Daily Papers

Structured representations like graphs and parse trees play a crucial role in many Natural Language Processing systems. In recent years, the advancements in multi-turn user interfaces necessitate the need for controlling and updating these structured representations given new sources of information. Although there have been many efforts focusing on improving the performance of the parsers that map text to graphs or parse trees, very few have explored the problem of directly manipulating these representations. In this paper, we explore the novel problem of graph modification, where the systems need to learn how to update an existing scene graph given a new user's command. Our novel models based on graph-based sparse transformer and cross attention information fusion outperform previous systems adapted from the machine translation and graph generation literature. We further contribute our large graph modification datasets to the research community to encourage future research for this new problem.

Graph transformers have emerged as a promising architecture for a variety of graph learning and representation tasks. Despite their successes, though, it remains challenging to scale graph transformers to large graphs while maintaining accuracy competitive with message-passing networks. In this paper, we introduce Exphormer, a framework for building powerful and scalable graph transformers. Exphormer consists of a sparse attention mechanism based on two mechanisms: virtual global nodes and expander graphs, whose mathematical characteristics, such as spectral expansion, pseduorandomness, and sparsity, yield graph transformers with complexity only linear in the size of the graph, while allowing us to prove desirable theoretical properties of the resulting transformer models. We show that incorporating Exphormer into the recently-proposed GraphGPS framework produces models with competitive empirical results on a wide variety of graph datasets, including state-of-the-art results on three datasets. We also show that Exphormer can scale to datasets on larger graphs than shown in previous graph transformer architectures. Code can be found at https://github.com/hamed1375/Exphormer.

Graph Neural Networks (GNNs) that are based on the message passing (MP) paradigm generally exchange information between 1-hop neighbors to build node representations at each layer. In principle, such networks are not able to capture long-range interactions (LRI) that may be desired or necessary for learning a given task on graphs. Recently, there has been an increasing interest in development of Transformer-based methods for graphs that can consider full node connectivity beyond the original sparse structure, thus enabling the modeling of LRI. However, MP-GNNs that simply rely on 1-hop message passing often fare better in several existing graph benchmarks when combined with positional feature representations, among other innovations, hence limiting the perceived utility and ranking of Transformer-like architectures. Here, we present the Long Range Graph Benchmark (LRGB) with 5 graph learning datasets: PascalVOC-SP, COCO-SP, PCQM-Contact, Peptides-func and Peptides-struct that arguably require LRI reasoning to achieve strong performance in a given task. We benchmark both baseline GNNs and Graph Transformer networks to verify that the models which capture long-range dependencies perform significantly better on these tasks. Therefore, these datasets are suitable for benchmarking and exploration of MP-GNNs and Graph Transformer architectures that are intended to capture LRI.

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.

We propose a recipe on how to build a general, powerful, scalable (GPS) graph Transformer with linear complexity and state-of-the-art results on a diverse set of benchmarks. Graph Transformers (GTs) have gained popularity in the field of graph representation learning with a variety of recent publications but they lack a common foundation about what constitutes a good positional or structural encoding, and what differentiates them. In this paper, we summarize the different types of encodings with a clearer definition and categorize them as being local, global or relative. The prior GTs are constrained to small graphs with a few hundred nodes, here we propose the first architecture with a complexity linear in the number of nodes and edges O(N+E) by decoupling the local real-edge aggregation from the fully-connected Transformer. We argue that this decoupling does not negatively affect the expressivity, with our architecture being a universal function approximator on graphs. Our GPS recipe consists of choosing 3 main ingredients: (i) positional/structural encoding, (ii) local message-passing mechanism, and (iii) global attention mechanism. We provide a modular framework GraphGPS that supports multiple types of encodings and that provides efficiency and scalability both in small and large graphs. We test our architecture on 16 benchmarks and show highly competitive results in all of them, show-casing the empirical benefits gained by the modularity and the combination of different strategies.

We present an approach to modifying Transformer architectures by integrating graph-aware relational reasoning into the attention mechanism, merging concepts from graph neural networks and language modeling. Building on the inherent connection between attention and graph theory, we reformulate the Transformer's attention mechanism as a graph operation and propose Graph-Aware Isomorphic Attention. This method leverages advanced graph modeling strategies, including Graph Isomorphism Networks (GIN) and Principal Neighborhood Aggregation (PNA), to enrich the representation of relational structures. Our approach captures complex dependencies and generalizes across tasks, as evidenced by a reduced generalization gap and improved learning performance. Additionally, we expand the concept of graph-aware attention to introduce Sparse GIN-Attention, a fine-tuning approach that employs sparse GINs. By interpreting attention matrices as sparse adjacency graphs, this technique enhances the adaptability of pre-trained foundational models with minimal computational overhead, endowing them with graph-aware capabilities. Sparse GIN-Attention fine-tuning achieves improved training dynamics and better generalization compared to alternative methods like low-rank adaption (LoRA). We discuss latent graph-like structures within traditional attention mechanisms, offering a new lens through which Transformers can be understood. By evolving Transformers as hierarchical GIN models for relational reasoning. This perspective suggests profound implications for foundational model development, enabling the design of architectures that dynamically adapt to both local and global dependencies. Applications in bioinformatics, materials science, language modeling, and beyond could benefit from this synthesis of relational and sequential data modeling, setting the stage for interpretable and generalizable modeling strategies.

The Transformer architecture has become a dominant choice in many domains, such as natural language processing and computer vision. Yet, it has not achieved competitive performance on popular leaderboards of graph-level prediction compared to mainstream GNN variants. Therefore, it remains a mystery how Transformers could perform well for graph representation learning. In this paper, we solve this mystery by presenting Graphormer, which is built upon the standard Transformer architecture, and could attain excellent results on a broad range of graph representation learning tasks, especially on the recent OGB Large-Scale Challenge. Our key insight to utilizing Transformer in the graph is the necessity of effectively encoding the structural information of a graph into the model. To this end, we propose several simple yet effective structural encoding methods to help Graphormer better model graph-structured data. Besides, we mathematically characterize the expressive power of Graphormer and exhibit that with our ways of encoding the structural information of graphs, many popular GNN variants could be covered as the special cases of Graphormer.

Utilizing pre-trained language models has achieved great success for neural document ranking. Limited by the computational and memory requirements, long document modeling becomes a critical issue. Recent works propose to modify the full attention matrix in Transformer by designing sparse attention patterns. However, most of them only focus on local connections of terms within a fixed-size window. How to build suitable remote connections between terms to better model document representation remains underexplored. In this paper, we propose the model Socialformer, which introduces the characteristics of social networks into designing sparse attention patterns for long document modeling in document ranking. Specifically, we consider several attention patterns to construct a graph like social networks. Endowed with the characteristic of social networks, most pairs of nodes in such a graph can reach with a short path while ensuring the sparsity. To facilitate efficient calculation, we segment the graph into multiple subgraphs to simulate friend circles in social scenarios. Experimental results confirm the effectiveness of our model on long document modeling.

We propose a generalization of transformer neural network architecture for arbitrary graphs. The original transformer was designed for Natural Language Processing (NLP), which operates on fully connected graphs representing all connections between the words in a sequence. Such architecture does not leverage the graph connectivity inductive bias, and can perform poorly when the graph topology is important and has not been encoded into the node features. We introduce a graph transformer with four new properties compared to the standard model. First, the attention mechanism is a function of the neighborhood connectivity for each node in the graph. Second, the positional encoding is represented by the Laplacian eigenvectors, which naturally generalize the sinusoidal positional encodings often used in NLP. Third, the layer normalization is replaced by a batch normalization layer, which provides faster training and better generalization performance. Finally, the architecture is extended to edge feature representation, which can be critical to tasks s.a. chemistry (bond type) or link prediction (entity relationship in knowledge graphs). Numerical experiments on a graph benchmark demonstrate the performance of the proposed graph transformer architecture. This work closes the gap between the original transformer, which was designed for the limited case of line graphs, and graph neural networks, that can work with arbitrary graphs. As our architecture is simple and generic, we believe it can be used as a black box for future applications that wish to consider transformer and graphs.

Transformers have recently emerged as powerful neural networks for graph learning, showcasing state-of-the-art performance on several graph property prediction tasks. However, these results have been limited to small-scale graphs, where the computational feasibility of the global attention mechanism is possible. The next goal is to scale up these architectures to handle very large graphs on the scale of millions or even billions of nodes. With large-scale graphs, global attention learning is proven impractical due to its quadratic complexity w.r.t. the number of nodes. On the other hand, neighborhood sampling techniques become essential to manage large graph sizes, yet finding the optimal trade-off between speed and accuracy with sampling techniques remains challenging. This work advances representation learning on single large-scale graphs with a focus on identifying model characteristics and critical design constraints for developing scalable graph transformer (GT) architectures. We argue such GT requires layers that can adeptly learn both local and global graph representations while swiftly sampling the graph topology. As such, a key innovation of this work lies in the creation of a fast neighborhood sampling technique coupled with a local attention mechanism that encompasses a 4-hop reception field, but achieved through just 2-hop operations. This local node embedding is then integrated with a global node embedding, acquired via another self-attention layer with an approximate global codebook, before finally sent through a downstream layer for node predictions. The proposed GT framework, named LargeGT, overcomes previous computational bottlenecks and is validated on three large-scale node classification benchmarks. We report a 3x speedup and 16.8% performance gain on ogbn-products and snap-patents, while we also scale LargeGT on ogbn-papers100M with a 5.9% performance improvement.

We consider the problem of computing the Walsh-Hadamard Transform (WHT) of some N-length input vector in the presence of noise, where the N-point Walsh spectrum is K-sparse with K = {O}(N^{delta}) scaling sub-linearly in the input dimension N for some 0<delta<1. Over the past decade, there has been a resurgence in research related to the computation of Discrete Fourier Transform (DFT) for some length-N input signal that has a K-sparse Fourier spectrum. In particular, through a sparse-graph code design, our earlier work on the Fast Fourier Aliasing-based Sparse Transform (FFAST) algorithm computes the K-sparse DFT in time {O}(Klog K) by taking {O}(K) noiseless samples. Inspired by the coding-theoretic design framework, Scheibler et al. proposed the Sparse Fast Hadamard Transform (SparseFHT) algorithm that elegantly computes the K-sparse WHT in the absence of noise using {O}(Klog N) samples in time {O}(Klog^2 N). However, the SparseFHT algorithm explicitly exploits the noiseless nature of the problem, and is not equipped to deal with scenarios where the observations are corrupted by noise. Therefore, a question of critical interest is whether this coding-theoretic framework can be made robust to noise. Further, if the answer is yes, what is the extra price that needs to be paid for being robust to noise? In this paper, we show, quite interestingly, that there is {\it no extra price} that needs to be paid for being robust to noise other than a constant factor. In other words, we can maintain the same sample complexity {O}(Klog N) and the computational complexity {O}(Klog^2 N) as those of the noiseless case, using our SParse Robust Iterative Graph-based Hadamard Transform (SPRIGHT) algorithm.

Despite that going deep has proven successful in many neural architectures, the existing graph transformers are relatively shallow. In this work, we explore whether more layers are beneficial to graph transformers, and find that current graph transformers suffer from the bottleneck of improving performance by increasing depth. Our further analysis reveals the reason is that deep graph transformers are limited by the vanishing capacity of global attention, restricting the graph transformer from focusing on the critical substructure and obtaining expressive features. To this end, we propose a novel graph transformer model named DeepGraph that explicitly employs substructure tokens in the encoded representation, and applies local attention on related nodes to obtain substructure based attention encoding. Our model enhances the ability of the global attention to focus on substructures and promotes the expressiveness of the representations, addressing the limitation of self-attention as the graph transformer deepens. Experiments show that our method unblocks the depth limitation of graph transformers and results in state-of-the-art performance across various graph benchmarks with deeper models.

Graph Transformer (GT) recently has emerged as a new paradigm of graph learning algorithms, outperforming the previously popular Message Passing Neural Network (MPNN) on multiple benchmarks. Previous work (Kim et al., 2022) shows that with proper position embedding, GT can approximate MPNN arbitrarily well, implying that GT is at least as powerful as MPNN. In this paper, we study the inverse connection and show that MPNN with virtual node (VN), a commonly used heuristic with little theoretical understanding, is powerful enough to arbitrarily approximate the self-attention layer of GT. In particular, we first show that if we consider one type of linear transformer, the so-called Performer/Linear Transformer (Choromanski et al., 2020; Katharopoulos et al., 2020), then MPNN + VN with only O(1) depth and O(1) width can approximate a self-attention layer in Performer/Linear Transformer. Next, via a connection between MPNN + VN and DeepSets, we prove the MPNN + VN with O(n^d) width and O(1) depth can approximate the self-attention layer arbitrarily well, where d is the input feature dimension. Lastly, under some assumptions, we provide an explicit construction of MPNN + VN with O(1) width and O(n) depth approximating the self-attention layer in GT arbitrarily well. On the empirical side, we demonstrate that 1) MPNN + VN is a surprisingly strong baseline, outperforming GT on the recently proposed Long Range Graph Benchmark (LRGB) dataset, 2) our MPNN + VN improves over early implementation on a wide range of OGB datasets and 3) MPNN + VN outperforms Linear Transformer and MPNN on the climate modeling task.

Transformers were originally proposed as a sequence-to-sequence model for text but have become vital for a wide range of modalities, including images, audio, video, and undirected graphs. However, transformers for directed graphs are a surprisingly underexplored topic, despite their applicability to ubiquitous domains including source code and logic circuits. In this work, we propose two direction- and structure-aware positional encodings for directed graphs: (1) the eigenvectors of the Magnetic Laplacian - a direction-aware generalization of the combinatorial Laplacian; (2) directional random walk encodings. Empirically, we show that the extra directionality information is useful in various downstream tasks, including correctness testing of sorting networks and source code understanding. Together with a data-flow-centric graph construction, our model outperforms the prior state of the art on the Open Graph Benchmark Code2 relatively by 14.7%.

Transformers for graph data are increasingly widely studied and successful in numerous learning tasks. Graph inductive biases are crucial for Graph Transformers, and previous works incorporate them using message-passing modules and/or positional encodings. However, Graph Transformers that use message-passing inherit known issues of message-passing, and differ significantly from Transformers used in other domains, thus making transfer of research advances more difficult. On the other hand, Graph Transformers without message-passing often perform poorly on smaller datasets, where inductive biases are more crucial. To bridge this gap, we propose the Graph Inductive bias Transformer (GRIT) -- a new Graph Transformer that incorporates graph inductive biases without using message passing. GRIT is based on several architectural changes that are each theoretically and empirically justified, including: learned relative positional encodings initialized with random walk probabilities, a flexible attention mechanism that updates node and node-pair representations, and injection of degree information in each layer. We prove that GRIT is expressive -- it can express shortest path distances and various graph propagation matrices. GRIT achieves state-of-the-art empirical performance across a variety of graph datasets, thus showing the power that Graph Transformers without message-passing can deliver.

Graph learning has become indispensable for interpreting and harnessing relational data in diverse fields, ranging from recommendation systems to social network analysis. In this context, a variety of GNNs have emerged as promising methodologies for encoding the structural information of graphs. By effectively capturing the graph's underlying structure, these GNNs have shown great potential in enhancing performance in graph learning tasks, such as link prediction and node classification. However, despite their successes, a significant challenge persists: these advanced methods often face difficulties in generalizing to unseen graph data that significantly differs from the training instances. In this work, our aim is to advance the graph learning paradigm by developing a general graph foundation model. This model is designed to understand the complex topological patterns present in diverse graph data, enabling it to excel in zero-shot graph learning tasks across different downstream datasets. To achieve this goal, we address several key technical challenges in our OpenGraph model. Firstly, we propose a unified graph tokenizer to adapt our graph model to generalize well on unseen graph data, even when the underlying graph properties differ significantly from those encountered during training. Secondly, we develop a scalable graph transformer as the foundational encoder, which effectively captures node-wise dependencies within the global topological context. Thirdly, we introduce a data augmentation mechanism enhanced by a LLM to alleviate the limitations of data scarcity in real-world scenarios. Extensive experiments validate the effectiveness of our framework. By adapting our OpenGraph to new graph characteristics and comprehending the nuances of diverse graphs, our approach achieves remarkable zero-shot graph learning performance across various settings and domains.

Transformers are powerful sequence models, but require time and memory that grows quadratically with the sequence length. In this paper we introduce sparse factorizations of the attention matrix which reduce this to O(n n). We also introduce a) a variation on architecture and initialization to train deeper networks, b) the recomputation of attention matrices to save memory, and c) fast attention kernels for training. We call networks with these changes Sparse Transformers, and show they can model sequences tens of thousands of timesteps long using hundreds of layers. We use the same architecture to model images, audio, and text from raw bytes, setting a new state of the art for density modeling of Enwik8, CIFAR-10, and ImageNet-64. We generate unconditional samples that demonstrate global coherence and great diversity, and show it is possible in principle to use self-attention to model sequences of length one million or more.

