yet underutilized capabilities for graph structural understanding, particularly for problems requiring global topological awareness and scale-invariant reasoning. These findings open new avenues to leverage this underappreciated potential for developing more effective graph foundation models for tasks dominated by holistic pattern recognition.

Graphs are essential data structures for modeling complex interactions in domains such as social networks, molecular structures, and biological systems. Graph-level tasks, which predict properties or classes for the entire graph, are critical for applications, such as molecular property prediction and subgraph counting. Graph Neural Networks (GNNs) have shown promise in these tasks, but their evaluations are often limited to narrow datasets, tasks, and inconsistent experimental setups, restricting their generalizability. To address these limitations, we propose a unified evaluation framework for graph-level GNNs. This framework provides a standardized setting to evaluate GNNs across diverse datasets, various graph tasks (e.g., graph classification and regression), and challenging scenarios, including noisy, imbalanced, and few-shot graphs. Additionally, we propose a novel GNN model with enhanced expressivity and generalization capabilities. Specifically, we enhance the expressivity of GNNs through a k-path rooted subgraph approach, enabling the model to effectively count subgraphs (e.g., paths and cycles). Moreover, we introduce a unified graph contrastive learning algorithm for graphs across diverse domains, which adaptively removes unimportant edges to augment graphs, thereby significantly improving generalization performance. Extensive experiments demonstrate that our model achieves superior performance against fourteen effective baselines across twenty-seven graph datasets, establishing it as a robust and generalizable model for graph-level tasks.

Graph Neural Networks (GNNs) are an effective framework for representation learning of graphs. GNNs follow a neighborhood aggregation scheme, where the representation vector of a node is computed by recursively aggregating and transforming representation vectors of its neighboring nodes. Many GNN variants have been proposed and have achieved state-of-the-art results on both node and graph classification tasks. However, despite GNNs revolutionizing graph representation learning, there is limited understanding of their representational properties and limitations. Here, we present a theoretical framework for analyzing the expressive power of GNNs to capture different graph structures. Our results characterize the discriminative power of popular GNN variants, such as Graph Convolutional Networks and GraphSAGE, and show that they cannot learn to distinguish certain simple graph structures. We then develop a simple architecture that is provably the most expressive among the class of GNNs and is as powerful as the Weisfeiler-Lehman graph isomorphism test. We empirically validate our theoretical findings on a number of graph classification benchmarks, and demonstrate that our model achieves state-of-the-art performance.

We present a simple yet powerful neural network that implicitly represents and renders 3D objects and scenes only from 2D observations. The network models 3D geometries as a general radiance field, which takes a set of 2D images with camera poses and intrinsics as input, constructs an internal representation for each point of the 3D space, and then renders the corresponding appearance and geometry of that point viewed from an arbitrary position. The key to our approach is to learn local features for each pixel in 2D images and to then project these features to 3D points, thus yielding general and rich point representations. We additionally integrate an attention mechanism to aggregate pixel features from multiple 2D views, such that visual occlusions are implicitly taken into account. Extensive experiments demonstrate that our method can generate high-quality and realistic novel views for novel objects, unseen categories and challenging real-world scenes.

Sound can convey significant information for spatial reasoning in our daily lives. To endow deep networks with such ability, we address the challenge of dense indoor prediction with sound in both 2D and 3D via cross-modal knowledge distillation. In this work, we propose a Spatial Alignment via Matching (SAM) distillation framework that elicits local correspondence between the two modalities in vision-to-audio knowledge transfer. SAM integrates audio features with visually coherent learnable spatial embeddings to resolve inconsistencies in multiple layers of a student model. Our approach does not rely on a specific input representation, allowing for flexibility in the input shapes or dimensions without performance degradation. With a newly curated benchmark named Dense Auditory Prediction of Surroundings (DAPS), we are the first to tackle dense indoor prediction of omnidirectional surroundings in both 2D and 3D with audio observations. Specifically, for audio-based depth estimation, semantic segmentation, and challenging 3D scene reconstruction, the proposed distillation framework consistently achieves state-of-the-art performance across various metrics and backbone architectures.

Graphs or networks are a very convenient way to represent data with lots of interaction. Recently, Machine Learning on Graph data has gained a lot of traction. In particular, vertex classification and missing edge detection have very interesting applications, ranging from drug discovery to recommender systems. To achieve such tasks, tremendous work has been accomplished to learn embedding of nodes and edges into finite-dimension vector spaces. This task is called Graph Representation Learning. However, Graph Representation Learning techniques often display prohibitive time and memory complexities, preventing their use in real-time with business size graphs. In this paper, we address this issue by leveraging a degeneracy property of Graphs - the K-Core Decomposition. We present two techniques taking advantage of this decomposition to reduce the time and memory consumption of walk-based Graph Representation Learning algorithms. We evaluate the performances, expressed in terms of quality of embedding and computational resources, of the proposed techniques on several academic datasets. Our code is available at https://github.com/SBrandeis/kcore-embedding

Complex networks provide a means to describe cities through their street mesh, expressing characteristics that refer to the structure and organization of an urban zone. Although other studies have used complex networks to model street meshes, we observed a lack of methods to characterize the relationship between cities by using their topological features. Accordingly, this paper aims to describe interactions between cities by using vectors of topological features extracted from their street meshes represented as complex networks. The methodology of this study is based on the use of digital maps. Over the computational representation of such maps, we extract global complex-network features that embody the characteristics of the cities. These vectors allow for the use of multidimensional projection and clustering techniques, enabling a similarity-based comparison of the street meshes. We experiment with 645 cities from the Brazilian state of Sao Paulo. Our results show how the joint of global features describes urban indicators that are deep-rooted in the network's topology and how they reveal characteristics and similarities among sets of cities that are separated from each other.

Convolutional Neural Networks (CNNs) and Vision Transformers (ViT) have been pivotal in biomedical image segmentation, yet their ability to manage long-range dependencies remains constrained by inherent locality and computational overhead. To overcome these challenges, in this technical report, we first propose xLSTM-UNet, a UNet structured deep learning neural network that leverages Vision-LSTM (xLSTM) as its backbone for medical image segmentation. xLSTM is a recently proposed as the successor of Long Short-Term Memory (LSTM) networks and have demonstrated superior performance compared to Transformers and State Space Models (SSMs) like Mamba in Neural Language Processing (NLP) and image classification (as demonstrated in Vision-LSTM, or ViL implementation). Here, xLSTM-UNet we designed extend the success in biomedical image segmentation domain. By integrating the local feature extraction strengths of convolutional layers with the long-range dependency capturing abilities of xLSTM, xLSTM-UNet offers a robust solution for comprehensive image analysis. We validate the efficacy of xLSTM-UNet through experiments. Our findings demonstrate that xLSTM-UNet consistently surpasses the performance of leading CNN-based, Transformer-based, and Mamba-based segmentation networks in multiple datasets in biomedical segmentation including organs in abdomen MRI, instruments in endoscopic images, and cells in microscopic images. With comprehensive experiments performed, this technical report highlights the potential of xLSTM-based architectures in advancing biomedical image analysis in both 2D and 3D. The code, models, and datasets are publicly available at http://tianrun-chen.github.io/xLSTM-UNet/{http://tianrun-chen.github.io/xLSTM-Unet/}

Multi-layer perceptrons (MLP) have proven to be effective scene encoders when combined with higher-dimensional projections of the input, commonly referred to as positional encoding. However, scenes with a wide frequency spectrum remain a challenge: choosing high frequencies for positional encoding introduces noise in low structure areas, while low frequencies result in poor fitting of detailed regions. To address this, we propose a progressive positional encoding, exposing a hierarchical MLP structure to incremental sets of frequency encodings. Our model accurately reconstructs scenes with wide frequency bands and learns a scene representation at progressive level of detail without explicit per-level supervision. The architecture is modular: each level encodes a continuous implicit representation that can be leveraged separately for its respective resolution, meaning a smaller network for coarser reconstructions. Experiments on several 2D and 3D datasets show improvements in reconstruction accuracy, representational capacity and training speed compared to baselines.

Semantic segmentation networks are usually pre-trained once and not updated during deployment. As a consequence, misclassifications commonly occur if the distribution of the training data deviates from the one encountered during the robot's operation. We propose to mitigate this problem by adapting the neural network to the robot's environment during deployment, without any need for external supervision. Leveraging complementary data representations, we generate a supervision signal, by probabilistically accumulating consecutive 2D semantic predictions in a volumetric 3D map. We then train the network on renderings of the accumulated semantic map, effectively resolving ambiguities and enforcing multi-view consistency through the 3D representation. In contrast to scene adaptation methods, we aim to retain the previously-learned knowledge, and therefore employ a continual learning experience replay strategy to adapt the network. Through extensive experimental evaluation, we show successful adaptation to real-world indoor scenes both on the ScanNet dataset and on in-house data recorded with an RGB-D sensor. Our method increases the segmentation accuracy on average by 9.9% compared to the fixed pre-trained neural network, while retaining knowledge from the pre-training dataset.

Message Passing Neural Networks (MPNNs) are instances of Graph Neural Networks that leverage the graph to send messages over the edges. This inductive bias leads to a phenomenon known as over-squashing, where a node feature is insensitive to information contained at distant nodes. Despite recent methods introduced to mitigate this issue, an understanding of the causes for over-squashing and of possible solutions are lacking. In this theoretical work, we prove that: (i) Neural network width can mitigate over-squashing, but at the cost of making the whole network more sensitive; (ii) Conversely, depth cannot help mitigate over-squashing: increasing the number of layers leads to over-squashing being dominated by vanishing gradients; (iii) The graph topology plays the greatest role, since over-squashing occurs between nodes at high commute (access) time. Our analysis provides a unified framework to study different recent methods introduced to cope with over-squashing and serves as a justification for a class of methods that fall under graph rewiring.

