Daily Papers

Normalization layers and activation functions are fundamental components in deep networks and typically co-locate with each other. Here we propose to design them using an automated approach. Instead of designing them separately, we unify them into a single tensor-to-tensor computation graph, and evolve its structure starting from basic mathematical functions. Examples of such mathematical functions are addition, multiplication and statistical moments. The use of low-level mathematical functions, in contrast to the use of high-level modules in mainstream NAS, leads to a highly sparse and large search space which can be challenging for search methods. To address the challenge, we develop efficient rejection protocols to quickly filter out candidate layers that do not work well. We also use multi-objective evolution to optimize each layer's performance across many architectures to prevent overfitting. Our method leads to the discovery of EvoNorms, a set of new normalization-activation layers with novel, and sometimes surprising structures that go beyond existing design patterns. For example, some EvoNorms do not assume that normalization and activation functions must be applied sequentially, nor need to center the feature maps, nor require explicit activation functions. Our experiments show that EvoNorms work well on image classification models including ResNets, MobileNets and EfficientNets but also transfer well to Mask R-CNN with FPN/SpineNet for instance segmentation and to BigGAN for image synthesis, outperforming BatchNorm and GroupNorm based layers in many cases.

Advancing research in the emerging field of deep graph learning requires new tools to support tensor computation over graphs. In this paper, we present the design principles and implementation of Deep Graph Library (DGL). DGL distills the computational patterns of GNNs into a few generalized sparse tensor operations suitable for extensive parallelization. By advocating graph as the central programming abstraction, DGL can perform optimizations transparently. By cautiously adopting a framework-neutral design, DGL allows users to easily port and leverage the existing components across multiple deep learning frameworks. Our evaluation shows that DGL significantly outperforms other popular GNN-oriented frameworks in both speed and memory consumption over a variety of benchmarks and has little overhead for small scale workloads.

In the past decade, Deep Learning (DL) systems have been widely deployed in various domains to facilitate our daily life. Meanwhile, it is extremely challenging to ensure the correctness of DL systems (e.g., due to their intrinsic nondeterminism), and bugs in DL systems can cause serious consequences and may even threaten human lives. In the literature, researchers have explored various techniques to test, analyze, and verify DL models, since their quality directly affects the corresponding system behaviors. Recently, researchers have also proposed novel techniques for testing the underlying operator-level DL libraries (such as TensorFlow and PyTorch), which provide general binary implementations for each high-level DL operator for running various DL models on many platforms. However, there is still limited work targeting the reliability of the emerging tensor compilers, which aim to directly compile high-level tensor computation graphs into high-performance binaries for better efficiency, portability, and scalability. In this paper, we target the important problem of tensor compiler testing, and have proposed Tzer, a practical fuzzing technique for the widely used TVM tensor compiler. Tzer focuses on mutating the low-level Intermediate Representation (IR) for TVM due to the limited mutation space for the high-level IR. More specifically, Tzer leverages both general-purpose and tensor-compiler-specific mutators guided by coverage feedback for evolutionary IR mutation; furthermore, Tzer also performs pass mutation in tandem with IR mutation for more effective fuzzing. Our results show that Tzer substantially outperforms existing fuzzing techniques on tensor compiler testing, with 75% higher coverage and 50% more valuable tests than the 2nd-best technique. To date, Tzer has detected 49 previously unknown bugs for TVM, with 37 bugs confirmed and 25 bugs fixed (PR merged).

Graph Neural Networks (GNN) are inherently limited in their expressive power. Recent seminal works (Xu et al., 2019; Morris et al., 2019b) introduced the Weisfeiler-Lehman (WL) hierarchy as a measure of expressive power. Although this hierarchy has propelled significant advances in GNN analysis and architecture developments, it suffers from several significant limitations. These include a complex definition that lacks direct guidance for model improvement and a WL hierarchy that is too coarse to study current GNNs. This paper introduces an alternative expressive power hierarchy based on the ability of GNNs to calculate equivariant polynomials of a certain degree. As a first step, we provide a full characterization of all equivariant graph polynomials by introducing a concrete basis, significantly generalizing previous results. Each basis element corresponds to a specific multi-graph, and its computation over some graph data input corresponds to a tensor contraction problem. Second, we propose algorithmic tools for evaluating the expressiveness of GNNs using tensor contraction sequences, and calculate the expressive power of popular GNNs. Finally, we enhance the expressivity of common GNN architectures by adding polynomial features or additional operations / aggregations inspired by our theory. These enhanced GNNs demonstrate state-of-the-art results in experiments across multiple graph learning benchmarks.

Optimizing neural networks with loss that contain high-dimensional and high-order differential operators is expensive to evaluate with back-propagation due to O(d^{k}) scaling of the derivative tensor size and the O(2^{k-1}L) scaling in the computation graph, where d is the dimension of the domain, L is the number of ops in the forward computation graph, and k is the derivative order. In previous works, the polynomial scaling in d was addressed by amortizing the computation over the optimization process via randomization. Separately, the exponential scaling in k for univariate functions (d=1) was addressed with high-order auto-differentiation (AD). In this work, we show how to efficiently perform arbitrary contraction of the derivative tensor of arbitrary order for multivariate functions, by properly constructing the input tangents to univariate high-order AD, which can be used to efficiently randomize any differential operator. When applied to Physics-Informed Neural Networks (PINNs), our method provides >1000times speed-up and >30times memory reduction over randomization with first-order AD, and we can now solve 1-million-dimensional PDEs in 8 minutes on a single NVIDIA A100 GPU. This work opens the possibility of using high-order differential operators in large-scale problems.

We introduce GraphNet, a dataset of 2.7K real-world deep learning computational graphs with rich metadata, spanning six major task categories across multiple deep learning frameworks. To evaluate tensor compiler performance on these samples, we propose the benchmark metric Speedup Score S(t), which jointly considers runtime speedup and execution correctness under tunable tolerance levels, offering a reliable measure of general optimization capability. Furthermore, we extend S(t) to the Error-aware Speedup Score ES(t), which incorporates error information and helps compiler developers identify key performance bottlenecks. In this report, we benchmark the default tensor compilers, CINN for PaddlePaddle and TorchInductor for PyTorch, on computer vision (CV) and natural language processing (NLP) samples to demonstrate the practicality of GraphNet. The full construction pipeline with graph extraction and compiler evaluation tools is available at https://github.com/PaddlePaddle/GraphNet .

We present GSPMD, an automatic, compiler-based parallelization system for common machine learning computations. It allows users to write programs in the same way as for a single device, then give hints through a few annotations on how to distribute tensors, based on which GSPMD will parallelize the computation. Its representation of partitioning is simple yet general, allowing it to express different or mixed paradigms of parallelism on a wide variety of models. GSPMD infers the partitioning for every operator based on limited user annotations, making it convenient to scale existing single-device programs. It solves several technical challenges for production usage, allowing GSPMD to achieve 50% to 62% compute utilization on up to 2048 Cloud TPUv3 cores for models with up to one trillion parameters.

Dynamic shape computations have become critical in modern machine learning workloads, especially in emerging large language models. The success of these models has driven demand for deploying them to a diverse set of backend environments. In this paper, we present Relax, a compiler abstraction for optimizing end-to-end dynamic machine learning workloads. Relax introduces first-class symbolic shape annotations to track dynamic shape computations globally across the program. It also introduces a cross-level abstraction that encapsulates computational graphs, loop-level tensor programs, and library calls in a single representation to enable cross-level optimizations. We build an end-to-end compilation framework using the proposed approach to optimize dynamic shape models. Experimental results on large language models show that Relax delivers performance competitive with state-of-the-art hand-optimized systems across platforms and enables deployment of emerging dynamic models to a broader set of environments, including mobile phones, embedded devices, and web browsers.

Low-precision formats such as float8 have been introduced in machine learning accelerated hardware to improve computational efficiency for large language models training and inference. Nevertheless, adoption by the ML community has been slowed down by the complex, and sometimes brittle, techniques required to match higher precision training accuracy. In this work, we present Scalify, a end-to-end scale propagation paradigm for computational graphs, generalizing and formalizing existing tensor scaling methods. Experiment results show that Scalify supports out-of-the-box float8 matrix multiplication and gradients representation, as well as float16 optimizer state storage. Our JAX implementation of Scalify is open-sourced at https://github.com/graphcore-research/jax-scalify

Heterogeneous Graph Neural Networks (HGNNs) are powerful tools for deep learning on heterogeneous graphs. Typical HGNNs require repetitive message passing during training, limiting efficiency for large-scale real-world graphs. Recent pre-computation-based HGNNs use one-time message passing to transform a heterogeneous graph into regular-shaped tensors, enabling efficient mini-batch training. Existing pre-computation-based HGNNs can be mainly categorized into two styles, which differ in how much information loss is allowed and efficiency. We propose a hybrid pre-computation-based HGNN, named Random Projection Heterogeneous Graph Neural Network (RpHGNN), which combines the benefits of one style's efficiency with the low information loss of the other style. To achieve efficiency, the main framework of RpHGNN consists of propagate-then-update iterations, where we introduce a Random Projection Squashing step to ensure that complexity increases only linearly. To achieve low information loss, we introduce a Relation-wise Neighbor Collection component with an Even-odd Propagation Scheme, which aims to collect information from neighbors in a finer-grained way. Experimental results indicate that our approach achieves state-of-the-art results on seven small and large benchmark datasets while also being 230% faster compared to the most effective baseline. Surprisingly, our approach not only surpasses pre-processing-based baselines but also outperforms end-to-end methods.

Hamiltonian matrix prediction is pivotal in computational chemistry, serving as the foundation for determining a wide range of molecular properties. While SE(3) equivariant graph neural networks have achieved remarkable success in this domain, their substantial computational cost--driven by high-order tensor product (TP) operations--restricts their scalability to large molecular systems with extensive basis sets. To address this challenge, we introduce SPHNet, an efficient and scalable equivariant network, that incorporates adaptive SParsity into Hamiltonian prediction. SPHNet employs two innovative sparse gates to selectively constrain non-critical interaction combinations, significantly reducing tensor product computations while maintaining accuracy. To optimize the sparse representation, we develop a Three-phase Sparsity Scheduler, ensuring stable convergence and achieving high performance at sparsity rates of up to 70%. Extensive evaluations on QH9 and PubchemQH datasets demonstrate that SPHNet achieves state-of-the-art accuracy while providing up to a 7x speedup over existing models. Beyond Hamiltonian prediction, the proposed sparsification techniques also hold significant potential for improving the efficiency and scalability of other SE(3) equivariant networks, further broadening their applicability and impact. Our code can be found at https://github.com/microsoft/SPHNet.

The deployment and training of neural networks on edge computing devices pose many challenges. The low memory nature of edge devices is often one of the biggest limiting factors encountered in the deployment of large neural network models. Tensor rematerialization or recompute is a way to address high memory requirements for neural network training and inference. In this paper we consider the problem of execution time minimization of compute graphs subject to a memory budget. In particular, we develop a new constraint programming formulation called Moccasin with only O(n) integer variables, where n is the number of nodes in the compute graph. This is a significant improvement over the works in the recent literature that propose formulations with O(n^2) Boolean variables. We present numerical studies that show that our approach is up to an order of magnitude faster than recent work especially for large-scale graphs.