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

Transformers provide a class of expressive architectures that are extremely effective for sequence modeling. However, the key limitation of transformers is their quadratic memory and time complexity O(L^2) with respect to the sequence length in attention layers, which restricts application in extremely long sequences. Most existing approaches leverage sparsity or low-rank assumptions in the attention matrix to reduce cost, but sacrifice expressiveness. Instead, we propose Combiner, which provides full attention capability in each attention head while maintaining low computation and memory complexity. The key idea is to treat the self-attention mechanism as a conditional expectation over embeddings at each location, and approximate the conditional distribution with a structured factorization. Each location can attend to all other locations, either via direct attention, or through indirect attention to abstractions, which are again conditional expectations of embeddings from corresponding local regions. We show that most sparse attention patterns used in existing sparse transformers are able to inspire the design of such factorization for full attention, resulting in the same sub-quadratic cost (O(Llog(L)) or O(LL)). Combiner is a drop-in replacement for attention layers in existing transformers and can be easily implemented in common frameworks. An experimental evaluation on both autoregressive and bidirectional sequence tasks demonstrates the effectiveness of this approach, yielding state-of-the-art results on several image and text modeling tasks.

Human visual recognition is a sparse process, where only a few salient visual cues are attended to rather than traversing every detail uniformly. However, most current vision networks follow a dense paradigm, processing every single visual unit (e.g,, pixel or patch) in a uniform manner. In this paper, we challenge this dense paradigm and present a new method, coined SparseFormer, to imitate human's sparse visual recognition in an end-to-end manner. SparseFormer learns to represent images using a highly limited number of tokens (down to 49) in the latent space with sparse feature sampling procedure instead of processing dense units in the original pixel space. Therefore, SparseFormer circumvents most of dense operations on the image space and has much lower computational costs. Experiments on the ImageNet classification benchmark dataset show that SparseFormer achieves performance on par with canonical or well-established models while offering better accuracy-throughput tradeoff. Moreover, the design of our network can be easily extended to the video classification with promising performance at lower computational costs. We hope that our work can provide an alternative way for visual modeling and inspire further research on sparse neural architectures. The code will be publicly available at https://github.com/showlab/sparseformer

Sparse attention offers a promising strategy to extend long-context capabilities in Transformer LLMs, yet its viability, its efficiency-accuracy trade-offs, and systematic scaling studies remain unexplored. To address this gap, we perform a careful comparison of training-free sparse attention methods at varying model scales, sequence lengths, and sparsity levels on a diverse collection of long-sequence tasks-including novel ones that rely on natural language while remaining controllable and easy to evaluate. Based on our experiments, we report a series of key findings: 1) an isoFLOPS analysis reveals that for very long sequences, larger and highly sparse models are preferable to smaller and dense ones. 2) The level of sparsity attainable while statistically guaranteeing accuracy preservation is higher during decoding than prefilling, and correlates with model size in the former. 3) There is no clear strategy that performs best across tasks and phases, with different units of sparsification or budget adaptivity needed for different scenarios. Even moderate sparsity levels often result in significant performance degradation on at least one task, highlighting that sparse attention is not a universal solution. 4) We introduce and validate novel scaling laws specifically tailored for sparse attention, providing evidence that our findings are likely to hold true beyond our range of experiments. Through these insights, we demonstrate that sparse attention is a key tool to enhance the capabilities of Transformer LLMs for processing longer sequences, but requires careful evaluation of trade-offs for performance-sensitive applications.

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.

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.

Graph transformers (GTs) have emerged as a promising architecture that is theoretically more expressive than message-passing graph neural networks (GNNs). However, typical GT models have at least quadratic complexity and thus cannot scale to large graphs. While there are several linear GTs recently proposed, they still lag behind GNN counterparts on several popular graph datasets, which poses a critical concern on their practical expressivity. To balance the trade-off between expressivity and scalability of GTs, we propose Polynormer, a polynomial-expressive GT model with linear complexity. Polynormer is built upon a novel base model that learns a high-degree polynomial on input features. To enable the base model permutation equivariant, we integrate it with graph topology and node features separately, resulting in local and global equivariant attention models. Consequently, Polynormer adopts a linear local-to-global attention scheme to learn high-degree equivariant polynomials whose coefficients are controlled by attention scores. Polynormer has been evaluated on 13 homophilic and heterophilic datasets, including large graphs with millions of nodes. Our extensive experiment results show that Polynormer outperforms state-of-the-art GNN and GT baselines on most datasets, even without the use of nonlinear activation functions.

Search is an ability foundational in many important tasks, and recent studies have shown that large language models (LLMs) struggle to perform search robustly. It is unknown whether this inability is due to a lack of data, insufficient model parameters, or fundamental limitations of the transformer architecture. In this work, we use the foundational graph connectivity problem as a testbed to generate effectively limitless high-coverage data to train small transformers and test whether they can learn to perform search. We find that, when given the right training distribution, the transformer is able to learn to search. We analyze the algorithm that the transformer has learned through a novel mechanistic interpretability technique that enables us to extract the computation graph from the trained model. We find that for each vertex in the input graph, transformers compute the set of vertices reachable from that vertex. Each layer then progressively expands these sets, allowing the model to search over a number of vertices exponential in the number of layers. However, we find that as the input graph size increases, the transformer has greater difficulty in learning the task. This difficulty is not resolved even as the number of parameters is increased, suggesting that increasing model scale will not lead to robust search abilities. We also find that performing search in-context (i.e., chain-of-thought) does not resolve this inability to learn to search on larger graphs.

In this paper, we propose the Hierarchical Document Transformer (HDT), a novel sparse Transformer architecture tailored for structured hierarchical documents. Such documents are extremely important in numerous domains, including science, law or medicine. However, most existing solutions are inefficient and fail to make use of the structure inherent to documents. HDT exploits document structure by introducing auxiliary anchor tokens and redesigning the attention mechanism into a sparse multi-level hierarchy. This approach facilitates information exchange between tokens at different levels while maintaining sparsity, thereby enhancing computational and memory efficiency while exploiting the document structure as an inductive bias. We address the technical challenge of implementing HDT's sample-dependent hierarchical attention pattern by developing a novel sparse attention kernel that considers the hierarchical structure of documents. As demonstrated by our experiments, utilizing structural information present in documents leads to faster convergence, higher sample efficiency and better performance on downstream tasks.

Temporal Graph Neural Networks have garnered substantial attention for their capacity to model evolving structural and temporal patterns while exhibiting impressive performance. However, it is known that these architectures are encumbered by issues that constrain their performance, such as over-squashing and over-smoothing. Meanwhile, Transformers have demonstrated exceptional computational capacity to effectively address challenges related to long-range dependencies. Consequently, we introduce Todyformer-a novel Transformer-based neural network tailored for dynamic graphs. It unifies the local encoding capacity of Message-Passing Neural Networks (MPNNs) with the global encoding of Transformers through i) a novel patchifying paradigm for dynamic graphs to improve over-squashing, ii) a structure-aware parametric tokenization strategy leveraging MPNNs, iii) a Transformer with temporal positional-encoding to capture long-range dependencies, and iv) an encoding architecture that alternates between local and global contextualization, mitigating over-smoothing in MPNNs. Experimental evaluations on public benchmark datasets demonstrate that Todyformer consistently outperforms the state-of-the-art methods for downstream tasks. Furthermore, we illustrate the underlying aspects of the proposed model in effectively capturing extensive temporal dependencies in dynamic graphs.

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.

Modern sequence models (e.g., Transformers, linear RNNs, etc.) emerged as dominant backbones of recent deep learning frameworks, mainly due to their efficiency, representational power, and/or ability to capture long-range dependencies. Adopting these sequence models for graph-structured data has recently gained popularity as the alternative to Message Passing Neural Networks (MPNNs). There is, however, a lack of a common foundation about what constitutes a good graph sequence model, and a mathematical description of the benefits and deficiencies in adopting different sequence models for learning on graphs. To this end, we first present Graph Sequence Model (GSM), a unifying framework for adopting sequence models for graphs, consisting of three main steps: (1) Tokenization, which translates the graph into a set of sequences; (2) Local Encoding, which encodes local neighborhoods around each node; and (3) Global Encoding, which employs a scalable sequence model to capture long-range dependencies within the sequences. This framework allows us to understand, evaluate, and compare the power of different sequence model backbones in graph tasks. Our theoretical evaluations of the representation power of Transformers and modern recurrent models through the lens of global and local graph tasks show that there are both negative and positive sides for both types of models. Building on this observation, we present GSM++, a fast hybrid model that uses the Hierarchical Affinity Clustering (HAC) algorithm to tokenize the graph into hierarchical sequences, and then employs a hybrid architecture of Transformer to encode these sequences. Our theoretical and experimental results support the design of GSM++, showing that GSM++ outperforms baselines in most benchmark evaluations.

Which transformer scaling regimes are able to perfectly solve different classes of algorithmic problems? While tremendous empirical advances have been attained by transformer-based neural networks, a theoretical understanding of their algorithmic reasoning capabilities in realistic parameter regimes is lacking. We investigate this question in terms of the network's depth, width, and number of extra tokens for algorithm execution. Our novel representational hierarchy separates 9 algorithmic reasoning problems into classes solvable by transformers in different realistic parameter scaling regimes. We prove that logarithmic depth is necessary and sufficient for tasks like graph connectivity, while single-layer transformers with small embedding dimensions can solve contextual retrieval tasks. We also support our theoretical analysis with ample empirical evidence using the GraphQA benchmark. These results show that transformers excel at many graph reasoning tasks, even outperforming specialized graph neural networks.

We show for the first time that large-scale generative pretrained transformer (GPT) family models can be pruned to at least 50% sparsity in one-shot, without any retraining, at minimal loss of accuracy. This is achieved via a new pruning method called SparseGPT, specifically designed to work efficiently and accurately on massive GPT-family models. We can execute SparseGPT on the largest available open-source models, OPT-175B and BLOOM-176B, in under 4.5 hours, and can reach 60% unstructured sparsity with negligible increase in perplexity: remarkably, more than 100 billion weights from these models can be ignored at inference time. SparseGPT generalizes to semi-structured (2:4 and 4:8) patterns, and is compatible with weight quantization approaches. The code is available at: https://github.com/IST-DASLab/sparsegpt.

In the field of deep learning, Graph Neural Networks (GNNs) and Graph Transformer models, with their outstanding performance and flexible architectural designs, have become leading technologies for processing structured data, especially graph data. Traditional GNNs often face challenges in capturing information from distant vertices effectively. In contrast, Graph Transformer models are particularly adept at managing long-distance node relationships. Despite these advantages, Graph Transformer models still encounter issues with computational and storage efficiency when scaled to large graph datasets. To address these challenges, we propose an innovative Graph Neural Network (GNN) architecture that integrates a Top-m attention mechanism aggregation component and a neighborhood aggregation component, effectively enhancing the model's ability to aggregate relevant information from both local and extended neighborhoods at each layer. This method not only improves computational efficiency but also enriches the node features, facilitating a deeper analysis of complex graph structures. Additionally, to assess the effectiveness of our proposed model, we have applied it to citation sentiment prediction, a novel task previously unexplored in the GNN field. Accordingly, we constructed a dedicated citation network, ArXivNet. In this dataset, we specifically annotated the sentiment polarity of the citations (positive, neutral, negative) to enable in-depth sentiment analysis. Our approach has shown superior performance across a variety of tasks including vertex classification, link prediction, sentiment prediction, graph regression, and visualization. It outperforms existing methods in terms of effectiveness, as demonstrated by experimental results on multiple datasets.

We propose DyGFormer, a new Transformer-based architecture for dynamic graph learning. DyGFormer is conceptually simple and only needs to learn from nodes' historical first-hop interactions by: (1) a neighbor co-occurrence encoding scheme that explores the correlations of the source node and destination node based on their historical sequences; (2) a patching technique that divides each sequence into multiple patches and feeds them to Transformer, allowing the model to effectively and efficiently benefit from longer histories. We also introduce DyGLib, a unified library with standard training pipelines, extensible coding interfaces, and comprehensive evaluating protocols to promote reproducible, scalable, and credible dynamic graph learning research. By performing exhaustive experiments on thirteen datasets for dynamic link prediction and dynamic node classification tasks, we find that DyGFormer achieves state-of-the-art performance on most of the datasets, demonstrating its effectiveness in capturing nodes' correlations and long-term temporal dependencies. Moreover, some results of baselines are inconsistent with previous reports, which may be caused by their diverse but less rigorous implementations, showing the importance of DyGLib. All the used resources are publicly available at https://github.com/yule-BUAA/DyGLib.

Large language models have become the cornerstone of natural language processing, but their use comes with substantial costs in terms of compute and memory resources. Sparsification provides a solution to alleviate these resource constraints, and recent works have shown that trained models can be sparsified post-hoc. Existing sparsification techniques face challenges as they need additional data structures and offer constrained speedup with current hardware. In this paper we present SliceGPT, a new post-training sparsification scheme which replaces each weight matrix with a smaller (dense) matrix, reducing the embedding dimension of the network. Through extensive experimentation, we show that SliceGPT can remove up to 25% of the model parameters (including embeddings) for LLAMA2-70B, OPT 66B and Phi-2 models while maintaining 99%, 99% and 90% zero-shot task performance of the dense model respectively. Our sliced models run on fewer GPUs and run faster without any additional code optimization: on 24GB consumer GPUs we reduce the total compute for inference on LLAMA2-70B to 64% of that of the dense model; on 40GB A100 GPUs we reduce it to 66%. We offer a new insight, computational invariance in transformer networks, which enables SliceGPT and we hope it will inspire and enable future avenues to reduce memory and computation demands for pre-trained models. Code is available at: https://github.com/microsoft/TransformerCompression

Transformer-based models dominate NLP tasks like sentiment analysis, machine translation, and claim verification. However, their massive computational demands and lack of interpretability pose challenges for real-world applications requiring efficiency and transparency. In this work, we explore Graph Neural Networks (GNNs) and Hyperbolic Graph Neural Networks (HGNNs) as lightweight yet effective alternatives for Environmental Claim Detection, reframing it as a graph classification problem. We construct dependency parsing graphs to explicitly model syntactic structures, using simple word embeddings (word2vec) for node features with dependency relations encoded as edge features. Our results demonstrate that these graph-based models achieve comparable or superior performance to state-of-the-art transformers while using 30x fewer parameters. This efficiency highlights the potential of structured, interpretable, and computationally efficient graph-based approaches.

Recent advances in Graph Neural Networks (GNNs) and Graph Transformers (GTs) have been driven by innovations in architectures and Positional Encodings (PEs), which are critical for augmenting node features and capturing graph topology. PEs are essential for GTs, where topological information would otherwise be lost without message-passing. However, PEs are often tested alongside novel architectures, making it difficult to isolate their effect on established models. To address this, we present a comprehensive benchmark of PEs in a unified framework that includes both message-passing GNNs and GTs. We also establish theoretical connections between MPNNs and GTs and introduce a sparsified GRIT attention mechanism to examine the influence of global connectivity. Our findings demonstrate that previously untested combinations of GNN architectures and PEs can outperform existing methods and offer a more comprehensive picture of the state-of-the-art. To support future research and experimentation in our framework, we make the code publicly available.

We introduce GRM, a large-scale reconstructor capable of recovering a 3D asset from sparse-view images in around 0.1s. GRM is a feed-forward transformer-based model that efficiently incorporates multi-view information to translate the input pixels into pixel-aligned Gaussians, which are unprojected to create a set of densely distributed 3D Gaussians representing a scene. Together, our transformer architecture and the use of 3D Gaussians unlock a scalable and efficient reconstruction framework. Extensive experimental results demonstrate the superiority of our method over alternatives regarding both reconstruction quality and efficiency. We also showcase the potential of GRM in generative tasks, i.e., text-to-3D and image-to-3D, by integrating it with existing multi-view diffusion models. Our project website is at: https://justimyhxu.github.io/projects/grm/.