Implicit Neural Representations (INRs) approximate discrete data through continuous functions and are commonly used for encoding 2D images. Traditional image-based INRs employ neural networks to map pixel coordinates to RGB values, capturing shapes, colors, and textures within the network's weights. Recently, GaussianImage has been proposed as an alternative, using Gaussian functions instead of neural networks to achieve comparable quality and compression. Such a solution obtains a quality and compression ratio similar to classical INR models but does not allow image modification. In contrast, our work introduces a novel method, MiraGe, which uses mirror reflections to perceive 2D images in 3D space and employs flat-controlled Gaussians for precise 2D image editing. Our approach improves the rendering quality and allows realistic image modifications, including human-inspired perception of photos in the 3D world. Thanks to modeling images in 3D space, we obtain the illusion of 3D-based modification in 2D images. We also show that our Gaussian representation can be easily combined with a physics engine to produce physics-based modification of 2D images. Consequently, MiraGe allows for better quality than the standard approach and natural modification of 2D images

Automatic organ segmentation is an important yet challenging problem for medical image analysis. The pancreas is an abdominal organ with very high anatomical variability. This inhibits previous segmentation methods from achieving high accuracies, especially compared to other organs such as the liver, heart or kidneys. In this paper, we present a probabilistic bottom-up approach for pancreas segmentation in abdominal computed tomography (CT) scans, using multi-level deep convolutional networks (ConvNets). We propose and evaluate several variations of deep ConvNets in the context of hierarchical, coarse-to-fine classification on image patches and regions, i.e. superpixels. We first present a dense labeling of local image patches via P{-}ConvNet and nearest neighbor fusion. Then we describe a regional ConvNet (R_1{-}ConvNet) that samples a set of bounding boxes around each image superpixel at different scales of contexts in a "zoom-out" fashion. Our ConvNets learn to assign class probabilities for each superpixel region of being pancreas. Last, we study a stacked R_2{-}ConvNet leveraging the joint space of CT intensities and the P{-}ConvNet dense probability maps. Both 3D Gaussian smoothing and 2D conditional random fields are exploited as structured predictions for post-processing. We evaluate on CT images of 82 patients in 4-fold cross-validation. We achieve a Dice Similarity Coefficient of 83.6pm6.3% in training and 71.8pm10.7% in testing.

Message-passing graph neural networks (MPNNs) emerged as powerful tools for processing graph-structured input. However, they operate on a fixed input graph structure, ignoring potential noise and missing information. Furthermore, their local aggregation mechanism can lead to problems such as over-squashing and limited expressive power in capturing relevant graph structures. Existing solutions to these challenges have primarily relied on heuristic methods, often disregarding the underlying data distribution. Hence, devising principled approaches for learning to infer graph structures relevant to the given prediction task remains an open challenge. In this work, leveraging recent progress in exact and differentiable k-subset sampling, we devise probabilistically rewired MPNNs (PR-MPNNs), which learn to add relevant edges while omitting less beneficial ones. For the first time, our theoretical analysis explores how PR-MPNNs enhance expressive power, and we identify precise conditions under which they outperform purely randomized approaches. Empirically, we demonstrate that our approach effectively mitigates issues like over-squashing and under-reaching. In addition, on established real-world datasets, our method exhibits competitive or superior predictive performance compared to traditional MPNN models and recent graph transformer architectures.

The presence of linear paths in parameter space between two different network solutions in certain cases, i.e., linear mode connectivity (LMC), has garnered interest from both theoretical and practical fronts. There has been significant research that either practically designs algorithms catered for connecting networks by adjusting for the permutation symmetries as well as some others that more theoretically construct paths through which networks can be connected. Yet, the core reasons for the occurrence of LMC, when in fact it does occur, in the highly non-convex loss landscapes of neural networks are far from clear. In this work, we take a step towards understanding it by providing a model of how the loss landscape needs to behave topographically for LMC (or the lack thereof) to manifest. Concretely, we present a `mountainside and ridge' perspective that helps to neatly tie together different geometric features that can be spotted in the loss landscape along the training runs. We also complement this perspective by providing a theoretical analysis of the barrier height, for which we provide empirical support, and which additionally extends as a faithful predictor of layer-wise LMC. We close with a toy example that provides further intuition on how barriers arise in the first place, all in all, showcasing the larger aim of the work -- to provide a working model of the landscape and its topography for the occurrence of LMC.

Graph neural networks (GNNs) have recently become the standard approach for learning with graph-structured data. Prior work has shed light into their potential, but also their limitations. Unfortunately, it was shown that standard GNNs are limited in their expressive power. These models are no more powerful than the 1-dimensional Weisfeiler-Leman (1-WL) algorithm in terms of distinguishing non-isomorphic graphs. In this paper, we propose Path Neural Networks (PathNNs), a model that updates node representations by aggregating paths emanating from nodes. We derive three different variants of the PathNN model that aggregate single shortest paths, all shortest paths and all simple paths of length up to K. We prove that two of these variants are strictly more powerful than the 1-WL algorithm, and we experimentally validate our theoretical results. We find that PathNNs can distinguish pairs of non-isomorphic graphs that are indistinguishable by 1-WL, while our most expressive PathNN variant can even distinguish between 3-WL indistinguishable graphs. The different PathNN variants are also evaluated on graph classification and graph regression datasets, where in most cases, they outperform the baseline methods.

Modern recurrent architectures, such as xLSTM and Mamba, have recently challenged the Transformer in language modeling. However, their structure constrains their applicability to sequences only or requires processing multi-dimensional data structures, such as images or molecular graphs, in a pre-defined sequential order. In contrast, Multi-Dimensional RNNs (MDRNNs) are well suited for data with a higher level structure, like 2D grids, trees, and directed acyclic graphs (DAGs). In this work, we extend the notion of multi-dimensionality to linear RNNs. We introduce parallelizable Linear Source Transition Mark networks (pLSTMs) using Source, Transition, and Mark gates that act on the line graph of a general DAG. This enables parallelization in analogy to parallel associative scans and the chunkwise-recurrent form of sequential linear RNNs, but for DAGs. For regular grids (1D and 2D), like images, this scheme can be efficiently implemented using einsum operations, concatenations, and padding in logarithmic time. pLSTMs tackle the vanishing/exploding activation/gradient problem for long distances in DAGs via two distinct modes: a directed propagation mode (P-mode) and a diffusive distribution mode (D-mode). To showcase the long-range capabilities of pLSTM, we introduce arrow-pointing extrapolation as a synthetic computer vision task that contains long-distance directional information. We demonstrate that pLSTMs generalize well to larger image sizes, whereas Transformers struggle to extrapolate. On established molecular graph and computer vision benchmarks, pLSTMs also show strong performance. Code and Datasets are available at: https://github.com/ml-jku/plstm_experiments.

We identify and overcome two key obstacles in extending the success of BERT-style pre-training, or the masked image modeling, to convolutional networks (convnets): (i) convolution operation cannot handle irregular, random-masked input images; (ii) the single-scale nature of BERT pre-training is inconsistent with convnet's hierarchical structure. For (i), we treat unmasked pixels as sparse voxels of 3D point clouds and use sparse convolution to encode. This is the first use of sparse convolution for 2D masked modeling. For (ii), we develop a hierarchical decoder to reconstruct images from multi-scale encoded features. Our method called Sparse masKed modeling (SparK) is general: it can be used directly on any convolutional model without backbone modifications. We validate it on both classical (ResNet) and modern (ConvNeXt) models: on three downstream tasks, it surpasses both state-of-the-art contrastive learning and transformer-based masked modeling by similarly large margins (around +1.0%). Improvements on object detection and instance segmentation are more substantial (up to +3.5%), verifying the strong transferability of features learned. We also find its favorable scaling behavior by observing more gains on larger models. All this evidence reveals a promising future of generative pre-training on convnets. Codes and models are released at https://github.com/keyu-tian/SparK.

Single-atom catalysts (SACs) have emerged as frontiers for catalyzing chemical reactions, yet the diverse combinations of active elements and support materials, the nature of coordination environments, elude traditional methodologies in searching optimal SAC systems with superior catalytic performance. Herein, by integrating multi-branch Convolutional Neural Network (CNN) analysis models to hybrid descriptor based activity volcano plot, 2D SAC system composed of diverse metallic single atoms anchored on six type of 2D supports, including graphitic carbon nitride, nitrogen-doped graphene, graphene with dual-vacancy, black phosphorous, boron nitride, and C2N, are screened for efficient CO2RR. Starting from establishing a correlation map between the adsorption energies of intermediates and diverse electronic and elementary descriptors, sole singular descriptor lost magic to predict catalytic activity. Deep learning method utilizing multi-branch CNN model therefore was employed, using 2D electronic density of states as input to predict adsorption energies. Hybrid-descriptor enveloping both C- and O-types of CO2RR intermediates was introduced to construct volcano plots and limiting potential periodic table, aiming for intuitive screening of catalyst candidates for efficient CO2 reduction to CH4. The eDOS occlusion experiments were performed to unravel individual orbital contribution to adsorption energy. To explore the electronic scale principle governing practical engineering catalytic CO2RR activity, orbitalwise eDOS shifting experiments based on CNN model were employed. The study involves examining the adsorption energy and, consequently, catalytic activities while varying supported single atoms. This work offers a tangible framework to inform both theoretical screening and experimental synthesis, thereby paving the way for systematically designing efficient SACs.

We introduce Lagrangian Flow Networks (LFlows) for modeling fluid densities and velocities continuously in space and time. By construction, the proposed LFlows satisfy the continuity equation, a PDE describing mass conservation in its differentiable form. Our model is based on the insight that solutions to the continuity equation can be expressed as time-dependent density transformations via differentiable and invertible maps. This follows from classical theory of the existence and uniqueness of Lagrangian flows for smooth vector fields. Hence, we model fluid densities by transforming a base density with parameterized diffeomorphisms conditioned on time. The key benefit compared to methods relying on numerical ODE solvers or PINNs is that the analytic expression of the velocity is always consistent with changes in density. Furthermore, we require neither expensive numerical solvers, nor additional penalties to enforce the PDE. LFlows show higher predictive accuracy in density modeling tasks compared to competing models in 2D and 3D, while being computationally efficient. As a real-world application, we model bird migration based on sparse weather radar measurements.