Tensor Networks (TN) offer a powerful framework to efficiently represent very high-dimensional objects. TN have recently shown their potential for machine learning applications and offer a unifying view of common tensor decomposition models such as Tucker, tensor train (TT) and tensor ring (TR). However, identifying the best tensor network structure from data for a given task is challenging. In this work, we leverage the TN formalism to develop a generic and efficient adaptive algorithm to jointly learn the structure and the parameters of a TN from data. Our method is based on a simple greedy approach starting from a rank one tensor and successively identifying the most promising tensor network edges for small rank increments. Our algorithm can adaptively identify TN structures with small number of parameters that effectively optimize any differentiable objective function. Experiments on tensor decomposition, tensor completion and model compression tasks demonstrate the effectiveness of the proposed algorithm. In particular, our method outperforms the state-of-the-art evolutionary topology search [Li and Sun, 2020] for tensor decomposition of images (while being orders of magnitude faster) and finds efficient tensor network structures to compress neural networks outperforming popular TT based approaches [Novikov et al., 2015].

We present a new class of fast polylog-linear algorithms based on the theory of structured matrices (in particular low displacement rank) for integrating tensor fields defined on weighted trees. Several applications of the resulting fast tree-field integrators (FTFIs) are presented, including (a) approximation of graph metrics with tree metrics, (b) graph classification, (c) modeling on meshes, and finally (d) Topological Transformers (TTs) (Choromanski et al., 2022) for images. For Topological Transformers, we propose new relative position encoding (RPE) masking mechanisms with as few as three extra learnable parameters per Transformer layer, leading to 1.0-1.5%+ accuracy gains. Importantly, most of FTFIs are exact methods, thus numerically equivalent to their brute-force counterparts. When applied to graphs with thousands of nodes, those exact algorithms provide 5.7-13x speedups. We also provide an extensive theoretical analysis of our methods.

E(3)-equivariant neural networks have demonstrated success across a wide range of 3D modelling tasks. A fundamental operation in these networks is the tensor product, which interacts two geometric features in an equivariant manner to create new features. Due to the high computational complexity of the tensor product, significant effort has been invested to optimize the runtime of this operation. For example, Luo et al. (2024) recently proposed the Gaunt tensor product (GTP) which promises a significant speedup. In this work, we provide a careful, systematic analysis of a number of tensor product operations. In particular, we emphasize that different tensor products are not performing the same operation. The reported speedups typically come at the cost of expressivity. We introduce measures of expressivity and interactability to characterize these differences. In addition, we realized the original implementation of GTP can be greatly simplified by directly using a spherical grid at no cost in asymptotic runtime. This spherical grid approach is faster on our benchmarks and in actual training of the MACE interatomic potential by 30%. Finally, we provide the first systematic microbenchmarks of the various tensor product operations. We find that the theoretical runtime guarantees can differ wildly from empirical performance, demonstrating the need for careful application-specific benchmarking. Code is available at https://github.com/atomicarchitects/PriceofFreedom.

Design of neural networks that incorporate symmetry is crucial for geometric deep learning. Central to this effort is the development of invariant and equivariant operations. This works presents a systematic method for constructing valid invariant and equivariant operations. It can handle inputs and outputs in the form of Cartesian tensors with different rank, as well as spherical tensors with different types. In addition, our method features a graphical representation utilizing the symmetric tensor network, which simplifies both the proofs and constructions related to invariant and equivariant functions. We also apply this approach to design the equivariant interaction message for the geometry graph neural network, and equivariant machine learning model to learn the constitutive law of materials.

Tensor networks are efficient representations of high-dimensional tensors which have been very successful for physics and mathematics applications. We demonstrate how algorithms for optimizing such networks can be adapted to supervised learning tasks by using matrix product states (tensor trains) to parameterize models for classifying images. For the MNIST data set we obtain less than 1% test set classification error. We discuss how the tensor network form imparts additional structure to the learned model and suggest a possible generative interpretation.

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

This work studies the combinatorial optimization problem of finding an optimal core tensor shape, also called multilinear rank, for a size-constrained Tucker decomposition. We give an algorithm with provable approximation guarantees for its reconstruction error via connections to higher-order singular values. Specifically, we introduce a novel Tucker packing problem, which we prove is NP-hard, and give a polynomial-time approximation scheme based on a reduction to the 2-dimensional knapsack problem with a matroid constraint. We also generalize our techniques to tree tensor network decompositions. We implement our algorithm using an integer programming solver, and show that its solution quality is competitive with (and sometimes better than) the greedy algorithm that uses the true Tucker decomposition loss at each step, while also running up to 1000x faster.

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.

The development of efficient machine learning models for molecular systems representation is becoming crucial in scientific research. We introduce TensorNet, an innovative O(3)-equivariant message-passing neural network architecture that leverages Cartesian tensor representations. By using Cartesian tensor atomic embeddings, feature mixing is simplified through matrix product operations. Furthermore, the cost-effective decomposition of these tensors into rotation group irreducible representations allows for the separate processing of scalars, vectors, and tensors when necessary. Compared to higher-rank spherical tensor models, TensorNet demonstrates state-of-the-art performance with significantly fewer parameters. For small molecule potential energies, this can be achieved even with a single interaction layer. As a result of all these properties, the model's computational cost is substantially decreased. Moreover, the accurate prediction of vector and tensor molecular quantities on top of potential energies and forces is possible. In summary, TensorNet's framework opens up a new space for the design of state-of-the-art equivariant models.

We give explicit low-rank bilinear non-commutative schemes for multiplying structured n times n matrices with 2 leq n leq 5, which serve as building blocks for recursive algorithms with improved multiplicative factors in asymptotic complexity. Our schemes are discovered over F_2 or F_3 and lifted to Z or Q. Using a flip graph search over tensor decompositions, we derive schemes for general, upper-triangular, lower-triangular, symmetric, and skew-symmetric inputs, as well as products of a structured matrix with its transpose. In particular, we obtain 4 times 4 rank-34 schemes: (i) multiplying a general matrix by its transpose using 10 recursive calls, improving the factor from 26/41 (0.634) to 8/13 (0.615); and (ii) multiplying an upper-triangular matrix by a general matrix using 12 recursive calls, improving the factor from 8/13 (0.615) to 22/37 (0.595). Additionally, using F_3 flip graphs, we discover schemes over Q that fundamentally require the inverse of 2, including a 2 times 2 symmetric-symmetric multiplication of rank 5 and a 3 times 3 skew-symmetric-general multiplication of rank 14 (improving upon AlphaTensor's 15).

Deploying deep learning models on various devices has become an important topic. The wave of hardware specialization brings a diverse set of acceleration primitives for multi-dimensional tensor computations. These new acceleration primitives, along with the emerging machine learning models, bring tremendous engineering challenges. In this paper, we present TensorIR, a compiler abstraction for optimizing programs with these tensor computation primitives. TensorIR generalizes the loop nest representation used in existing machine learning compilers to bring tensor computation as the first-class citizen. Finally, we build an end-to-end framework on top of our abstraction to automatically optimize deep learning models for given tensor computation primitives. Experimental results show that TensorIR compilation automatically uses the tensor computation primitives for given hardware backends and delivers performance that is competitive to state-of-art hand-optimized systems across platforms.

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.

Tensor computations, with matrix multiplication being the primary operation, serve as the fundamental basis for data analysis, physics, machine learning, and deep learning. As the scale and complexity of data continue to grow rapidly, the demand for tensor computations has also increased significantly. To meet this demand, several research institutions have started developing dedicated hardware for tensor computations. To further improve the computational performance of tensor process units, we have reexamined the issue of computation reuse that was previously overlooked in existing architectures. As a result, we propose a novel EN-T architecture that can reduce chip area and power consumption. Furthermore, our method is compatible with existing tensor processing units. We evaluated our method on prevalent microarchitectures, the results demonstrate an average improvement in area efficiency of 8.7\%, 12.2\%, and 11.0\% for tensor computing units at computational scales of 256 GOPS, 1 TOPS, and 4 TOPS, respectively. Similarly, there were energy efficiency enhancements of 13.0\%, 17.5\%, and 15.5\%.

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.

The NeuroEvolution of Augmenting Topologies (NEAT) algorithm has received considerable recognition in the field of neuroevolution. Its effectiveness is derived from initiating with simple networks and incrementally evolving both their topologies and weights. Although its capability across various challenges is evident, the algorithm's computational efficiency remains an impediment, limiting its scalability potential. In response, this paper introduces a tensorization method for the NEAT algorithm, enabling the transformation of its diverse network topologies and associated operations into uniformly shaped tensors for computation. This advancement facilitates the execution of the NEAT algorithm in a parallelized manner across the entire population. Furthermore, we develop TensorNEAT, a library that implements the tensorized NEAT algorithm and its variants, such as CPPN and HyperNEAT. Building upon JAX, TensorNEAT promotes efficient parallel computations via automated function vectorization and hardware acceleration. Moreover, the TensorNEAT library supports various benchmark environments including Gym, Brax, and gymnax. Through evaluations across a spectrum of robotics control environments in Brax, TensorNEAT achieves up to 500x speedups compared to the existing implementations such as NEAT-Python. Source codes are available at: https://github.com/EMI-Group/tensorneat.

The expressive power of Graph Neural Networks (GNNs) has been studied extensively through the Weisfeiler-Leman (WL) graph isomorphism test. However, standard GNNs and the WL framework are inapplicable for geometric graphs embedded in Euclidean space, such as biomolecules, materials, and other physical systems. In this work, we propose a geometric version of the WL test (GWL) for discriminating geometric graphs while respecting the underlying physical symmetries: permutations, rotation, reflection, and translation. We use GWL to characterise the expressive power of geometric GNNs that are invariant or equivariant to physical symmetries in terms of distinguishing geometric graphs. GWL unpacks how key design choices influence geometric GNN expressivity: (1) Invariant layers have limited expressivity as they cannot distinguish one-hop identical geometric graphs; (2) Equivariant layers distinguish a larger class of graphs by propagating geometric information beyond local neighbourhoods; (3) Higher order tensors and scalarisation enable maximally powerful geometric GNNs; and (4) GWL's discrimination-based perspective is equivalent to universal approximation. Synthetic experiments supplementing our results are available at https://github.com/chaitjo/geometric-gnn-dojo

Simulating physics using Graph Neural Networks (GNNs) is predominantly driven by message-passing architectures, which face challenges in scaling and efficiency, particularly in handling large, complex meshes. These architectures have inspired numerous enhancements, including multigrid approaches and K-hop aggregation (using neighbours of distance K), yet they often introduce significant complexity and suffer from limited in-depth investigations. In response to these challenges, we propose a novel Graph Transformer architecture that leverages the adjacency matrix as an attention mask. The proposed approach incorporates innovative augmentations, including Dilated Sliding Windows and Global Attention, to extend receptive fields without sacrificing computational efficiency. Through extensive experimentation, we evaluate model size, adjacency matrix augmentations, positional encoding and K-hop configurations using challenging 3D computational fluid dynamics (CFD) datasets. We also train over 60 models to find a scaling law between training FLOPs and parameters. The introduced models demonstrate remarkable scalability, performing on meshes with up to 300k nodes and 3 million edges. Notably, the smallest model achieves parity with MeshGraphNet while being 7times faster and 6times smaller. The largest model surpasses the previous state-of-the-art by 38.8\% on average and outperforms MeshGraphNet by 52\% on the all-rollout RMSE, while having a similar training speed. Code and datasets are available at https://github.com/DonsetPG/graph-physics.