Transformer-based large language models (e.g., BERT and GPT) achieve great success, and fine-tuning, which tunes a pre-trained model on a task-specific dataset, is the standard practice to utilize these models for downstream tasks. However, Transformer fine-tuning has long running time and high memory consumption due to the large size of the models. We propose the SPT system to fine-tune Transformer-based models efficiently by introducing sparsity. We observe that the memory consumption of Transformer mainly comes from storing attention weights for multi-head attention (MHA), and the majority of running time is spent on feed-forward network (FFN). Thus, we design the sparse MHA module, which computes and stores only large attention weights to reduce memory consumption, and the routed FFN module, which dynamically activates a subset of model parameters for each token to reduce computation cost. We implement SPT on PyTorch and customize CUDA kernels to run sparse MHA and routed FFN efficiently. Specifically, we use product quantization to identify the large attention weights and compute attention via sparse matrix multiplication for sparse MHA. For routed FFN, we batch the tokens according to their activated model parameters for efficient computation. We conduct extensive experiments to evaluate SPT on various model configurations. The results show that SPT consistently outperforms well-optimized baselines, reducing the peak memory consumption by up to 50% and accelerating fine-tuning by up to 2.2x.

Attention mechanisms have become ubiquitous in NLP. Recent architectures, notably the Transformer, learn powerful context-aware word representations through layered, multi-headed attention. The multiple heads learn diverse types of word relationships. However, with standard softmax attention, all attention heads are dense, assigning a non-zero weight to all context words. In this work, we introduce the adaptively sparse Transformer, wherein attention heads have flexible, context-dependent sparsity patterns. This sparsity is accomplished by replacing softmax with alpha-entmax: a differentiable generalization of softmax that allows low-scoring words to receive precisely zero weight. Moreover, we derive a method to automatically learn the alpha parameter -- which controls the shape and sparsity of alpha-entmax -- allowing attention heads to choose between focused or spread-out behavior. Our adaptively sparse Transformer improves interpretability and head diversity when compared to softmax Transformers on machine translation datasets. Findings of the quantitative and qualitative analysis of our approach include that heads in different layers learn different sparsity preferences and tend to be more diverse in their attention distributions than softmax Transformers. Furthermore, at no cost in accuracy, sparsity in attention heads helps to uncover different head specializations.

This work presents a sparse-attention Transformer architecture for modeling documents that contain large tables. Tables are ubiquitous on the web, and are rich in information. However, more than 20% of relational tables on the web have 20 or more rows (Cafarella et al., 2008), and these large tables present a challenge for current Transformer models, which are typically limited to 512 tokens. Here we propose MATE, a novel Transformer architecture designed to model the structure of web tables. MATE uses sparse attention in a way that allows heads to efficiently attend to either rows or columns in a table. This architecture scales linearly with respect to speed and memory, and can handle documents containing more than 8000 tokens with current accelerators. MATE also has a more appropriate inductive bias for tabular data, and sets a new state-of-the-art for three table reasoning datasets. For HybridQA (Chen et al., 2020b), a dataset that involves large documents containing tables, we improve the best prior result by 19 points.

Self-attention has recently been adopted for a wide range of sequence modeling problems. Despite its effectiveness, self-attention suffers from quadratic compute and memory requirements with respect to sequence length. Successful approaches to reduce this complexity focused on attending to local sliding windows or a small set of locations independent of content. Our work proposes to learn dynamic sparse attention patterns that avoid allocating computation and memory to attend to content unrelated to the query of interest. This work builds upon two lines of research: it combines the modeling flexibility of prior work on content-based sparse attention with the efficiency gains from approaches based on local, temporal sparse attention. Our model, the Routing Transformer, endows self-attention with a sparse routing module based on online k-means while reducing the overall complexity of attention to Oleft(n^{1.5}dright) from Oleft(n^2dright) for sequence length n and hidden dimension d. We show that our model outperforms comparable sparse attention models on language modeling on Wikitext-103 (15.8 vs 18.3 perplexity) as well as on image generation on ImageNet-64 (3.43 vs 3.44 bits/dim) while using fewer self-attention layers. Additionally, we set a new state-of-the-art on the newly released PG-19 data-set, obtaining a test perplexity of 33.2 with a 22 layer Routing Transformer model trained on sequences of length 8192.

Transformer-based architectures have become the prevailing backbone of large language models. However, the quadratic time and memory complexity of self-attention remains a fundamental obstacle to efficient long-context modeling. To address this limitation, recent research has introduced two principal categories of efficient attention mechanisms. Linear attention methods achieve linear complexity through kernel approximations, recurrent formulations, or fastweight dynamics, thereby enabling scalable inference with reduced computational overhead. Sparse attention techniques, in contrast, limit attention computation to selected subsets of tokens based on fixed patterns, block-wise routing, or clustering strategies, enhancing efficiency while preserving contextual coverage. This survey provides a systematic and comprehensive overview of these developments, integrating both algorithmic innovations and hardware-level considerations. In addition, we analyze the incorporation of efficient attention into largescale pre-trained language models, including both architectures built entirely on efficient attention and hybrid designs that combine local and global components. By aligning theoretical foundations with practical deployment strategies, this work aims to serve as a foundational reference for advancing the design of scalable and efficient language models.

Transformers have revolutionized performance in Natural Language Processing and Vision, paving the way for their integration with Graph Neural Networks (GNNs). One key challenge in enhancing graph transformers is strengthening the discriminative power of distinguishing isomorphisms of graphs, which plays a crucial role in boosting their predictive performances. To address this challenge, we introduce 'Topology-Informed Graph Transformer (TIGT)', a novel transformer enhancing both discriminative power in detecting graph isomorphisms and the overall performance of Graph Transformers. TIGT consists of four components: A topological positional embedding layer using non-isomorphic universal covers based on cyclic subgraphs of graphs to ensure unique graph representation: A dual-path message-passing layer to explicitly encode topological characteristics throughout the encoder layers: A global attention mechanism: And a graph information layer to recalibrate channel-wise graph features for better feature representation. TIGT outperforms previous Graph Transformers in classifying synthetic dataset aimed at distinguishing isomorphism classes of graphs. Additionally, mathematical analysis and empirical evaluations highlight our model's competitive edge over state-of-the-art Graph Transformers across various benchmark datasets.

Graph-structured scene descriptions can be efficiently used in generative models to control the composition of the generated image. Previous approaches are based on the combination of graph convolutional networks and adversarial methods for layout prediction and image generation, respectively. In this work, we show how employing multi-head attention to encode the graph information, as well as using a transformer-based model in the latent space for image generation can improve the quality of the sampled data, without the need to employ adversarial models with the subsequent advantage in terms of training stability. The proposed approach, specifically, is entirely based on transformer architectures both for encoding scene graphs into intermediate object layouts and for decoding these layouts into images, passing through a lower dimensional space learned by a vector-quantized variational autoencoder. Our approach shows an improved image quality with respect to state-of-the-art methods as well as a higher degree of diversity among multiple generations from the same scene graph. We evaluate our approach on three public datasets: Visual Genome, COCO, and CLEVR. We achieve an Inception Score of 13.7 and 12.8, and an FID of 52.3 and 60.3, on COCO and Visual Genome, respectively. We perform ablation studies on our contributions to assess the impact of each component. Code is available at https://github.com/perceivelab/trf-sg2im

Transformers have greatly advanced the state-of-the-art in Natural Language Processing (NLP) in recent years, but present very large computation and storage requirements. We observe that the design process of Transformers (pre-train a foundation model on a large dataset in a self-supervised manner, and subsequently fine-tune it for different downstream tasks) leads to task-specific models that are highly over-parameterized, adversely impacting both accuracy and inference efficiency. We propose AxFormer, a systematic framework that applies accuracy-driven approximations to create optimized transformer models for a given downstream task. AxFormer combines two key optimizations -- accuracy-driven pruning and selective hard attention. Accuracy-driven pruning identifies and removes parts of the fine-tuned transformer that hinder performance on the given downstream task. Sparse hard-attention optimizes attention blocks in selected layers by eliminating irrelevant word aggregations, thereby helping the model focus only on the relevant parts of the input. In effect, AxFormer leads to models that are more accurate, while also being faster and smaller. Our experiments on GLUE and SQUAD tasks show that AxFormer models are up to 4.5% more accurate, while also being up to 2.5X faster and up to 3.2X smaller than conventional fine-tuned models. In addition, we demonstrate that AxFormer can be combined with previous efforts such as distillation or quantization to achieve further efficiency gains.

We introduceGraphGPT, a novel self-supervised generative pre-trained model for graph learning based on the Graph Eulerian Transformer (GET). First, we propose GET, which combines a standard transformer encoder or decoder architecture with an innovative graph-to-sequence transformation method. This method converts graphs or sampled subgraphs into sequences of tokens representing nodes, edges, and attributes in a reversible manner using Eulerian paths. We pre-train GET using either of the two self-supervised tasks: next-token prediction (NTP) and scheduled masked-token prediction (SMTP). The pre-trained model is then fine-tuned for downstream tasks such as graph-, edge-, and node-level prediction. Despite its simplicity, GraphGPT achieves performance comparable to or surpassing state-of-the-art methods on multiple large-scale Open Graph Benchmark (OGB) datasets. It demonstrates exceptional results on the molecular property prediction dataset PCQM4Mv2 and the protein-protein interaction dataset ogbl-ppa. Notably, generative pre-training enables scaling GraphGPT to 2 billion parameters while maintaining performance gains - a breakthrough that overcomes the scalability limitations of traditional Graph Neural Networks (GNNs) and prior graph transformers (GTs). To advance research in graph foundation models and facilitate scientific discovery in chemistry, materials science, and related fields, we will release the source code (https://github.com/alibaba/graph-gpt) and pre-trained checkpoints.

Image classification is a computer vision task where a model analyzes an image to categorize it into a specific label. Vision Transformers (ViT) improve this task by leveraging self-attention to capture complex patterns and long range relationships between image patches. However, a key challenge for ViTs is efficiently incorporating multiscale feature representations, which is inherent in CNNs through their hierarchical structure. In this paper, we introduce the Scale-Aware Graph Attention Vision Transformer (SAG-ViT), a novel framework that addresses this challenge by integrating multi-scale features. Using EfficientNet as a backbone, the model extracts multi-scale feature maps, which are divided into patches to preserve semantic information. These patches are organized into a graph based on spatial and feature similarities, with a Graph Attention Network (GAT) refining the node embeddings. Finally, a Transformer encoder captures long-range dependencies and complex interactions. The SAG-ViT is evaluated on benchmark datasets, demonstrating its effectiveness in enhancing image classification performance.

We aim to tackle the problem of point-based interactive segmentation, in which the key challenge is to propagate the user-provided annotations to unlabeled regions efficiently. Existing methods tackle this challenge by utilizing computationally expensive fully connected graphs or transformer architectures that sacrifice important fine-grained information required for accurate segmentation. To overcome these limitations, we propose a cascade sparse feature propagation network that learns a click-augmented feature representation for propagating user-provided information to unlabeled regions. The sparse design of our network enables efficient information propagation on high-resolution features, resulting in more detailed object segmentation. We validate the effectiveness of our method through comprehensive experiments on various benchmarks, and the results demonstrate the superior performance of our approach. Code is available at https://github.com/kleinzcy/CSFPN{https://github.com/kleinzcy/CSFPN}.

The Vision Transformer architecture is a deep learning model inspired by the success of the Transformer model in Natural Language Processing. However, the self-attention mechanism, large number of parameters, and the requirement for a substantial amount of training data still make Vision Transformers computationally burdensome. In this research, we investigate the possibility of applying Sparse Regularization to Vision Transformers and the impact of Pruning, either after Sparse Regularization or without it, on the trade-off between performance and efficiency. To accomplish this, we apply Sparse Regularization and Pruning methods to the Vision Transformer architecture for image classification tasks on the CIFAR-10, CIFAR-100, and ImageNet-100 datasets. The training process for the Vision Transformer model consists of two parts: pre-training and fine-tuning. Pre-training utilizes ImageNet21K data, followed by fine-tuning for 20 epochs. The results show that when testing with CIFAR-100 and ImageNet-100 data, models with Sparse Regularization can increase accuracy by 0.12%. Furthermore, applying pruning to models with Sparse Regularization yields even better results. Specifically, it increases the average accuracy by 0.568% on CIFAR-10 data, 1.764% on CIFAR-100, and 0.256% on ImageNet-100 data compared to pruning models without Sparse Regularization. Code can be accesed here: https://github.com/yogiprsty/Sparse-ViT

We present the Power Law Graph Transformer, a transformer model with well defined deductive and inductive tasks for prediction and representation learning. The deductive task learns the dataset level (global) and instance level (local) graph structures in terms of learnable power law distribution parameters. The inductive task outputs the prediction probabilities using the deductive task output, similar to a transductive model. We trained our model with Turkish-English and Portuguese-English datasets from TED talk transcripts for machine translation and compared the model performance and characteristics to a transformer model with scaled dot product attention trained on the same experimental setup. We report BLEU scores of 17.79 and 28.33 on the Turkish-English and Portuguese-English translation tasks with our model, respectively. We also show how a duality between a quantization set and N-dimensional manifold representation can be leveraged to transform between local and global deductive-inductive outputs using successive application of linear and non-linear transformations end-to-end.

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.

We explore the impact of parameter sparsity on the scaling behavior of Transformers trained on massive datasets (i.e., "foundation models"), in both vision and language domains. In this setting, we identify the first scaling law describing the relationship between weight sparsity, number of non-zero parameters, and amount of training data, which we validate empirically across model and data scales; on ViT/JFT-4B and T5/C4. These results allow us to characterize the "optimal sparsity", the sparsity level which yields the best performance for a given effective model size and training budget. For a fixed number of non-zero parameters, we identify that the optimal sparsity increases with the amount of data used for training. We also extend our study to different sparsity structures (such as the hardware-friendly n:m pattern) and strategies (such as starting from a pretrained dense model). Our findings shed light on the power and limitations of weight sparsity across various parameter and computational settings, offering both theoretical understanding and practical implications for leveraging sparsity towards computational efficiency improvements.

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.

With the tremendous success of large transformer models in natural language understanding, down-sizing them for cost-effective deployments has become critical. Recent studies have explored the low-rank weight factorization techniques which are efficient to train, and apply out-of-the-box to any transformer architecture. Unfortunately, the low-rank assumption tends to be over-restrictive and hinders the expressiveness of the compressed model. This paper proposes, DSFormer, a simple alternative factorization scheme which expresses a target weight matrix as the product of a small dense and a semi-structured sparse matrix. The resulting approximation is more faithful to the weight distribution in transformers and therefore achieves a stronger efficiency-accuracy trade-off. Another concern with existing factorizers is their dependence on a task-unaware initialization step which degrades the accuracy of the resulting model. DSFormer addresses this issue through a novel Straight-Through Factorizer (STF) algorithm that jointly learns all the weight factorizations to directly maximize the final task accuracy. Extensive experiments on multiple natural language understanding benchmarks demonstrate that DSFormer obtains up to 40% better compression than the state-of-the-art low-rank factorizers, leading semi-structured sparsity baselines and popular knowledge distillation approaches. Our approach is also orthogonal to mainstream compressors and offers up to 50% additional compression when added to popular distilled, layer-shared and quantized transformers. We empirically evaluate the benefits of STF over conventional optimization practices.

Attention-based graph neural networks (GNNs), such as graph attention networks (GATs), have become popular neural architectures for processing graph-structured data and learning node embeddings. Despite their empirical success, these models rely on labeled data and the theoretical properties of these models have yet to be fully understood. In this work, we propose a novel attention-based node embedding framework for graphs. Our framework builds upon a hierarchical kernel for multisets of subgraphs around nodes (e.g. neighborhoods) and each kernel leverages the geometry of a smooth statistical manifold to compare pairs of multisets, by "projecting" the multisets onto the manifold. By explicitly computing node embeddings with a manifold of Gaussian mixtures, our method leads to a new attention mechanism for neighborhood aggregation. We provide theoretical insights into generalizability and expressivity of our embeddings, contributing to a deeper understanding of attention-based GNNs. We propose both efficient unsupervised and supervised methods for learning the embeddings. Through experiments on several node classification benchmarks, we demonstrate that our proposed method outperforms existing attention-based graph models like GATs. Our code is available at https://github.com/BorgwardtLab/fisher_information_embedding.