Effective communication is key to successful, decentralized, multi-robot path planning. Yet, it is far from obvious what information is crucial to the task at hand, and how and when it must be shared among robots. To side-step these issues and move beyond hand-crafted heuristics, we propose a combined model that automatically synthesizes local communication and decision-making policies for robots navigating in constrained workspaces. Our architecture is composed of a convolutional neural network (CNN) that extracts adequate features from local observations, and a graph neural network (GNN) that communicates these features among robots. We train the model to imitate an expert algorithm, and use the resulting model online in decentralized planning involving only local communication and local observations. We evaluate our method in simulations {by navigating teams of robots to their destinations in 2D} cluttered workspaces. We measure the success rates and sum of costs over the planned paths. The results show a performance close to that of our expert algorithm, demonstrating the validity of our approach. In particular, we show our model's capability to generalize to previously unseen cases (involving larger environments and larger robot teams).

In the realm of generative models for graphs, extensive research has been conducted. However, most existing methods struggle with large graphs due to the complexity of representing the entire joint distribution across all node pairs and capturing both global and local graph structures simultaneously. To overcome these issues, we introduce a method that generates a graph by progressively expanding a single node to a target graph. In each step, nodes and edges are added in a localized manner through denoising diffusion, building first the global structure, and then refining the local details. The local generation avoids modeling the entire joint distribution over all node pairs, achieving substantial computational savings with subquadratic runtime relative to node count while maintaining high expressivity through multiscale generation. Our experiments show that our model achieves state-of-the-art performance on well-established benchmark datasets while successfully scaling to graphs with at least 5000 nodes. Our method is also the first to successfully extrapolate to graphs outside of the training distribution, showcasing a much better generalization capability over existing methods.

The self-attention mechanism utilizes large implicit weight matrices, programmed through dot product-based activations with very few trainable parameters, to enable long sequence modeling. In this paper, we investigate the possibility of discarding residual learning by employing large implicit kernels to achieve full context interaction at each layer of the network. To accomplish it, we introduce coordinate-based implicit MLPs as a slow network to generate hyper-kernels for another fast convolutional network. To get context-varying weights for fast dynamic encoding, we propose a HyperZ{cdotZ{cdot}W} operator that connects hyper-kernels (W) and hidden activations (Z) through simple elementwise multiplication, followed by convolution of Z using the context-dependent W. Based on this design, we present a novel Terminator architecture that integrates hyper-kernels of different sizes to produce multi-branch hidden representations for enhancing the feature extraction capability of each layer. Additionally, a bottleneck layer is employed to compress the concatenated channels, allowing only valuable information to propagate to the subsequent layers. Notably, our model incorporates several innovative components and exhibits excellent properties, such as introducing local feedback error for updating the slow network, stable zero-mean features, faster training convergence, and fewer model parameters. Extensive experimental results on pixel-level 1D and 2D image classification benchmarks demonstrate the superior performance of our architecture.

Kolmogorov-Arnold Networks (KANs) have recently emerged as a promising alternative to traditional neural architectures, yet their application to speech processing remains under explored. This work presents the first investigation of KANs for Spoken Language Understanding (SLU) tasks. We experiment with 2D-CNN models on two datasets, integrating KAN layers in five different configurations within the dense block. The best-performing setup, which places a KAN layer between two linear layers, is directly applied to transformer-based models and evaluated on five SLU datasets with increasing complexity. Our results show that KAN layers can effectively replace the linear layers, achieving comparable or superior performance in most cases. Finally, we provide insights into how KAN and linear layers on top of transformers differently attend to input regions of the raw waveforms.

Tooth segmentation is a pivotal step in modern digital dentistry, essential for applications across orthodontic diagnosis and treatment planning. Despite its importance, this process is fraught with challenges due to the high noise and low contrast inherent in 2D and 3D tooth data. Both Convolutional Neural Networks (CNNs) and Transformers has shown promise in medical image segmentation, yet each method has limitations in handling long-range dependencies and computational complexity. To address this issue, this paper introduces T-Mamba, integrating frequency-based features and shared bi-positional encoding into vision mamba to address limitations in efficient global feature modeling. Besides, we design a gate selection unit to integrate two features in spatial domain and one feature in frequency domain adaptively. T-Mamba is the first work to introduce frequency-based features into vision mamba, and its flexibility allows it to process both 2D and 3D tooth data without the need for separate modules. Also, the TED3, a large-scale public tooth 2D dental X-ray dataset, has been presented in this paper. Extensive experiments demonstrate that T-Mamba achieves new SOTA results on a public tooth CBCT dataset and outperforms previous SOTA methods on TED3 dataset. The code and models are publicly available at: https://github.com/isbrycee/T-Mamba.

The 2D human pose estimation is a basic visual problem. However, supervised learning of a model requires massive labeled images, which is expensive and labor-intensive. In this paper, we aim at boosting the accuracy of a pose estimator by excavating extra unlabeled images in a semi-supervised learning (SSL) way. Most previous consistency-based SSL methods strive to constraint the model to predict consistent results for differently augmented images. Following this consensus, we revisit two core aspects including advanced data augmentation methods and concise consistency training frameworks. Specifically, we heuristically dig various collaborative combinations of existing data augmentations, and discover novel superior data augmentation schemes to more effectively add noise on unlabeled samples. They can compose easy-hard augmentation pairs with larger transformation difficulty gaps, which play a crucial role in consistency-based SSL. Moreover, we propose to strongly augment unlabeled images repeatedly with diverse augmentations, generate multi-path predictions sequentially, and optimize corresponding unsupervised consistency losses using one single network. This simple and compact design is on a par with previous methods consisting of dual or triple networks. Furthermore, it can also be integrated with multiple networks to produce better performance. Comparing to state-of-the-art SSL approaches, our method brings substantial improvements on public datasets. Code is released for academic use in https://github.com/hnuzhy/MultiAugs.

Generating 3D images of complex objects conditionally from a few 2D views is a difficult synthesis problem, compounded by issues such as domain gap and geometric misalignment. For instance, a unified framework such as Generative Adversarial Networks cannot achieve this unless they explicitly define both a domain-invariant and geometric-invariant joint latent distribution, whereas Neural Radiance Fields are generally unable to handle both issues as they optimize at the pixel level. By contrast, we propose a simple and novel 2D to 3D synthesis approach based on conditional diffusion with vector-quantized codes. Operating in an information-rich code space enables high-resolution 3D synthesis via full-coverage attention across the views. Specifically, we generate the 3D codes (e.g. for CT images) conditional on previously generated 3D codes and the entire codebook of two 2D views (e.g. 2D X-rays). Qualitative and quantitative results demonstrate state-of-the-art performance over specialized methods across varied evaluation criteria, including fidelity metrics such as density, coverage, and distortion metrics for two complex volumetric imagery datasets from in real-world scenarios.

Deep learning has revolutionized the computer vision and image classification domains. In this context Convolutional Neural Networks (CNNs) based architectures are the most widely applied models. In this article, we introduced two procedures for training Convolutional Neural Networks (CNNs) and Deep Neural Network based on Gradient Boosting (GB), namely GB-CNN and GB-DNN. These models are trained to fit the gradient of the loss function or pseudo-residuals of previous models. At each iteration, the proposed method adds one dense layer to an exact copy of the previous deep NN model. The weights of the dense layers trained on previous iterations are frozen to prevent over-fitting, permitting the model to fit the new dense as well as to fine-tune the convolutional layers (for GB-CNN) while still utilizing the information already learned. Through extensive experimentation on different 2D-image classification and tabular datasets, the presented models show superior performance in terms of classification accuracy with respect to standard CNN and Deep-NN with the same architectures.

There have been remarkable successes in computer vision with deep learning. While such breakthroughs show robust performance, there have still been many challenges in learning in-depth knowledge, like occlusion or predicting physical interactions. Although some recent works show the potential of 3D data in serving such context, it is unclear how we efficiently provide 3D input to the 2D models due to the misalignment in dimensionality between 2D and 3D. To leverage the successes of 2D models in predicting self-occlusions, we design Ray-marching in Camera Space (RiCS), a new method to represent the self-occlusions of foreground objects in 3D into a 2D self-occlusion map. We test the effectiveness of our representation on the human image harmonization task by predicting shading that is coherent with a given background image. Our experiments demonstrate that our representation map not only allows us to enhance the image quality but also to model temporally coherent complex shadow effects compared with the simulation-to-real and harmonization methods, both quantitatively and qualitatively. We further show that we can significantly improve the performance of human parts segmentation networks trained on existing synthetic datasets by enhancing the harmonization quality with our method.

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.

This paper investigates how far a very deep neural network is from attaining close to saturating performance on existing 2D and 3D face alignment datasets. To this end, we make the following 5 contributions: (a) we construct, for the first time, a very strong baseline by combining a state-of-the-art architecture for landmark localization with a state-of-the-art residual block, train it on a very large yet synthetically expanded 2D facial landmark dataset and finally evaluate it on all other 2D facial landmark datasets. (b) We create a guided by 2D landmarks network which converts 2D landmark annotations to 3D and unifies all existing datasets, leading to the creation of LS3D-W, the largest and most challenging 3D facial landmark dataset to date ~230,000 images. (c) Following that, we train a neural network for 3D face alignment and evaluate it on the newly introduced LS3D-W. (d) We further look into the effect of all "traditional" factors affecting face alignment performance like large pose, initialization and resolution, and introduce a "new" one, namely the size of the network. (e) We show that both 2D and 3D face alignment networks achieve performance of remarkable accuracy which is probably close to saturating the datasets used. Training and testing code as well as the dataset can be downloaded from https://www.adrianbulat.com/face-alignment/

Comprehending 3D environments is vital for intelligent systems in domains like robotics and autonomous navigation. Voxel grids offer a structured representation of 3D space, but extracting high-level semantic meaning remains challenging. This paper proposes a novel approach utilizing a Vision-Language Model (VLM) to extract "voxel semantics"-object identity, color, and location-from voxel data. Critically, instead of employing complex 3D networks, our method processes the voxel space by systematically slicing it along a primary axis (e.g., the Z-axis, analogous to CT scan slices). These 2D slices are then formatted and sequentially fed into the image encoder of a standard VLM. The model learns to aggregate information across slices and correlate spatial patterns with semantic concepts provided by the language component. This slice-based strategy aims to leverage the power of pre-trained 2D VLMs for efficient 3D semantic understanding directly from voxel representations.

