Daily Papers

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.

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.

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.

The existence of a plethora of language models makes the problem of selecting the best one for a custom task challenging. Most state-of-the-art methods leverage transformer-based models (e.g., BERT) or their variants. Training such models and exploring their hyperparameter space, however, is computationally expensive. Prior work proposes several neural architecture search (NAS) methods that employ performance predictors (e.g., surrogate models) to address this issue; however, analysis has been limited to homogeneous models that use fixed dimensionality throughout the network. This leads to sub-optimal architectures. To address this limitation, we propose a suite of heterogeneous and flexible models, namely FlexiBERT, that have varied encoder layers with a diverse set of possible operations and different hidden dimensions. For better-posed surrogate modeling in this expanded design space, we propose a new graph-similarity-based embedding scheme. We also propose a novel NAS policy, called BOSHNAS, that leverages this new scheme, Bayesian modeling, and second-order optimization, to quickly train and use a neural surrogate model to converge to the optimal architecture. A comprehensive set of experiments shows that the proposed policy, when applied to the FlexiBERT design space, pushes the performance frontier upwards compared to traditional models. FlexiBERT-Mini, one of our proposed models, has 3% fewer parameters than BERT-Mini and achieves 8.9% higher GLUE score. A FlexiBERT model with equivalent performance as the best homogeneous model achieves 2.6x smaller size. FlexiBERT-Large, another proposed model, achieves state-of-the-art results, outperforming the baseline models by at least 5.7% on the GLUE benchmark.

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.

We report a flexible language-model based deep learning strategy, applied here to solve complex forward and inverse problems in protein modeling, based on an attention neural network that integrates transformer and graph convolutional architectures in a causal multi-headed graph mechanism, to realize a generative pretrained model. The model is applied to predict secondary structure content (per-residue level and overall content), protein solubility, and sequencing tasks. Further trained on inverse tasks, the model is rendered capable of designing proteins with these properties as target features. The model is formulated as a general framework, completely prompt-based, and can be adapted for a variety of downstream tasks. We find that adding additional tasks yields emergent synergies that the model exploits in improving overall performance, beyond what would be possible by training a model on each dataset alone. Case studies are presented to validate the method, yielding protein designs specifically focused on structural proteins, but also exploring the applicability in the design of soluble, antimicrobial biomaterials. While our model is trained to ultimately perform 8 distinct tasks, with available datasets it can be extended to solve additional problems. In a broader sense, this work illustrates a form of multiscale modeling that relates a set of ultimate building blocks (here, byte-level utf8 characters) to complex output. This materiomic scheme captures complex emergent relationships between universal building block and resulting properties via a synergizing learning capacity to express a set of potentialities embedded in the knowledge used in training, via the interplay of universality and diversity.

Contemporary machine learning models, such as language models, are powerful, but come with immense resource requirements both at training and inference time. It has been shown that decoder-only language models can be trained to a competitive state with ternary weights (1.58 bits per weight), facilitating efficient inference. Here, we start our exploration with non-transformer model architectures, investigating 1.58-bit training for multi-layer perceptrons and graph neural networks. Then, we explore 1.58-bit training in other transformer-based language models, namely encoder-only and encoder-decoder models. Our results show that in all of these settings, 1.58-bit training is on par with or sometimes even better than the standard 32/16-bit models.

Document AI aims to automatically analyze documents by leveraging natural language processing and computer vision techniques. One of the major tasks of Document AI is document layout analysis, which structures document pages by interpreting the content and spatial relationships of layout, image, and text. This task can be image-centric, wherein the aim is to identify and label various regions such as authors and paragraphs, or text-centric, where the focus is on classifying individual words in a document. Although there are increasingly sophisticated methods for improving layout analysis, doubts remain about the extent to which their findings can be generalized to a broader context. Specifically, prior work developed systems based on very different architectures, such as transformer-based, graph-based, and CNNs. However, no work has mentioned the effectiveness of these models in a comparative analysis. Moreover, while language-independent Document AI models capable of knowledge transfer have been developed, it remains to be investigated to what degree they can effectively transfer knowledge. In this study, we aim to fill these gaps by conducting a comparative evaluation of state-of-the-art models in document layout analysis and investigating the potential of cross-lingual layout analysis by utilizing machine translation techniques.

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.

Structural pruning enables model acceleration by removing structurally-grouped parameters from neural networks. However, the parameter-grouping patterns vary widely across different models, making architecture-specific pruners, which rely on manually-designed grouping schemes, non-generalizable to new architectures. In this work, we study a highly-challenging yet barely-explored task, any structural pruning, to tackle general structural pruning of arbitrary architecture like CNNs, RNNs, GNNs and Transformers. The most prominent obstacle towards this goal lies in the structural coupling, which not only forces different layers to be pruned simultaneously, but also expects all removed parameters to be consistently unimportant, thereby avoiding structural issues and significant performance degradation after pruning. To address this problem, we propose a general and {fully automatic} method, Dependency Graph (DepGraph), to explicitly model the dependency between layers and comprehensively group coupled parameters for pruning. In this work, we extensively evaluate our method on several architectures and tasks, including ResNe(X)t, DenseNet, MobileNet and Vision transformer for images, GAT for graph, DGCNN for 3D point cloud, alongside LSTM for language, and demonstrate that, even with a simple norm-based criterion, the proposed method consistently yields gratifying performances.

This paper presents a novel approach to representation learning in recommender systems by integrating generative self-supervised learning with graph transformer architecture. We highlight the importance of high-quality data augmentation with relevant self-supervised pretext tasks for improving performance. Towards this end, we propose a new approach that automates the self-supervision augmentation process through a rationale-aware generative SSL that distills informative user-item interaction patterns. The proposed recommender with Graph TransFormer (GFormer) that offers parameterized collaborative rationale discovery for selective augmentation while preserving global-aware user-item relationships. In GFormer, we allow the rationale-aware SSL to inspire graph collaborative filtering with task-adaptive invariant rationalization in graph transformer. The experimental results reveal that our GFormer has the capability to consistently improve the performance over baselines on different datasets. Several in-depth experiments further investigate the invariant rationale-aware augmentation from various aspects. The source code for this work is publicly available at: https://github.com/HKUDS/GFormer.