Transformers-based methods have achieved significant performance in image deraining as they can model the non-local information which is vital for high-quality image reconstruction. In this paper, we find that most existing Transformers usually use all similarities of the tokens from the query-key pairs for the feature aggregation. However, if the tokens from the query are different from those of the key, the self-attention values estimated from these tokens also involve in feature aggregation, which accordingly interferes with the clear image restoration. To overcome this problem, we propose an effective DeRaining network, Sparse Transformer (DRSformer) that can adaptively keep the most useful self-attention values for feature aggregation so that the aggregated features better facilitate high-quality image reconstruction. Specifically, we develop a learnable top-k selection operator to adaptively retain the most crucial attention scores from the keys for each query for better feature aggregation. Simultaneously, as the naive feed-forward network in Transformers does not model the multi-scale information that is important for latent clear image restoration, we develop an effective mixed-scale feed-forward network to generate better features for image deraining. To learn an enriched set of hybrid features, which combines local context from CNN operators, we equip our model with mixture of experts feature compensator to present a cooperation refinement deraining scheme. Extensive experimental results on the commonly used benchmarks demonstrate that the proposed method achieves favorable performance against state-of-the-art approaches. The source code and trained models are available at https://github.com/cschenxiang/DRSformer.

In this paper, we contend that the objective of representation learning is to compress and transform the distribution of the data, say sets of tokens, towards a mixture of low-dimensional Gaussian distributions supported on incoherent subspaces. The quality of the final representation can be measured by a unified objective function called sparse rate reduction. From this perspective, popular deep networks such as transformers can be naturally viewed as realizing iterative schemes to optimize this objective incrementally. Particularly, we show that the standard transformer block can be derived from alternating optimization on complementary parts of this objective: the multi-head self-attention operator can be viewed as a gradient descent step to compress the token sets by minimizing their lossy coding rate, and the subsequent multi-layer perceptron can be viewed as attempting to sparsify the representation of the tokens. This leads to a family of white-box transformer-like deep network architectures which are mathematically fully interpretable. Despite their simplicity, experiments show that these networks indeed learn to optimize the designed objective: they compress and sparsify representations of large-scale real-world vision datasets such as ImageNet, and achieve performance very close to thoroughly engineered transformers such as ViT. Code is at https://github.com/Ma-Lab-Berkeley/CRATE.

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.

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

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.

Recent advances in efficient Transformers have exploited either the sparsity or low-rank properties of attention matrices to reduce the computational and memory bottlenecks of modeling long sequences. However, it is still challenging to balance the trade-off between model quality and efficiency to perform a one-size-fits-all approximation for different tasks. To better understand this trade-off, we observe that sparse and low-rank approximations excel in different regimes, determined by the softmax temperature in attention, and sparse + low-rank can outperform each individually. Inspired by the classical robust-PCA algorithm for sparse and low-rank decomposition, we propose Scatterbrain, a novel way to unify sparse (via locality sensitive hashing) and low-rank (via kernel feature map) attention for accurate and efficient approximation. The estimation is unbiased with provably low error. We empirically show that Scatterbrain can achieve 2.1x lower error than baselines when serving as a drop-in replacement in BigGAN image generation and pre-trained T2T-ViT. On a pre-trained T2T Vision transformer, even without fine-tuning, Scatterbrain can reduce 98% of attention memory at the cost of only 1% drop in accuracy. We demonstrate Scatterbrain for end-to-end training with up to 4 points better perplexity and 5 points better average accuracy than sparse or low-rank efficient transformers on language modeling and long-range-arena tasks.

The deployment of Deep Neural Networks (DNNs) on edge devices is hindered by the substantial gap between performance requirements and available processing power. While recent research has made significant strides in developing pruning methods to build a sparse network for reducing the computing overhead of DNNs, there remains considerable accuracy loss, especially at high pruning ratios. We find that the architectures designed for dense networks by differentiable architecture search methods are ineffective when pruning mechanisms are applied to them. The main reason is that the current method does not support sparse architectures in their search space and uses a search objective that is made for dense networks and does not pay any attention to sparsity. In this paper, we propose a new method to search for sparsity-friendly neural architectures. We do this by adding two new sparse operations to the search space and modifying the search objective. We propose two novel parametric SparseConv and SparseLinear operations in order to expand the search space to include sparse operations. In particular, these operations make a flexible search space due to using sparse parametric versions of linear and convolution operations. The proposed search objective lets us train the architecture based on the sparsity of the search space operations. Quantitative analyses demonstrate that our search architectures outperform those used in the stateof-the-art sparse networks on the CIFAR-10 and ImageNet datasets. In terms of performance and hardware effectiveness, DASS increases the accuracy of the sparse version of MobileNet-v2 from 73.44% to 81.35% (+7.91% improvement) with 3.87x faster inference time.

Designing an efficient yet deployment-friendly 3D backbone to handle sparse point clouds is a fundamental problem in 3D perception. Compared with the customized sparse convolution, the attention mechanism in Transformers is more appropriate for flexibly modeling long-range relationships and is easier to be deployed in real-world applications. However, due to the sparse characteristics of point clouds, it is non-trivial to apply a standard transformer on sparse points. In this paper, we present Dynamic Sparse Voxel Transformer (DSVT), a single-stride window-based voxel Transformer backbone for outdoor 3D perception. In order to efficiently process sparse points in parallel, we propose Dynamic Sparse Window Attention, which partitions a series of local regions in each window according to its sparsity and then computes the features of all regions in a fully parallel manner. To allow the cross-set connection, we design a rotated set partitioning strategy that alternates between two partitioning configurations in consecutive self-attention layers. To support effective downsampling and better encode geometric information, we also propose an attention-style 3D pooling module on sparse points, which is powerful and deployment-friendly without utilizing any customized CUDA operations. Our model achieves state-of-the-art performance with a broad range of 3D perception tasks. More importantly, DSVT can be easily deployed by TensorRT with real-time inference speed (27Hz). Code will be available at https://github.com/Haiyang-W/DSVT.

Transformers use the dense self-attention mechanism which gives a lot of flexibility for long-range connectivity. Over multiple layers of a deep transformer, the number of possible connectivity patterns increases exponentially. However, very few of these contribute to the performance of the network, and even fewer are essential. We hypothesize that there are sparsely connected sub-networks within a transformer, called information pathways which can be trained independently. However, the dynamic (i.e., input-dependent) nature of these pathways makes it difficult to prune dense self-attention during training. But the overall distribution of these pathways is often predictable. We take advantage of this fact to propose Stochastically Subsampled self-Attention (SSA) - a general-purpose training strategy for transformers that can reduce both the memory and computational cost of self-attention by 4 to 8 times during training while also serving as a regularization method - improving generalization over dense training. We show that an ensemble of sub-models can be formed from the subsampled pathways within a network, which can achieve better performance than its densely attended counterpart. We perform experiments on a variety of NLP, computer vision and graph learning tasks in both generative and discriminative settings to provide empirical evidence for our claims and show the effectiveness of the proposed method.

Attention mechanisms have been widely used to capture long-range dependencies among nodes in Graph Transformers. Bottlenecked by the quadratic computational cost, attention mechanisms fail to scale in large graphs. Recent improvements in computational efficiency are mainly achieved by attention sparsification with random or heuristic-based graph subsampling, which falls short in data-dependent context reasoning. State space models (SSMs), such as Mamba, have gained prominence for their effectiveness and efficiency in modeling long-range dependencies in sequential data. However, adapting SSMs to non-sequential graph data presents a notable challenge. In this work, we introduce Graph-Mamba, the first attempt to enhance long-range context modeling in graph networks by integrating a Mamba block with the input-dependent node selection mechanism. Specifically, we formulate graph-centric node prioritization and permutation strategies to enhance context-aware reasoning, leading to a substantial improvement in predictive performance. Extensive experiments on ten benchmark datasets demonstrate that Graph-Mamba outperforms state-of-the-art methods in long-range graph prediction tasks, with a fraction of the computational cost in both FLOPs and GPU memory consumption. The code and models are publicly available at https://github.com/bowang-lab/Graph-Mamba.

In this paper, we present a novel generative task: joint scene graph - image generation. While previous works have explored image generation conditioned on scene graphs or layouts, our task is distinctive and important as it involves generating scene graphs themselves unconditionally from noise, enabling efficient and interpretable control for image generation. Our task is challenging, requiring the generation of plausible scene graphs with heterogeneous attributes for nodes (objects) and edges (relations among objects), including continuous object bounding boxes and discrete object and relation categories. We introduce a novel diffusion model, DiffuseSG, that jointly models the adjacency matrix along with heterogeneous node and edge attributes. We explore various types of encodings for the categorical data, relaxing it into a continuous space. With a graph transformer being the denoiser, DiffuseSG successively denoises the scene graph representation in a continuous space and discretizes the final representation to generate the clean scene graph. Additionally, we introduce an IoU regularization to enhance the empirical performance. Our model significantly outperforms existing methods in scene graph generation on the Visual Genome and COCO-Stuff datasets, both on standard and newly introduced metrics that better capture the problem complexity. Moreover, we demonstrate the additional benefits of our model in two downstream applications: 1) excelling in a series of scene graph completion tasks, and 2) improving scene graph detection models by using extra training samples generated from DiffuseSG.

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.

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

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.

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.

This paper studies the curious phenomenon for machine learning models with Transformer architectures that their activation maps are sparse. By activation map we refer to the intermediate output of the multi-layer perceptrons (MLPs) after a ReLU activation function, and by sparse we mean that on average very few entries (e.g., 3.0% for T5-Base and 6.3% for ViT-B16) are nonzero for each input to MLP. Moreover, larger Transformers with more layers and wider MLP hidden dimensions are sparser as measured by the percentage of nonzero entries. Through extensive experiments we demonstrate that the emergence of sparsity is a prevalent phenomenon that occurs for both natural language processing and vision tasks, on both training and evaluation data, for Transformers of various configurations, at layers of all depth levels, as well as for other architectures including MLP-mixers and 2-layer MLPs. We show that sparsity also emerges using training datasets with random labels, or with random inputs, or with infinite amount of data, demonstrating that sparsity is not a result of a specific family of datasets. We discuss how sparsity immediately implies a way to significantly reduce the FLOP count and improve efficiency for Transformers. Moreover, we demonstrate perhaps surprisingly that enforcing an even sparser activation via Top-k thresholding with a small value of k brings a collection of desired but missing properties for Transformers, namely less sensitivity to noisy training data, more robustness to input corruptions, and better calibration for their prediction confidence.

Scene graph generation (SGG) aims to predict graph-structured descriptions of input images, in the form of objects and relationships between them. This task is becoming increasingly useful for progress at the interface of vision and language. Here, it is important - yet challenging - to perform well on novel (zero-shot) or rare (few-shot) compositions of objects and relationships. In this paper, we identify two key issues that limit such generalization. Firstly, we show that the standard loss used in this task is unintentionally a function of scene graph density. This leads to the neglect of individual edges in large sparse graphs during training, even though these contain diverse few-shot examples that are important for generalization. Secondly, the frequency of relationships can create a strong bias in this task, such that a blind model predicting the most frequent relationship achieves good performance. Consequently, some state-of-the-art models exploit this bias to improve results. We show that such models can suffer the most in their ability to generalize to rare compositions, evaluating two different models on the Visual Genome dataset and its more recent, improved version, GQA. To address these issues, we introduce a density-normalized edge loss, which provides more than a two-fold improvement in certain generalization metrics. Compared to other works in this direction, our enhancements require only a few lines of code and no added computational cost. We also highlight the difficulty of accurately evaluating models using existing metrics, especially on zero/few shots, and introduce a novel weighted metric.

As the core building block of vision transformers, attention is a powerful tool to capture long-range dependency. However, such power comes at a cost: it incurs a huge computation burden and heavy memory footprint as pairwise token interaction across all spatial locations is computed. A series of works attempt to alleviate this problem by introducing handcrafted and content-agnostic sparsity into attention, such as restricting the attention operation to be inside local windows, axial stripes, or dilated windows. In contrast to these approaches, we propose a novel dynamic sparse attention via bi-level routing to enable a more flexible allocation of computations with content awareness. Specifically, for a query, irrelevant key-value pairs are first filtered out at a coarse region level, and then fine-grained token-to-token attention is applied in the union of remaining candidate regions (\ie, routed regions). We provide a simple yet effective implementation of the proposed bi-level routing attention, which utilizes the sparsity to save both computation and memory while involving only GPU-friendly dense matrix multiplications. Built with the proposed bi-level routing attention, a new general vision transformer, named BiFormer, is then presented. As BiFormer attends to a small subset of relevant tokens in a query adaptive manner without distraction from other irrelevant ones, it enjoys both good performance and high computational efficiency, especially in dense prediction tasks. Empirical results across several computer vision tasks such as image classification, object detection, and semantic segmentation verify the effectiveness of our design. Code is available at https://github.com/rayleizhu/BiFormer.

The recently proposed SparseFormer architecture provides an alternative approach to visual understanding by utilizing a significantly lower number of visual tokens via adjusting RoIs, greatly reducing computational costs while still achieving promising performance. However, training SparseFormers from scratch is still expensive, and scaling up the number of parameters can be challenging. In this paper, we propose to bootstrap SparseFormers from ViT-based vision foundation models in a simple and efficient way. Since the majority of SparseFormer blocks are the standard transformer ones, we can inherit weights from large-scale pre-trained vision transformers and freeze them as much as possible. Therefore, we only need to train the SparseFormer-specific lightweight focusing transformer to adjust token RoIs and fine-tune a few early pre-trained blocks to align the final token representation. In such a way, we can bootstrap SparseFormer architectures from various large-scale pre-trained models (e.g., IN-21K pre-trained AugRegs or CLIPs) using a rather smaller amount of training samples (e.g., IN-1K) and without labels or captions within just a few hours. As a result, the bootstrapped unimodal SparseFormer (from AugReg-ViT-L/16-384) can reach 84.9% accuracy on IN-1K with only 49 tokens, and the multimodal SparseFormer from CLIPs also demonstrates notable zero-shot performance with highly reduced computational cost without seeing any caption during the bootstrapping procedure. In addition, CLIP-bootstrapped SparseFormers, which align the output space with language without seeing a word, can serve as efficient vision encoders in multimodal large language models. Code will be publicly available at https://github.com/showlab/sparseformer

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.

Since the pioneering work on the lottery ticket hypothesis for graph neural networks (GNNs) was proposed in Chen et al. (2021), the study on finding graph lottery tickets (GLT) has become one of the pivotal focus in the GNN community, inspiring researchers to discover sparser GLT while achieving comparable performance to original dense networks. In parallel, the graph structure has gained substantial attention as a crucial factor in GNN training dynamics, also elucidated by several recent studies. Despite this, contemporary studies on GLT, in general, have not fully exploited inherent pathways in the graph structure and identified tickets in an iterative manner, which is time-consuming and inefficient. To address these limitations, we introduce TEDDY, a one-shot edge sparsification framework that leverages structural information by incorporating edge-degree information. Following edge sparsification, we encourage the parameter sparsity during training via simple projected gradient descent on the ell_0 ball. Given the target sparsity levels for both the graph structure and the model parameters, our TEDDY facilitates efficient and rapid realization of GLT within a single training. Remarkably, our experimental results demonstrate that TEDDY significantly surpasses conventional iterative approaches in generalization, even when conducting one-shot sparsification that solely utilizes graph structures, without taking feature information into account.

Can we model non-Euclidean graphs as pure language or even Euclidean vectors while retaining their inherent information? The non-Euclidean property have posed a long term challenge in graph modeling. Despite recent GNN and Graphformer efforts encoding graphs as Euclidean vectors, recovering original graph from the vectors remains a challenge. We introduce GraphsGPT, featuring a Graph2Seq encoder that transforms non-Euclidean graphs into learnable graph words in a Euclidean space, along with a GraphGPT decoder that reconstructs the original graph from graph words to ensure information equivalence. We pretrain GraphsGPT on 100M molecules and yield some interesting findings: (1) Pretrained Graph2Seq excels in graph representation learning, achieving state-of-the-art results on 8/9 graph classification and regression tasks. (2) Pretrained GraphGPT serves as a strong graph generator, demonstrated by its ability to perform both unconditional and conditional graph generation. (3) Graph2Seq+GraphGPT enables effective graph mixup in the Euclidean space, overcoming previously known non-Euclidean challenge. (4) Our proposed novel edge-centric GPT pretraining task is effective in graph fields, underscoring its success in both representation and generation.

Sparse models, including sparse Mixture-of-Experts (MoE) models, have emerged as an effective approach for scaling Transformer models. However, they often suffer from computational inefficiency since a significant number of parameters are unnecessarily involved in computations via multiplying values by zero or low activation values. To address this issue, we present \tool, a novel MoE designed to enhance both the efficacy and efficiency of sparse MoE models. \tool leverages small experts and a threshold-based router to enable tokens to selectively engage only essential parameters. Our extensive experiments on language modeling and machine translation tasks demonstrate that \tool can enhance model performance while decreasing the computation load at MoE layers by over 50\% without sacrificing performance. Furthermore, we present the versatility of \tool by applying it to dense models, enabling sparse computation during inference. We provide a comprehensive analysis and make our code available at https://anonymous.4open.science/r/XMoE.