Quantum many-body physics simulation has important impacts on understanding fundamental science and has applications to quantum materials design and quantum technology. However, due to the exponentially growing size of the Hilbert space with respect to the particle number, a direct simulation is intractable. While representing quantum states with tensor networks and neural networks are the two state-of-the-art methods for approximate simulations, each has its own limitations in terms of expressivity and inductive bias. To address these challenges, we develop a novel architecture, Autoregressive Neural TensorNet (ANTN), which bridges tensor networks and autoregressive neural networks. We show that Autoregressive Neural TensorNet parameterizes normalized wavefunctions, allows for exact sampling, generalizes the expressivity of tensor networks and autoregressive neural networks, and inherits a variety of symmetries from autoregressive neural networks. We demonstrate our approach on quantum state learning as well as finding the ground state of the challenging 2D J_1-J_2 Heisenberg model with different systems sizes and coupling parameters, outperforming both tensor networks and autoregressive neural networks. Our work opens up new opportunities for scientific simulations of quantum many-body physics and quantum technology.

In-Context Operator Networks (ICONs) have demonstrated the ability to learn operators across diverse partial differential equations using few-shot, in-context learning. However, existing ICONs process each spatial point as an individual token, severely limiting computational efficiency when handling dense data in higher spatial dimensions. We propose Vision In-Context Operator Networks (VICON), which integrates vision transformer architectures to efficiently process 2D data through patch-wise operations while preserving ICON's adaptability to multiphysics systems and varying timesteps. Evaluated across three fluid dynamics benchmarks, VICON significantly outperforms state-of-the-art baselines: DPOT and MPP, reducing the averaged last-step rollout error by 37.9% compared to DPOT and 44.7% compared to MPP, while requiring only 72.5% and 34.8% of their respective inference times. VICON naturally supports flexible rollout strategies with varying timestep strides, enabling immediate deployment in imperfect measurement systems where sampling frequencies may differ or frames might be dropped - common challenges in real-world settings - without requiring retraining or interpolation. In these realistic scenarios, VICON exhibits remarkable robustness, experiencing only 24.41% relative performance degradation compared to 71.37%-74.49% degradation in baseline methods, demonstrating its versatility for deploying in realistic applications. Our scripts for processing datasets and code are publicly available at https://github.com/Eydcao/VICON.

Inverse problems in image reconstruction are fundamentally complicated by unknown noise properties. Classical iterative deconvolution approaches amplify noise and require careful parameter selection for an optimal trade-off between sharpness and grain. Deep learning methods allow for flexible parametrization of the noise and learning its properties directly from the data. Recently, self-supervised blind-spot neural networks were successfully adopted for image deconvolution by including a known point-spread function in the end-to-end training. However, their practical application has been limited to 2D images in the biomedical domain because it implies large kernels that are poorly optimized. We tackle this problem with Fast Fourier Transform convolutions that provide training speed-up in 3D microscopy deconvolution tasks. Further, we propose to adopt a Siamese invariance loss for deconvolution and empirically identify its optimal position in the neural network between blind-spot and full image branches. The experimental results show that our improved framework outperforms the previous state-of-the-art deconvolution methods with a known point spread function.

In this paper, we study the problem of temporal video grounding (TVG), which aims to predict the starting/ending time points of moments described by a text sentence within a long untrimmed video. Benefiting from fine-grained 3D visual features, the TVG techniques have achieved remarkable progress in recent years. However, the high complexity of 3D convolutional neural networks (CNNs) makes extracting dense 3D visual features time-consuming, which calls for intensive memory and computing resources. Towards efficient TVG, we propose a novel text-visual prompting (TVP) framework, which incorporates optimized perturbation patterns (that we call 'prompts') into both visual inputs and textual features of a TVG model. In sharp contrast to 3D CNNs, we show that TVP allows us to effectively co-train vision encoder and language encoder in a 2D TVG model and improves the performance of crossmodal feature fusion using only low-complexity sparse 2D visual features. Further, we propose a Temporal-Distance IoU (TDIoU) loss for efficient learning of TVG. Experiments on two benchmark datasets, Charades-STA and ActivityNet Captions datasets, empirically show that the proposed TVP significantly boosts the performance of 2D TVG (e.g., 9.79% improvement on Charades-STA and 30.77% improvement on ActivityNet Captions) and achieves 5x inference acceleration over TVG using 3D visual features. Codes are available at Open.Intel.

Convolutional Neural Networks have revolutionized vision applications. There are image domains and representations, however, that cannot be handled by standard CNNs (e.g., spherical images, superpixels). Such data are usually processed using networks and algorithms specialized for each type. In this work, we show that it may not always be necessary to use specialized neural networks to operate on such spaces. Instead, we introduce a new structured graph convolution operator that can copy 2D convolution weights, transferring the capabilities of already trained traditional CNNs to our new graph network. This network can then operate on any data that can be represented as a positional graph. By converting non-rectilinear data to a graph, we can apply these convolutions on these irregular image domains without requiring training on large domain-specific datasets. Results of transferring pre-trained image networks for segmentation, stylization, and depth prediction are demonstrated for a variety of such data forms.

Bayesian parameter inference is useful to improve Li-ion battery diagnostics and can help formulate battery aging models. However, it is computationally intensive and cannot be easily repeated for multiple cycles, multiple operating conditions, or multiple replicate cells. To reduce the computational cost of Bayesian calibration, numerical solvers for physics-based models can be replaced with faster surrogates. A physics-informed neural network (PINN) is developed as a surrogate for the pseudo-2D (P2D) battery model calibration. For the P2D surrogate, additional training regularization was needed as compared to the PINN single-particle model (SPM) developed in Part I. Both the PINN SPM and P2D surrogate models are exercised for parameter inference and compared to data obtained from a direct numerical solution of the governing equations. A parameter inference study highlights the ability to use these PINNs to calibrate scaling parameters for the cathode Li diffusion and the anode exchange current density. By realizing computational speed-ups of 2250x for the P2D model, as compared to using standard integrating methods, the PINN surrogates enable rapid state-of-health diagnostics. In the low-data availability scenario, the testing error was estimated to 2mV for the SPM surrogate and 10mV for the P2D surrogate which could be mitigated with additional data.

We introduce Open3DIS, a novel solution designed to tackle the problem of Open-Vocabulary Instance Segmentation within 3D scenes. Objects within 3D environments exhibit diverse shapes, scales, and colors, making precise instance-level identification a challenging task. Recent advancements in Open-Vocabulary scene understanding have made significant strides in this area by employing class-agnostic 3D instance proposal networks for object localization and learning queryable features for each 3D mask. While these methods produce high-quality instance proposals, they struggle with identifying small-scale and geometrically ambiguous objects. The key idea of our method is a new module that aggregates 2D instance masks across frames and maps them to geometrically coherent point cloud regions as high-quality object proposals addressing the above limitations. These are then combined with 3D class-agnostic instance proposals to include a wide range of objects in the real world. To validate our approach, we conducted experiments on three prominent datasets, including ScanNet200, S3DIS, and Replica, demonstrating significant performance gains in segmenting objects with diverse categories over the state-of-the-art approaches.

Molecular interactions often involve high-order relationships that cannot be fully captured by traditional graph-based models limited to pairwise connections. Hypergraphs naturally extend graphs by enabling multi-way interactions, making them well-suited for modeling complex molecular systems. In this work, we introduce EquiHGNN, an Equivariant HyperGraph Neural Network framework that integrates symmetry-aware representations to improve molecular modeling. By enforcing the equivariance under relevant transformation groups, our approach preserves geometric and topological properties, leading to more robust and physically meaningful representations. We examine a range of equivariant architectures and demonstrate that integrating symmetry constraints leads to notable performance gains on large-scale molecular datasets. Experiments on both small and large molecules show that high-order interactions offer limited benefits for small molecules but consistently outperform 2D graphs on larger ones. Adding geometric features to these high-order structures further improves the performance, emphasizing the value of spatial information in molecular learning. Our source code is available at https://github.com/HySonLab/EquiHGNN/

Convolutional neural networks are now seeing widespread use in a variety of fields, including image classification, facial and object recognition, medical imaging analysis, and many more. In addition, there are applications such as physics-informed simulators in which accurate forecasts in real time with a minimal lag are required. The present neural network designs include millions of parameters, which makes it difficult to install such complex models on devices that have limited memory. Compression techniques might be able to resolve these issues by decreasing the size of CNN models that are created by reducing the number of parameters that contribute to the complexity of the models. We propose a compressed tensor format of convolutional layer, a priori, before the training of the neural network. 3-way kernels or 2-way kernels in convolutional layers are replaced by one-way fiters. The overfitting phenomena will be reduced also. The time needed to make predictions or time required for training using the original Convolutional Neural Networks model would be cut significantly if there were fewer parameters to deal with. In this paper we present a method of a priori compressing convolutional neural networks for finite element (FE) predictions of physical data. Afterwards we validate our a priori compressed models on physical data from a FE model solving a 2D wave equation. We show that the proposed convolutinal compression technique achieves equivalent performance as classical convolutional layers with fewer trainable parameters and lower memory footprint.

Unsupervised generation of high-quality multi-view-consistent images and 3D shapes using only collections of single-view 2D photographs has been a long-standing challenge. Existing 3D GANs are either compute-intensive or make approximations that are not 3D-consistent; the former limits quality and resolution of the generated images and the latter adversely affects multi-view consistency and shape quality. In this work, we improve the computational efficiency and image quality of 3D GANs without overly relying on these approximations. We introduce an expressive hybrid explicit-implicit network architecture that, together with other design choices, synthesizes not only high-resolution multi-view-consistent images in real time but also produces high-quality 3D geometry. By decoupling feature generation and neural rendering, our framework is able to leverage state-of-the-art 2D CNN generators, such as StyleGAN2, and inherit their efficiency and expressiveness. We demonstrate state-of-the-art 3D-aware synthesis with FFHQ and AFHQ Cats, among other experiments.

Bayesian neural networks (BNNs) require scalable sampling algorithms to approximate posterior distributions over parameters. Existing stochastic gradient Markov Chain Monte Carlo (SGMCMC) methods are highly sensitive to the choice of stepsize and adaptive variants such as pSGLD typically fail to sample the correct invariant measure without addition of a costly divergence correction term. In this work, we build on the recently proposed `SamAdams' framework for timestep adaptation (Leimkuhler, Lohmann, and Whalley 2025), introducing an adaptive scheme: SA-SGLD, which employs time rescaling to modulate the stepsize according to a monitored quantity (typically the local gradient norm). SA-SGLD can automatically shrink stepsizes in regions of high curvature and expand them in flatter regions, improving both stability and mixing without introducing bias. We show that our method can achieve more accurate posterior sampling than SGLD on high-curvature 2D toy examples and in image classification with BNNs using sharp priors.