Tensor network (TN) is a powerful framework in machine learning, but selecting a good TN model, known as TN structure search (TN-SS), is a challenging and computationally intensive task. The recent approach TNLS~li2022permutation showed promising results for this task, however, its computational efficiency is still unaffordable, requiring too many evaluations of the objective function. We propose TnALE, a new algorithm that updates each structure-related variable alternately by local enumeration, greatly reducing the number of evaluations compared to TNLS. We theoretically investigate the descent steps for TNLS and TnALE, proving that both algorithms can achieve linear convergence up to a constant if a sufficient reduction of the objective is reached in each neighborhood. We also compare the evaluation efficiency of TNLS and TnALE, revealing that Omega(2^N) evaluations are typically required in TNLS for reaching the objective reduction in the neighborhood, while ideally O(N^2R) evaluations are sufficient in TnALE, where N denotes the tensor order and R reflects the ``low-rankness'' of the neighborhood. Experimental results verify that TnALE can find practically good TN-ranks and permutations with vastly fewer evaluations than the state-of-the-art algorithms.

Modelling compositionality has been a longstanding area of research in the field of vector space semantics. The categorical approach to compositionality maps grammar onto vector spaces in a principled way, but comes under fire for requiring the formation of very high-dimensional matrices and tensors, and therefore being computationally infeasible. In this paper I show how a linear simplification of recursive neural tensor network models can be mapped directly onto the categorical approach, giving a way of computing the required matrices and tensors. This mapping suggests a number of lines of research for both categorical compositional vector space models of meaning and for recursive neural network models of compositionality.

A Sheaf Neural Network (SNN) is a type of Graph Neural Network (GNN) that operates on a sheaf, an object that equips a graph with vector spaces over its nodes and edges and linear maps between these spaces. SNNs have been shown to have useful theoretical properties that help tackle issues arising from heterophily and over-smoothing. One complication intrinsic to these models is finding a good sheaf for the task to be solved. Previous works proposed two diametrically opposed approaches: manually constructing the sheaf based on domain knowledge and learning the sheaf end-to-end using gradient-based methods. However, domain knowledge is often insufficient, while learning a sheaf could lead to overfitting and significant computational overhead. In this work, we propose a novel way of computing sheaves drawing inspiration from Riemannian geometry: we leverage the manifold assumption to compute manifold-and-graph-aware orthogonal maps, which optimally align the tangent spaces of neighbouring data points. We show that this approach achieves promising results with less computational overhead when compared to previous SNN models. Overall, this work provides an interesting connection between algebraic topology and differential geometry, and we hope that it will spark future research in this direction.

For any graph G having n vertices and its automorphism group Aut(G), we provide a full characterisation of all of the possible Aut(G)-equivariant neural networks whose layers are some tensor power of R^{n}. In particular, we find a spanning set of matrices for the learnable, linear, Aut(G)-equivariant layer functions between such tensor power spaces in the standard basis of R^{n}.

We introduce PyTorch Geometric, a library for deep learning on irregularly structured input data such as graphs, point clouds and manifolds, built upon PyTorch. In addition to general graph data structures and processing methods, it contains a variety of recently published methods from the domains of relational learning and 3D data processing. PyTorch Geometric achieves high data throughput by leveraging sparse GPU acceleration, by providing dedicated CUDA kernels and by introducing efficient mini-batch handling for input examples of different size. In this work, we present the library in detail and perform a comprehensive comparative study of the implemented methods in homogeneous evaluation scenarios.

We present a neural operator architecture to simulate Lagrangian dynamics, such as fluid flow, granular flows, and elastoplasticity. Traditional numerical methods, such as the finite element method (FEM), suffer from long run times and large memory consumption. On the other hand, approaches based on graph neural networks are faster but still suffer from long computation times on dense graphs, which are often required for high-fidelity simulations. Our model, GIOROM or Graph Interaction Operator for Reduced-Order Modeling, learns temporal dynamics within a reduced-order setting, capturing spatial features from a highly sparse graph representation of the input and generalizing to arbitrary spatial locations during inference. The model is geometry-aware and discretization-agnostic and can generalize to different initial conditions, velocities, and geometries after training. We show that point clouds of the order of 100,000 points can be inferred from sparse graphs with sim1000 points, with negligible change in computation time. We empirically evaluate our model on elastic solids, Newtonian fluids, Non-Newtonian fluids, Drucker-Prager granular flows, and von Mises elastoplasticity. On these benchmarks, our approach results in a 25times speedup compared to other neural network-based physics simulators while delivering high-fidelity predictions of complex physical systems and showing better performance on most benchmarks. The code and the demos are provided at https://github.com/HrishikeshVish/GIOROM.

In the classical transformer attention scheme, we are given three n times d size matrices Q, K, V (the query, key, and value tokens), and the goal is to compute a new n times d size matrix D^{-1} exp(QK^top) V where D = diag( exp(QK^top) {bf 1}_n ). In this work, we study a generalization of attention which captures triple-wise correlations. This generalization is able to solve problems about detecting triple-wise connections that were shown to be impossible for transformers. The potential downside of this generalization is that it appears as though computations are even more difficult, since the straightforward algorithm requires cubic time in n. However, we show that in the bounded-entry setting (which arises in practice, and which is well-studied in both theory and practice), there is actually a near-linear time algorithm. More precisely, we show that bounded entries are both necessary and sufficient for quickly performing generalized computations: bullet On the positive side, if all entries of the input matrices are bounded above by o(sqrt[3]{log n}) then we show how to approximate the ``tensor-type'' attention matrix in n^{1+o(1)} time. bullet On the negative side, we show that if the entries of the input matrices may be as large as Omega(sqrt[3]{log n}), then there is no algorithm that runs faster than n^{3-o(1)} (assuming the Strong Exponential Time Hypothesis from fine-grained complexity theory). We also show that our construction, algorithms, and lower bounds naturally generalize to higher-order tensors and correlations. Interestingly, the higher the order of the tensors, the lower the bound on the entries needs to be for an efficient algorithm. Our results thus yield a natural tradeoff between the boundedness of the entries, and order of the tensor one may use for more expressive, efficient attention computation.

We present an end-to-end reconfigurable algorithmic pipeline for solving a famous problem in knot theory using a noisy digital quantum computer, namely computing the value of the Jones polynomial at the fifth root of unity within additive error for any input link, i.e. a closed braid. This problem is DQC1-complete for Markov-closed braids and BQP-complete for Plat-closed braids, and we accommodate both versions of the problem. Even though it is widely believed that DQC1 is strictly contained in BQP, and so is 'less quantum', the resource requirements of classical algorithms for the DQC1 version are at least as high as for the BQP version, and so we potentially gain 'more advantage' by focusing on Markov-closed braids in our exposition. We demonstrate our quantum algorithm on Quantinuum's H2-2 quantum computer and show the effect of problem-tailored error-mitigation techniques. Further, leveraging that the Jones polynomial is a link invariant, we construct an efficiently verifiable benchmark to characterise the effect of noise present in a given quantum processor. In parallel, we implement and benchmark the state-of-the-art tensor-network-based classical algorithms for computing the Jones polynomial. The practical tools provided in this work allow for precise resource estimation to identify near-term quantum advantage for a meaningful quantum-native problem in knot theory.

Proposing an effective and flexible matrix to represent a graph is a fundamental challenge that has been explored from multiple perspectives, e.g., filtering in Graph Fourier Transforms. In this work, we develop a novel and general framework which unifies many existing GNN models from the view of parameterized decomposition and filtering, and show how it helps to enhance the flexibility of GNNs while alleviating the smoothness and amplification issues of existing models. Essentially, we show that the extensively studied spectral graph convolutions with learnable polynomial filters are constrained variants of this formulation, and releasing these constraints enables our model to express the desired decomposition and filtering simultaneously. Based on this generalized framework, we develop models that are simple in implementation but achieve significant improvements and computational efficiency on a variety of graph learning tasks. Code is available at https://github.com/qslim/PDF.

The inductive bias of a graph neural network (GNN) is largely encoded in its specified graph. Latent graph inference relies on latent geometric representations to dynamically rewire or infer a GNN's graph to maximize the GNN's predictive downstream performance, but it lacks solid theoretical foundations in terms of embedding-based representation guarantees. This paper addresses this issue by introducing a trainable deep learning architecture, coined neural snowflake, that can adaptively implement fractal-like metrics on R^d. We prove that any given finite weights graph can be isometrically embedded by a standard MLP encoder. Furthermore, when the latent graph can be represented in the feature space of a sufficiently regular kernel, we show that the combined neural snowflake and MLP encoder do not succumb to the curse of dimensionality by using only a low-degree polynomial number of parameters in the number of nodes. This implementation enables a low-dimensional isometric embedding of the latent graph. We conduct synthetic experiments to demonstrate the superior metric learning capabilities of neural snowflakes when compared to more familiar spaces like Euclidean space. Additionally, we carry out latent graph inference experiments on graph benchmarks. Consistently, the neural snowflake model achieves predictive performance that either matches or surpasses that of the state-of-the-art latent graph inference models. Importantly, this performance improvement is achieved without requiring random search for optimal latent geometry. Instead, the neural snowflake model achieves this enhancement in a differentiable manner.

We present the Evolving Graph Fourier Transform (EFT), the first invertible spectral transform that captures evolving representations on temporal graphs. We motivate our work by the inadequacy of existing methods for capturing the evolving graph spectra, which are also computationally expensive due to the temporal aspect along with the graph vertex domain. We view the problem as an optimization over the Laplacian of the continuous time dynamic graph. Additionally, we propose pseudo-spectrum relaxations that decompose the transformation process, making it highly computationally efficient. The EFT method adeptly captures the evolving graph's structural and positional properties, making it effective for downstream tasks on evolving graphs. Hence, as a reference implementation, we develop a simple neural model induced with EFT for capturing evolving graph spectra. We empirically validate our theoretical findings on a number of large-scale and standard temporal graph benchmarks and demonstrate that our model achieves state-of-the-art performance.

Machine learning (ML) and deep learning (DL) techniques have gained significant attention as reduced order models (ROMs) to computationally expensive structural analysis methods, such as finite element analysis (FEA). Graph neural network (GNN) is a particular type of neural network which processes data that can be represented as graphs. This allows for efficient representation of complex geometries that can change during conceptual design of a structure or a product. In this study, we propose a novel graph embedding technique for efficient representation of 3D stiffened panels by considering separate plate domains as vertices. This approach is considered using Graph Sampling and Aggregation (GraphSAGE) to predict stress distributions in stiffened panels with varying geometries. A comparison between a finite-element-vertex graph representation is conducted to demonstrate the effectiveness of the proposed approach. A comprehensive parametric study is performed to examine the effect of structural geometry on the prediction performance. Our results demonstrate the immense potential of graph neural networks with the proposed graph embedding method as robust reduced-order models for 3D structures.

Tensorial neural networks (TNNs) combine the successes of multilinear algebra with those of deep learning to enable extremely efficient reduced-order models of high-dimensional problems. Here, I describe a deep neural network architecture that fuses multiple TNNs into a larger network, intended to solve a broader class of problems than a single TNN. I evaluate this architecture, referred to as a "stacked tensorial neural network" (STNN), on a parametric PDE with three independent variables and three parameters. The three parameters correspond to one PDE coefficient and two quantities describing the domain geometry. The STNN provides an accurate reduced-order description of the solution manifold over a wide range of parameters. There is also evidence of meaningful generalization to parameter values outside its training data. Finally, while the STNN architecture is relatively simple and problem agnostic, it can be regularized to incorporate problem-specific features like symmetries and physical modeling assumptions.