Tracking 3D objects accurately and consistently is crucial for autonomous vehicles, enabling more reliable downstream tasks such as trajectory prediction and motion planning. Based on the substantial progress in object detection in recent years, the tracking-by-detection paradigm has become a popular choice due to its simplicity and efficiency. State-of-the-art 3D multi-object tracking (MOT) approaches typically rely on non-learned model-based algorithms such as Kalman Filter but require many manually tuned parameters. On the other hand, learning-based approaches face the problem of adapting the training to the online setting, leading to inevitable distribution mismatch between training and inference as well as suboptimal performance. In this work, we propose 3DMOTFormer, a learned geometry-based 3D MOT framework building upon the transformer architecture. We use an Edge-Augmented Graph Transformer to reason on the track-detection bipartite graph frame-by-frame and conduct data association via edge classification. To reduce the distribution mismatch between training and inference, we propose a novel online training strategy with an autoregressive and recurrent forward pass as well as sequential batch optimization. Using CenterPoint detections, our approach achieves 71.2% and 68.2% AMOTA on the nuScenes validation and test split, respectively. In addition, a trained 3DMOTFormer model generalizes well across different object detectors. Code is available at: https://github.com/dsx0511/3DMOTFormer.

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.

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.

Despite the widespread applications of machine learning force field (MLFF) on solids and small molecules, there is a notable gap in applying MLFF to complex liquid electrolytes. In this work, we introduce BAMBOO (ByteDance AI Molecular Simulation Booster), a novel framework for molecular dynamics (MD) simulations, with a demonstration of its capabilities in the context of liquid electrolytes for lithium batteries. We design a physics-inspired graph equivariant transformer architecture as the backbone of BAMBOO to learn from quantum mechanical simulations. Additionally, we pioneer an ensemble knowledge distillation approach and apply it on MLFFs to improve the stability of MD simulations. Finally, we propose the density alignment algorithm to align BAMBOO with experimental measurements. BAMBOO demonstrates state-of-the-art accuracy in predicting key electrolyte properties such as density, viscosity, and ionic conductivity across various solvents and salt combinations. Our current model, trained on more than 15 chemical species, achieves the average density error of 0.01 g/cm^3 on various compositions compared with experimental data. Moreover, our model demonstrates transferability to molecules not included in the quantum mechanical dataset. We envision this work as paving the way to a "universal MLFF" capable of simulating properties of common organic liquids.

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}.

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.

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.

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.

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

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.

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.

Scene Graph Generation (SGG) offers a structured representation critical in many computer vision applications. Traditional SGG approaches, however, are limited by a closed-set assumption, restricting their ability to recognize only predefined object and relation categories. To overcome this, we categorize SGG scenarios into four distinct settings based on the node and edge: Closed-set SGG, Open Vocabulary (object) Detection-based SGG (OvD-SGG), Open Vocabulary Relation-based SGG (OvR-SGG), and Open Vocabulary Detection + Relation-based SGG (OvD+R-SGG). While object-centric open vocabulary SGG has been studied recently, the more challenging problem of relation-involved open-vocabulary SGG remains relatively unexplored. To fill this gap, we propose a unified framework named OvSGTR towards fully open vocabulary SGG from a holistic view. The proposed framework is an end-toend transformer architecture, which learns a visual-concept alignment for both nodes and edges, enabling the model to recognize unseen categories. For the more challenging settings of relation-involved open vocabulary SGG, the proposed approach integrates relation-aware pre-training utilizing image-caption data and retains visual-concept alignment through knowledge distillation. Comprehensive experimental results on the Visual Genome benchmark demonstrate the effectiveness and superiority of the proposed framework.

Programming languages possess rich semantic information such as data flow that is represented by graphs and not available from the surface form of source code. Recent code language models have scaled to billions of parameters, but model source code solely as text tokens while ignoring any other structural information. Conversely, models that do encode structural information of code make modifications to the Transformer architecture, limiting their scale and compatibility with pretrained LLMs. In this work, we take the best of both worlds with GALLa - Graph Aligned Large Language Model. GALLa utilizes graph neural networks and cross-modal alignment technologies to inject the structural information of code into LLMs as an auxiliary task during finetuning. This framework is both model-agnostic and task-agnostic, as it can be applied to any code LLM for any code downstream task, and requires the structural graph data only at training time from a corpus unrelated to the finetuning data, while incurring no cost at inference time over the baseline LLM. Experiments on five code tasks with four different baseline LLMs ranging in size from 350M to 8B validate the effectiveness of GALLa, demonstrating consistent improvement over the baseline, even for powerful models such as LLaMA3.

The paper presents a novel approach for vector-floorplan generation via a diffusion model, which denoises 2D coordinates of room/door corners with two inference objectives: 1) a single-step noise as the continuous quantity to precisely invert the continuous forward process; and 2) the final 2D coordinate as the discrete quantity to establish geometric incident relationships such as parallelism, orthogonality, and corner-sharing. Our task is graph-conditioned floorplan generation, a common workflow in floorplan design. We represent a floorplan as 1D polygonal loops, each of which corresponds to a room or a door. Our diffusion model employs a Transformer architecture at the core, which controls the attention masks based on the input graph-constraint and directly generates vector-graphics floorplans via a discrete and continuous denoising process. We have evaluated our approach on RPLAN dataset. The proposed approach makes significant improvements in all the metrics against the state-of-the-art with significant margins, while being capable of generating non-Manhattan structures and controlling the exact number of corners per room. A project website with supplementary video and document is here https://aminshabani.github.io/housediffusion.

Spider webs are incredible biological structures, comprising thin but strong silk filament and arranged into complex hierarchical architectures with striking mechanical properties (e.g., lightweight but high strength, achieving diverse mechanical responses). While simple 2D orb webs can easily be mimicked, the modeling and synthesis of 3D-based web structures remain challenging, partly due to the rich set of design features. Here we provide a detailed analysis of the heterogenous graph structures of spider webs, and use deep learning as a way to model and then synthesize artificial, bio-inspired 3D web structures. The generative AI models are conditioned based on key geometric parameters (including average edge length, number of nodes, average node degree, and others). To identify graph construction principles, we use inductive representation sampling of large experimentally determined spider web graphs, to yield a dataset that is used to train three conditional generative models: 1) An analog diffusion model inspired by nonequilibrium thermodynamics, with sparse neighbor representation, 2) a discrete diffusion model with full neighbor representation, and 3) an autoregressive transformer architecture with full neighbor representation. All three models are scalable, produce complex, de novo bio-inspired spider web mimics, and successfully construct graphs that meet the design objectives. We further propose algorithm that assembles web samples produced by the generative models into larger-scale structures based on a series of geometric design targets, including helical and parametric shapes, mimicking, and extending natural design principles towards integration with diverging engineering objectives. Several webs are manufactured using 3D printing and tested to assess mechanical properties.