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

Accommodating long sequences efficiently in autoregressive Transformers, especially within an extended context window, poses significant challenges due to the quadratic computational complexity and substantial KV memory requirements inherent in self-attention mechanisms. In this work, we introduce SPARSEK Attention, a novel sparse attention mechanism designed to overcome these computational and memory obstacles while maintaining performance. Our approach integrates a scoring network and a differentiable top-k mask operator, SPARSEK, to select a constant number of KV pairs for each query, thereby enabling gradient-based optimization. As a result, SPARSEK Attention offers linear time complexity and constant memory footprint during generation. Experimental results reveal that SPARSEK Attention outperforms previous sparse attention methods and provides significant speed improvements during both training and inference, particularly in language modeling and downstream tasks. Furthermore, our method can be seamlessly integrated into pre-trained Large Language Models (LLMs) with minimal fine-tuning, offering a practical solution for effectively managing long-range dependencies in diverse applications.

Transformers serve as the backbone architectures of Foundational Models, where a domain-specific tokenizer helps them adapt to various domains. Graph Transformers (GTs) have recently emerged as a leading model in geometric deep learning, outperforming Graph Neural Networks (GNNs) in various graph learning tasks. However, the development of tokenizers for graphs has lagged behind other modalities, with existing approaches relying on heuristics or GNNs co-trained with Transformers. To address this, we introduce GQT (Graph Quantized Tokenizer), which decouples tokenizer training from Transformer training by leveraging multi-task graph self-supervised learning, yielding robust and generalizable graph tokens. Furthermore, the GQT utilizes Residual Vector Quantization (RVQ) to learn hierarchical discrete tokens, resulting in significantly reduced memory requirements and improved generalization capabilities. By combining the GQT with token modulation, a Transformer encoder achieves state-of-the-art performance on 16 out of 18 benchmarks, including large-scale homophilic and heterophilic datasets. The code is available at: https://github.com/limei0307/graph-tokenizer

The transformer extends its success from the language to the vision domain. Because of the stacked self-attention and cross-attention blocks, the acceleration deployment of vision transformer on GPU hardware is challenging and also rarely studied. This paper thoroughly designs a compression scheme to maximally utilize the GPU-friendly 2:4 fine-grained structured sparsity and quantization. Specially, an original large model with dense weight parameters is first pruned into a sparse one by 2:4 structured pruning, which considers the GPU's acceleration of 2:4 structured sparse pattern with FP16 data type, then the floating-point sparse model is further quantized into a fixed-point one by sparse-distillation-aware quantization aware training, which considers GPU can provide an extra speedup of 2:4 sparse calculation with integer tensors. A mixed-strategy knowledge distillation is used during the pruning and quantization process. The proposed compression scheme is flexible to support supervised and unsupervised learning styles. Experiment results show GPUSQ-ViT scheme achieves state-of-the-art compression by reducing vision transformer models 6.4-12.7 times on model size and 30.3-62 times on FLOPs with negligible accuracy degradation on ImageNet classification, COCO detection and ADE20K segmentation benchmarking tasks. Moreover, GPUSQ-ViT can boost actual deployment performance by 1.39-1.79 times and 3.22-3.43 times of latency and throughput on A100 GPU, and 1.57-1.69 times and 2.11-2.51 times improvement of latency and throughput on AGX Orin.

Diffusion-based generative graph models have been proven effective in generating high-quality small graphs. However, they need to be more scalable for generating large graphs containing thousands of nodes desiring graph statistics. In this work, we propose EDGE, a new diffusion-based generative graph model that addresses generative tasks with large graphs. To improve computation efficiency, we encourage graph sparsity by using a discrete diffusion process that randomly removes edges at each time step and finally obtains an empty graph. EDGE only focuses on a portion of nodes in the graph at each denoising step. It makes much fewer edge predictions than previous diffusion-based models. Moreover, EDGE admits explicitly modeling the node degrees of the graphs, further improving the model performance. The empirical study shows that EDGE is much more efficient than competing methods and can generate large graphs with thousands of nodes. It also outperforms baseline models in generation quality: graphs generated by our approach have more similar graph statistics to those of the training graphs.

In this paper, we introduce a new task for code completion that focuses on handling long code input and propose a sparse Transformer model, called LongCoder, to address this task. LongCoder employs a sliding window mechanism for self-attention and introduces two types of globally accessible tokens - bridge tokens and memory tokens - to improve performance and efficiency. Bridge tokens are inserted throughout the input sequence to aggregate local information and facilitate global interaction, while memory tokens are included to highlight important statements that may be invoked later and need to be memorized, such as package imports and definitions of classes, functions, or structures. We conduct experiments on a newly constructed dataset that contains longer code context and the publicly available CodeXGLUE benchmark. Experimental results demonstrate that LongCoder achieves superior performance on code completion tasks compared to previous models while maintaining comparable efficiency in terms of computational resources during inference. All the codes and data are available at https://github.com/microsoft/CodeBERT.

Sparse expert models are a thirty-year old concept re-emerging as a popular architecture in deep learning. This class of architecture encompasses Mixture-of-Experts, Switch Transformers, Routing Networks, BASE layers, and others, all with the unifying idea that each example is acted on by a subset of the parameters. By doing so, the degree of sparsity decouples the parameter count from the compute per example allowing for extremely large, but efficient models. The resulting models have demonstrated significant improvements across diverse domains such as natural language processing, computer vision, and speech recognition. We review the concept of sparse expert models, provide a basic description of the common algorithms, contextualize the advances in the deep learning era, and conclude by highlighting areas for future work.

Obtaining versions of deep neural networks that are both highly-accurate and highly-sparse is one of the main challenges in the area of model compression, and several high-performance pruning techniques have been investigated by the community. Yet, much less is known about the interaction between sparsity and the standard stochastic optimization techniques used for training sparse networks, and most existing work uses standard dense schedules and hyperparameters for training sparse networks. In this work, we examine the impact of high sparsity on model training using the standard computer vision and natural language processing sparsity benchmarks. We begin by showing that using standard dense training recipes for sparse training is suboptimal, and results in under-training. We provide new approaches for mitigating this issue for both sparse pre-training of vision models (e.g. ResNet50/ImageNet) and sparse fine-tuning of language models (e.g. BERT/GLUE), achieving state-of-the-art results in both settings in the high-sparsity regime, and providing detailed analyses for the difficulty of sparse training in both scenarios. Our work sets a new threshold in terms of the accuracies that can be achieved under high sparsity, and should inspire further research into improving sparse model training, to reach higher accuracies under high sparsity, but also to do so efficiently.

We present graph attention networks (GATs), novel neural network architectures that operate on graph-structured data, leveraging masked self-attentional layers to address the shortcomings of prior methods based on graph convolutions or their approximations. By stacking layers in which nodes are able to attend over their neighborhoods' features, we enable (implicitly) specifying different weights to different nodes in a neighborhood, without requiring any kind of costly matrix operation (such as inversion) or depending on knowing the graph structure upfront. In this way, we address several key challenges of spectral-based graph neural networks simultaneously, and make our model readily applicable to inductive as well as transductive problems. Our GAT models have achieved or matched state-of-the-art results across four established transductive and inductive graph benchmarks: the Cora, Citeseer and Pubmed citation network datasets, as well as a protein-protein interaction dataset (wherein test graphs remain unseen during training).

Dictionary learning is a key tool for representation learning, that explains the data as linear combination of few basic elements. Yet, this analysis is not amenable in the context of graph learning, as graphs usually belong to different metric spaces. We fill this gap by proposing a new online Graph Dictionary Learning approach, which uses the Gromov Wasserstein divergence for the data fitting term. In our work, graphs are encoded through their nodes' pairwise relations and modeled as convex combination of graph atoms, i.e. dictionary elements, estimated thanks to an online stochastic algorithm, which operates on a dataset of unregistered graphs with potentially different number of nodes. Our approach naturally extends to labeled graphs, and is completed by a novel upper bound that can be used as a fast approximation of Gromov Wasserstein in the embedding space. We provide numerical evidences showing the interest of our approach for unsupervised embedding of graph datasets and for online graph subspace estimation and tracking.

Graph Neural Networks (GNNs) are widely deployed in vast fields, but they often struggle to maintain accurate representations as graphs evolve. We theoretically establish a lower bound, proving that under mild conditions, representation distortion inevitably occurs over time. To estimate the temporal distortion without human annotation after deployment, one naive approach is to pre-train a recurrent model (e.g., RNN) before deployment and use this model afterwards, but the estimation is far from satisfactory. In this paper, we analyze the representation distortion from an information theory perspective, and attribute it primarily to inaccurate feature extraction during evolution. Consequently, we introduce Smart, a straightforward and effective baseline enhanced by an adaptive feature extractor through self-supervised graph reconstruction. In synthetic random graphs, we further refine the former lower bound to show the inevitable distortion over time and empirically observe that Smart achieves good estimation performance. Moreover, we observe that Smart consistently shows outstanding generalization estimation on four real-world evolving graphs. The ablation studies underscore the necessity of graph reconstruction. For example, on OGB-arXiv dataset, the estimation metric MAPE deteriorates from 2.19% to 8.00% without reconstruction.

High-resolution images enable neural networks to learn richer visual representations. However, this improved performance comes at the cost of growing computational complexity, hindering their usage in latency-sensitive applications. As not all pixels are equal, skipping computations for less-important regions offers a simple and effective measure to reduce the computation. This, however, is hard to be translated into actual speedup for CNNs since it breaks the regularity of the dense convolution workload. In this paper, we introduce SparseViT that revisits activation sparsity for recent window-based vision transformers (ViTs). As window attentions are naturally batched over blocks, actual speedup with window activation pruning becomes possible: i.e., ~50% latency reduction with 60% sparsity. Different layers should be assigned with different pruning ratios due to their diverse sensitivities and computational costs. We introduce sparsity-aware adaptation and apply the evolutionary search to efficiently find the optimal layerwise sparsity configuration within the vast search space. SparseViT achieves speedups of 1.5x, 1.4x, and 1.3x compared to its dense counterpart in monocular 3D object detection, 2D instance segmentation, and 2D semantic segmentation, respectively, with negligible to no loss of accuracy.

As deep learning models grow, sparsity is becoming an increasingly critical component of deep neural networks, enabling improved performance and reduced storage. However, existing frameworks offer poor support for sparsity. Specialized sparsity engines focus exclusively on sparse inference, while general frameworks primarily focus on sparse tensors in classical formats and neglect the broader sparsification pipeline necessary for using sparse models, especially during training. Further, existing frameworks are not easily extensible: adding a new sparse tensor format or operator is challenging and time-consuming. To address this, we propose STen, a sparsity programming model and interface for PyTorch, which incorporates sparsity layouts, operators, and sparsifiers, in an efficient, customizable, and extensible framework that supports virtually all sparsification methods. We demonstrate this by developing a high-performance grouped n:m sparsity layout for CPU inference at moderate sparsity. STen brings high performance and ease of use to the ML community, making sparsity easily accessible.

In this paper, we propose the first framework that enables solving graph learning tasks of all levels (node, edge and graph) and all types (generation, regression and classification) with one model. We first propose Latent Graph Diffusion (LGD), a generative model that can generate node, edge, and graph-level features of all categories simultaneously. We achieve this goal by embedding the graph structures and features into a latent space leveraging a powerful encoder which can also be decoded, then training a diffusion model in the latent space. LGD is also capable of conditional generation through a specifically designed cross-attention mechanism. Then we formulate prediction tasks including regression and classification as (conditional) generation, which enables our LGD to solve tasks of all levels and all types with provable guarantees. We verify the effectiveness of our framework with extensive experiments, where our models achieve state-of-the-art or highly competitive results across generation and regression tasks.

Deployment of Transformer models on edge devices is becoming increasingly challenging due to the exponentially growing inference cost that scales quadratically with the number of tokens in the input sequence. Token pruning is an emerging solution to address this challenge due to its ease of deployment on various Transformer backbones. However, most token pruning methods require computationally expensive fine-tuning, which is undesirable in many edge deployment cases. In this work, we propose Zero-TPrune, the first zero-shot method that considers both the importance and similarity of tokens in performing token pruning. It leverages the attention graph of pre-trained Transformer models to produce an importance distribution for tokens via our proposed Weighted Page Rank (WPR) algorithm. This distribution further guides token partitioning for efficient similarity-based pruning. Due to the elimination of the fine-tuning overhead, Zero-TPrune can prune large models at negligible computational cost, switch between different pruning configurations at no computational cost, and perform hyperparameter tuning efficiently. We evaluate the performance of Zero-TPrune on vision tasks by applying it to various vision Transformer backbones and testing them on ImageNet. Without any fine-tuning, Zero-TPrune reduces the FLOPs cost of DeiT-S by 34.7\% and improves its throughput by 45.3\% with only 0.4\% accuracy loss. Compared with state-of-the-art pruning methods that require fine-tuning, Zero-TPrune not only eliminates the need for fine-tuning after pruning but also does so with only 0.1\% accuracy loss. Compared with state-of-the-art fine-tuning-free pruning methods, Zero-TPrune reduces accuracy loss by up to 49\% with the same or higher throughput.

Graph-structured data plays a vital role in numerous domains, such as social networks, citation networks, commonsense reasoning graphs and knowledge graphs. While graph neural networks have been employed for graph processing, recent advancements have explored integrating large language models for graph-based tasks. In this paper, we propose a novel approach named Learnable Graph Pooling Token (LGPT), which addresses the limitations of the scalability issues in node-level projection and information loss in graph-level projection. LGPT enables flexible and efficient graph representation by introducing learnable parameters that act as tokens in large language models, balancing fine-grained and global graph information. Additionally, we investigate an Early Query Fusion technique, which fuses query context before constructing the graph representation, leading to more effective graph embeddings. Our method achieves a 4.13\% performance improvement on the GraphQA benchmark without training the large language model, demonstrating significant gains in handling complex textual-attributed graph data.

We propose an effective lightweight dynamic local and global self-attention network (DLGSANet) to solve image super-resolution. Our method explores the properties of Transformers while having low computational costs. Motivated by the network designs of Transformers, we develop a simple yet effective multi-head dynamic local self-attention (MHDLSA) module to extract local features efficiently. In addition, we note that existing Transformers usually explore all similarities of the tokens between the queries and keys for the feature aggregation. However, not all the tokens from the queries are relevant to those in keys, using all the similarities does not effectively facilitate the high-resolution image reconstruction. To overcome this problem, we develop a sparse global self-attention (SparseGSA) module to select the most useful similarity values so that the most useful global features can be better utilized for the high-resolution image reconstruction. We develop a hybrid dynamic-Transformer block(HDTB) that integrates the MHDLSA and SparseGSA for both local and global feature exploration. To ease the network training, we formulate the HDTBs into a residual hybrid dynamic-Transformer group (RHDTG). By embedding the RHDTGs into an end-to-end trainable network, we show that our proposed method has fewer network parameters and lower computational costs while achieving competitive performance against state-of-the-art ones in terms of accuracy. More information is available at https://neonleexiang.github.io/DLGSANet/

Long-Context Transformer Models (LCTMs) are vital for real-world applications but suffer high computational costs due to attention's quadratic complexity. Block-sparse attention mitigates this by focusing computation on critical regions, yet existing methods struggle with balancing accuracy and efficiency due to costly block importance measurements. In this paper, we introduce XAttention, a plug-and-play framework that dramatically accelerates long-context inference in Transformers models using sparse attention. XAttention's key innovation is the insight that the sum of antidiagonal values (i.e., from the lower-left to upper-right) in the attention matrix provides a powerful proxy for block importance. This allows for precise identification and pruning of non-essential blocks, resulting in high sparsity and dramatically accelerated inference. Across comprehensive evaluations on demanding long-context benchmarks-including RULER and LongBench for language, VideoMME for video understanding, and VBench for video generation. XAttention achieves accuracy comparable to full attention while delivering substantial computational gains. We demonstrate up to 13.5x acceleration in attention computation. These results underscore XAttention's ability to unlock the practical potential of block sparse attention, paving the way for scalable and efficient deployment of LCTMs in real-world applications. Code is available at https://github.com/mit-han-lab/x-attention.