Progress in AI is hindered by the lack of a programming language with all the requisite features. Libraries like PyTorch and TensorFlow provide automatic differentiation and efficient GPU implementation, but are additions to Python, which was never intended for AI. Their lack of support for automated reasoning and knowledge acquisition has led to a long and costly series of hacky attempts to tack them on. On the other hand, AI languages like LISP an Prolog lack scalability and support for learning. This paper proposes tensor logic, a language that solves these problems by unifying neural and symbolic AI at a fundamental level. The sole construct in tensor logic is the tensor equation, based on the observation that logical rules and Einstein summation are essentially the same operation, and all else can be reduced to them. I show how to elegantly implement key forms of neural, symbolic and statistical AI in tensor logic, including transformers, formal reasoning, kernel machines and graphical models. Most importantly, tensor logic makes new directions possible, such as sound reasoning in embedding space. This combines the scalability and learnability of neural networks with the reliability and transparency of symbolic reasoning, and is potentially a basis for the wider adoption of AI.

With the increasing adoption of graph neural networks (GNNs) in the machine learning community, GPUs have become an essential tool to accelerate GNN training. However, training GNNs on very large graphs that do not fit in GPU memory is still a challenging task. Unlike conventional neural networks, mini-batching input samples in GNNs requires complicated tasks such as traversing neighboring nodes and gathering their feature values. While this process accounts for a significant portion of the training time, we find existing GNN implementations using popular deep neural network (DNN) libraries such as PyTorch are limited to a CPU-centric approach for the entire data preparation step. This "all-in-CPU" approach has negative impact on the overall GNN training performance as it over-utilizes CPU resources and hinders GPU acceleration of GNN training. To overcome such limitations, we introduce PyTorch-Direct, which enables a GPU-centric data accessing paradigm for GNN training. In PyTorch-Direct, GPUs are capable of efficiently accessing complicated data structures in host memory directly without CPU intervention. Our microbenchmark and end-to-end GNN training results show that PyTorch-Direct reduces data transfer time by 47.1% on average and speeds up GNN training by up to 1.6x. Furthermore, by reducing CPU utilization, PyTorch-Direct also saves system power by 12.4% to 17.5% during training. To minimize programmer effort, we introduce a new "unified tensor" type along with necessary changes to the PyTorch memory allocator, dispatch logic, and placement rules. As a result, users need to change at most two lines of their PyTorch GNN training code for each tensor object to take advantage of PyTorch-Direct.

In this work, we demonstrate that a simple two-layer neural network with standard activation functions can learn an arbitrary word operation in any finite group, provided sufficient width is available and exhibits grokking while doing so. To explain the mechanism by which this is achieved, we reframe the problem as that of learning a particular 3-tensor, which we show is typically of low rank. A key insight is that low-rank implementations of this tensor can be obtained by decomposing it along triplets of basic self-conjugate representations of the group and leveraging the fusion structure to rule out many components. Focusing on a phenomenologically similar but more tractable surrogate model, we show that the network is able to find such low-rank implementations (or approximations thereof), thereby using limited width to approximate the word-tensor in a generalizable way. In the case of the simple multiplication word, we further elucidate the form of these low-rank implementations, showing that the network effectively implements efficient matrix multiplication in the sense of Strassen. Our work also sheds light on the mechanism by which a network reaches such a solution under gradient descent.

Computational materials discovery is limited by the high cost of first-principles calculations. Machine learning (ML) potentials that predict energies from crystal structures are promising, but existing methods face computational bottlenecks. Steerable graph neural networks (GNNs) encode geometry with spherical harmonics, respecting atomic symmetries -- permutation, rotation, and translation -- for physically realistic predictions. Yet maintaining equivariance is difficult: activation functions must be modified, and each layer must handle multiple data types for different harmonic orders. We present Facet, a GNN architecture for efficient ML potentials, developed through systematic analysis of steerable GNNs. Our innovations include replacing expensive multi-layer perceptrons (MLPs) for interatomic distances with splines, which match performance while cutting computational and memory demands. We also introduce a general-purpose equivariant layer that mixes node information via spherical grid projection followed by standard MLPs -- faster than tensor products and more expressive than linear or gate layers. On the MPTrj dataset, Facet matches leading models with far fewer parameters and under 10% of their training compute. On a crystal relaxation task, it runs twice as fast as MACE models. We further show SevenNet-0's parameters can be reduced by over 25% with no accuracy loss. These techniques enable more than 10x faster training of large-scale foundation models for ML potentials, potentially reshaping computational materials discovery.

The computing cost and memory demand of deep learning pipelines have grown fast in recent years and thus a variety of pruning techniques have been developed to reduce model parameters. The majority of these techniques focus on reducing inference costs by pruning the network after a pass of full training. A smaller number of methods address the reduction of training costs, mostly based on compressing the network via low-rank layer factorizations. Despite their efficiency for linear layers, these methods fail to effectively handle convolutional filters. In this work, we propose a low-parametric training method that factorizes the convolutions into tensor Tucker format and adaptively prunes the Tucker ranks of the convolutional kernel during training. Leveraging fundamental results from geometric integration theory of differential equations on tensor manifolds, we obtain a robust training algorithm that provably approximates the full baseline performance and guarantees loss descent. A variety of experiments against the full model and alternative low-rank baselines are implemented, showing that the proposed method drastically reduces the training costs, while achieving high performance, comparable to or better than the full baseline, and consistently outperforms competing low-rank approaches.

We introduce Clifford Group Equivariant Simplicial Message Passing Networks, a method for steerable E(n)-equivariant message passing on simplicial complexes. Our method integrates the expressivity of Clifford group-equivariant layers with simplicial message passing, which is topologically more intricate than regular graph message passing. Clifford algebras include higher-order objects such as bivectors and trivectors, which express geometric features (e.g., areas, volumes) derived from vectors. Using this knowledge, we represent simplex features through geometric products of their vertices. To achieve efficient simplicial message passing, we share the parameters of the message network across different dimensions. Additionally, we restrict the final message to an aggregation of the incoming messages from different dimensions, leading to what we term shared simplicial message passing. Experimental results show that our method is able to outperform both equivariant and simplicial graph neural networks on a variety of geometric tasks.

We study the estimation of a planted signal hidden in a recently introduced nested matrix-tensor model, which is an extension of the classical spiked rank-one tensor model, motivated by multi-view clustering. Prior work has theoretically examined the performance of a tensor-based approach, which relies on finding a best rank-one approximation, a problem known to be computationally hard. A tractable alternative approach consists in computing instead the best rank-one (matrix) approximation of an unfolding of the observed tensor data, but its performance was hitherto unknown. We quantify here the performance gap between these two approaches, in particular by deriving the precise algorithmic threshold of the unfolding approach and demonstrating that it exhibits a BBP-type transition behavior. This work is therefore in line with recent contributions which deepen our understanding of why tensor-based methods surpass matrix-based methods in handling structured tensor data.

Applications of machine learning techniques for materials modeling typically involve functions known to be equivariant or invariant to specific symmetries. While graph neural networks (GNNs) have proven successful in such tasks, they enforce symmetries via the model architecture, which often reduces their expressivity, scalability and comprehensibility. In this paper, we introduce (1) a flexible framework relying on stochastic frame-averaging (SFA) to make any model E(3)-equivariant or invariant through data transformations. (2) FAENet: a simple, fast and expressive GNN, optimized for SFA, that processes geometric information without any symmetrypreserving design constraints. We prove the validity of our method theoretically and empirically demonstrate its superior accuracy and computational scalability in materials modeling on the OC20 dataset (S2EF, IS2RE) as well as common molecular modeling tasks (QM9, QM7-X). A package implementation is available at https://faenet.readthedocs.io.

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.

Developing equivariant neural networks for the E(3) group plays an important role in modeling 3D data across real-world applications. Enforcing this equivariance primarily involves the tensor products of irreducible representations (irreps). However, the computational complexity of such operations increases significantly as higher-order tensors are used. In this work, we propose a systematic approach to substantially accelerate the computation of the tensor products of irreps. We mathematically connect the commonly used Clebsch-Gordan coefficients to the Gaunt coefficients, which are integrals of products of three spherical harmonics. Through Gaunt coefficients, the tensor product of irreps becomes equivalent to the multiplication between spherical functions represented by spherical harmonics. This perspective further allows us to change the basis for the equivariant operations from spherical harmonics to a 2D Fourier basis. Consequently, the multiplication between spherical functions represented by a 2D Fourier basis can be efficiently computed via the convolution theorem and Fast Fourier Transforms. This transformation reduces the complexity of full tensor products of irreps from O(L^6) to O(L^3), where L is the max degree of irreps. Leveraging this approach, we introduce the Gaunt Tensor Product, which serves as a new method to construct efficient equivariant operations across different model architectures. Our experiments on the Open Catalyst Project and 3BPA datasets demonstrate both the increased efficiency and improved performance of our approach.

Graph neural networks (GNNs) have gained significant attention in recent years for their ability to process data that may be represented as graphs. This has prompted several studies to explore their representational capability based on the graph isomorphism task. Notably, these works inherently assume a countable node feature representation, potentially limiting their applicability. Interestingly, only a few study GNNs with uncountable node feature representation. In the paper, a new perspective on the representational capability of GNNs is investigated across all levelsx2014node-level, neighborhood-level, and graph-levelx2014when the space of node feature representation is uncountable. Specifically, the injective and metric requirements of previous works are softly relaxed by employing a pseudometric distance on the space of input to create a soft-injective function such that distinct inputs may produce similar outputs if and only if the pseudometric deems the inputs to be sufficiently similar on some representation. As a consequence, a simple and computationally efficient soft-isomorphic relational graph convolution network (SIR-GCN) that emphasizes the contextualized transformation of neighborhood feature representations via anisotropic and dynamic message functions is proposed. Furthermore, a mathematical discussion on the relationship between SIR-GCN and key GNNs in literature is laid out to put the contribution into context, establishing SIR-GCN as a generalization of classical GNN methodologies. To close, experiments on synthetic and benchmark datasets demonstrate the relative superiority of SIR-GCN, outperforming comparable models in node and graph property prediction tasks.

Tuning tensor program generation involves searching for various possible program transformation combinations for a given program on target hardware to optimize the tensor program execution. It is already a complex process because of the massive search space and exponential combinations of transformations make auto-tuning tensor program generation more challenging, especially when we have a heterogeneous target. In this research, we attempt to address these problems by learning the joint neural network and hardware features and transferring them to the new target hardware. We extensively study the existing state-of-the-art dataset, TenSet, perform comparative analysis on the test split strategies and propose methodologies to prune the dataset. We adopt an attention-inspired approach for tuning the tensor programs enabling them to embed neural network and hardware-specific features. Our approach could prune the dataset up to 45\% of the baseline without compromising the Pairwise Comparison Accuracy (PCA). Further, the proposed methodology can achieve on-par or improved mean inference time with 25%-40% of the baseline tuning time across different networks and target hardware.

The learnable, linear neural network layers between tensor power spaces of R^{n} that are equivariant to the orthogonal group, O(n), the special orthogonal group, SO(n), and the symplectic group, Sp(n), were characterised in arXiv:2212.08630. We present an algorithm for multiplying a vector by any weight matrix for each of these groups, using category theoretic constructions to implement the procedure. We achieve a significant reduction in computational cost compared with a naive implementation by making use of Kronecker product matrices to perform the multiplication. We show that our approach extends to the symmetric group, S_n, recovering the algorithm of arXiv:2303.06208 in the process.

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.