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

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

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.

This paper introduces GET-Zero, a model architecture and training procedure for learning an embodiment-aware control policy that can immediately adapt to new hardware changes without retraining. To do so, we present Graph Embodiment Transformer (GET), a transformer model that leverages the embodiment graph connectivity as a learned structural bias in the attention mechanism. We use behavior cloning to distill demonstration data from embodiment-specific expert policies into an embodiment-aware GET model that conditions on the hardware configuration of the robot to make control decisions. We conduct a case study on a dexterous in-hand object rotation task using different configurations of a four-fingered robot hand with joints removed and with link length extensions. Using the GET model along with a self-modeling loss enables GET-Zero to zero-shot generalize to unseen variation in graph structure and link length, yielding a 20% improvement over baseline methods. All code and qualitative video results are on https://get-zero-paper.github.io

A proper scene representation is central to the pursuit of spatial intelligence where agents can robustly reconstruct and efficiently understand 3D scenes. A scene representation is either metric, such as landmark maps in 3D reconstruction, 3D bounding boxes in object detection, or voxel grids in occupancy prediction, or topological, such as pose graphs with loop closures in SLAM or visibility graphs in SfM. In this work, we propose to build Multiview Scene Graphs (MSG) from unposed images, representing a scene topologically with interconnected place and object nodes. The task of building MSG is challenging for existing representation learning methods since it needs to jointly address both visual place recognition, object detection, and object association from images with limited fields of view and potentially large viewpoint changes. To evaluate any method tackling this task, we developed an MSG dataset and annotation based on a public 3D dataset. We also propose an evaluation metric based on the intersection-over-union score of MSG edges. Moreover, we develop a novel baseline method built on mainstream pretrained vision models, combining visual place recognition and object association into one Transformer decoder architecture. Experiments demonstrate our method has superior performance compared to existing relevant baselines.

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 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.

In this paper, we propose a novel method for joint entity and relation extraction from unstructured text by framing it as a conditional sequence generation problem. In contrast to conventional generative information extraction models that are left-to-right token-level generators, our approach is span-based. It generates a linearized graph where nodes represent text spans and edges represent relation triplets. Our method employs a transformer encoder-decoder architecture with pointing mechanism on a dynamic vocabulary of spans and relation types. Our model can capture the structural characteristics and boundaries of entities and relations through span representations while simultaneously grounding the generated output in the original text thanks to the pointing mechanism. Evaluation on benchmark datasets validates the effectiveness of our approach, demonstrating competitive results. Code is available at https://github.com/urchade/ATG.

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.

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.

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.

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.

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 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 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 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%.

In recent years, the transformer architecture has become the de facto standard for machine learning algorithms applied to natural language processing and computer vision. Despite notable evidence of successful deployment of this architecture in the context of robot learning, we claim that vanilla transformers do not fully exploit the structure of the robot learning problem. Therefore, we propose Body Transformer (BoT), an architecture that leverages the robot embodiment by providing an inductive bias that guides the learning process. We represent the robot body as a graph of sensors and actuators, and rely on masked attention to pool information throughout the architecture. The resulting architecture outperforms the vanilla transformer, as well as the classical multilayer perceptron, in terms of task completion, scaling properties, and computational efficiency when representing either imitation or reinforcement learning policies. Additional material including the open-source code is available at https://sferrazza.cc/bot_site.

This paper develops a graph reinforcement learning approach to online planning of the schedule and destinations of electric aircraft that comprise an urban air mobility (UAM) fleet operating across multiple vertiports. This fleet scheduling problem is formulated to consider time-varying demand, constraints related to vertiport capacity, aircraft capacity and airspace safety guidelines, uncertainties related to take-off delay, weather-induced route closures, and unanticipated aircraft downtime. Collectively, such a formulation presents greater complexity, and potentially increased realism, than in existing UAM fleet planning implementations. To address these complexities, a new policy architecture is constructed, primary components of which include: graph capsule conv-nets for encoding vertiport and aircraft-fleet states both abstracted as graphs; transformer layers encoding time series information on demand and passenger fare; and a Multi-head Attention-based decoder that uses the encoded information to compute the probability of selecting each available destination for an aircraft. Trained with Proximal Policy Optimization, this policy architecture shows significantly better performance in terms of daily averaged profits on unseen test scenarios involving 8 vertiports and 40 aircraft, when compared to a random baseline and genetic algorithm-derived optimal solutions, while being nearly 1000 times faster in execution than the latter.

Heavy computation is a bottleneck limiting deep-learningbased feature matching algorithms to be applied in many realtime applications. However, existing lightweight networks optimized for Euclidean data cannot address classical feature matching tasks, since sparse keypoint based descriptors are expected to be matched. This paper tackles this problem and proposes two concepts: 1) a novel parallel attention model entitled ParaFormer and 2) a graph based U-Net architecture with attentional pooling. First, ParaFormer fuses features and keypoint positions through the concept of amplitude and phase, and integrates self- and cross-attention in a parallel manner which achieves a win-win performance in terms of accuracy and efficiency. Second, with U-Net architecture and proposed attentional pooling, the ParaFormer-U variant significantly reduces computational complexity, and minimize performance loss caused by downsampling. Sufficient experiments on various applications, including homography estimation, pose estimation, and image matching, demonstrate that ParaFormer achieves state-of-the-art performance while maintaining high efficiency. The efficient ParaFormer-U variant achieves comparable performance with less than 50% FLOPs of the existing attention-based models.

The task of text-to-SQL parsing, which aims at converting natural language questions into executable SQL queries, has garnered increasing attention in recent years, as it can assist end users in efficiently extracting vital information from databases without the need for technical background. One of the major challenges in text-to-SQL parsing is domain generalization, i.e., how to generalize well to unseen databases. Recently, the pre-trained text-to-text transformer model, namely T5, though not specialized for text-to-SQL parsing, has achieved state-of-the-art performance on standard benchmarks targeting domain generalization. In this work, we explore ways to further augment the pre-trained T5 model with specialized components for text-to-SQL parsing. Such components are expected to introduce structural inductive bias into text-to-SQL parsers thus improving model's capacity on (potentially multi-hop) reasoning, which is critical for generating structure-rich SQLs. To this end, we propose a new architecture GRAPHIX-T5, a mixed model with the standard pre-trained transformer model augmented by some specially-designed graph-aware layers. Extensive experiments and analysis demonstrate the effectiveness of GRAPHIX-T5 across four text-to-SQL benchmarks: SPIDER, SYN, REALISTIC and DK. GRAPHIX-T5 surpass all other T5-based parsers with a significant margin, achieving new state-of-the-art performance. Notably, GRAPHIX-T5-large reach performance superior to the original T5-large by 5.7% on exact match (EM) accuracy and 6.6% on execution accuracy (EX). This even outperforms the T5-3B by 1.2% on EM and 1.5% on EX.