Graph Structure Learning (GSL) focuses on capturing intrinsic dependencies and interactions among nodes in graph-structured data by generating novel graph structures. Graph Neural Networks (GNNs) have emerged as promising GSL solutions, utilizing recursive message passing to encode node-wise inter-dependencies. However, many existing GSL methods heavily depend on explicit graph structural information as supervision signals, leaving them susceptible to challenges such as data noise and sparsity. In this work, we propose GraphEdit, an approach that leverages large language models (LLMs) to learn complex node relationships in graph-structured data. By enhancing the reasoning capabilities of LLMs through instruction-tuning over graph structures, we aim to overcome the limitations associated with explicit graph structural information and enhance the reliability of graph structure learning. Our approach not only effectively denoises noisy connections but also identifies node-wise dependencies from a global perspective, providing a comprehensive understanding of the graph structure. We conduct extensive experiments on multiple benchmark datasets to demonstrate the effectiveness and robustness of GraphEdit across various settings. We have made our model implementation available at: https://github.com/HKUDS/GraphEdit.

In neural Information Retrieval, ongoing research is directed towards improving the first retriever in ranking pipelines. Learning dense embeddings to conduct retrieval using efficient approximate nearest neighbors methods has proven to work well. Meanwhile, there has been a growing interest in learning sparse representations for documents and queries, that could inherit from the desirable properties of bag-of-words models such as the exact matching of terms and the efficiency of inverted indexes. In this work, we present a new first-stage ranker based on explicit sparsity regularization and a log-saturation effect on term weights, leading to highly sparse representations and competitive results with respect to state-of-the-art dense and sparse methods. Our approach is simple, trained end-to-end in a single stage. We also explore the trade-off between effectiveness and efficiency, by controlling the contribution of the sparsity regularization.

DETR introduces a simplified one-stage framework for scene graph generation (SGG) but faces challenges of sparse supervision and false negative samples. The former occurs because each image typically contains fewer than 10 relation annotations, while DETR-based SGG models employ over 100 relation queries. Each ground truth relation is assigned to only one query during training. The latter arises when one ground truth relation may have multiple queries with similar matching scores, leading to suboptimally matched queries being treated as negative samples. To address these, we propose Hydra-SGG, a one-stage SGG method featuring a Hybrid Relation Assignment. This approach combines a One-to-One Relation Assignment with an IoU-based One-to-Many Relation Assignment, increasing positive training samples and mitigating sparse supervision. In addition, we empirically demonstrate that removing self-attention between relation queries leads to duplicate predictions, which actually benefits the proposed One-to-Many Relation Assignment. With this insight, we introduce Hydra Branch, an auxiliary decoder without self-attention layers, to further enhance One-to-Many Relation Assignment by promoting different queries to make the same relation prediction. Hydra-SGG achieves state-of-the-art performance on multiple datasets, including VG150 (16.0 mR@50), Open Images V6 (50.1 weighted score), and GQA (12.7 mR@50).

Graph Transformers have recently been successful in various graph representation learning tasks, providing a number of advantages over message-passing Graph Neural Networks. Utilizing Graph Transformers for learning the representation of the brain functional connectivity network is also gaining interest. However, studies to date have underlooked the temporal dynamics of functional connectivity, which fluctuates over time. Here, we propose a method for learning the representation of dynamic functional connectivity with Graph Transformers. Specifically, we define the connectome embedding, which holds the position, structure, and time information of the functional connectivity graph, and use Transformers to learn its representation across time. We perform experiments with over 50,000 resting-state fMRI samples obtained from three datasets, which is the largest number of fMRI data used in studies by far. The experimental results show that our proposed method outperforms other competitive baselines in gender classification and age regression tasks based on the functional connectivity extracted from the fMRI data.

Many real-world graphs frequently present challenges for graph learning due to the presence of both heterophily and heterogeneity. However, existing benchmarks for graph learning often focus on heterogeneous graphs with homophily or homogeneous graphs with heterophily, leaving a gap in understanding how methods perform on graphs that are both heterogeneous and heterophilic. To bridge this gap, we introduce H2GB, a novel graph benchmark that brings together the complexities of both the heterophily and heterogeneity properties of graphs. Our benchmark encompasses 9 diverse real-world datasets across 5 domains, 28 baseline model implementations, and 26 benchmark results. In addition, we present a modular graph transformer framework UnifiedGT and a new model variant, H2G-former, that excels at this challenging benchmark. By integrating masked label embeddings, cross-type heterogeneous attention, and type-specific FFNs, H2G-former effectively tackles graph heterophily and heterogeneity. Extensive experiments across 26 baselines on H2GB reveal inadequacies of current models on heterogeneous heterophilic graph learning, and demonstrate the superiority of our H2G-former over existing solutions. Both the benchmark and the framework are available on GitHub (https://github.com/junhongmit/H2GB) and PyPI (https://pypi.org/project/H2GB), and documentation can be found at https://junhongmit.github.io/H2GB/.

While Graph Neural Networks have gained popularity in multiple domains, graph-structured input remains a major challenge due to (a) over-smoothing, (b) noisy neighbours (heterophily), and (c) the suspended animation problem. To address all these problems simultaneously, we propose a novel graph neural network FDGATII, inspired by attention mechanism's ability to focus on selective information supplemented with two feature preserving mechanisms. FDGATII combines Initial Residuals and Identity Mapping with the more expressive dynamic self-attention to handle noise prevalent from the neighbourhoods in heterophilic data sets. By using sparse dynamic attention, FDGATII is inherently parallelizable in design, whist efficient in operation; thus theoretically able to scale to arbitrary graphs with ease. Our approach has been extensively evaluated on 7 datasets. We show that FDGATII outperforms GAT and GCN based benchmarks in accuracy and performance on fully supervised tasks, obtaining state-of-the-art results on Chameleon and Cornell datasets with zero domain-specific graph pre-processing, and demonstrate its versatility and fairness.

Sparse dictionary learning has been a rapidly growing technique in mechanistic interpretability to attack superposition and extract more human-understandable features from model activations. We ask a further question based on the extracted more monosemantic features: How do we recognize circuits connecting the enormous amount of dictionary features? We propose a circuit discovery framework alternative to activation patching. Our framework suffers less from out-of-distribution and proves to be more efficient in terms of asymptotic complexity. The basic unit in our framework is dictionary features decomposed from all modules writing to the residual stream, including embedding, attention output and MLP output. Starting from any logit, dictionary feature or attention score, we manage to trace down to lower-level dictionary features of all tokens and compute their contribution to these more interpretable and local model behaviors. We dig in a small transformer trained on a synthetic task named Othello and find a number of human-understandable fine-grained circuits inside of it.

Advances in Visually Rich Document Understanding (VrDU) have enabled information extraction and question answering over documents with complex layouts. Two tropes of architectures have emerged -- transformer-based models inspired by LLMs, and Graph Neural Networks. In this paper, we introduce DocGraphLM, a novel framework that combines pre-trained language models with graph semantics. To achieve this, we propose 1) a joint encoder architecture to represent documents, and 2) a novel link prediction approach to reconstruct document graphs. DocGraphLM predicts both directions and distances between nodes using a convergent joint loss function that prioritizes neighborhood restoration and downweighs distant node detection. Our experiments on three SotA datasets show consistent improvement on IE and QA tasks with the adoption of graph features. Moreover, we report that adopting the graph features accelerates convergence in the learning process during training, despite being solely constructed through link prediction.

Sparse neural networks have shown similar or better generalization performance than their dense counterparts while having higher parameter efficiency. This has motivated a number of works to learn or search for high performing sparse networks. While reports of task performance or efficiency gains are impressive, standard baselines are lacking leading to poor comparability and unreliable reproducibility across methods. In this work, we propose Random Search as a baseline algorithm for finding good sparse configurations and study its performance. We apply Random Search on the node space of an overparameterized network with the goal of finding better initialized sparse sub-networks that are positioned more advantageously in the loss landscape. We record the post-training performances of the found sparse networks and at various levels of sparsity, and compare against both their fully connected parent networks and random sparse configurations at the same sparsity levels. First, we demonstrate performance at different levels of sparsity and highlight that a significant level of performance can still be preserved even when the network is highly sparse. Second, we observe that for this sparse architecture search task, initialized sparse networks found by Random Search neither perform better nor converge more efficiently than their random counterparts. Thus we conclude that Random Search may be viewed as a reasonable neutral baseline for sparsity search methods.

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.

The attention mechanism of a transformer has a quadratic complexity, leading to high inference costs and latency for long sequences. However, attention matrices are mostly sparse, which implies that many entries may be omitted from computation for efficient inference. Sparse attention inference methods aim to reduce this computational burden; however, they also come with a troublesome performance degradation. We discover that one reason for this degradation is that the sparse calculation induces a distributional shift in the attention outputs. The distributional shift causes decoding-time queries to fail to align well with the appropriate keys from the prefill stage, leading to a drop in performance. We propose a simple, novel, and effective procedure for correcting this distributional shift, bringing the distribution of sparse attention outputs closer to that of quadratic attention. Our method can be applied on top of any sparse attention method, and results in an average 36%pt performance increase, recovering 88% of quadratic attention accuracy on the 131K RULER benchmark when applied on top of sliding window attention with sink tokens while only adding a small overhead. Our method can maintain approximately 98.5% sparsity over full quadratic attention, making our model 32 times faster than Flash Attention 2 when processing 1M token prefills.

Sparsely-gated Mixture of Experts networks (MoEs) have demonstrated excellent scalability in Natural Language Processing. In Computer Vision, however, almost all performant networks are "dense", that is, every input is processed by every parameter. We present a Vision MoE (V-MoE), a sparse version of the Vision Transformer, that is scalable and competitive with the largest dense networks. When applied to image recognition, V-MoE matches the performance of state-of-the-art networks, while requiring as little as half of the compute at inference time. Further, we propose an extension to the routing algorithm that can prioritize subsets of each input across the entire batch, leading to adaptive per-image compute. This allows V-MoE to trade-off performance and compute smoothly at test-time. Finally, we demonstrate the potential of V-MoE to scale vision models, and train a 15B parameter model that attains 90.35% on ImageNet.

Language Models (LMs) are increasingly challenging the dominance of domain-specific models, including Graph Neural Networks (GNNs) and Graph Transformers (GTs), in graph learning tasks. Following this trend, we propose a novel approach that empowers off-the-shelf LMs to achieve performance comparable to state-of-the-art GNNs on node classification tasks, without requiring any architectural modification. By preserving the LM's original architecture, our approach retains a key benefit of LM instruction tuning: the ability to jointly train on diverse datasets, fostering greater flexibility and efficiency. To achieve this, we introduce two key augmentation strategies: (1) Enriching LMs' input using topological and semantic retrieval methods, which provide richer contextual information, and (2) guiding the LMs' classification process through a lightweight GNN classifier that effectively prunes class candidates. Our experiments on real-world datasets show that backbone Flan-T5 models equipped with these augmentation strategies outperform state-of-the-art text-output node classifiers and are comparable to top-performing vector-output node classifiers. By bridging the gap between specialized task-specific node classifiers and general LMs, this work paves the way for more versatile and widely applicable graph learning models. We will open-source the code upon publication.

In this paper, we contend that a natural objective of representation learning is to compress and transform the distribution of the data, say sets of tokens, towards a low-dimensional Gaussian mixture supported on incoherent subspaces. The goodness of such a representation can be evaluated by a principled measure, called sparse rate reduction, that simultaneously maximizes the intrinsic information gain and extrinsic sparsity of the learned representation. From this perspective, popular deep network architectures, including transformers, can be viewed as realizing iterative schemes to optimize this measure. Particularly, we derive a transformer block from alternating optimization on parts of this objective: the multi-head self-attention operator compresses the representation by implementing an approximate gradient descent step on the coding rate of the features, and the subsequent multi-layer perceptron sparsifies the features. This leads to a family of white-box transformer-like deep network architectures, named CRATE, which are mathematically fully interpretable. We show, by way of a novel connection between denoising and compression, that the inverse to the aforementioned compressive encoding can be realized by the same class of CRATE architectures. Thus, the so-derived white-box architectures are universal to both encoders and decoders. Experiments show that these networks, despite their simplicity, indeed learn to compress and sparsify representations of large-scale real-world image and text datasets, and achieve performance very close to highly engineered transformer-based models: ViT, MAE, DINO, BERT, and GPT2. We believe the proposed computational framework demonstrates great potential in bridging the gap between theory and practice of deep learning, from a unified perspective of data compression. Code is available at: https://ma-lab-berkeley.github.io/CRATE .

The transformer architecture has driven breakthroughs in recent years on tasks which require modeling pairwise relationships between sequential elements, as is the case in natural language understanding. However, long seqeuences pose a problem due to the quadratic complexity of the attention operation. Previous research has aimed to lower the complexity by sparsifying or linearly approximating the attention matrix. Yet, these approaches cannot straightforwardly distill knowledge from a teacher's attention matrix and often require complete retraining from scratch. Furthermore, previous sparse and linear approaches lose interpretability if they cannot produce full attention matrices. To address these challenges, we propose SEA: Sparse linear attention with an Estimated Attention mask. SEA estimates the attention matrix with linear complexity via kernel-based linear attention, then subsequently creates a sparse attention matrix with a top-k selection to perform a sparse attention operation. For language modeling tasks (Wikitext2), previous linear and sparse attention methods show roughly two-fold worse perplexity scores over the quadratic OPT-1.3B baseline, while SEA achieves better perplexity than OPT-1.3B, using roughly half the memory of OPT-1.3B, providing interpretable attention matrix. We believe that our work will have a large practical impact, as it opens the possibility of running large transformers on resource-limited devices with less memory.

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.

To address the challenge of increasing network size, researchers have developed sparse models through network pruning. However, maintaining model accuracy while achieving significant speedups on general computing devices remains an open problem. In this paper, we present a novel mobile inference acceleration framework SparseByteNN, which leverages fine-grained kernel sparsity to achieve real-time execution as well as high accuracy. Our framework consists of two parts: (a) A fine-grained kernel sparsity schema with a sparsity granularity between structured pruning and unstructured pruning. It designs multiple sparse patterns for different operators. Combined with our proposed whole network rearrangement strategy, the schema achieves a high compression rate and high precision at the same time. (b) Inference engine co-optimized with the sparse pattern. The conventional wisdom is that this reduction in theoretical FLOPs does not translate into real-world efficiency gains. We aim to correct this misconception by introducing a family of efficient sparse kernels for ARM and WebAssembly. Equipped with our efficient implementation of sparse primitives, we show that sparse versions of MobileNet-v1 outperform strong dense baselines on the efficiency-accuracy curve. Experimental results on Qualcomm 855 show that for 30% sparse MobileNet-v1, SparseByteNN achieves 1.27x speedup over the dense version and 1.29x speedup over the state-of-the-art sparse inference engine MNN with a slight accuracy drop of 0.224%. The source code of SparseByteNN will be available at https://github.com/lswzjuer/SparseByteNN

Transformer-based language models are applied to a wide range of applications in natural language processing. However, they are inefficient and difficult to deploy. In recent years, many compression algorithms have been proposed to increase the implementation efficiency of large Transformer-based models on target hardware. In this work we present a new method for training sparse pre-trained Transformer language models by integrating weight pruning and model distillation. These sparse pre-trained models can be used to transfer learning for a wide range of tasks while maintaining their sparsity pattern. We demonstrate our method with three known architectures to create sparse pre-trained BERT-Base, BERT-Large and DistilBERT. We show how the compressed sparse pre-trained models we trained transfer their knowledge to five different downstream natural language tasks with minimal accuracy loss. Moreover, we show how to further compress the sparse models' weights to 8bit precision using quantization-aware training. For example, with our sparse pre-trained BERT-Large fine-tuned on SQuADv1.1 and quantized to 8bit we achieve a compression ratio of 40X for the encoder with less than 1% accuracy loss. To the best of our knowledge, our results show the best compression-to-accuracy ratio for BERT-Base, BERT-Large, and DistilBERT.

Graph Convolutional Networks (GCNs) and their variants have experienced significant attention and have become the de facto methods for learning graph representations. GCNs derive inspiration primarily from recent deep learning approaches, and as a result, may inherit unnecessary complexity and redundant computation. In this paper, we reduce this excess complexity through successively removing nonlinearities and collapsing weight matrices between consecutive layers. We theoretically analyze the resulting linear model and show that it corresponds to a fixed low-pass filter followed by a linear classifier. Notably, our experimental evaluation demonstrates that these simplifications do not negatively impact accuracy in many downstream applications. Moreover, the resulting model scales to larger datasets, is naturally interpretable, and yields up to two orders of magnitude speedup over FastGCN.