We propose a systematic approach to reduce the memory consumption of deep neural network training. Specifically, we design an algorithm that costs O(sqrt(n)) memory to train a n layer network, with only the computational cost of an extra forward pass per mini-batch. As many of the state-of-the-art models hit the upper bound of the GPU memory, our algorithm allows deeper and more complex models to be explored, and helps advance the innovations in deep learning research. We focus on reducing the memory cost to store the intermediate feature maps and gradients during training. Computation graph analysis is used for automatic in-place operation and memory sharing optimizations. We show that it is possible to trade computation for memory - giving a more memory efficient training algorithm with a little extra computation cost. In the extreme case, our analysis also shows that the memory consumption can be reduced to O(log n) with as little as O(n log n) extra cost for forward computation. Our experiments show that we can reduce the memory cost of a 1,000-layer deep residual network from 48G to 7G with only 30 percent additional running time cost on ImageNet problems. Similarly, significant memory cost reduction is observed in training complex recurrent neural networks on very long sequences.

The existing definitions of graph convolution, either from spatial or spectral perspectives, are inflexible and not unified. Defining a general convolution operator in the graph domain is challenging due to the lack of canonical coordinates, the presence of irregular structures, and the properties of graph symmetries. In this work, we propose a novel and general graph convolution framework by parameterizing the kernels as continuous functions of pseudo-coordinates derived via graph positional encoding. We name this Continuous Kernel Graph Convolution (CKGConv). Theoretically, we demonstrate that CKGConv is flexible and expressive. CKGConv encompasses many existing graph convolutions, and exhibits a stronger expressiveness, as powerful as graph transformers in terms of distinguishing non-isomorphic graphs. Empirically, we show that CKGConv-based Networks outperform existing graph convolutional networks and perform comparably to the best graph transformers across a variety of graph datasets. The code and models are publicly available at https://github.com/networkslab/CKGConv.

Communication is a key bottleneck for distributed graph neural network (GNN) training. This paper proposes GNNPipe, a new approach that scales the distributed full-graph deep GNN training. Being the first to use layer-level model parallelism for GNN training, GNNPipe partitions GNN layers among GPUs, each device performs the computation for a disjoint subset of consecutive GNN layers on the whole graph. Compared to graph parallelism with each GPU handling a graph partition, GNNPipe reduces the communication volume by a factor of the number of GNN layers. GNNPipe overcomes the unique challenges for pipelined layer-level model parallelism on the whole graph by partitioning it into dependent chunks, allowing the use of historical vertex embeddings, and applying specific training techniques to ensure convergence. We also propose a hybrid approach by combining GNNPipe with graph parallelism to handle large graphs, achieve better computer resource utilization and ensure model convergence. We build a general GNN training system supporting all three parallelism setting. Extensive experiments show that our method reduces the per-epoch training time by up to 2.45x (on average 1.58x) and reduces the communication volume and overhead by up to 22.89x and 27.21x (on average 8.69x and 11.60x), respectively, while achieving a comparable level of model accuracy and convergence speed compared to graph parallelism.

We propose Strivec, a novel neural representation that models a 3D scene as a radiance field with sparsely distributed and compactly factorized local tensor feature grids. Our approach leverages tensor decomposition, following the recent work TensoRF, to model the tensor grids. In contrast to TensoRF which uses a global tensor and focuses on their vector-matrix decomposition, we propose to utilize a cloud of local tensors and apply the classic CANDECOMP/PARAFAC (CP) decomposition to factorize each tensor into triple vectors that express local feature distributions along spatial axes and compactly encode a local neural field. We also apply multi-scale tensor grids to discover the geometry and appearance commonalities and exploit spatial coherence with the tri-vector factorization at multiple local scales. The final radiance field properties are regressed by aggregating neural features from multiple local tensors across all scales. Our tri-vector tensors are sparsely distributed around the actual scene surface, discovered by a fast coarse reconstruction, leveraging the sparsity of a 3D scene. We demonstrate that our model can achieve better rendering quality while using significantly fewer parameters than previous methods, including TensoRF and Instant-NGP.

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.

Computing the numerical solution to high-dimensional tensor differential equations can lead to prohibitive computational costs and memory requirements. To reduce the memory and computational footprint, dynamical low-rank approximation (DLRA) has proven to be a promising approach. DLRA represents the solution as a low-rank tensor factorization and evolves the resulting low-rank factors in time. A central challenge in DLRA is to find time integration schemes that are robust to the arising small singular values. A robust parallel basis update & Galerkin integrator, which simultaneously evolves all low-rank factors, has recently been derived for matrix differential equations. This work extends the parallel low-rank matrix integrator to Tucker tensors and general tree tensor networks, yielding an algorithm in which all bases and connecting tensors are evolved in parallel over a time step. We formulate the algorithm, provide a robust error bound, and demonstrate the efficiency of the new integrators for problems in quantum many-body physics, uncertainty quantification, and radiative transfer.

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.

In this paper, we introduce a mesh-free two-level hybrid Tucker tensor format for approximation of multivariate functions, which combines the product Chebyshev interpolation with the ALS-based Tucker decomposition of the tensor of Chebyshev coefficients. It allows to avoid the expenses of the rank-structured approximation of function-related tensors defined on large spacial grids, while benefiting from the Tucker decomposition of the rather small core tensor of Chebyshev coefficients. This leads to nearly optimal Tucker rank parameters which are close to the results for well established Tucker-ALS algorithm applied to the large grid-based tensors. These rank parameters inherited from the Tucker-ALS decomposition of the coefficient tensor can be much less than the polynomial degrees of the initial Chebyshev interpolant via function independent basis set. Furthermore, the tensor product Chebyshev polynomials discretized on a tensor grid leads to a low-rank two-level orthogonal algebraic Tucker tensor that approximates the initial function with controllable accuracy. It is shown that our techniques could be gainfully applied to the long-range part of the electrostatic potential of multi-particle systems approximated in the range-separated tensor format. Error and complexity estimates of the proposed methods are presented. We demonstrate the efficiency of the suggested method numerically on examples of the long-range components of multi-particle interaction potentials generated by 3D Newton kernel for large bio-molecule systems and lattice-type compounds.

Large model inference is shifting from cloud to edge due to concerns about the privacy of user interaction data. However, edge devices often struggle with limited computing power, memory, and bandwidth, requiring collaboration across multiple devices to run and speed up LLM inference. Pipeline parallelism, the mainstream solution, is inefficient for single-user scenarios, while tensor parallelism struggles with frequent communications. In this paper, we argue that tensor parallelism can be more effective than pipeline on low-resource devices, and present a compute- and memory-efficient tensor parallel inference system, named TPI-LLM, to serve 70B-scale models. TPI-LLM keeps sensitive raw data local in the users' devices and introduces a sliding window memory scheduler to dynamically manage layer weights during inference, with disk I/O latency overlapped with the computation and communication. This allows larger models to run smoothly on memory-limited devices. We analyze the communication bottleneck and find that link latency, not bandwidth, emerges as the main issue, so a star-based allreduce algorithm is implemented. Through extensive experiments on both emulated and real testbeds, TPI-LLM demonstrated over 80% less time-to-first-token and token latency compared to Accelerate, and over 90% compared to Transformers and Galaxy, while cutting the peak memory footprint of Llama 2-70B by 90%, requiring only 3.1 GB of memory for 70B-scale models.

Boosting the runtime performance of deep neural networks (DNNs) is critical due to their wide adoption in real-world tasks. Existing approaches to optimizing the tensor algebra expression of a DNN only consider expressions representable by a fixed set of predefined operators, missing possible optimization opportunities between general expressions. We propose OLLIE, the first derivation-based tensor program optimizer. OLLIE optimizes tensor programs by leveraging transformations between general tensor algebra expressions, enabling a significantly larger expression search space that includes those supported by prior work as special cases. OLLIE uses a hybrid derivation-based optimizer that effectively combines explorative and guided derivations to quickly discover highly optimized expressions. Evaluation on seven DNNs shows that OLLIE can outperform existing optimizers by up to 2.73times (1.46times on average) on an A100 GPU and up to 2.68times (1.51times) on a V100 GPU, respectively.

We define the bicategory of Graph Convolutional Neural Networks GCNN_n for an arbitrary graph with n nodes. We show it can be factored through the already existing categorical constructions for deep learning called Para and Lens with the base category set to the CoKleisli category of the product comonad. We prove that there exists an injective-on-objects, faithful 2-functor GCNN_n to Para(CoKl(R^{n times n} times -)). We show that this construction allows us to treat the adjacency matrix of a GCNN as a global parameter instead of a a local, layer-wise one. This gives us a high-level categorical characterisation of a particular kind of inductive bias GCNNs possess. Lastly, we hypothesize about possible generalisations of GCNNs to general message-passing graph neural networks, connections to equivariant learning, and the (lack of) functoriality of activation functions.

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.

Graph generation with Machine Learning is an open problem with applications in various research fields. In this work, we propose to cast the generative process of a graph into a sequential one, relying on a node ordering procedure. We use this sequential process to design a novel generative model composed of two recurrent neural networks that learn to predict the edges of graphs: the first network generates one endpoint of each edge, while the second network generates the other endpoint conditioned on the state of the first. We test our approach extensively on five different datasets, comparing with two well-known baselines coming from graph literature, and two recurrent approaches, one of which holds state of the art performances. Evaluation is conducted considering quantitative and qualitative characteristics of the generated samples. Results show that our approach is able to yield novel, and unique graphs originating from very different distributions, while retaining structural properties very similar to those in the training sample. Under the proposed evaluation framework, our approach is able to reach performances comparable to the current state of the art on the graph generation task.

Fundamental tasks in computational chemistry, from transition state search to vibrational analysis, rely on molecular Hessians, which are the second derivatives of the potential energy. Yet, Hessians are computationally expensive to calculate and scale poorly with system size, with both quantum mechanical methods and neural networks. In this work, we demonstrate that Hessians can be predicted directly from a deep learning model, without relying on automatic differentiation or finite differences. We observe that one can construct SE(3)-equivariant, symmetric Hessians from irreducible representations (irrep) features up to degree l=2 computed during message passing in graph neural networks. This makes HIP Hessians one to two orders of magnitude faster, more accurate, more memory efficient, easier to train, and enables more favorable scaling with system size. We validate our predictions across a wide range of downstream tasks, demonstrating consistently superior performance for transition state search, accelerated geometry optimization, zero-point energy corrections, and vibrational analysis benchmarks. We open-source the HIP codebase and model weights to enable further development of the direct prediction of Hessians at https://github.com/BurgerAndreas/hip

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.

TensorFlow is a machine learning system that operates at large scale and in heterogeneous environments. TensorFlow uses dataflow graphs to represent computation, shared state, and the operations that mutate that state. It maps the nodes of a dataflow graph across many machines in a cluster, and within a machine across multiple computational devices, including multicore CPUs, general-purpose GPUs, and custom designed ASICs known as Tensor Processing Units (TPUs). This architecture gives flexibility to the application developer: whereas in previous "parameter server" designs the management of shared state is built into the system, TensorFlow enables developers to experiment with novel optimizations and training algorithms. TensorFlow supports a variety of applications, with particularly strong support for training and inference on deep neural networks. Several Google services use TensorFlow in production, we have released it as an open-source project, and it has become widely used for machine learning research. In this paper, we describe the TensorFlow dataflow model in contrast to existing systems, and demonstrate the compelling performance that TensorFlow achieves for several real-world applications.

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.