Mamba, a special case of the State Space Model, is gaining popularity as an alternative to template-based deep learning approaches in medical image analysis. While transformers are powerful architectures, they have drawbacks, including quadratic computational complexity and an inability to address long-range dependencies efficiently. This limitation affects the analysis of large and complex datasets in medical imaging, where there are many spatial and temporal relationships. In contrast, Mamba offers benefits that make it well-suited for medical image analysis. It has linear time complexity, which is a significant improvement over transformers. Mamba processes longer sequences without attention mechanisms, enabling faster inference and requiring less memory. Mamba also demonstrates strong performance in merging multimodal data, improving diagnosis accuracy and patient outcomes. The organization of this paper allows readers to appreciate the capabilities of Mamba in medical imaging step by step. We begin by defining core concepts of SSMs and models, including S4, S5, and S6, followed by an exploration of Mamba architectures such as pure Mamba, U-Net variants, and hybrid models with convolutional neural networks, transformers, and Graph Neural Networks. We also cover Mamba optimizations, techniques and adaptations, scanning, datasets, applications, experimental results, and conclude with its challenges and future directions in medical imaging. This review aims to demonstrate the transformative potential of Mamba in overcoming existing barriers within medical imaging while paving the way for innovative advancements in the field. A comprehensive list of Mamba architectures applied in the medical field, reviewed in this work, is available at Github.

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.

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.

Recent years have seen a phenomenal rise in performance and applications of transformer neural networks. The family of transformer networks, including Bidirectional Encoder Representations from Transformer (BERT), Generative Pretrained Transformer (GPT) and Vision Transformer (ViT), have shown their effectiveness across Natural Language Processing (NLP) and Computer Vision (CV) domains. Transformer-based networks such as ChatGPT have impacted the lives of common men. However, the quest for high predictive performance has led to an exponential increase in transformers' memory and compute footprint. Researchers have proposed techniques to optimize transformer inference at all levels of abstraction. This paper presents a comprehensive survey of techniques for optimizing the inference phase of transformer networks. We survey techniques such as knowledge distillation, pruning, quantization, neural architecture search and lightweight network design at the algorithmic level. We further review hardware-level optimization techniques and the design of novel hardware accelerators for transformers. We summarize the quantitative results on the number of parameters/FLOPs and accuracy of several models/techniques to showcase the tradeoff exercised by them. We also outline future directions in this rapidly evolving field of research. We believe that this survey will educate both novice and seasoned researchers and also spark a plethora of research efforts in this field.

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.

Vision transformers have shown unprecedented levels of performance in tackling various visual perception tasks in recent years. However, the architectural and computational complexity of such network architectures have made them challenging to deploy in real-world applications with high-throughput, low-memory requirements. As such, there has been significant research recently on the design of efficient vision transformer architectures. In this study, we explore the generation of fast vision transformer architecture designs via generative architecture search (GAS) to achieve a strong balance between accuracy and architectural and computational efficiency. Through this generative architecture search process, we create TurboViT, a highly efficient hierarchical vision transformer architecture design that is generated around mask unit attention and Q-pooling design patterns. The resulting TurboViT architecture design achieves significantly lower architectural computational complexity (>2.47times smaller than FasterViT-0 while achieving same accuracy) and computational complexity (>3.4times fewer FLOPs and 0.9% higher accuracy than MobileViT2-2.0) when compared to 10 other state-of-the-art efficient vision transformer network architecture designs within a similar range of accuracy on the ImageNet-1K dataset. Furthermore, TurboViT demonstrated strong inference latency and throughput in both low-latency and batch processing scenarios (>3.21times lower latency and >3.18times higher throughput compared to FasterViT-0 for low-latency scenario). These promising results demonstrate the efficacy of leveraging generative architecture search for generating efficient transformer architecture designs for high-throughput scenarios.

Transformer architecture currently represents the main driver behind many successes in a variety of tasks addressed by deep learning, especially the recent advances in natural language processing (NLP) culminating with large language models (LLM). In addition, transformer architecture has found a wide spread of interest from computer vision (CV) researchers and practitioners, allowing for many advancements in vision-related tasks and opening the door for multi-task and multi-modal deep learning architectures that share the same principle of operation. One drawback to these architectures is their reliance on the scaled dot product attention mechanism with the softmax activation function, which is computationally expensive and requires large compute capabilities both for training and inference. This paper investigates substituting the attention mechanism usually adopted for transformer architecture with an architecture incorporating gated linear unit (GLU) activation within a multi-layer perceptron (MLP) structure in conjunction with the default MLP incorporated in the traditional transformer design. Another step forward taken by this paper is to eliminate the second non-gated MLP to further reduce the computational cost. Experimental assessments conducted by this research show that both proposed modifications and reductions offer competitive performance in relation to baseline architectures, in support of the aims of this work in establishing a more efficient yet capable alternative to the traditional attention mechanism as the core component in designing transformer architectures.

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.

Transformers have revolutionized machine learning with their simple yet effective architecture. Pre-training Transformers on massive text datasets from the Internet has led to unmatched generalization for natural language understanding (NLU) tasks. However, such language models remain fragile when tasked with algorithmic forms of reasoning, where computations must be precise and robust. To address this limitation, we propose a novel approach that combines the Transformer's language understanding with the robustness of graph neural network (GNN)-based neural algorithmic reasoners (NARs). Such NARs proved effective as generic solvers for algorithmic tasks, when specified in graph form. To make their embeddings accessible to a Transformer, we propose a hybrid architecture with a two-phase training procedure, allowing the tokens in the language model to cross-attend to the node embeddings from the NAR. We evaluate our resulting TransNAR model on CLRS-Text, the text-based version of the CLRS-30 benchmark, and demonstrate significant gains over Transformer-only models for algorithmic reasoning, both in and out of distribution.

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.