In pose estimation for seen objects, a prevalent pipeline involves using neural networks to predict dense 3D coordinates of the object surface on 2D images, which are then used to establish dense 2D-3D correspondences. However, current methods primarily focus on more efficient encoding techniques to improve the precision of predicted 3D coordinates on the object's front surface, overlooking the potential benefits of incorporating the back surface and interior of the object. To better utilize the full surface and interior of the object, this study predicts 3D coordinates of both the object's front and back surfaces and densely samples 3D coordinates between them. This process creates ultra-dense 2D-3D correspondences, effectively enhancing pose estimation accuracy based on the Perspective-n-Point (PnP) algorithm. Additionally, we propose Hierarchical Continuous Coordinate Encoding (HCCE) to provide a more accurate and efficient representation of front and back surface coordinates. Experimental results show that, compared to existing state-of-the-art (SOTA) methods on the BOP website, the proposed approach outperforms across seven classic BOP core datasets. Code is available at https://github.com/WangYuLin-SEU/HCCEPose.

Image segmentation plays an essential role in medicine for both diagnostic and interventional tasks. Segmentation approaches are either manual, semi-automated or fully-automated. Manual segmentation offers full control over the quality of the results, but is tedious, time consuming and prone to operator bias. Fully automated methods require no human effort, but often deliver sub-optimal results without providing users with the means to make corrections. Semi-automated approaches keep users in control of the results by providing means for interaction, but the main challenge is to offer a good trade-off between precision and required interaction. In this paper we present a deep learning (DL) based semi-automated segmentation approach that aims to be a "smart" interactive tool for region of interest delineation in medical images. We demonstrate its use for segmenting multiple organs on computed tomography (CT) of the abdomen. Our approach solves some of the most pressing clinical challenges: (i) it requires only one to a few user clicks to deliver excellent 2D segmentations in a fast and reliable fashion; (ii) it can generalize to previously unseen structures and "corner cases"; (iii) it delivers results that can be corrected quickly in a smart and intuitive way up to an arbitrary degree of precision chosen by the user and (iv) ensures high accuracy. We present our approach and compare it to other techniques and previous work to show the advantages brought by our method.

Based on the theory of homogeneous spaces we derive geometrically optimal edge attributes to be used within the flexible message-passing framework. We formalize the notion of weight sharing in convolutional networks as the sharing of message functions over point-pairs that should be treated equally. We define equivalence classes of point-pairs that are identical up to a transformation in the group and derive attributes that uniquely identify these classes. Weight sharing is then obtained by conditioning message functions on these attributes. As an application of the theory, we develop an efficient equivariant group convolutional network for processing 3D point clouds. The theory of homogeneous spaces tells us how to do group convolutions with feature maps over the homogeneous space of positions R^3, position and orientations R^3 {times} S^2, and the group SE(3) itself. Among these, R^3 {times} S^2 is an optimal choice due to the ability to represent directional information, which R^3 methods cannot, and it significantly enhances computational efficiency compared to indexing features on the full SE(3) group. We support this claim with state-of-the-art results -- in accuracy and speed -- on five different benchmarks in 2D and 3D, including interatomic potential energy prediction, trajectory forecasting in N-body systems, and generating molecules via equivariant diffusion models.

We propose a method for adapting neural networks to distribution shifts at test-time. In contrast to training-time robustness mechanisms that attempt to anticipate and counter the shift, we create a closed-loop system and make use of a test-time feedback signal to adapt a network on the fly. We show that this loop can be effectively implemented using a learning-based function, which realizes an amortized optimizer for the network. This leads to an adaptation method, named Rapid Network Adaptation (RNA), that is notably more flexible and orders of magnitude faster than the baselines. Through a broad set of experiments using various adaptation signals and target tasks, we study the efficiency and flexibility of this method. We perform the evaluations using various datasets (Taskonomy, Replica, ScanNet, Hypersim, COCO, ImageNet), tasks (depth, optical flow, semantic segmentation, classification), and distribution shifts (Cross-datasets, 2D and 3D Common Corruptions) with promising results. We end with a discussion on general formulations for handling distribution shifts and our observations from comparing with similar approaches from other domains.

We introduce a framework for multi-camera 3D object detection. In contrast to existing works, which estimate 3D bounding boxes directly from monocular images or use depth prediction networks to generate input for 3D object detection from 2D information, our method manipulates predictions directly in 3D space. Our architecture extracts 2D features from multiple camera images and then uses a sparse set of 3D object queries to index into these 2D features, linking 3D positions to multi-view images using camera transformation matrices. Finally, our model makes a bounding box prediction per object query, using a set-to-set loss to measure the discrepancy between the ground-truth and the prediction. This top-down approach outperforms its bottom-up counterpart in which object bounding box prediction follows per-pixel depth estimation, since it does not suffer from the compounding error introduced by a depth prediction model. Moreover, our method does not require post-processing such as non-maximum suppression, dramatically improving inference speed. We achieve state-of-the-art performance on the nuScenes autonomous driving benchmark.

Recent successful applications of convolutional neural networks (CNNs) to audio classification and speech recognition have motivated the search for better input representations for more efficient training. Visual displays of an audio signal, through various time-frequency representations such as spectrograms offer a rich representation of the temporal and spectral structure of the original signal. In this letter, we compare various popular signal processing methods to obtain this representation, such as short-time Fourier transform (STFT) with linear and Mel scales, constant-Q transform (CQT) and continuous Wavelet transform (CWT), and assess their impact on the classification performance of two environmental sound datasets using CNNs. This study supports the hypothesis that time-frequency representations are valuable in learning useful features for sound classification. Moreover, the actual transformation used is shown to impact the classification accuracy, with Mel-scaled STFT outperforming the other discussed methods slightly and baseline MFCC features to a large degree. Additionally, we observe that the optimal window size during transformation is dependent on the characteristics of the audio signal and architecturally, 2D convolution yielded better results in most cases compared to 1D.

Graph neural networks achieve high accuracy in link prediction by jointly leveraging graph topology and node attributes. Topology, however, is represented indirectly; state-of-the-art methods based on subgraph classification label nodes with distance to the target link, so that, although topological information is present, it is tempered by pooling. This makes it challenging to leverage features like loops and motifs associated with network formation mechanisms. We propose a link prediction algorithm based on a new pooling scheme called WalkPool. WalkPool combines the expressivity of topological heuristics with the feature-learning ability of neural networks. It summarizes a putative link by random walk probabilities of adjacent paths. Instead of extracting transition probabilities from the original graph, it computes the transition matrix of a "predictive" latent graph by applying attention to learned features; this may be interpreted as feature-sensitive topology fingerprinting. WalkPool can leverage unsupervised node features or be combined with GNNs and trained end-to-end. It outperforms state-of-the-art methods on all common link prediction benchmarks, both homophilic and heterophilic, with and without node attributes. Applying WalkPool to a set of unsupervised GNNs significantly improves prediction accuracy, suggesting that it may be used as a general-purpose graph pooling scheme.

Accurate, real-time 3D reconstruction of human heads from monocular images and videos underlies numerous visual applications. As 3D ground truth data is hard to come by at scale, previous methods have sought to learn from abundant 2D videos in a self-supervised manner. Typically, this involves the use of differentiable mesh rendering, which is effective but faces limitations. To improve on this, we propose SHeaP (Self-supervised Head Geometry Predictor Learned via 2D Gaussians). Given a source image, we predict a 3DMM mesh and a set of Gaussians that are rigged to this mesh. We then reanimate this rigged head avatar to match a target frame, and backpropagate photometric losses to both the 3DMM and Gaussian prediction networks. We find that using Gaussians for rendering substantially improves the effectiveness of this self-supervised approach. Training solely on 2D data, our method surpasses existing self-supervised approaches in geometric evaluations on the NoW benchmark for neutral faces and a new benchmark for non-neutral expressions. Our method also produces highly expressive meshes, outperforming state-of-the-art in emotion classification.

Recently, there has been a surge of interest in employing neural networks for graph generation, a fundamental statistical learning problem with critical applications like molecule design and community analysis. However, most approaches encounter significant limitations when generating large-scale graphs. This is due to their requirement to output the full adjacency matrices whose size grows quadratically with the number of nodes. In response to this challenge, we introduce a new, simple, and scalable graph representation named gap encoded edge list (GEEL) that has a small representation size that aligns with the number of edges. In addition, GEEL significantly reduces the vocabulary size by incorporating the gap encoding and bandwidth restriction schemes. GEEL can be autoregressively generated with the incorporation of node positional encoding, and we further extend GEEL to deal with attributed graphs by designing a new grammar. Our findings reveal that the adoption of this compact representation not only enhances scalability but also bolsters performance by simplifying the graph generation process. We conduct a comprehensive evaluation across ten non-attributed and two molecular graph generation tasks, demonstrating the effectiveness of GEEL.

Graph neural networks are popular architectures for graph machine learning, based on iterative computation of node representations of an input graph through a series of invariant transformations. A large class of graph neural networks follow a standard message-passing paradigm: at every layer, each node state is updated based on an aggregate of messages from its neighborhood. In this work, we propose a novel framework for training graph neural networks, where every node is viewed as a player that can choose to either 'listen', 'broadcast', 'listen and broadcast', or to 'isolate'. The standard message propagation scheme can then be viewed as a special case of this framework where every node 'listens and broadcasts' to all neighbors. Our approach offers a more flexible and dynamic message-passing paradigm, where each node can determine its own strategy based on their state, effectively exploring the graph topology while learning. We provide a theoretical analysis of the new message-passing scheme which is further supported by an extensive empirical analysis on a synthetic dataset and on real-world datasets.