Recent works in geometric deep learning have introduced neural networks that allow performing inference tasks on three-dimensional geometric data by defining convolution, and sometimes pooling, operations on triangle meshes. These methods, however, either consider the input mesh as a graph, and do not exploit specific geometric properties of meshes for feature aggregation and downsampling, or are specialized for meshes, but rely on a rigid definition of convolution that does not properly capture the local topology of the mesh. We propose a method that combines the advantages of both types of approaches, while addressing their limitations: we extend a primal-dual framework drawn from the graph-neural-network literature to triangle meshes, and define convolutions on two types of graphs constructed from an input mesh. Our method takes features for both edges and faces of a 3D mesh as input and dynamically aggregates them using an attention mechanism. At the same time, we introduce a pooling operation with a precise geometric interpretation, that allows handling variations in the mesh connectivity by clustering mesh faces in a task-driven fashion. We provide theoretical insights of our approach using tools from the mesh-simplification literature. In addition, we validate experimentally our method in the tasks of shape classification and shape segmentation, where we obtain comparable or superior performance to the state of the art.

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.

General matrix-matrix multiplication (GEMM) is a cornerstone of AI computations, making tensor processing engines (TPEs) increasingly critical in GPUs and domain-specific architectures. Existing architectures primarily optimize dataflow or operand reuse strategies. However, considering the interaction between matrix multiplication and multiply-accumulators (MACs) offers greater optimization potential. This work introduces a novel hardware perspective on matrix multiplication, focusing on the bit-weight dimension of MACs. We propose a finer-grained TPE notation using matrix triple loops as an example, introducing new methods for designing and optimizing PE microarchitectures. Based on this notation and its transformations, we propose four optimization techniques that improve timing, area, and power consumption. Implementing our design in RTL using the SMIC-28nm process, we evaluate its effectiveness across four classic TPE architectures: systolic array, 3D-Cube, multiplier-adder tree, and 2D-Matrix. Our techniques achieve area efficiency improvements of 1.27x, 1.28x, 1.56x, and 1.44x, and energy efficiency gains of 1.04x, 1.56x, 1.49x, and 1.20x, respectively. Applied to a bit-slice architecture, our approach achieves a 12.10x improvement in energy efficiency and 2.85x in area efficiency compared to Laconic. Our Verilog HDL code, along with timing, area, and power reports, is available at https://github.com/wqzustc/High-Performance-Tensor-Processing-Engines

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.

Large language models have led to state-of-the-art accuracies across a range of tasks. However, training these models efficiently is challenging for two reasons: a) GPU memory capacity is limited, making it impossible to fit large models on even a multi-GPU server, and b) the number of compute operations required to train these models can result in unrealistically long training times. Consequently, new methods of model parallelism such as tensor and pipeline parallelism have been proposed. Unfortunately, naive usage of these methods leads to fundamental scaling issues at thousands of GPUs, e.g., due to expensive cross-node communication or devices spending significant time waiting on other devices to make progress. In this paper, we show how different types of parallelism methods (tensor, pipeline, and data parallelism) can be composed to scale to thousands of GPUs and models with trillions of parameters. We survey techniques for pipeline parallelism and propose a novel interleaved pipeline parallelism schedule that can improve throughput by 10+% with memory footprint comparable to existing approaches. We quantitatively study the trade-offs between tensor, pipeline, and data parallelism, and provide intuition as to how to configure distributed training of a large model. Our approach allows us to perform training iterations on a model with 1 trillion parameters at 502 petaFLOP/s on 3072 GPUs with achieved per-GPU throughput of 52% of theoretical peak. Our code is open sourced at https://github.com/nvidia/megatron-lm.

We investigate novel random graph embeddings that can be computed in expected polynomial time and that are able to distinguish all non-isomorphic graphs in expectation. Previous graph embeddings have limited expressiveness and either cannot distinguish all graphs or cannot be computed efficiently for every graph. To be able to approximate arbitrary functions on graphs, we are interested in efficient alternatives that become arbitrarily expressive with increasing resources. Our approach is based on Lov\'asz' characterisation of graph isomorphism through an infinite dimensional vector of homomorphism counts. Our empirical evaluation shows competitive results on several benchmark graph learning tasks.

Graph embedding methods produce unsupervised node features from graphs that can then be used for a variety of machine learning tasks. Modern graphs, particularly in industrial applications, contain billions of nodes and trillions of edges, which exceeds the capability of existing embedding systems. We present PyTorch-BigGraph (PBG), an embedding system that incorporates several modifications to traditional multi-relation embedding systems that allow it to scale to graphs with billions of nodes and trillions of edges. PBG uses graph partitioning to train arbitrarily large embeddings on either a single machine or in a distributed environment. We demonstrate comparable performance with existing embedding systems on common benchmarks, while allowing for scaling to arbitrarily large graphs and parallelization on multiple machines. We train and evaluate embeddings on several large social network graphs as well as the full Freebase dataset, which contains over 100 million nodes and 2 billion edges.

Recent advances in molecular representation learning have produced highly effective encodings of molecules for numerous cheminformatics and bioinformatics tasks. However, extracting general chemical insight while balancing predictive accuracy, interpretability, and computational efficiency remains a major challenge. In this work, we introduce a novel Graph Neural Network (GNN) architecture that combines compressed higher-order topological signals with standard molecular features. Our approach captures global geometric information while preserving computational tractability and human-interpretable structure. We evaluate our model across a range of benchmarks, from small-molecule datasets to complex material datasets, and demonstrate superior performance using a parameter-efficient architecture. We achieve the best performing results in both accuracy and robustness across almost all benchmarks. We open source all code All code and results can be found on Github https://github.com/rahulkhorana/TFC-PACT-Net.

Graph Neural Networks (GNNs) are the dominant architecture for molecular machine learning, particularly for molecular property prediction and machine learning interatomic potentials (MLIPs). GNNs perform message passing on predefined graphs often induced by a fixed radius cutoff or k-nearest neighbor scheme. While this design aligns with the locality present in many molecular tasks, a hard-coded graph can limit expressivity due to the fixed receptive field and slows down inference with sparse graph operations. In this work, we investigate whether pure, unmodified Transformers trained directly on Cartesian coordinatesx2013without predefined graphs or physical priorsx2013can approximate molecular energies and forces. As a starting point for our analysis, we demonstrate how to train a Transformer to competitive energy and force mean absolute errors under a matched training compute budget, relative to a state-of-the-art equivariant GNN on the OMol25 dataset. We discover that the Transformer learns physically consistent patternsx2013such as attention weights that decay inversely with interatomic distancex2013and flexibly adapts them across different molecular environments due to the absence of hard-coded biases. The use of a standard Transformer also unlocks predictable improvements with respect to scaling training resources, consistent with empirical scaling laws observed in other domains. Our results demonstrate that many favorable properties of GNNs can emerge adaptively in Transformers, challenging the necessity of hard-coded graph inductive biases and pointing toward standardized, scalable architectures for molecular modeling.

Deep graph generative modeling has proven capable of learning the distribution of complex, multi-scale structures characterizing real-world graphs. However, one of the main limitations of existing methods is their large output space, which limits generation scalability and hinders accurate modeling of the underlying distribution. To overcome these limitations, we propose a novel approach that significantly reduces the output space of existing graph generative models. Specifically, starting from the observation that many real-world graphs have low graph bandwidth, we restrict graph bandwidth during training and generation. Our strategy improves both generation scalability and quality without increasing architectural complexity or reducing expressiveness. Our approach is compatible with existing graph generative methods, and we describe its application to both autoregressive and one-shot models. We extensively validate our strategy on synthetic and real datasets, including molecular graphs. Our experiments show that, in addition to improving generation efficiency, our approach consistently improves generation quality and reconstruction accuracy. The implementation is made available.

Knowledge Graphs (KGs) are symbolically structured storages of facts. The KG embedding contains concise data used in NLP tasks requiring implicit information about the real world. Furthermore, the size of KGs that may be useful in actual NLP assignments is enormous, and creating embedding over it has memory cost issues. We represent KG as a 3rd-order binary tensor and move beyond the standard CP decomposition by using a data-specific generalized version of it. The generalization of the standard CP-ALS algorithm allows obtaining optimization gradients without a backpropagation mechanism. It reduces the memory needed in training while providing computational benefits. We propose a MEKER, a memory-efficient KG embedding model, which yields SOTA-comparable performance on link prediction tasks and KG-based Question Answering.

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.

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.

In this paper, we delve into the foundational principles of tensor categories, harnessing the universal property of the tensor product to pioneer novel methodologies in deep network architectures. Our primary contribution is the introduction of the Tensor Attention and Tensor Interaction Mechanism, a groundbreaking approach that leverages the tensor category to enhance the computational efficiency and the expressiveness of deep networks, and can even be generalized into the quantum realm.

When learning simulations for modeling physical phenomena in industrial designs, geometrical variabilities are of prime interest. While classical regression techniques prove effective for parameterized geometries, practical scenarios often involve the absence of shape parametrization during the inference stage, leaving us with only mesh discretizations as available data. Learning simulations from such mesh-based representations poses significant challenges, with recent advances relying heavily on deep graph neural networks to overcome the limitations of conventional machine learning approaches. Despite their promising results, graph neural networks exhibit certain drawbacks, including their dependency on extensive datasets and limitations in providing built-in predictive uncertainties or handling large meshes. In this work, we propose a machine learning method that do not rely on graph neural networks. Complex geometrical shapes and variations with fixed topology are dealt with using well-known mesh morphing onto a common support, combined with classical dimensionality reduction techniques and Gaussian processes. The proposed methodology can easily deal with large meshes without the need for explicit shape parameterization and provides crucial predictive uncertainties, which are essential for informed decision-making. In the considered numerical experiments, the proposed method is competitive with respect to existing graph neural networks, regarding training efficiency and accuracy of the predictions.

We study the problem of visualizing large-scale and high-dimensional data in a low-dimensional (typically 2D or 3D) space. Much success has been reported recently by techniques that first compute a similarity structure of the data points and then project them into a low-dimensional space with the structure preserved. These two steps suffer from considerable computational costs, preventing the state-of-the-art methods such as the t-SNE from scaling to large-scale and high-dimensional data (e.g., millions of data points and hundreds of dimensions). We propose the LargeVis, a technique that first constructs an accurately approximated K-nearest neighbor graph from the data and then layouts the graph in the low-dimensional space. Comparing to t-SNE, LargeVis significantly reduces the computational cost of the graph construction step and employs a principled probabilistic model for the visualization step, the objective of which can be effectively optimized through asynchronous stochastic gradient descent with a linear time complexity. The whole procedure thus easily scales to millions of high-dimensional data points. Experimental results on real-world data sets demonstrate that the LargeVis outperforms the state-of-the-art methods in both efficiency and effectiveness. The hyper-parameters of LargeVis are also much more stable over different data sets.

Graph neural networks (GNNs) are the most widely adopted model in graph-structured data oriented learning and representation. Despite their extraordinary success in real-world applications, understanding their working mechanism by theory is still on primary stage. In this paper, we move towards this goal from the perspective of generalization. To be specific, we first establish high probability bounds of generalization gap and gradients in transductive learning with consideration of stochastic optimization. After that, we provide high probability bounds of generalization gap for popular GNNs. The theoretical results reveal the architecture specific factors affecting the generalization gap. Experimental results on benchmark datasets show the consistency between theoretical results and empirical evidence. Our results provide new insights in understanding the generalization of GNNs.