Dynamic Sparse Training (DST) methods achieve state-of-the-art results in sparse neural network training, matching the generalization of dense models while enabling sparse training and inference. Although the resulting models are highly sparse and theoretically less computationally expensive, achieving speedups with unstructured sparsity on real-world hardware is challenging. In this work, we propose a sparse-to-sparse DST method, Structured RigL (SRigL), to learn a variant of fine-grained structured N:M sparsity by imposing a constant fan-in constraint. Using our empirical analysis of existing DST methods at high sparsity, we additionally employ a neuron ablation method which enables SRigL to achieve state-of-the-art sparse-to-sparse structured DST performance on a variety of Neural Network (NN) architectures. We demonstrate reduced real-world timings on CPU for online inference -- 3.6x/2x faster at 90% sparsity than equivalent dense/unstructured sparse layers, respectively. Our source code is available at https://github.com/calgaryml/condensed-sparsity

Recent improvements in KG-to-text generation are due to additional auxiliary pre-training tasks designed to give the fine-tune task a boost in performance. These tasks require extensive computational resources while only suggesting marginal improvements. Here, we demonstrate that by fusing graph-aware elements into existing pre-trained language models, we are able to outperform state-of-the-art models and close the gap imposed by additional pre-training tasks. We do so by proposing a mask structure to capture neighborhood information and a novel type encoder that adds a bias to the graph-attention weights depending on the connection type. Experiments on two KG-to-text benchmark datasets show our models are competitive while involving fewer parameters and no additional pre-training tasks. By formulating the problem as a framework, we can interchange the various proposed components and begin interpreting KG-to-text generative models based on the topological and type information found in a graph.

Transformer models, despite their impressive performance, often face practical limitations due to their high computational requirements. At the same time, previous studies have revealed significant activation sparsity in these models, indicating the presence of redundant computations. In this paper, we propose Dynamic Sparsified Transformer Inference (DSTI), a method that radically reduces the inference cost of Transformer models by enforcing activation sparsity and subsequently transforming a dense model into its sparse Mixture of Experts (MoE) version. We demonstrate that it is possible to train small gating networks that successfully predict the relative contribution of each expert during inference. Furthermore, we introduce a mechanism that dynamically determines the number of executed experts individually for each token. DSTI can be applied to any Transformer-based architecture and has negligible impact on the accuracy. For the BERT-base classification model, we reduce inference cost by almost 60%.

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.

Autoregressive decoding limits the efficiency of transformers for Machine Translation (MT). The community proposed specific network architectures and learning-based methods to solve this issue, which are expensive and require changes to the MT model, trading inference speed at the cost of the translation quality. In this paper, we propose to address the problem from the point of view of decoding algorithms, as a less explored but rather compelling direction. We propose to reframe the standard greedy autoregressive decoding of MT with a parallel formulation leveraging Jacobi and Gauss-Seidel fixed-point iteration methods for fast inference. This formulation allows to speed up existing models without training or modifications while retaining translation quality. We present three parallel decoding algorithms and test them on different languages and models showing how the parallelization introduces a speedup up to 38% w.r.t. the standard autoregressive decoding and nearly 2x when scaling the method on parallel resources. Finally, we introduce a decoding dependency graph visualizer (DDGviz) that let us see how the model has learned the conditional dependence between tokens and inspect the decoding procedure.

Transformers trained with self-supervised learning using self-distillation loss (DINO) have been shown to produce attention maps that highlight salient foreground objects. In this paper, we demonstrate a graph-based approach that uses the self-supervised transformer features to discover an object from an image. Visual tokens are viewed as nodes in a weighted graph with edges representing a connectivity score based on the similarity of tokens. Foreground objects can then be segmented using a normalized graph-cut to group self-similar regions. We solve the graph-cut problem using spectral clustering with generalized eigen-decomposition and show that the second smallest eigenvector provides a cutting solution since its absolute value indicates the likelihood that a token belongs to a foreground object. Despite its simplicity, this approach significantly boosts the performance of unsupervised object discovery: we improve over the recent state of the art LOST by a margin of 6.9%, 8.1%, and 8.1% respectively on the VOC07, VOC12, and COCO20K. The performance can be further improved by adding a second stage class-agnostic detector (CAD). Our proposed method can be easily extended to unsupervised saliency detection and weakly supervised object detection. For unsupervised saliency detection, we improve IoU for 4.9%, 5.2%, 12.9% on ECSSD, DUTS, DUT-OMRON respectively compared to previous state of the art. For weakly supervised object detection, we achieve competitive performance on CUB and ImageNet.

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

Graph neural networks have recently achieved remarkable success in representing graph-structured data, with rapid progress in both the node embedding and graph pooling methods. Yet, they mostly focus on capturing information from the nodes considering their connectivity, and not much work has been done in representing the edges, which are essential components of a graph. However, for tasks such as graph reconstruction and generation, as well as graph classification tasks for which the edges are important for discrimination, accurately representing edges of a given graph is crucial to the success of the graph representation learning. To this end, we propose a novel edge representation learning framework based on Dual Hypergraph Transformation (DHT), which transforms the edges of a graph into the nodes of a hypergraph. This dual hypergraph construction allows us to apply message-passing techniques for node representations to edges. After obtaining edge representations from the hypergraphs, we then cluster or drop edges to obtain holistic graph-level edge representations. We validate our edge representation learning method with hypergraphs on diverse graph datasets for graph representation and generation performance, on which our method largely outperforms existing graph representation learning methods. Moreover, our edge representation learning and pooling method also largely outperforms state-of-the-art graph pooling methods on graph classification, not only because of its accurate edge representation learning, but also due to its lossless compression of the nodes and removal of irrelevant edges for effective message-passing.

We propose GS-LRM, a scalable large reconstruction model that can predict high-quality 3D Gaussian primitives from 2-4 posed sparse images in 0.23 seconds on single A100 GPU. Our model features a very simple transformer-based architecture; we patchify input posed images, pass the concatenated multi-view image tokens through a sequence of transformer blocks, and decode final per-pixel Gaussian parameters directly from these tokens for differentiable rendering. In contrast to previous LRMs that can only reconstruct objects, by predicting per-pixel Gaussians, GS-LRM naturally handles scenes with large variations in scale and complexity. We show that our model can work on both object and scene captures by training it on Objaverse and RealEstate10K respectively. In both scenarios, the models outperform state-of-the-art baselines by a wide margin. We also demonstrate applications of our model in downstream 3D generation tasks. Our project webpage is available at: https://sai-bi.github.io/project/gs-lrm/ .

Sparse autoencoders provide a promising unsupervised approach for extracting interpretable features from a language model by reconstructing activations from a sparse bottleneck layer. Since language models learn many concepts, autoencoders need to be very large to recover all relevant features. However, studying the properties of autoencoder scaling is difficult due to the need to balance reconstruction and sparsity objectives and the presence of dead latents. We propose using k-sparse autoencoders [Makhzani and Frey, 2013] to directly control sparsity, simplifying tuning and improving the reconstruction-sparsity frontier. Additionally, we find modifications that result in few dead latents, even at the largest scales we tried. Using these techniques, we find clean scaling laws with respect to autoencoder size and sparsity. We also introduce several new metrics for evaluating feature quality based on the recovery of hypothesized features, the explainability of activation patterns, and the sparsity of downstream effects. These metrics all generally improve with autoencoder size. To demonstrate the scalability of our approach, we train a 16 million latent autoencoder on GPT-4 activations for 40 billion tokens. We release training code and autoencoders for open-source models, as well as a visualizer.

Attention layers, as commonly used in transformers, form the backbone of modern deep learning, yet there is no mathematical description of their benefits and deficiencies as compared with other architectures. In this work we establish both positive and negative results on the representation power of attention layers, with a focus on intrinsic complexity parameters such as width, depth, and embedding dimension. On the positive side, we present a sparse averaging task, where recurrent networks and feedforward networks all have complexity scaling polynomially in the input size, whereas transformers scale merely logarithmically in the input size; furthermore, we use the same construction to show the necessity and role of a large embedding dimension in a transformer. On the negative side, we present a triple detection task, where attention layers in turn have complexity scaling linearly in the input size; as this scenario seems rare in practice, we also present natural variants that can be efficiently solved by attention layers. The proof techniques emphasize the value of communication complexity in the analysis of transformers and related models, and the role of sparse averaging as a prototypical attention task, which even finds use in the analysis of triple detection.

Graph Attention Networks (GATs) are one of the most popular GNN architectures and are considered as the state-of-the-art architecture for representation learning with graphs. In GAT, every node attends to its neighbors given its own representation as the query. However, in this paper we show that GAT computes a very limited kind of attention: the ranking of the attention scores is unconditioned on the query node. We formally define this restricted kind of attention as static attention and distinguish it from a strictly more expressive dynamic attention. Because GATs use a static attention mechanism, there are simple graph problems that GAT cannot express: in a controlled problem, we show that static attention hinders GAT from even fitting the training data. To remove this limitation, we introduce a simple fix by modifying the order of operations and propose GATv2: a dynamic graph attention variant that is strictly more expressive than GAT. We perform an extensive evaluation and show that GATv2 outperforms GAT across 11 OGB and other benchmarks while we match their parametric costs. Our code is available at https://github.com/tech-srl/how_attentive_are_gats . GATv2 is available as part of the PyTorch Geometric library, the Deep Graph Library, and the TensorFlow GNN library.

Given a graph G and the desired size k in bits, how can we summarize G within k bits, while minimizing the information loss? Large-scale graphs have become omnipresent, posing considerable computational challenges. Analyzing such large graphs can be fast and easy if they are compressed sufficiently to fit in main memory or even cache. Graph summarization, which yields a coarse-grained summary graph with merged nodes, stands out with several advantages among graph compression techniques. Thus, a number of algorithms have been developed for obtaining a concise summary graph with little information loss or equivalently small reconstruction error. However, the existing methods focus solely on reducing the number of nodes, and they often yield dense summary graphs, failing to achieve better compression rates. Moreover, due to their limited scalability, they can be applied only to moderate-size graphs. In this work, we propose SSumM, a scalable and effective graph-summarization algorithm that yields a sparse summary graph. SSumM not only merges nodes together but also sparsifies the summary graph, and the two strategies are carefully balanced based on the minimum description length principle. Compared with state-of-the-art competitors, SSumM is (a) Concise: yields up to 11.2X smaller summary graphs with similar reconstruction error, (b) Accurate: achieves up to 4.2X smaller reconstruction error with similarly concise outputs, and (c) Scalable: summarizes 26X larger graphs while exhibiting linear scalability. We validate these advantages through extensive experiments on 10 real-world graphs.

We introduce a self-supervised approach for learning node and graph level representations by contrasting structural views of graphs. We show that unlike visual representation learning, increasing the number of views to more than two or contrasting multi-scale encodings do not improve performance, and the best performance is achieved by contrasting encodings from first-order neighbors and a graph diffusion. We achieve new state-of-the-art results in self-supervised learning on 8 out of 8 node and graph classification benchmarks under the linear evaluation protocol. For example, on Cora (node) and Reddit-Binary (graph) classification benchmarks, we achieve 86.8% and 84.5% accuracy, which are 5.5% and 2.4% relative improvements over previous state-of-the-art. When compared to supervised baselines, our approach outperforms them in 4 out of 8 benchmarks. Source code is released at: https://github.com/kavehhassani/mvgrl

Ever since their conception, Transformers have taken over traditional sequence models in many tasks, such as NLP, image classification, and video/audio processing, for their fast training and superior performance. Much of the merit is attributable to positional encoding and multi-head attention. However, Transformers fall short in learning long-range dependencies mainly due to the quadratic complexity scaled with context length, in terms of both time and space. Consequently, over the past five years, a myriad of methods has been proposed to make Transformers more efficient. In this work, we first take a step back, study and compare existing solutions to long-sequence modeling in terms of their pure mathematical formulation. Specifically, we summarize them using a unified template, given their shared nature of token mixing. Through benchmarks, we then demonstrate that long context length does yield better performance, albeit application-dependent, and traditional Transformer models fall short in taking advantage of long-range dependencies. Next, inspired by emerging sparse models of huge capacity, we propose a machine learning system for handling million-scale dependencies. As a proof of concept, we evaluate the performance of one essential component of this system, namely, the distributed multi-head attention. We show that our algorithm can scale up attention computation by almost 40times using four GeForce RTX 4090 GPUs, compared to vanilla multi-head attention mechanism. We believe this study is an instrumental step towards modeling million-scale dependencies.

Following the success of Word2Vec embeddings, graph embeddings (GEs) have gained substantial traction. GEs are commonly generated and evaluated extrinsically on downstream applications, but intrinsic evaluations of the original graph properties in terms of topological structure and semantic information have been lacking. Understanding these will help identify the deficiency of the various families of GE methods when vectorizing graphs in terms of preserving the relevant knowledge or learning incorrect knowledge. To address this, we propose RESTORE, a framework for intrinsic GEs assessment through graph reconstruction. We show that reconstructing the original graph from the underlying GEs yields insights into the relative amount of information preserved in a given vector form. We first introduce the graph reconstruction task. We generate GEs from three GE families based on factorization methods, random walks, and deep learning (with representative algorithms from each family) on the CommonSense Knowledge Graph (CSKG). We analyze their effectiveness in preserving the (a) topological structure of node-level graph reconstruction with an increasing number of hops and (b) semantic information on various word semantic and analogy tests. Our evaluations show deep learning-based GE algorithm (SDNE) is overall better at preserving (a) with a mean average precision (mAP) of 0.54 and 0.35 for 2 and 3-hop reconstruction respectively, while the factorization-based algorithm (HOPE) is better at encapsulating (b) with an average Euclidean distance of 0.14, 0.17, and 0.11 for 1, 2, and 3-hop reconstruction respectively. The modest performance of these GEs leaves room for further research avenues on better graph representation learning.

In existing joint detection and tracking methods, pairwise relational features are used to match previous tracklets to current detections. However, the features may not be discriminative enough for a tracker to identify a target from a large number of detections. Selecting only high-scored detections for tracking may lead to missed detections whose confidence score is low. Consequently, in the online setting, this results in disconnections of tracklets which cannot be recovered. In this regard, we present Sparse Graph Tracker (SGT), a novel online graph tracker using higher-order relational features which are more discriminative by aggregating the features of neighboring detections and their relations. SGT converts video data into a graph where detections, their connections, and the relational features of two connected nodes are represented by nodes, edges, and edge features, respectively. The strong edge features allow SGT to track targets with tracking candidates selected by top-K scored detections with large K. As a result, even low-scored detections can be tracked, and the missed detections are also recovered. The robustness of K value is shown through the extensive experiments. In the MOT16/17/20 and HiEve Challenge, SGT outperforms the state-of-the-art trackers with real-time inference speed. Especially, a large improvement in MOTA is shown in the MOT20 and HiEve Challenge. Code is available at https://github.com/HYUNJS/SGT.

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.

Motivated by the factorization inherent in the original fast multipole method and the improved fast Gauss transform we introduce a factorable form of attention that operates efficiently in high dimensions. This approach reduces the computational and memory complexity of the attention mechanism in transformers from O(N^2) to O(N). In comparison to previous attempts, our work presents a linearly scaled attention mechanism that maintains the full representation of the attention matrix without compromising on sparsification and incorporates the all-to-all relationship between tokens. We explore the properties of our new attention metric and conduct tests in various standard settings. Results indicate that our attention mechanism has a robust performance and holds significant promise for diverse applications where self-attention is used.

Neural networks can be significantly compressed by pruning, yielding sparse models with reduced storage and computational demands while preserving predictive performance. Model soups (Wortsman et al., 2022) enhance generalization and out-of-distribution (OOD) performance by averaging the parameters of multiple models into a single one, without increasing inference time. However, achieving both sparsity and parameter averaging is challenging as averaging arbitrary sparse models reduces the overall sparsity due to differing sparse connectivities. This work addresses these challenges by demonstrating that exploring a single retraining phase of Iterative Magnitude Pruning (IMP) with varied hyperparameter configurations such as batch ordering or weight decay yields models suitable for averaging, sharing identical sparse connectivity by design. Averaging these models significantly enhances generalization and OOD performance over their individual counterparts. Building on this, we introduce Sparse Model Soups (SMS), a novel method for merging sparse models by initiating each prune-retrain cycle with the averaged model from the previous phase. SMS preserves sparsity, exploits sparse network benefits, is modular and fully parallelizable, and substantially improves IMP's performance. We further demonstrate that SMS can be adapted to enhance state-of-the-art pruning-during-training approaches.

We propose sparsemax, a new activation function similar to the traditional softmax, but able to output sparse probabilities. After deriving its properties, we show how its Jacobian can be efficiently computed, enabling its use in a network trained with backpropagation. Then, we propose a new smooth and convex loss function which is the sparsemax analogue of the logistic loss. We reveal an unexpected connection between this new loss and the Huber classification loss. We obtain promising empirical results in multi-label classification problems and in attention-based neural networks for natural language inference. For the latter, we achieve a similar performance as the traditional softmax, but with a selective, more compact, attention focus.