Large models based on the Transformer architecture play increasingly vital roles in artificial intelligence, particularly within the realms of natural language processing (NLP) and computer vision (CV). Model compression methods reduce their memory and computational cost, which is a necessary step to implement the transformer models on practical devices. Given the unique architecture of transformer, featuring alternative attention and Feedforward Neural Network (FFN) modules, specific compression techniques are required. The efficiency of these compression methods is also paramount, as it is usually impractical to retrain large models on the entire training dataset.This survey provides a comprehensive review of recent compression methods, with a specific focus on their application to transformer models. The compression methods are primarily categorized into pruning, quantization, knowledge distillation, and efficient architecture design. In each category, we discuss compression methods for both CV and NLP tasks, highlighting common underlying principles. At last, we delve into the relation between various compression methods, and discuss the further directions in this domain.

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.

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.

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.

Transformers have become the predominant architecture in foundation models due to their excellent performance across various domains. However, the substantial cost of scaling these models remains a significant concern. This problem arises primarily from their dependence on a fixed number of parameters within linear projections. When architectural modifications (e.g., channel dimensions) are introduced, the entire model typically requires retraining from scratch. As model sizes continue growing, this strategy results in increasingly high computational costs and becomes unsustainable. To overcome this problem, we introduce TokenFormer, a natively scalable architecture that leverages the attention mechanism not only for computations among input tokens but also for interactions between tokens and model parameters, thereby enhancing architectural flexibility. By treating model parameters as tokens, we replace all the linear projections in Transformers with our token-parameter attention layer, where input tokens act as queries and model parameters as keys and values. This reformulation allows for progressive and efficient scaling without necessitating retraining from scratch. Our model scales from 124M to 1.4B parameters by incrementally adding new key-value parameter pairs, achieving performance comparable to Transformers trained from scratch while greatly reducing training costs. Code and models are available at https://github.com/Haiyang-W/TokenFormer.

Powerful foundation models, including large language models (LLMs), with Transformer architectures have ushered in a new era of Generative AI across various industries. Industry and research community have witnessed a large number of new applications, based on those foundation models. Such applications include question and answer, customer services, image and video generation, and code completions, among others. However, as the number of model parameters reaches to hundreds of billions, their deployment incurs prohibitive inference costs and high latency in real-world scenarios. As a result, the demand for cost-effective and fast inference using AI accelerators is ever more higher. To this end, our tutorial offers a comprehensive discussion on complementary inference optimization techniques using AI accelerators. Beginning with an overview of basic Transformer architectures and deep learning system frameworks, we deep dive into system optimization techniques for fast and memory-efficient attention computations and discuss how they can be implemented efficiently on AI accelerators. Next, we describe architectural elements that are key for fast transformer inference. Finally, we examine various model compression and fast decoding strategies in the same context.

Vision Transformer has shown great visual representation power in substantial vision tasks such as recognition and detection, and thus been attracting fast-growing efforts on manually designing more effective architectures. In this paper, we propose to use neural architecture search to automate this process, by searching not only the architecture but also the search space. The central idea is to gradually evolve different search dimensions guided by their E-T Error computed using a weight-sharing supernet. Moreover, we provide design guidelines of general vision transformers with extensive analysis according to the space searching process, which could promote the understanding of vision transformer. Remarkably, the searched models, named S3 (short for Searching the Search Space), from the searched space achieve superior performance to recently proposed models, such as Swin, DeiT and ViT, when evaluated on ImageNet. The effectiveness of S3 is also illustrated on object detection, semantic segmentation and visual question answering, demonstrating its generality to downstream vision and vision-language tasks. Code and models will be available at https://github.com/microsoft/Cream.

Transformer architecture has widespread applications, particularly in Natural Language Processing and computer vision. Recently Transformers have been employed in various aspects of time-series analysis. This tutorial provides an overview of the Transformer architecture, its applications, and a collection of examples from recent research papers in time-series analysis. We delve into an explanation of the core components of the Transformer, including the self-attention mechanism, positional encoding, multi-head, and encoder/decoder. Several enhancements to the initial, Transformer architecture are highlighted to tackle time-series tasks. The tutorial also provides best practices and techniques to overcome the challenge of effectively training Transformers for time-series analysis.

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.

Transformer models serve as the backbone of many state-ofthe-art language models, and most use the scaled dot-product attention (SDPA) mechanism to capture relationships between tokens. However, the straightforward implementation of SDPA has quadratic compute and memory complexity with respect to the sequence length. On processor architectures such as GPUs and TPUs, there is a robust body of prior work. However, little work has been performed on non-processor architectures.In this work, we show how the architecture and execution model of Streaming Dataflow Accelerators can help tackle this challenge. We first define abstract hardware that adopts a streaming execution model, and we implement a cycle-accurate simulator of the abstract hardware using the Dataflow Abstract Machine simulation framework. Second, we implement the naive SDPA algorithm on this abstract hardware and show it requires linear (O(N)) intermediate memory. Third, we then modify the naive algorithm, taking inspiration from prior processor-oriented works, by reordering the multiplication and division operations. Finally, we map the modified algorithm to abstract hardware, and confirm that the implementation computes SDPA at full throughput while only using a constant amount (O(1)) of intermediate memory.

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.

With Artificial Intelligence (AI) increasingly permeating various aspects of society, including healthcare, the adoption of the Transformers neural network architecture is rapidly changing many applications. Transformer is a type of deep learning architecture initially developed to solve general-purpose Natural Language Processing (NLP) tasks and has subsequently been adapted in many fields, including healthcare. In this survey paper, we provide an overview of how this architecture has been adopted to analyze various forms of data, including medical imaging, structured and unstructured Electronic Health Records (EHR), social media, physiological signals, and biomolecular sequences. Those models could help in clinical diagnosis, report generation, data reconstruction, and drug/protein synthesis. We identified relevant studies using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We also discuss the benefits and limitations of using transformers in healthcare and examine issues such as computational cost, model interpretability, fairness, alignment with human values, ethical implications, and environmental impact.

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.

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.

The transformer architecture by Vaswani et al. (2017) is now ubiquitous across application domains, from natural language processing to speech processing and image understanding. We propose DenseFormer, a simple modification to the standard architecture that improves the perplexity of the model without increasing its size -- adding a few thousand parameters for large-scale models in the 100B parameters range. Our approach relies on an additional averaging step after each transformer block, which computes a weighted average of current and past representations -- we refer to this operation as Depth-Weighted-Average (DWA). The learned DWA weights exhibit coherent patterns of information flow, revealing the strong and structured reuse of activations from distant layers. Experiments demonstrate that DenseFormer is more data efficient, reaching the same perplexity of much deeper transformer models, and that for the same perplexity, these new models outperform transformer baselines in terms of memory efficiency and inference time.