Multi-channel imaging data is a prevalent data format in scientific fields such as astronomy and biology. The structured information and the high dimensionality of these 3-D tensor data makes the analysis an intriguing but challenging topic for statisticians and practitioners. The low-rank scalar-on-tensor regression model, in particular, has received widespread attention and has been re-formulated as a tensor Gaussian Process (Tensor-GP) model with multi-linear kernel in Yu et al. (2018). In this paper, we extend the Tensor-GP model by integrating a dimensionality reduction technique, called tensor contraction, with a Tensor-GP for a scalar-on-tensor regression task with multi-channel imaging data. This is motivated by the solar flare forecasting problem with high dimensional multi-channel imaging data. We first estimate a latent, reduced-size tensor for each data tensor and then apply a multi-linear Tensor-GP on the latent tensor data for prediction. We introduce an anisotropic total-variation regularization when conducting the tensor contraction to obtain a sparse and smooth latent tensor. We then propose an alternating proximal gradient descent algorithm for estimation. We validate our approach via extensive simulation studies and applying it to the solar flare forecasting problem.

Graph Structure Learning (GSL) has recently garnered considerable attention due to its ability to optimize both the parameters of Graph Neural Networks (GNNs) and the computation graph structure simultaneously. Despite the proliferation of GSL methods developed in recent years, there is no standard experimental setting or fair comparison for performance evaluation, which creates a great obstacle to understanding the progress in this field. To fill this gap, we systematically analyze the performance of GSL in different scenarios and develop a comprehensive Graph Structure Learning Benchmark (GSLB) curated from 20 diverse graph datasets and 16 distinct GSL algorithms. Specifically, GSLB systematically investigates the characteristics of GSL in terms of three dimensions: effectiveness, robustness, and complexity. We comprehensively evaluate state-of-the-art GSL algorithms in node- and graph-level tasks, and analyze their performance in robust learning and model complexity. Further, to facilitate reproducible research, we have developed an easy-to-use library for training, evaluating, and visualizing different GSL methods. Empirical results of our extensive experiments demonstrate the ability of GSL and reveal its potential benefits on various downstream tasks, offering insights and opportunities for future research. The code of GSLB is available at: https://github.com/GSL-Benchmark/GSLB.

Feature-based image matching has extensive applications in computer vision. Keypoints detected in images can be naturally represented as graph structures, and Graph Neural Networks (GNNs) have been shown to outperform traditional deep learning techniques. Consequently, the paradigm of image matching via GNNs has gained significant prominence in recent academic research. In this paper, we first introduce an innovative adaptive graph construction method that utilizes a filtering mechanism based on distance and dynamic threshold similarity. This method dynamically adjusts the criteria for incorporating new vertices based on the characteristics of existing vertices, allowing for the construction of more precise and robust graph structures while avoiding redundancy. We further combine the vertex processing capabilities of GNNs with the global awareness capabilities of Transformers to enhance the model's representation of spatial and feature information within graph structures. This hybrid model provides a deeper understanding of the interrelationships between vertices and their contributions to the matching process. Additionally, we employ the Sinkhorn algorithm to iteratively solve for optimal matching results. Finally, we validate our system using extensive image datasets and conduct comprehensive comparative experiments. Experimental results demonstrate that our system achieves an average improvement of 3.8x-40.3x in overall matching performance. Additionally, the number of vertices and edges significantly impacts training efficiency and memory usage; therefore, we employ multi-GPU technology to accelerate the training process. Our code is available at https://github.com/songxf1024/GIMS.

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.

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

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 convolutional networks (GCNs) enable end-to-end learning on graph structured data. However, many works assume a given graph structure. When the input graph is noisy or unavailable, one approach is to construct or learn a latent graph structure. These methods typically fix the choice of node degree for the entire graph, which is suboptimal. Instead, we propose a novel end-to-end differentiable graph generator which builds graph topologies where each node selects both its neighborhood and its size. Our module can be readily integrated into existing pipelines involving graph convolution operations, replacing the predetermined or existing adjacency matrix with one that is learned, and optimized, as part of the general objective. As such it is applicable to any GCN. We integrate our module into trajectory prediction, point cloud classification and node classification pipelines resulting in improved accuracy over other structure-learning methods across a wide range of datasets and GCN backbones.

Knowledge graph (KG) learning offers a powerful framework for generating new knowledge and making inferences. Training KG embedding can take a significantly long time, especially for larger datasets. Our analysis shows that the gradient computation of embedding is one of the dominant functions in the translation-based KG embedding training loop. We address this issue by replacing the core embedding computation with SpMM (Sparse-Dense Matrix Multiplication) kernels. This allows us to unify multiple scatter (and gather) operations as a single operation, reducing training time and memory usage. We create a general framework for training KG models using sparse kernels and implement four models, namely TransE, TransR, TransH, and TorusE. Our sparse implementations exhibit up to 5.3x speedup on the CPU and up to 4.2x speedup on the GPU with a significantly low GPU memory footprint. The speedups are consistent across large and small datasets for a given model. Our proposed sparse approach can be extended to accelerate other translation-based (such as TransC, TransM, etc.) and non-translational (such as DistMult, ComplEx, RotatE, etc.) models as well. An implementation of the SpTransX framework is publicly available as a Python package in https://github.com/HipGraph/SpTransX.

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.

Neural networks that process the parameters of other neural networks find applications in domains as diverse as classifying implicit neural representations, generating neural network weights, and predicting generalization errors. However, existing approaches either overlook the inherent permutation symmetry in the neural network or rely on intricate weight-sharing patterns to achieve equivariance, while ignoring the impact of the network architecture itself. In this work, we propose to represent neural networks as computational graphs of parameters, which allows us to harness powerful graph neural networks and transformers that preserve permutation symmetry. Consequently, our approach enables a single model to encode neural computational graphs with diverse architectures. We showcase the effectiveness of our method on a wide range of tasks, including classification and editing of implicit neural representations, predicting generalization performance, and learning to optimize, while consistently outperforming state-of-the-art methods. The source code is open-sourced at https://github.com/mkofinas/neural-graphs.

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 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.

With the fast growth of parameter size, it becomes increasingly challenging to deploy large generative models as they typically require large GPU memory consumption and massive computation. Unstructured model pruning has been a common approach to reduce both GPU memory footprint and the overall computation while retaining good model accuracy. However, the existing solutions do not provide a highly-efficient support for handling unstructured sparsity on modern GPUs, especially on the highly-structured Tensor Core hardware. Therefore, we propose Flash-LLM for enabling low-cost and highly-efficient large generative model inference with the sophisticated support of unstructured sparsity on high-performance but highly restrictive Tensor Cores. Based on our key observation that the main bottleneck of generative model inference is the several skinny matrix multiplications for which Tensor Cores would be significantly under-utilized due to low computational intensity, we propose a general Load-as-Sparse and Compute-as-Dense methodology for unstructured sparse matrix multiplication. The basic insight is to address the significant memory bandwidth bottleneck while tolerating redundant computations that are not critical for end-to-end performance on Tensor Cores. Based on this, we design an effective software framework for Tensor Core based unstructured SpMM, leveraging on-chip resources for efficient sparse data extraction and computation/memory-access overlapping. At SpMM kernel level, Flash-LLM significantly outperforms the state-of-the-art library, i.e., Sputnik and SparTA by an average of 2.9x and 1.5x, respectively. At end-to-end framework level on OPT-30B/66B/175B models, for tokens per GPU-second, Flash-LLM achieves up to 3.8x and 3.6x improvement over DeepSpeed and FasterTransformer, respectively, with significantly lower inference cost.

We propose the convergent graph solver (CGS), a deep learning method that learns iterative mappings to predict the properties of a graph system at its stationary state (fixed point) with guaranteed convergence. CGS systematically computes the fixed points of a target graph system and decodes them to estimate the stationary properties of the system without the prior knowledge of existing solvers or intermediate solutions. The forward propagation of CGS proceeds in three steps: (1) constructing the input dependent linear contracting iterative maps, (2) computing the fixed-points of the linear maps, and (3) decoding the fixed-points to estimate the properties. The contractivity of the constructed linear maps guarantees the existence and uniqueness of the fixed points following the Banach fixed point theorem. To train CGS efficiently, we also derive a tractable analytical expression for its gradient by leveraging the implicit function theorem. We evaluate the performance of CGS by applying it to various network-analytic and graph benchmark problems. The results indicate that CGS has competitive capabilities for predicting the stationary properties of graph systems, irrespective of whether the target systems are linear or non-linear. CGS also shows high performance for graph classification problems where the existence or the meaning of a fixed point is hard to be clearly defined, which highlights the potential of CGS as a general graph neural network architecture.

We propose Riemannian Flow Matching (RFM), a simple yet powerful framework for training continuous normalizing flows on manifolds. Existing methods for generative modeling on manifolds either require expensive simulation, are inherently unable to scale to high dimensions, or use approximations for limiting quantities that result in biased training objectives. Riemannian Flow Matching bypasses these limitations and offers several advantages over previous approaches: it is simulation-free on simple geometries, does not require divergence computation, and computes its target vector field in closed-form. The key ingredient behind RFM is the construction of a relatively simple premetric for defining target vector fields, which encompasses the existing Euclidean case. To extend to general geometries, we rely on the use of spectral decompositions to efficiently compute premetrics on the fly. Our method achieves state-of-the-art performance on many real-world non-Euclidean datasets, and we demonstrate tractable training on general geometries, including triangular meshes with highly non-trivial curvature and boundaries.

We study the implications of the modeling choice to use a graph, instead of a hypergraph, to represent real-world interconnected systems whose constituent relationships are of higher order by nature. Such a modeling choice typically involves an underlying projection process that maps the original hypergraph onto a graph, and is common in graph-based analysis. While hypergraph projection can potentially lead to loss of higher-order relations, there exists very limited studies on the consequences of doing so, as well as its remediation. This work fills this gap by doing two things: (1) we develop analysis based on graph and set theory, showing two ubiquitous patterns of hyperedges that are root to structural information loss in all hypergraph projections; we also quantify the combinatorial impossibility of recovering the lost higher-order structures if no extra help is provided; (2) we still seek to recover the lost higher-order structures in hypergraph projection, and in light of (1)'s findings we propose to relax the problem into a learning-based setting. Under this setting, we develop a learning-based hypergraph reconstruction method based on an important statistic of hyperedge distributions that we find. Our reconstruction method is evaluated on 8 real-world datasets under different settings, and exhibits consistently good performance. We also demonstrate benefits of the reconstructed hypergraphs via use cases of protein rankings and link predictions.

Graph Transformers (GTs) have achieved impressive results on various graph-related tasks. However, the huge computational cost of GTs hinders their deployment and application, especially in resource-constrained environments. Therefore, in this paper, we explore the feasibility of sparsifying GTs, a significant yet under-explored topic. We first discuss the redundancy of GTs based on the characteristics of existing GT models, and then propose a comprehensive Graph Transformer SParsification (GTSP) framework that helps to reduce the computational complexity of GTs from four dimensions: the input graph data, attention heads, model layers, and model weights. Specifically, GTSP designs differentiable masks for each individual compressible component, enabling effective end-to-end pruning. We examine our GTSP through extensive experiments on prominent GTs, including GraphTrans, Graphormer, and GraphGPS. The experimental results substantiate that GTSP effectively cuts computational costs, accompanied by only marginal decreases in accuracy or, in some cases, even improvements. For instance, GTSP yields a reduction of 30\% in Floating Point Operations while contributing to a 1.8\% increase in Area Under the Curve accuracy on OGBG-HIV dataset. Furthermore, we provide several insights on the characteristics of attention heads and the behavior of attention mechanisms, all of which have immense potential to inspire future research endeavors in this domain.