Subgraph matching is vital in knowledge graph (KG) question answering, molecule design, scene graph, code and circuit search, etc. Neural methods have shown promising results for subgraph matching. Our study of recent systems suggests refactoring them into a unified design space for graph matching networks. Existing methods occupy only a few isolated patches in this space, which remains largely uncharted. We undertake the first comprehensive exploration of this space, featuring such axes as attention-based vs. soft permutation-based interaction between query and corpus graphs, aligning nodes vs. edges, and the form of the final scoring network that integrates neural representations of the graphs. Our extensive experiments reveal that judicious and hitherto-unexplored combinations of choices in this space lead to large performance benefits. Beyond better performance, our study uncovers valuable insights and establishes general design principles for neural graph representation and interaction, which may be of wider interest.

Scaling deep learning models has been at the heart of recent revolutions in language modelling and image generation. Practitioners have observed a strong relationship between model size, dataset size, and performance. However, structure-based architectures such as Graph Neural Networks (GNNs) are yet to show the benefits of scale mainly due to the lower efficiency of sparse operations, large data requirements, and lack of clarity about the effectiveness of various architectures. We address this drawback of GNNs by studying their scaling behavior. Specifically, we analyze message-passing networks, graph Transformers, and hybrid architectures on the largest public collection of 2D molecular graphs. For the first time, we observe that GNNs benefit tremendously from the increasing scale of depth, width, number of molecules, number of labels, and the diversity in the pretraining datasets, resulting in a 30.25% improvement when scaling to 1 billion parameters and 28.98% improvement when increasing size of dataset to eightfold. We further demonstrate strong finetuning scaling behavior on 38 tasks, outclassing previous large models. We hope that our work paves the way for an era where foundational GNNs drive pharmaceutical drug discovery.

Recent advances in representation learning on graphs, mainly leveraging graph convolutional networks, have brought a substantial improvement on many graph-based benchmark tasks. While novel approaches to learning node embeddings are highly suitable for node classification and link prediction, their application to graph classification (predicting a single label for the entire graph) remains mostly rudimentary, typically using a single global pooling step to aggregate node features or a hand-designed, fixed heuristic for hierarchical coarsening of the graph structure. An important step towards ameliorating this is differentiable graph coarsening---the ability to reduce the size of the graph in an adaptive, data-dependent manner within a graph neural network pipeline, analogous to image downsampling within CNNs. However, the previous prominent approach to pooling has quadratic memory requirements during training and is therefore not scalable to large graphs. Here we combine several recent advances in graph neural network design to demonstrate that competitive hierarchical graph classification results are possible without sacrificing sparsity. Our results are verified on several established graph classification benchmarks, and highlight an important direction for future research in graph-based neural networks.

Graph Neural Networks (GNNs) are popular models for machine learning on graphs that typically follow the message-passing paradigm, whereby the feature of a node is updated recursively upon aggregating information over its neighbors. While exchanging messages over the input graph endows GNNs with a strong inductive bias, it can also make GNNs susceptible to over-squashing, thereby preventing them from capturing long-range interactions in the given graph. To rectify this issue, graph rewiring techniques have been proposed as a means of improving information flow by altering the graph connectivity. In this work, we identify three desiderata for graph-rewiring: (i) reduce over-squashing, (ii) respect the locality of the graph, and (iii) preserve the sparsity of the graph. We highlight fundamental trade-offs that occur between spatial and spectral rewiring techniques; while the former often satisfy (i) and (ii) but not (iii), the latter generally satisfy (i) and (iii) at the expense of (ii). We propose a novel rewiring framework that satisfies all of (i)--(iii) through a locality-aware sequence of rewiring operations. We then discuss a specific instance of such rewiring framework and validate its effectiveness on several real-world benchmarks, showing that it either matches or significantly outperforms existing rewiring approaches.

Graph neural networks aim to learn representations for graph-structured data and show impressive performance, particularly in node classification. Recently, many methods have studied the representations of GNNs from the perspective of optimization goals and spectral graph theory. However, the feature space that dominates representation learning has not been systematically studied in graph neural networks. In this paper, we propose to fill this gap by analyzing the feature space of both spatial and spectral models. We decompose graph neural networks into determined feature spaces and trainable weights, providing the convenience of studying the feature space explicitly using matrix space analysis. In particular, we theoretically find that the feature space tends to be linearly correlated due to repeated aggregations. Motivated by these findings, we propose 1) feature subspaces flattening and 2) structural principal components to expand the feature space. Extensive experiments verify the effectiveness of our proposed more comprehensive feature space, with comparable inference time to the baseline, and demonstrate its efficient convergence capability.

This paper introduces a new model to learn graph neural networks equivariant to rotations, translations, reflections and permutations called E(n)-Equivariant Graph Neural Networks (EGNNs). In contrast with existing methods, our work does not require computationally expensive higher-order representations in intermediate layers while it still achieves competitive or better performance. In addition, whereas existing methods are limited to equivariance on 3 dimensional spaces, our model is easily scaled to higher-dimensional spaces. We demonstrate the effectiveness of our method on dynamical systems modelling, representation learning in graph autoencoders and predicting molecular properties.

We present Graph Neural Diffusion (GRAND) that approaches deep learning on graphs as a continuous diffusion process and treats Graph Neural Networks (GNNs) as discretisations of an underlying PDE. In our model, the layer structure and topology correspond to the discretisation choices of temporal and spatial operators. Our approach allows a principled development of a broad new class of GNNs that are able to address the common plights of graph learning models such as depth, oversmoothing, and bottlenecks. Key to the success of our models are stability with respect to perturbations in the data and this is addressed for both implicit and explicit discretisation schemes. We develop linear and nonlinear versions of GRAND, which achieve competitive results on many standard graph benchmarks.

Graph representation learning resurges as a trending research subject owing to the widespread use of deep learning for Euclidean data, which inspire various creative designs of neural networks in the non-Euclidean domain, particularly graphs. With the success of these graph neural networks (GNN) in the static setting, we approach further practical scenarios where the graph dynamically evolves. Existing approaches typically resort to node embeddings and use a recurrent neural network (RNN, broadly speaking) to regulate the embeddings and learn the temporal dynamics. These methods require the knowledge of a node in the full time span (including both training and testing) and are less applicable to the frequent change of the node set. In some extreme scenarios, the node sets at different time steps may completely differ. To resolve this challenge, we propose EvolveGCN, which adapts the graph convolutional network (GCN) model along the temporal dimension without resorting to node embeddings. The proposed approach captures the dynamism of the graph sequence through using an RNN to evolve the GCN parameters. Two architectures are considered for the parameter evolution. We evaluate the proposed approach on tasks including link prediction, edge classification, and node classification. The experimental results indicate a generally higher performance of EvolveGCN compared with related approaches. The code is available at https://github.com/IBM/EvolveGCN.

Large-language models (LLMs) have demonstrated powerful problem-solving capabilities, in particular when organized in multi-agent systems. However, the advent of such systems also raises several questions on the ability of a complex network of agents to effectively self-organize and collaborate. While measuring performance on standard reasoning benchmarks indicates how well multi-agent systems can solve reasoning tasks, it is unclear whether these systems are able to leverage their topology effectively. Here, we propose AgentsNet, a new benchmark for multi-agent reasoning. By drawing inspiration from classical problems in distributed systems and graph theory, AgentsNet measures the ability of multi-agent systems to collaboratively form strategies for problem-solving, self-organization, and effective communication given a network topology. We evaluate a variety of baseline methods on AgentsNet including homogeneous networks of agents which first have to agree on basic protocols for organization and communication. We find that some frontier LLMs are already demonstrating strong performance for small networks but begin to fall off once the size of the network scales. While existing multi-agent benchmarks cover at most 2-5 agents, AgentsNet is practically unlimited in size and can scale with new generations of LLMs. As such, we also probe frontier models in a setup with up to 100 agents.

State-of-the-art Graph Neural Networks (GNNs) have limited scalability with respect to the graph and model sizes. On large graphs, increasing the model depth often means exponential expansion of the scope (i.e., receptive field). Beyond just a few layers, two fundamental challenges emerge: 1. degraded expressivity due to oversmoothing, and 2. expensive computation due to neighborhood explosion. We propose a design principle to decouple the depth and scope of GNNs -- to generate representation of a target entity (i.e., a node or an edge), we first extract a localized subgraph as the bounded-size scope, and then apply a GNN of arbitrary depth on top of the subgraph. A properly extracted subgraph consists of a small number of critical neighbors, while excluding irrelevant ones. The GNN, no matter how deep it is, smooths the local neighborhood into informative representation rather than oversmoothing the global graph into "white noise". Theoretically, decoupling improves the GNN expressive power from the perspectives of graph signal processing (GCN), function approximation (GraphSAGE) and topological learning (GIN). Empirically, on seven graphs (with up to 110M nodes) and six backbone GNN architectures, our design achieves significant accuracy improvement with orders of magnitude reduction in computation and hardware cost.

Neural networks efficiently encode learned information within their parameters. Consequently, many tasks can be unified by treating neural networks themselves as input data. When doing so, recent studies demonstrated the importance of accounting for the symmetries and geometry of parameter spaces. However, those works developed architectures tailored to specific networks such as MLPs and CNNs without normalization layers, and generalizing such architectures to other types of networks can be challenging. In this work, we overcome these challenges by building new metanetworks - neural networks that take weights from other neural networks as input. Put simply, we carefully build graphs representing the input neural networks and process the graphs using graph neural networks. Our approach, Graph Metanetworks (GMNs), generalizes to neural architectures where competing methods struggle, such as multi-head attention layers, normalization layers, convolutional layers, ResNet blocks, and group-equivariant linear layers. We prove that GMNs are expressive and equivariant to parameter permutation symmetries that leave the input neural network functions unchanged. We validate the effectiveness of our method on several metanetwork tasks over diverse neural network architectures.

With the increasing number of new neural architecture designs and substantial existing neural architectures, it becomes difficult for the researchers to situate their contributions compared with existing neural architectures or establish the connections between their designs and other relevant ones. To discover similar neural architectures in an efficient and automatic manner, we define a new problem Neural Architecture Retrieval which retrieves a set of existing neural architectures which have similar designs to the query neural architecture. Existing graph pre-training strategies cannot address the computational graph in neural architectures due to the graph size and motifs. To fulfill this potential, we propose to divide the graph into motifs which are used to rebuild the macro graph to tackle these issues, and introduce multi-level contrastive learning to achieve accurate graph representation learning. Extensive evaluations on both human-designed and synthesized neural architectures demonstrate the superiority of our algorithm. Such a dataset which contains 12k real-world network architectures, as well as their embedding, is built for neural architecture retrieval.