After their initial success in natural language processing, transformer architectures have rapidly gained traction in computer vision, providing state-of-the-art results for tasks such as image classification, detection, segmentation, and video analysis. We offer three insights based on simple and easy to implement variants of vision transformers. (1) The residual layers of vision transformers, which are usually processed sequentially, can to some extent be processed efficiently in parallel without noticeably affecting the accuracy. (2) Fine-tuning the weights of the attention layers is sufficient to adapt vision transformers to a higher resolution and to other classification tasks. This saves compute, reduces the peak memory consumption at fine-tuning time, and allows sharing the majority of weights across tasks. (3) Adding MLP-based patch pre-processing layers improves Bert-like self-supervised training based on patch masking. We evaluate the impact of these design choices using the ImageNet-1k dataset, and confirm our findings on the ImageNet-v2 test set. Transfer performance is measured across six smaller datasets.

The Transformer is a sequence model that forgoes traditional recurrent architectures in favor of a fully attention-based approach. Besides improving performance, an advantage of using attention is that it can also help to interpret a model by showing how the model assigns weight to different input elements. However, the multi-layer, multi-head attention mechanism in the Transformer model can be difficult to decipher. To make the model more accessible, we introduce an open-source tool that visualizes attention at multiple scales, each of which provides a unique perspective on the attention mechanism. We demonstrate the tool on BERT and OpenAI GPT-2 and present three example use cases: detecting model bias, locating relevant attention heads, and linking neurons to model behavior.

Besides natural language processing, transformers exhibit extraordinary performance in solving broader applications, including scientific computing and computer vision. Previous works try to explain this from the expressive power and capability perspectives that standard transformers are capable of performing some algorithms. To empower transformers with algorithmic capabilities and motivated by the recently proposed looped transformer (Yang et al., 2024; Giannou et al., 2023), we design a novel transformer block, dubbed Algorithm Transformer (abbreviated as AlgoFormer). Compared with the standard transformer and vanilla looped transformer, the proposed AlgoFormer can achieve significantly higher expressiveness in algorithm representation when using the same number of parameters. In particular, inspired by the structure of human-designed learning algorithms, our transformer block consists of a pre-transformer that is responsible for task pre-processing, a looped transformer for iterative optimization algorithms, and a post-transformer for producing the desired results after post-processing. We provide theoretical evidence of the expressive power of the AlgoFormer in solving some challenging problems, mirroring human-designed algorithms. Furthermore, some theoretical and empirical results are presented to show that the designed transformer has the potential to be smarter than human-designed algorithms. Experimental results demonstrate the empirical superiority of the proposed transformer in that it outperforms the standard transformer and vanilla looped transformer in some challenging tasks.

Transformer is a new kind of neural architecture which encodes the input data as powerful features via the attention mechanism. Basically, the visual transformers first divide the input images into several local patches and then calculate both representations and their relationship. Since natural images are of high complexity with abundant detail and color information, the granularity of the patch dividing is not fine enough for excavating features of objects in different scales and locations. In this paper, we point out that the attention inside these local patches are also essential for building visual transformers with high performance and we explore a new architecture, namely, Transformer iN Transformer (TNT). Specifically, we regard the local patches (e.g., 16times16) as "visual sentences" and present to further divide them into smaller patches (e.g., 4times4) as "visual words". The attention of each word will be calculated with other words in the given visual sentence with negligible computational costs. Features of both words and sentences will be aggregated to enhance the representation ability. Experiments on several benchmarks demonstrate the effectiveness of the proposed TNT architecture, e.g., we achieve an 81.5% top-1 accuracy on the ImageNet, which is about 1.7% higher than that of the state-of-the-art visual transformer with similar computational cost. The PyTorch code is available at https://github.com/huawei-noah/CV-Backbones, and the MindSpore code is available at https://gitee.com/mindspore/models/tree/master/research/cv/TNT.

In recent years roboticists have achieved remarkable progress in solving increasingly general tasks on dexterous robotic hardware by leveraging high capacity Transformer network architectures and generative diffusion models. Unfortunately, combining these two orthogonal improvements has proven surprisingly difficult, since there is no clear and well-understood process for making important design choices. In this paper, we identify, study and improve key architectural design decisions for high-capacity diffusion transformer policies. The resulting models can efficiently solve diverse tasks on multiple robot embodiments, without the excruciating pain of per-setup hyper-parameter tuning. By combining the results of our investigation with our improved model components, we are able to present a novel architecture, named \method, that significantly outperforms the state of the art in solving long-horizon (1500+ time-steps) dexterous tasks on a bi-manual ALOHA robot. In addition, we find that our policies show improved scaling performance when trained on 10 hours of highly multi-modal, language annotated ALOHA demonstration data. We hope this work will open the door for future robot learning techniques that leverage the efficiency of generative diffusion modeling with the scalability of large scale transformer architectures. Code, robot dataset, and videos are available at: https://dit-policy.github.io

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

Diagrams matter. Unfortunately, the deep learning community has no standard method for diagramming architectures. The current combination of linear algebra notation and ad-hoc diagrams fails to offer the necessary precision to understand architectures in all their detail. However, this detail is critical for faithful implementation, mathematical analysis, further innovation, and ethical assurances. I present neural circuit diagrams, a graphical language tailored to the needs of communicating deep learning architectures. Neural circuit diagrams naturally keep track of the changing arrangement of data, precisely show how operations are broadcast over axes, and display the critical parallel behavior of linear operations. A lingering issue with existing diagramming methods is the inability to simultaneously express the detail of axes and the free arrangement of data, which neural circuit diagrams solve. Their compositional structure is analogous to code, creating a close correspondence between diagrams and implementation. In this work, I introduce neural circuit diagrams for an audience of machine learning researchers. After introducing neural circuit diagrams, I cover a host of architectures to show their utility and breed familiarity. This includes the transformer architecture, convolution (and its difficult-to-explain extensions), residual networks, the U-Net, and the vision transformer. I include a Jupyter notebook that provides evidence for the close correspondence between diagrams and code. Finally, I examine backpropagation using neural circuit diagrams. I show their utility in providing mathematical insight and analyzing algorithms' time and space complexities.