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.

Message passing mechanism contributes to the success of GNNs in various applications, but also brings the oversquashing problem. Recent works combat oversquashing by improving the graph spectrums with rewiring techniques, disrupting the structural bias in graphs, and having limited improvement on oversquashing in terms of oversquashing measure. Motivated by unitary RNN, we propose Graph Unitary Message Passing (GUMP) to alleviate oversquashing in GNNs by applying unitary adjacency matrix for message passing. To design GUMP, a transformation is first proposed to make general graphs have unitary adjacency matrix and keep its structural bias. Then, unitary adjacency matrix is obtained with a unitary projection algorithm, which is implemented by utilizing the intrinsic structure of unitary adjacency matrix and allows GUMP to be permutation-equivariant. Experimental results show the effectiveness of GUMP in improving the performance on various graph learning tasks.

In this work we develop a new method, named Sub-graph Permutation Equivariant Networks (SPEN), which provides a framework for building graph neural networks that operate on sub-graphs, while using a base update function that is permutation equivariant, that are equivariant to a novel choice of automorphism group. Message passing neural networks have been shown to be limited in their expressive power and recent approaches to over come this either lack scalability or require structural information to be encoded into the feature space. The general framework presented here overcomes the scalability issues associated with global permutation equivariance by operating more locally on sub-graphs. In addition, through operating on sub-graphs the expressive power of higher-dimensional global permutation equivariant networks is improved; this is due to fact that two non-distinguishable graphs often contain distinguishable sub-graphs. Furthermore, the proposed framework only requires a choice of k-hops for creating ego-network sub-graphs and a choice of representation space to be used for each layer, which makes the method easily applicable across a range of graph based domains. We experimentally validate the method on a range of graph benchmark classification tasks, demonstrating statistically indistinguishable results from the state-of-the-art on six out of seven benchmarks. Further, we demonstrate that the use of local update functions offers a significant improvement in GPU memory over global methods.

Many graph representation learning (GRL) problems are dynamic, with millions of edges added or removed per second. A fundamental workload in this setting is dynamic link prediction: using a history of graph updates to predict whether a given pair of vertices will become connected. Recent schemes for link prediction in such dynamic settings employ Transformers, modeling individual graph updates as single tokens. In this work, we propose HOT: a model that enhances this line of works by harnessing higher-order (HO) graph structures; specifically, k-hop neighbors and more general subgraphs containing a given pair of vertices. Harnessing such HO structures by encoding them into the attention matrix of the underlying Transformer results in higher accuracy of link prediction outcomes, but at the expense of increased memory pressure. To alleviate this, we resort to a recent class of schemes that impose hierarchy on the attention matrix, significantly reducing memory footprint. The final design offers a sweetspot between high accuracy and low memory utilization. HOT outperforms other dynamic GRL schemes, for example achieving 9%, 7%, and 15% higher accuracy than - respectively - DyGFormer, TGN, and GraphMixer, for the MOOC dataset. Our design can be seamlessly extended towards other dynamic GRL workloads.

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

During early optimization passes, compilers must make predictions for machine-dependent characteristics such as execution unit utilization, number of register spills, latency, throughput etc. to generate better code. Often a hand-written static/analytical hardware cost model is built into the compiler. However, the need for more sophisticated and varied predictions has become more pronounced with the development of deep learning compilers which need to optimize dataflow graphs. Such compilers usually employ a much higher level MLIR form as an IR representation before lowering to traditional LLVM-IR. A static/analytical cost model in such a scenario is cumbersome and error prone as the opcodes represent very high level algebraic/arithmetic operations. Hence, we develop a machine learning-based cost model for high-level MLIR which can predict different target variables of interest such as CPU/GPU/xPU utilization, instructions executed, register usage etc. By considering the incoming MLIR as a text input a la NLP models we can apply well-known techniques from modern NLP research to help predict hardware characteristics more accurately. We expect such precise ML-driven hardware cost models to guide our deep learning compiler in graph level optimizations around operator fusion, local memory allocation, kernel scheduling etc. as well as in many kernel-level optimizations such as loop interchange, LICM and unroll. We report early work-in -progress results of developing such models on high-level MLIR representing dataflow graphs emitted by Pytorch/Tensorflow-like frameworks as well as lower-level dialects like affine. We show that these models can provide reasonably good estimates with low error bounds for various hardware characteristics of interest and can be a go-to mechanism for hardware cost modelling in the future.

CNNs achieve remarkable performance by leveraging deep, over-parametrized architectures, trained on large datasets. However, they have limited generalization ability to data outside the training domain, and a lack of robustness to noise and adversarial attacks. By building better inductive biases, we can improve robustness and also obtain smaller networks that are more memory and computationally efficient. While standard CNNs use matrix computations, we study tensor layers that involve higher-order computations and provide better inductive bias. Specifically, we impose low-rank tensor structures on the weights of tensor regression layers to obtain compact networks, and propose tensor dropout, a randomization in the tensor rank for robustness. We show that our approach outperforms other methods for large-scale image classification on ImageNet and CIFAR-100. We establish a new state-of-the-art accuracy for phenotypic trait prediction on the largest dataset of brain MRI, the UK Biobank brain MRI dataset, where multi-linear structure is paramount. In all cases, we demonstrate superior performance and significantly improved robustness, both to noisy inputs and to adversarial attacks. We rigorously validate the theoretical validity of our approach by establishing the link between our randomized decomposition and non-linear dropout.

Graph Neural Networks (GNNs) have demonstrated superior performance on various graph learning tasks, including recommendation, where they leverage user-item collaborative filtering signals in graphs. However, theoretical formulations of their capability are scarce, despite their empirical effectiveness in state-of-the-art recommender models. Recently, research has explored the expressiveness of GNNs in general, demonstrating that message passing GNNs are at most as powerful as the Weisfeiler-Lehman test, and that GNNs combined with random node initialization are universal. Nevertheless, the concept of "expressiveness" for GNNs remains vaguely defined. Most existing works adopt the graph isomorphism test as the metric of expressiveness, but this graph-level task may not effectively assess a model's ability in recommendation, where the objective is to distinguish nodes of different closeness. In this paper, we provide a comprehensive theoretical analysis of the expressiveness of GNNs in recommendation, considering three levels of expressiveness metrics: graph isomorphism (graph-level), node automorphism (node-level), and topological closeness (link-level). We propose the topological closeness metric to evaluate GNNs' ability to capture the structural distance between nodes, which aligns closely with the objective of recommendation. To validate the effectiveness of this new metric in evaluating recommendation performance, we introduce a learning-less GNN algorithm that is optimal on the new metric and can be optimal on the node-level metric with suitable modification. We conduct extensive experiments comparing the proposed algorithm against various types of state-of-the-art GNN models to explore the explainability of the new metric in the recommendation task. For reproducibility, implementation codes are available at https://github.com/HKUDS/GTE.

Recently proposed Graph Neural Networks (GNNs) for vertex clustering are trained with an unsupervised minimum cut objective, approximated by a Spectral Clustering (SC) relaxation. However, the SC relaxation is loose and, while it offers a closed-form solution, it also yields overly smooth cluster assignments that poorly separate the vertices. In this paper, we propose a GNN model that computes cluster assignments by optimizing a tighter relaxation of the minimum cut based on graph total variation (GTV). The cluster assignments can be used directly to perform vertex clustering or to implement graph pooling in a graph classification framework. Our model consists of two core components: i) a message-passing layer that minimizes the ell_1 distance in the features of adjacent vertices, which is key to achieving sharp transitions between clusters; ii) an unsupervised loss function that minimizes the GTV of the cluster assignments while ensuring balanced partitions. Experimental results show that our model outperforms other GNNs for vertex clustering and graph classification.

In the graph node embedding problem, embedding spaces can vary significantly for different data types, leading to the need for different GNN model types. In this paper, we model the embedding update of a node feature as a Hamiltonian orbit over time. Since the Hamiltonian orbits generalize the exponential maps, this approach allows us to learn the underlying manifold of the graph in training, in contrast to most of the existing literature that assumes a fixed graph embedding manifold with a closed exponential map solution. Our proposed node embedding strategy can automatically learn, without extensive tuning, the underlying geometry of any given graph dataset even if it has diverse geometries. We test Hamiltonian functions of different forms and verify the performance of our approach on two graph node embedding downstream tasks: node classification and link prediction. Numerical experiments demonstrate that our approach adapts better to different types of graph datasets than popular state-of-the-art graph node embedding GNNs. The code is available at https://github.com/zknus/Hamiltonian-GNN.

Graph neural networks (GNNs) emerged recently as a standard toolkit for learning from data on graphs. Current GNN designing works depend on immense human expertise to explore different message-passing mechanisms, and require manual enumeration to determine the proper message-passing depth. Inspired by the strong searching capability of neural architecture search (NAS) in CNN, this paper proposes Graph Neural Architecture Search (GNAS) with novel-designed search space. The GNAS can automatically learn better architecture with the optimal depth of message passing on the graph. Specifically, we design Graph Neural Architecture Paradigm (GAP) with tree-topology computation procedure and two types of fine-grained atomic operations (feature filtering and neighbor aggregation) from message-passing mechanism to construct powerful graph network search space. Feature filtering performs adaptive feature selection, and neighbor aggregation captures structural information and calculates neighbors' statistics. Experiments show that our GNAS can search for better GNNs with multiple message-passing mechanisms and optimal message-passing depth. The searched network achieves remarkable improvement over state-of-the-art manual designed and search-based GNNs on five large-scale datasets at three classical graph tasks. Codes can be found at https://github.com/phython96/GNAS-MP.

Recently, many works studied the expressive power of graph neural networks (GNNs) by linking it to the 1-dimensional Weisfeiler--Leman algorithm (1-WL). Here, the 1-WL is a well-studied heuristic for the graph isomorphism problem, which iteratively colors or partitions a graph's vertex set. While this connection has led to significant advances in understanding and enhancing GNNs' expressive power, it does not provide insights into their generalization performance, i.e., their ability to make meaningful predictions beyond the training set. In this paper, we study GNNs' generalization ability through the lens of Vapnik--Chervonenkis (VC) dimension theory in two settings, focusing on graph-level predictions. First, when no upper bound on the graphs' order is known, we show that the bitlength of GNNs' weights tightly bounds their VC dimension. Further, we derive an upper bound for GNNs' VC dimension using the number of colors produced by the 1-WL. Secondly, when an upper bound on the graphs' order is known, we show a tight connection between the number of graphs distinguishable by the 1-WL and GNNs' VC dimension. Our empirical study confirms the validity of our theoretical findings.

Machine learning frameworks such as graph neural networks typically rely on a given, fixed graph to exploit relational inductive biases and thus effectively learn from network data. However, when said graphs are (partially) unobserved, noisy, or dynamic, the problem of inferring graph structure from data becomes relevant. In this paper, we postulate a graph convolutional relationship between the observed and latent graphs, and formulate the graph learning task as a network inverse (deconvolution) problem. In lieu of eigendecomposition-based spectral methods or iterative optimization solutions, we unroll and truncate proximal gradient iterations to arrive at a parameterized neural network architecture that we call a Graph Deconvolution Network (GDN). GDNs can learn a distribution of graphs in a supervised fashion, perform link prediction or edge-weight regression tasks by adapting the loss function, and they are inherently inductive. We corroborate GDN's superior graph recovery performance and its generalization to larger graphs using synthetic data in supervised settings. Furthermore, we demonstrate the robustness and representation power of GDNs on real world neuroimaging and social network datasets.