Graph Neural Networks (GNNs) have shown great potential in the field of graph representation learning. Standard GNNs define a local message-passing mechanism which propagates information over the whole graph domain by stacking multiple layers. This paradigm suffers from two major limitations, over-squashing and poor long-range dependencies, that can be solved using global attention but significantly increases the computational cost to quadratic complexity. In this work, we propose an alternative approach to overcome these structural limitations by leveraging the ViT/MLP-Mixer architectures introduced in computer vision. We introduce a new class of GNNs, called Graph ViT/MLP-Mixer, that holds three key properties. First, they capture long-range dependency and mitigate the issue of over-squashing as demonstrated on Long Range Graph Benchmark and TreeNeighbourMatch datasets. Second, they offer better speed and memory efficiency with a complexity linear to the number of nodes and edges, surpassing the related Graph Transformer and expressive GNN models. Third, they show high expressivity in terms of graph isomorphism as they can distinguish at least 3-WL non-isomorphic graphs. We test our architecture on 4 simulated datasets and 7 real-world benchmarks, and show highly competitive results on all of them. The source code is available for reproducibility at: https://github.com/XiaoxinHe/Graph-ViT-MLPMixer.

Graph neural networks (GNN) has been successfully applied to operate on the graph-structured data. Given a specific scenario, rich human expertise and tremendous laborious trials are usually required to identify a suitable GNN architecture. It is because the performance of a GNN architecture is significantly affected by the choice of graph convolution components, such as aggregate function and hidden dimension. Neural architecture search (NAS) has shown its potential in discovering effective deep architectures for learning tasks in image and language modeling. However, existing NAS algorithms cannot be directly applied to the GNN search problem. First, the search space of GNN is different from the ones in existing NAS work. Second, the representation learning capacity of GNN architecture changes obviously with slight architecture modifications. It affects the search efficiency of traditional search methods. Third, widely used techniques in NAS such as parameter sharing might become unstable in GNN. To bridge the gap, we propose the automated graph neural networks (AGNN) framework, which aims to find an optimal GNN architecture within a predefined search space. A reinforcement learning based controller is designed to greedily validate architectures via small steps. AGNN has a novel parameter sharing strategy that enables homogeneous architectures to share parameters, based on a carefully-designed homogeneity definition. Experiments on real-world benchmark datasets demonstrate that the GNN architecture identified by AGNN achieves the best performance, comparing with existing handcrafted models and tradistional search methods.

Graph Neural Networks (GNNs) are popular models for graph learning problems. GNNs show strong empirical performance in many practical tasks. However, the theoretical properties have not been completely elucidated. In this paper, we investigate whether GNNs can exploit the graph structure from the perspective of the expressive power of GNNs. In our analysis, we consider graph generation processes that are controlled by hidden (or latent) node features, which contain all information about the graph structure. A typical example of this framework is kNN graphs constructed from the hidden features. In our main results, we show that GNNs can recover the hidden node features from the input graph alone, even when all node features, including the hidden features themselves and any indirect hints, are unavailable. GNNs can further use the recovered node features for downstream tasks. These results show that GNNs can fully exploit the graph structure by themselves, and in effect, GNNs can use both the hidden and explicit node features for downstream tasks. In the experiments, we confirm the validity of our results by showing that GNNs can accurately recover the hidden features using a GNN architecture built based on our theoretical analysis.

Networks have become indispensable and ubiquitous structures in many fields to model the interactions among different entities, such as friendship in social networks or protein interactions in biological graphs. A major challenge is to understand the structure and dynamics of these systems. Although networks evolve through time, most existing graph representation learning methods target only static networks. Whereas approaches have been developed for the modeling of dynamic networks, there is a lack of efficient continuous time dynamic graph representation learning methods that can provide accurate network characterization and visualization in low dimensions while explicitly accounting for prominent network characteristics such as homophily and transitivity. In this paper, we propose the Piecewise-Velocity Model (PiVeM) for the representation of continuous-time dynamic networks. It learns dynamic embeddings in which the temporal evolution of nodes is approximated by piecewise linear interpolations based on a latent distance model with piecewise constant node-specific velocities. The model allows for analytically tractable expressions of the associated Poisson process likelihood with scalable inference invariant to the number of events. We further impose a scalable Kronecker structured Gaussian Process prior to the dynamics accounting for community structure, temporal smoothness, and disentangled (uncorrelated) latent embedding dimensions optimally learned to characterize the network dynamics. We show that PiVeM can successfully represent network structure and dynamics in ultra-low two-dimensional spaces. It outperforms relevant state-of-art methods in downstream tasks such as link prediction. In summary, PiVeM enables easily interpretable dynamic network visualizations and characterizations that can further improve our understanding of the intrinsic dynamics of time-evolving networks.

The use of graph neural networks has produced significant advances in point cloud problems, such as those found in high energy physics. The question of how to produce a graph structure in these problems is usually treated as a matter of heuristics, employing fully connected graphs or K-nearest neighbors. In this work, we elevate this question to utmost importance as the Topology Problem. We propose an attention mechanism that allows a graph to be constructed in a learned space that handles geometrically the flow of relevance, providing one solution to the Topology Problem. We test this architecture, called GravNetNorm, on the task of top jet tagging, and show that it is competitive in tagging accuracy, and uses far fewer computational resources than all other comparable models.

Graph neural architecture search has sparked much attention as Graph Neural Networks (GNNs) have shown powerful reasoning capability in many relational tasks. However, the currently used graph search space overemphasizes learning node features and neglects mining hierarchical relational information. Moreover, due to diverse mechanisms in the message passing, the graph search space is much larger than that of CNNs. This hinders the straightforward application of classical search strategies for exploring complicated graph search space. We propose Automatic Relation-aware Graph Network Proliferation (ARGNP) for efficiently searching GNNs with a relation-guided message passing mechanism. Specifically, we first devise a novel dual relation-aware graph search space that comprises both node and relation learning operations. These operations can extract hierarchical node/relational information and provide anisotropic guidance for message passing on a graph. Second, analogous to cell proliferation, we design a network proliferation search paradigm to progressively determine the GNN architectures by iteratively performing network division and differentiation. The experiments on six datasets for four graph learning tasks demonstrate that GNNs produced by our method are superior to the current state-of-the-art hand-crafted and search-based GNNs. Codes are available at https://github.com/phython96/ARGNP.

In the last few years, graph neural networks (GNNs) have become the standard toolkit for analyzing and learning from data on graphs. This emerging field has witnessed an extensive growth of promising techniques that have been applied with success to computer science, mathematics, biology, physics and chemistry. But for any successful field to become mainstream and reliable, benchmarks must be developed to quantify progress. This led us in March 2020 to release a benchmark framework that i) comprises of a diverse collection of mathematical and real-world graphs, ii) enables fair model comparison with the same parameter budget to identify key architectures, iii) has an open-source, easy-to-use and reproducible code infrastructure, and iv) is flexible for researchers to experiment with new theoretical ideas. As of December 2022, the GitHub repository has reached 2,000 stars and 380 forks, which demonstrates the utility of the proposed open-source framework through the wide usage by the GNN community. In this paper, we present an updated version of our benchmark with a concise presentation of the aforementioned framework characteristics, an additional medium-sized molecular dataset AQSOL, similar to the popular ZINC, but with a real-world measured chemical target, and discuss how this framework can be leveraged to explore new GNN designs and insights. As a proof of value of our benchmark, we study the case of graph positional encoding (PE) in GNNs, which was introduced with this benchmark and has since spurred interest of exploring more powerful PE for Transformers and GNNs in a robust experimental setting.

Lattices are architected metamaterials whose properties strongly depend on their geometrical design. The analogy between lattices and graphs enables the use of graph neural networks (GNNs) as a faster surrogate model compared to traditional methods such as finite element modelling. In this work, we generate a big dataset of structure-property relationships for strut-based lattices. The dataset is made available to the community which can fuel the development of methods anchored in physical principles for the fitting of fourth-order tensors. In addition, we present a higher-order GNN model trained on this dataset. The key features of the model are (i) SE(3) equivariance, and (ii) consistency with the thermodynamic law of conservation of energy. We compare the model to non-equivariant models based on a number of error metrics and demonstrate its benefits in terms of predictive performance and reduced training requirements. Finally, we demonstrate an example application of the model to an architected material design task. The methods which we developed are applicable to fourth-order tensors beyond elasticity such as piezo-optical tensor etc.

In this work, we present a new network design paradigm. Our goal is to help advance the understanding of network design and discover design principles that generalize across settings. Instead of focusing on designing individual network instances, we design network design spaces that parametrize populations of networks. The overall process is analogous to classic manual design of networks, but elevated to the design space level. Using our methodology we explore the structure aspect of network design and arrive at a low-dimensional design space consisting of simple, regular networks that we call RegNet. The core insight of the RegNet parametrization is surprisingly simple: widths and depths of good networks can be explained by a quantized linear function. We analyze the RegNet design space and arrive at interesting findings that do not match the current practice of network design. The RegNet design space provides simple and fast networks that work well across a wide range of flop regimes. Under comparable training settings and flops, the RegNet models outperform the popular EfficientNet models while being up to 5x faster on GPUs.

Transformers often fail to learn generalizable algorithms, instead relying on brittle heuristics. Using graph connectivity as a testbed, we explain this phenomenon both theoretically and empirically. We consider a simplified Transformer architecture, the disentangled Transformer, and prove that an L-layer model has capacity to solve for graphs with diameters up to exactly 3^L, implementing an algorithm equivalent to computing powers of the adjacency matrix. We analyze the training-dynamics, and show that the learned strategy hinges on whether most training instances are within this model capacity. Within-capacity graphs (diameter leq 3^L) drive the learning of a correct algorithmic solution while beyond-capacity graphs drive the learning of a simple heuristic based on node degrees. Finally, we empirically demonstrate that restricting training data within a model's capacity leads to both standard and disentangled transformers learning the exact algorithm rather than the degree-based heuristic.