Transformer-based language models have recently been at the forefront of active research in text generation. However, these models' advances come at the price of prohibitive training costs, with parameter counts in the billions and compute requirements measured in petaflop/s-decades. In this paper, we investigate transformer-based architectures for improving model performance in a low-data regime by selectively replacing attention layers with feed-forward and quasi-recurrent neural network layers. We test these architectures on the standard Enwik8 and Wikitext-103 corpora. Our results show that our reduced architectures outperform existing models with a comparable number of parameters, and obtain comparable performance to larger models while significantly reducing the number of parameters.

In this paper, we present the findings of our Project ALPINE which stands for ``Autoregressive Learning for Planning In NEtworks." Project ALPINE initiates a theoretical investigation into the development of planning capabilities in Transformer-based language models through their autoregressive learning mechanisms, aiming to identify any potential limitations in their planning abilities. We abstract planning as a network path-finding task where the objective is to generate a valid path from a specified source node to a designated target node. In terms of expressiveness, we show that the Transformer is capable of executing path-finding by embedding the adjacency and reachability matrices within its weights. Our theoretical analysis of the gradient-based learning dynamic of the Transformer reveals that the Transformer is capable of learning both the adjacency matrix and a limited form of the reachability matrix. These theoretical insights are then validated through experiments, which demonstrate that the Transformer indeed learns the adjacency matrix and an incomplete reachability matrix, which aligns with the predictions made in our theoretical analysis. Additionally, when applying our methodology to a real-world planning benchmark, called Blocksworld, our observations remain consistent. Our theoretical and empirical analyses further unveil a potential limitation of Transformer in path-finding: it cannot identify reachability relationships through transitivity, and thus would fail when path concatenation is needed to generate a path. In summary, our findings shed new light on how the internal mechanisms of autoregressive learning enable planning in networks. This study may contribute to our understanding of the general planning capabilities in other related domains.

Transformers have become keystone models in natural language processing over the past decade. They have achieved great popularity in deep learning applications, but the increasing sizes of the parameter spaces required by transformer models generate a commensurate need to accelerate performance. Natural language processing problems are also routinely faced with variable-length sequences, as word counts commonly vary among sentences. Existing deep learning frameworks pad variable-length sequences to a maximal length, which adds significant memory and computational overhead. In this paper, we present ByteTransformer, a high-performance transformer boosted for variable-length inputs. We propose a padding-free algorithm that liberates the entire transformer from redundant computations on zero padded tokens. In addition to algorithmic-level optimization, we provide architecture-aware optimizations for transformer functional modules, especially the performance-critical algorithm Multi-Head Attention (MHA). Experimental results on an NVIDIA A100 GPU with variable-length sequence inputs validate that our fused MHA outperforms PyTorch by 6.13x. The end-to-end performance of ByteTransformer for a forward BERT transformer surpasses state-of-the-art transformer frameworks, such as PyTorch JIT, TensorFlow XLA, Tencent TurboTransformer, Microsoft DeepSpeed-Inference and NVIDIA FasterTransformer, by 87\%, 131\%, 138\%, 74\% and 55\%, respectively. We also demonstrate the general applicability of our optimization methods to other BERT-like models, including ALBERT, DistilBERT, and DeBERTa.

Transformer is a transformative framework that models sequential data and has achieved remarkable performance on a wide range of tasks, but with high computational and energy cost. To improve its efficiency, a popular choice is to compress the models via binarization which constrains the floating-point values into binary ones to save resource consumption owing to cheap bitwise operations significantly. However, existing binarization methods only aim at minimizing the information loss for the input distribution statistically, while ignoring the pairwise similarity modeling at the core of the attention. To this end, we propose a new binarization paradigm customized to high-dimensional softmax attention via kernelized hashing, called EcoFormer, to map the original queries and keys into low-dimensional binary codes in Hamming space. The kernelized hash functions are learned to match the ground-truth similarity relations extracted from the attention map in a self-supervised way. Based on the equivalence between the inner product of binary codes and the Hamming distance as well as the associative property of matrix multiplication, we can approximate the attention in linear complexity by expressing it as a dot-product of binary codes. Moreover, the compact binary representations of queries and keys enable us to replace most of the expensive multiply-accumulate operations in attention with simple accumulations to save considerable on-chip energy footprint on edge devices. Extensive experiments on both vision and language tasks show that EcoFormer consistently achieves comparable performance with standard attentions while consuming much fewer resources. For example, based on PVTv2-B0 and ImageNet-1K, Ecoformer achieves a 73% on-chip energy footprint reduction with only a 0.33% performance drop compared to the standard attention. Code is available at https://github.com/ziplab/EcoFormer.

Although purely transformer-based architectures showed promising performance in many computer vision tasks, many hybrid models consisting of CNN and transformer blocks are introduced to fit more specialized tasks. Nevertheless, despite the performance gain of both pure and hybrid transformer-based architectures compared to CNNs in medical imaging segmentation, their high training cost and complexity make it challenging to use them in real scenarios. In this work, we propose simple architectures based on purely convolutional layers, and show that by just taking advantage of the attention map visualizations obtained from a self-supervised pretrained vision transformer network (e.g., DINO) one can outperform complex transformer-based networks with much less computation costs. The proposed architecture is composed of two encoder branches with the original image as input in one branch and the attention map visualizations of the same image from multiple self-attention heads from a pre-trained DINO model (as multiple channels) in the other branch. The results of our experiments on two publicly available medical imaging datasets show that the proposed pipeline outperforms U-Net and the state-of-the-art medical image segmentation models.

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

Transformers have achieved remarkable success across diverse domains, but their monolithic architecture presents challenges in interpretability, adaptability, and scalability. This paper introduces a novel modular Transformer architecture that explicitly decouples knowledge and reasoning through a generalized cross-attention mechanism to a globally shared knowledge base with layer-specific transformations, specifically designed for effective knowledge retrieval. Critically, we provide a rigorous mathematical derivation demonstrating that the Feed-Forward Network (FFN) in a standard Transformer is a specialized case (a closure) of this generalized cross-attention, revealing its role in implicit knowledge retrieval and validating our design. This theoretical framework provides a new lens for understanding FFNs and lays the foundation for future research exploring enhanced interpretability, adaptability, and scalability, enabling richer interplay with external knowledge bases and other systems.