Within the graph learning community, conventional wisdom dictates that spectral convolutional networks may only be deployed on undirected graphs: Only there could the existence of a well-defined graph Fourier transform be guaranteed, so that information may be translated between spatial- and spectral domains. Here we show this traditional reliance on the graph Fourier transform to be superfluous and -- making use of certain advanced tools from complex analysis and spectral theory -- extend spectral convolutions to directed graphs. We provide a frequency-response interpretation of newly developed filters, investigate the influence of the basis used to express filters and discuss the interplay with characteristic operators on which networks are based. In order to thoroughly test the developed theory, we conduct experiments in real world settings, showcasing that directed spectral convolutional networks provide new state of the art results for heterophilic node classification on many datasets and -- as opposed to baselines -- may be rendered stable to resolution-scale varying topological perturbations.

Many large-scale systems rely on high-quality deep representations (embeddings) to facilitate tasks like retrieval, search, and generative modeling. Matryoshka Representation Learning (MRL) recently emerged as a solution for adaptive embedding lengths, but it requires full model retraining and suffers from noticeable performance degradations at short lengths. In this paper, we show that sparse coding offers a compelling alternative for achieving adaptive representation with minimal overhead and higher fidelity. We propose Contrastive Sparse Representation (CSR), a method that sparsifies pre-trained embeddings into a high-dimensional but selectively activated feature space. By leveraging lightweight autoencoding and task-aware contrastive objectives, CSR preserves semantic quality while allowing flexible, cost-effective inference at different sparsity levels. Extensive experiments on image, text, and multimodal benchmarks demonstrate that CSR consistently outperforms MRL in terms of both accuracy and retrieval speed-often by large margins-while also cutting training time to a fraction of that required by MRL. Our results establish sparse coding as a powerful paradigm for adaptive representation learning in real-world applications where efficiency and fidelity are both paramount. Code is available at https://github.com/neilwen987/CSR_Adaptive_Rep

Overparameterized neural networks generalize well but are expensive to train. Ideally, one would like to reduce their computational cost while retaining their generalization benefits. Sparse model training is a simple and promising approach to achieve this, but there remain challenges as existing methods struggle with accuracy loss, slow training runtime, or difficulty in sparsifying all model components. The core problem is that searching for a sparsity mask over a discrete set of sparse matrices is difficult and expensive. To address this, our main insight is to optimize over a continuous superset of sparse matrices with a fixed structure known as products of butterfly matrices. As butterfly matrices are not hardware efficient, we propose simple variants of butterfly (block and flat) to take advantage of modern hardware. Our method (Pixelated Butterfly) uses a simple fixed sparsity pattern based on flat block butterfly and low-rank matrices to sparsify most network layers (e.g., attention, MLP). We empirically validate that Pixelated Butterfly is 3x faster than butterfly and speeds up training to achieve favorable accuracy--efficiency tradeoffs. On the ImageNet classification and WikiText-103 language modeling tasks, our sparse models train up to 2.5x faster than the dense MLP-Mixer, Vision Transformer, and GPT-2 medium with no drop in accuracy.

Vision Transformers (ViT) have shown their competitive advantages performance-wise compared to convolutional neural networks (CNNs) though they often come with high computational costs. To this end, previous methods explore different attention patterns by limiting a fixed number of spatially nearby tokens to accelerate the ViT's multi-head self-attention (MHSA) operations. However, such structured attention patterns limit the token-to-token connections to their spatial relevance, which disregards learned semantic connections from a full attention mask. In this work, we propose a novel approach to learn instance-dependent attention patterns, by devising a lightweight connectivity predictor module to estimate the connectivity score of each pair of tokens. Intuitively, two tokens have high connectivity scores if the features are considered relevant either spatially or semantically. As each token only attends to a small number of other tokens, the binarized connectivity masks are often very sparse by nature and therefore provide the opportunity to accelerate the network via sparse computations. Equipped with the learned unstructured attention pattern, sparse attention ViT (Sparsifiner) produces a superior Pareto-optimal trade-off between FLOPs and top-1 accuracy on ImageNet compared to token sparsity. Our method reduces 48% to 69% FLOPs of MHSA while the accuracy drop is within 0.4%. We also show that combining attention and token sparsity reduces ViT FLOPs by over 60%.

Large language models (LLMs) now support extremely long context windows, but the quadratic complexity of vanilla attention results in significantly long Time-to-First-Token (TTFT) latency. Existing approaches to address this complexity require additional pretraining or finetuning, and often sacrifice model accuracy. In this paper, we first provide both theoretical and empirical foundations for near-lossless sparse attention. We find dynamically capturing head-specific sparse patterns at runtime with low overhead is crucial. To address this, we propose SampleAttention, an adaptive structured and near-lossless sparse attention. Leveraging observed significant sparse patterns, SampleAttention attends to a fixed percentage of adjacent tokens to capture local window patterns, and employs a two-stage query-guided key-value filtering approach, which adaptively select a minimum set of key-values with low overhead, to capture column stripe patterns. Comprehensive evaluations show that SampleAttention can seamlessly replace vanilla attention in off-the-shelf LLMs with nearly no accuracy loss, and reduces TTFT by up to 2.42times compared with FlashAttention.

In recent years, there has been a growing emphasis on compressing large pre-trained transformer models for resource-constrained devices. However, traditional pruning methods often leave the embedding layer untouched, leading to model over-parameterization. Additionally, they require extensive compression time with large datasets to maintain performance in pruned models. To address these challenges, we propose VTrans, an iterative pruning framework guided by the Variational Information Bottleneck (VIB) principle. Our method compresses all structural components, including embeddings, attention heads, and layers using VIB-trained masks. This approach retains only essential weights in each layer, ensuring compliance with specified model size or computational constraints. Notably, our method achieves upto 70% more compression than prior state-of-the-art approaches, both task-agnostic and task-specific. We further propose faster variants of our method: Fast-VTrans utilizing only 3% of the data and Faster-VTrans, a time efficient alternative that involves exclusive finetuning of VIB masks, accelerating compression by upto 25 times with minimal performance loss compared to previous methods. Extensive experiments on BERT, ROBERTa, and GPT-2 models substantiate the efficacy of our method. Moreover, our method demonstrates scalability in compressing large models such as LLaMA-2-7B, achieving superior performance compared to previous pruning methods. Additionally, we use attention-based probing to qualitatively assess model redundancy and interpret the efficiency of our approach. Notably, our method considers heads with high attention to special and current tokens in un-pruned model as foremost candidates for pruning while retained heads are observed to attend more to task-critical keywords.

Self-supervised learning (SSL) has been extensively explored in recent years. Particularly, generative SSL has seen emerging success in natural language processing and other AI fields, such as the wide adoption of BERT and GPT. Despite this, contrastive learning-which heavily relies on structural data augmentation and complicated training strategies-has been the dominant approach in graph SSL, while the progress of generative SSL on graphs, especially graph autoencoders (GAEs), has thus far not reached the potential as promised in other fields. In this paper, we identify and examine the issues that negatively impact the development of GAEs, including their reconstruction objective, training robustness, and error metric. We present a masked graph autoencoder GraphMAE that mitigates these issues for generative self-supervised graph pretraining. Instead of reconstructing graph structures, we propose to focus on feature reconstruction with both a masking strategy and scaled cosine error that benefit the robust training of GraphMAE. We conduct extensive experiments on 21 public datasets for three different graph learning tasks. The results manifest that GraphMAE-a simple graph autoencoder with careful designs-can consistently generate outperformance over both contrastive and generative state-of-the-art baselines. This study provides an understanding of graph autoencoders and demonstrates the potential of generative self-supervised pre-training on graphs.

In this work we introduce KERNELIZED TRANSFORMER, a generic, scalable, data driven framework for learning the kernel function in Transformers. Our framework approximates the Transformer kernel as a dot product between spectral feature maps and learns the kernel by learning the spectral distribution. This not only helps in learning a generic kernel end-to-end, but also reduces the time and space complexity of Transformers from quadratic to linear. We show that KERNELIZED TRANSFORMERS achieve performance comparable to existing efficient Transformer architectures, both in terms of accuracy as well as computational efficiency. Our study also demonstrates that the choice of the kernel has a substantial impact on performance, and kernel learning variants are competitive alternatives to fixed kernel Transformers, both in long as well as short sequence tasks.

We revisit the well-studied problem of approximating a matrix product, A^TB, based on small space sketches S(A) and S(B) of A in R^{n times d} and Bin R^{n times m}. We are interested in the setting where the sketches must be computed independently of each other, except for the use of a shared random seed. We prove that, when A and B are sparse, methods based on coordinated random sampling can outperform classical linear sketching approaches, like Johnson-Lindenstrauss Projection or CountSketch. For example, to obtain Frobenius norm error epsilon|A|_F|B|_F, coordinated sampling requires sketches of size O(s/epsilon^2) when A and B have at most s leq d,m non-zeros per row. In contrast, linear sketching leads to sketches of size O(d/epsilon^2) and O(m/epsilon^2) for A and B. We empirically evaluate our approach on two applications: 1) distributed linear regression in databases, a problem motivated by tasks like dataset discovery and augmentation, and 2) approximating attention matrices in transformer-based language models. In both cases, our sampling algorithms yield an order of magnitude improvement over linear sketching.

Large pre-trained transformers are show-stealer in modern-day deep learning, and it becomes crucial to comprehend the parsimonious patterns that exist within them as they grow in scale. With exploding parameter counts, Lottery Ticket Hypothesis (LTH) and its variants, have lost their pragmatism in sparsifying them due to high computation and memory bottleneck of repetitive train-prune-retrain routine of iterative magnitude pruning (IMP) which worsens with increasing model size. This paper comprehensively studies induced sparse patterns across multiple large pre-trained vision and language transformers. We propose the existence of -- essential sparsity defined with a sharp dropping point beyond which the performance declines much faster w.r.t the rise of sparsity level, when we directly remove weights with the smallest magnitudes in one-shot without re-training. We also find essential sparsity to hold valid for N:M sparsity patterns as well as on modern-scale large language models (Vicuna-7B). We also present an intriguing emerging phenomenon of abrupt sparsification during the pre-training of BERT, i.e., BERT suddenly becomes heavily sparse in pre-training after certain iterations. Moreover, our observations also indicate a counter-intuitive finding that BERT trained with a larger amount of pre-training data tends to have a better ability to condense knowledge in comparatively relatively fewer parameters. Lastly, we investigate the effect of the pre-training loss on essential sparsity and discover that self-supervised learning (SSL) objectives trigger stronger emergent sparsification properties than supervised learning (SL). Our codes are available at https://github.com/VITA-Group/essential_sparsity.

Electronic Health Records (EHR) are high-dimensional data with implicit connections among thousands of medical concepts. These connections, for instance, the co-occurrence of diseases and lab-disease correlations can be informative when only a subset of these variables is documented by the clinician. A feasible approach to improving the representation learning of EHR data is to associate relevant medical concepts and utilize these connections. Existing medical ontologies can be the reference for EHR structures, but they place numerous constraints on the data source. Recent progress on graph neural networks (GNN) enables end-to-end learning of topological structures for non-grid or non-sequential data. However, there are problems to be addressed on how to learn the medical graph adaptively and how to understand the effect of the medical graph on representation learning. In this paper, we propose a variationally regularized encoder-decoder graph network that achieves more robustness in graph structure learning by regularizing node representations. Our model outperforms the existing graph and non-graph based methods in various EHR predictive tasks based on both public data and real-world clinical data. Besides the improvements in empirical experiment performances, we provide an interpretation of the effect of variational regularization compared to standard graph neural network, using singular value analysis.

While Diffusion Transformers (DiTs) have achieved breakthroughs in video generation, this long sequence generation task remains constrained by the quadratic complexity of attention mechanisms, resulting in significant inference latency. Through detailed analysis of attention maps in Video Diffusion Transformer (vDiT), we identify three recurring sparsity patterns: diagonal, multi-diagonal, and vertical-stripe structures. And even 3-6\% attention heads can be skipped. Crucially, these patterns exhibit strong layer-depth and head-position correlations but show limited dependence on the input content. Leveraging these findings, we propose Sparse-vDiT, a sparsity acceleration framework for vDiT comprising: 1) Pattern-optimized sparse kernels that replace dense attention with computationally efficient implementations for each identified sparsity pattern. 2) An offline sparse diffusion search algorithm that selects the optimal sparse computation strategy per layer and head via hardware-aware cost modeling. After determining the optimal configuration, we fuse heads within the same layer that share the same attention strategy, enhancing inference efficiency. Integrated into state-of-the-art vDiT models (CogVideoX1.5, HunyuanVideo, and Wan2.1), Sparse-vDiT achieves 2.09times, 2.38times, and 1.67times theoretical FLOP reduction, and actual inference speedups of 1.76times, 1.85times, and 1.58times, respectively, while maintaining high visual fidelity, with PSNR values reaching 24.13, 27.09, and 22.59. Our work demonstrates that latent structural sparsity in vDiTs can be systematically exploited for long video synthesis.

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.

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

Transformer models are foundational to natural language processing (NLP) and computer vision. Despite various recent works devoted to reducing the quadratic cost of such models (as a function of the sequence length n), dealing with ultra long sequences efficiently (e.g., with more than 16K tokens) remains challenging. Applications such as answering questions based on an entire book or summarizing a scientific article are inefficient or infeasible. In this paper, we propose to significantly reduce the dependency of a Transformer model's complexity on n, by compressing the input into a representation whose size r is independent of n at each layer. Specifically, by exploiting the fact that in many tasks, only a small subset of special tokens (we call VIP-tokens) are most relevant to the final prediction, we propose a VIP-token centric compression (Vcc) scheme which selectively compresses the input sequence based on their impact on approximating the representation of these VIP-tokens. Compared with competitive baselines, the proposed algorithm not only is efficient (achieving more than 3times efficiency improvement compared to baselines on 4K and 16K lengths), but also achieves competitive or better performance on a large number of tasks. Further, we show that our algorithm can be scaled to 128K tokens (or more) while consistently offering accuracy improvement.

State-of-the-art LLMs often rely on scale with high computational costs, which has sparked a research agenda to reduce parameter counts and costs without significantly impacting performance. Our study focuses on Transformer-based LLMs, specifically applying low-rank parametrization to the computationally intensive feedforward networks (FFNs), which are less studied than attention blocks. In contrast to previous works, (i) we explore low-rank parametrization at scale, up to 1.3B parameters; (ii) within Transformer language models rather than convolutional architectures; and (iii) starting from training from scratch. Experiments on the large RefinedWeb dataset show that low-rank parametrization is both efficient (e.g., 2.6times FFN speed-up with 32\% parameters) and effective during training. Interestingly, these structured FFNs exhibit steeper scaling curves than the original models. Motivated by this finding, we develop the wide and structured networks surpassing the current medium-sized and large-sized Transformer in perplexity and throughput performance. Our code is available at https://github.com/CLAIRE-Labo/StructuredFFN/tree/main.

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.

Diffusion Transformers (DiTs) have shown remarkable performance in modeling and generating high-quality videos. However, the quadratic computational complexity of 3D full attention mechanism presents significant challenges in scaling video DiT training, especially for high-definition and lengthy videos, where attention can dominate up to 95% of the end-to-end time and necessitate specialized communication paradigms to handle large input sizes. This paper introduces DSV, a novel framework designed to accelerate and scale the training of video DiTs by leveraging the inherent dynamic attention sparsity throughout the training process. DSV employs a two-stage training algorithm that exploits sparsity patterns, focusing on critical elements supported by efficient, tailored kernels. To accommodate the new sparsity dimension, we develop a hybrid sparsity-aware context parallelism that effectively scales to large inputs by addressing the heterogeneity of sparsity across attention heads and blocks, resulting in optimized sparse computation and communication. Extensive evaluations demonstrate that DSV achieves up to 3.02x gain in training throughput with nearly no quality degradation.

Graph neural networks (GNNs) have been successfully applied to learning representation on graphs in many relational tasks. Recently, researchers study neural architecture search (NAS) to reduce the dependence of human expertise and explore better GNN architectures, but they over-emphasize entity features and ignore latent relation information concealed in the edges. To solve this problem, we incorporate edge features into graph search space and propose Edge-featured Graph Neural Architecture Search to find the optimal GNN architecture. Specifically, we design rich entity and edge updating operations to learn high-order representations, which convey more generic message passing mechanisms. Moreover, the architecture topology in our search space allows to explore complex feature dependence of both entities and edges, which can be efficiently optimized by differentiable search strategy. Experiments at three graph tasks on six datasets show EGNAS can search better GNNs with higher performance than current state-of-the-art human-designed and searched-based GNNs.