Message passing neural networks (MPNNs) have been shown to suffer from the phenomenon of over-squashing that causes poor performance for tasks relying on long-range interactions. This can be largely attributed to message passing only occurring locally, over a node's immediate neighbours. Rewiring approaches attempting to make graphs 'more connected', and supposedly better suited to long-range tasks, often lose the inductive bias provided by distance on the graph since they make distant nodes communicate instantly at every layer. In this paper we propose a framework, applicable to any MPNN architecture, that performs a layer-dependent rewiring to ensure gradual densification of the graph. We also propose a delay mechanism that permits skip connections between nodes depending on the layer and their mutual distance. We validate our approach on several long-range tasks and show that it outperforms graph Transformers and multi-hop MPNNs.

Graph Neural Networks have gained huge interest in the past few years. These powerful algorithms expanded deep learning models to non-Euclidean space and were able to achieve state of art performance in various applications including recommender systems and social networks. However, this performance is based on static graph structures assumption which limits the Graph Neural Networks performance when the data varies with time. Spatiotemporal Graph Neural Networks are extension of Graph Neural Networks that takes the time factor into account. Recently, various Spatiotemporal Graph Neural Network algorithms were proposed and achieved superior performance compared to other deep learning algorithms in several time dependent applications. This survey discusses interesting topics related to Spatiotemporal Graph Neural Networks, including algorithms, applications, and open challenges.

We present FastRP, a scalable and performant algorithm for learning distributed node representations in a graph. FastRP is over 4,000 times faster than state-of-the-art methods such as DeepWalk and node2vec, while achieving comparable or even better performance as evaluated on several real-world networks on various downstream tasks. We observe that most network embedding methods consist of two components: construct a node similarity matrix and then apply dimension reduction techniques to this matrix. We show that the success of these methods should be attributed to the proper construction of this similarity matrix, rather than the dimension reduction method employed. FastRP is proposed as a scalable algorithm for network embeddings. Two key features of FastRP are: 1) it explicitly constructs a node similarity matrix that captures transitive relationships in a graph and normalizes matrix entries based on node degrees; 2) it utilizes very sparse random projection, which is a scalable optimization-free method for dimension reduction. An extra benefit from combining these two design choices is that it allows the iterative computation of node embeddings so that the similarity matrix need not be explicitly constructed, which further speeds up FastRP. FastRP is also advantageous for its ease of implementation, parallelization and hyperparameter tuning. The source code is available at https://github.com/GTmac/FastRP.

Graph neural networks (GNNs) are a powerful architecture for tackling graph learning tasks, yet have been shown to be oblivious to eminent substructures such as cycles. We present TOGL, a novel layer that incorporates global topological information of a graph using persistent homology. TOGL can be easily integrated into any type of GNN and is strictly more expressive (in terms the Weisfeiler--Lehman graph isomorphism test) than message-passing GNNs. Augmenting GNNs with TOGL leads to improved predictive performance for graph and node classification tasks, both on synthetic data sets, which can be classified by humans using their topology but not by ordinary GNNs, and on real-world data.

Graph Neural Networks (GNNs) have been popularly used for analyzing non-Euclidean data such as social network data and biological data. Despite their success, the design of graph neural networks requires a lot of manual work and domain knowledge. In this paper, we propose a Graph Neural Architecture Search method (GraphNAS for short) that enables automatic search of the best graph neural architecture based on reinforcement learning. Specifically, GraphNAS first uses a recurrent network to generate variable-length strings that describe the architectures of graph neural networks, and then trains the recurrent network with reinforcement learning to maximize the expected accuracy of the generated architectures on a validation data set. Extensive experimental results on node classification tasks in both transductive and inductive learning settings demonstrate that GraphNAS can achieve consistently better performance on the Cora, Citeseer, Pubmed citation network, and protein-protein interaction network. On node classification tasks, GraphNAS can design a novel network architecture that rivals the best human-invented architecture in terms of test set accuracy.

Graph Neural Networks (GNNs) have shown great promise in learning node embeddings for link prediction (LP). While numerous studies aim to improve the overall LP performance of GNNs, none have explored its varying performance across different nodes and its underlying reasons. To this end, we aim to demystify which nodes will perform better from the perspective of their local topology. Despite the widespread belief that low-degree nodes exhibit poorer LP performance, our empirical findings provide nuances to this viewpoint and prompt us to propose a better metric, Topological Concentration (TC), based on the intersection of the local subgraph of each node with the ones of its neighbors. We empirically demonstrate that TC has a higher correlation with LP performance than other node-level topological metrics like degree and subgraph density, offering a better way to identify low-performing nodes than using cold-start. With TC, we discover a novel topological distribution shift issue in which newly joined neighbors of a node tend to become less interactive with that node's existing neighbors, compromising the generalizability of node embeddings for LP at testing time. To make the computation of TC scalable, We further propose Approximated Topological Concentration (ATC) and theoretically/empirically justify its efficacy in approximating TC and reducing the computation complexity. Given the positive correlation between node TC and its LP performance, we explore the potential of boosting LP performance via enhancing TC by re-weighting edges in the message-passing and discuss its effectiveness with limitations. Our code is publicly available at https://github.com/YuWVandy/Topo_LP_GNN.

Networks provide a powerful formalism for modeling complex systems by using a model of pairwise interactions. But much of the structure within these systems involves interactions that take place among more than two nodes at once; for example, communication within a group rather than person-to person, collaboration among a team rather than a pair of coauthors, or biological interaction between a set of molecules rather than just two. Such higher-order interactions are ubiquitous, but their empirical study has received limited attention, and little is known about possible organizational principles of such structures. Here we study the temporal evolution of 19 datasets with explicit accounting for higher-order interactions. We show that there is a rich variety of structure in our datasets but datasets from the same system types have consistent patterns of higher-order structure. Furthermore, we find that tie strength and edge density are competing positive indicators of higher-order organization, and these trends are consistent across interactions involving differing numbers of nodes. To systematically further the study of theories for such higher-order structures, we propose higher-order link prediction as a benchmark problem to assess models and algorithms that predict higher-order structure. We find a fundamental differences from traditional pairwise link prediction, with a greater role for local rather than long-range information in predicting the appearance of new interactions.

Neural networks have achieved tremendous success in a large variety of applications. However, their memory footprint and computational demand can render them impractical in application settings with limited hardware or energy resources. In this work, we propose a novel algorithm to find efficient low-rank subnetworks. Remarkably, these subnetworks are determined and adapted already during the training phase and the overall time and memory resources required by both training and evaluating them are significantly reduced. The main idea is to restrict the weight matrices to a low-rank manifold and to update the low-rank factors rather than the full matrix during training. To derive training updates that are restricted to the prescribed manifold, we employ techniques from dynamic model order reduction for matrix differential equations. This allows us to provide approximation, stability, and descent guarantees. Moreover, our method automatically and dynamically adapts the ranks during training to achieve the desired approximation accuracy. The efficiency of the proposed method is demonstrated through a variety of numerical experiments on fully-connected and convolutional networks.

Graph Neural Networks (GNNs) have shown promising potential in graph representation learning. The majority of GNNs define a local message-passing mechanism, propagating information over the graph by stacking multiple layers. These methods, however, are known to suffer from two major limitations: over-squashing and poor capturing of long-range dependencies. Recently, Graph Transformers (GTs) emerged as a powerful alternative to Message-Passing Neural Networks (MPNNs). GTs, however, have quadratic computational cost, lack inductive biases on graph structures, and rely on complex Positional/Structural Encodings (SE/PE). In this paper, we show that while Transformers, complex message-passing, and SE/PE are sufficient for good performance in practice, neither is necessary. Motivated by the recent success of State Space Models (SSMs), such as Mamba, we present Graph Mamba Networks (GMNs), a general framework for a new class of GNNs based on selective SSMs. We discuss and categorize the new challenges when adopting SSMs to graph-structured data, and present four required and one optional steps to design GMNs, where we choose (1) Neighborhood Tokenization, (2) Token Ordering, (3) Architecture of Bidirectional Selective SSM Encoder, (4) Local Encoding, and dispensable (5) PE and SE. We further provide theoretical justification for the power of GMNs. Experiments demonstrate that despite much less computational cost, GMNs attain an outstanding performance in long-range, small-scale, large-scale, and heterophilic benchmark datasets.

This tutorial serves as a comprehensive guide for understanding graph databases, focusing on the fundamentals of graph theory while showcasing practical applications across various fields. It starts by introducing foundational concepts and delves into the structure of graphs through nodes and edges, covering different types such as undirected, directed, weighted, and unweighted graphs. Key graph properties, terminologies, and essential algorithms for network analysis are outlined, including Dijkstras shortest path algorithm and methods for calculating node centrality and graph connectivity. The tutorial highlights the advantages of graph databases over traditional relational databases, particularly in efficiently managing complex, interconnected data. It examines leading graph database systems such as Neo4j, Amazon Neptune, and ArangoDB, emphasizing their unique features for handling large datasets. Practical instructions on graph operations using NetworkX and Neo4j are provided, covering node and edge creation, attribute assignment, and advanced queries with Cypher. Additionally, the tutorial explores common graph visualization techniques using tools like Plotly and Neo4j Bloom, which enhance the interpretation and usability of graph data. It also delves into community detection algorithms, including the Louvain method, which facilitates clustering in large networks. Finally, the paper concludes with recommendations for researchers interested in exploring the vast potential of graph technologies.

Graph generation is a critical task in numerous domains, including molecular design and social network analysis, due to its ability to model complex relationships and structured data. While most modern graph generative models utilize adjacency matrix representations, this work revisits an alternative approach that represents graphs as sequences of node set and edge set. We advocate for this approach due to its efficient encoding of graphs and propose a novel representation. Based on this representation, we introduce the Graph Generative Pre-trained Transformer (G2PT), an auto-regressive model that learns graph structures via next-token prediction. To further exploit G2PT's capabilities as a general-purpose foundation model, we explore fine-tuning strategies for two downstream applications: goal-oriented generation and graph property prediction. We conduct extensive experiments across multiple datasets. Results indicate that G2PT achieves superior generative performance on both generic graph and molecule datasets. Furthermore, G2PT exhibits strong adaptability and versatility in downstream tasks from molecular design to property prediction.