Vision Transformer (ViT) extends the application range of transformers from language processing to computer vision tasks as being an alternative architecture against the existing convolutional neural networks (CNN). Since the transformer-based architecture has been innovative for computer vision modeling, the design convention towards an effective architecture has been less studied yet. From the successful design principles of CNN, we investigate the role of spatial dimension conversion and its effectiveness on transformer-based architecture. We particularly attend to the dimension reduction principle of CNNs; as the depth increases, a conventional CNN increases channel dimension and decreases spatial dimensions. We empirically show that such a spatial dimension reduction is beneficial to a transformer architecture as well, and propose a novel Pooling-based Vision Transformer (PiT) upon the original ViT model. We show that PiT achieves the improved model capability and generalization performance against ViT. Throughout the extensive experiments, we further show PiT outperforms the baseline on several tasks such as image classification, object detection, and robustness evaluation. Source codes and ImageNet models are available at https://github.com/naver-ai/pit

Transformer-based architectures achieved breakthrough performance in natural language processing and computer vision, yet they remain inferior to simpler linear baselines in multivariate long-term forecasting. To better understand this phenomenon, we start by studying a toy linear forecasting problem for which we show that transformers are incapable of converging to their true solution despite their high expressive power. We further identify the attention of transformers as being responsible for this low generalization capacity. Building upon this insight, we propose a shallow lightweight transformer model that successfully escapes bad local minima when optimized with sharpness-aware optimization. We empirically demonstrate that this result extends to all commonly used real-world multivariate time series datasets. In particular, SAMformer surpasses current state-of-the-art methods and is on par with the biggest foundation model MOIRAI while having significantly fewer parameters. The code is available at https://github.com/romilbert/samformer.

Learning feature interaction is the critical backbone to building recommender systems. In web-scale applications, learning feature interaction is extremely challenging due to the sparse and large input feature space; meanwhile, manually crafting effective feature interactions is infeasible because of the exponential solution space. We propose to leverage a Transformer-based architecture with attention layers to automatically capture feature interactions. Transformer architectures have witnessed great success in many domains, such as natural language processing and computer vision. However, there has not been much adoption of Transformer architecture for feature interaction modeling in industry. We aim at closing the gap. We identify two key challenges for applying the vanilla Transformer architecture to web-scale recommender systems: (1) Transformer architecture fails to capture the heterogeneous feature interactions in the self-attention layer; (2) The serving latency of Transformer architecture might be too high to be deployed in web-scale recommender systems. We first propose a heterogeneous self-attention layer, which is a simple yet effective modification to the self-attention layer in Transformer, to take into account the heterogeneity of feature interactions. We then introduce Hiformer (Heterogeneous Interaction Transformer) to further improve the model expressiveness. With low-rank approximation and model pruning, \hiformer enjoys fast inference for online deployment. Extensive offline experiment results corroborates the effectiveness and efficiency of the Hiformer model. We have successfully deployed the Hiformer model to a real world large scale App ranking model at Google Play, with significant improvement in key engagement metrics (up to +2.66\%).

Recent prevailing works on graph machine learning typically follow a similar methodology that involves designing advanced variants of graph neural networks (GNNs) to maintain the superior performance of GNNs on different graphs. In this paper, we aim to streamline the GNN design process and leverage the advantages of Large Language Models (LLMs) to improve the performance of GNNs on downstream tasks. We formulate a new paradigm, coined "LLMs-as-Consultants," which integrates LLMs with GNNs in an interactive manner. A framework named LOGIN (LLM Consulted GNN training) is instantiated, empowering the interactive utilization of LLMs within the GNN training process. First, we attentively craft concise prompts for spotted nodes, carrying comprehensive semantic and topological information, and serving as input to LLMs. Second, we refine GNNs by devising a complementary coping mechanism that utilizes the responses from LLMs, depending on their correctness. We empirically evaluate the effectiveness of LOGIN on node classification tasks across both homophilic and heterophilic graphs. The results illustrate that even basic GNN architectures, when employed within the proposed LLMs-as-Consultants paradigm, can achieve comparable performance to advanced GNNs with intricate designs. Our codes are available at https://github.com/QiaoYRan/LOGIN.

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

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

Owing to their ability to both effectively integrate information over long time horizons and scale to massive amounts of data, self-attention architectures have recently shown breakthrough success in natural language processing (NLP), achieving state-of-the-art results in domains such as language modeling and machine translation. Harnessing the transformer's ability to process long time horizons of information could provide a similar performance boost in partially observable reinforcement learning (RL) domains, but the large-scale transformers used in NLP have yet to be successfully applied to the RL setting. In this work we demonstrate that the standard transformer architecture is difficult to optimize, which was previously observed in the supervised learning setting but becomes especially pronounced with RL objectives. We propose architectural modifications that substantially improve the stability and learning speed of the original Transformer and XL variant. The proposed architecture, the Gated Transformer-XL (GTrXL), surpasses LSTMs on challenging memory environments and achieves state-of-the-art results on the multi-task DMLab-30 benchmark suite, exceeding the performance of an external memory architecture. We show that the GTrXL, trained using the same losses, has stability and performance that consistently matches or exceeds a competitive LSTM baseline, including on more reactive tasks where memory is less critical. GTrXL offers an easy-to-train, simple-to-implement but substantially more expressive architectural alternative to the standard multi-layer LSTM ubiquitously used for RL agents in partially observable environments.

Transformers have become one of the most important architectural innovations in deep learning and have enabled many breakthroughs over the past few years. Here we propose a simple network architecture, gMLP, based on MLPs with gating, and show that it can perform as well as Transformers in key language and vision applications. Our comparisons show that self-attention is not critical for Vision Transformers, as gMLP can achieve the same accuracy. For BERT, our model achieves parity with Transformers on pretraining perplexity and is better on some downstream NLP tasks. On finetuning tasks where gMLP performs worse, making the gMLP model substantially larger can close the gap with Transformers. In general, our experiments show that gMLP can scale as well as Transformers over increased data and compute.

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

Vision Transformer (ViT) demonstrates that Transformer for natural language processing can be applied to computer vision tasks and result in comparable performance to convolutional neural networks (CNN), which have been studied and adopted in computer vision for years. This naturally raises the question of how the performance of ViT can be advanced with design techniques of CNN. To this end, we propose to incorporate two techniques and present ViT-ResNAS, an efficient multi-stage ViT architecture designed with neural architecture search (NAS). First, we propose residual spatial reduction to decrease sequence lengths for deeper layers and utilize a multi-stage architecture. When reducing lengths, we add skip connections to improve performance and stabilize training deeper networks. Second, we propose weight-sharing NAS with multi-architectural sampling. We enlarge a network and utilize its sub-networks to define a search space. A super-network covering all sub-networks is then trained for fast evaluation of their performance. To efficiently train the super-network, we propose to sample and train multiple sub-networks with one forward-backward pass. After that, evolutionary search is performed to discover high-performance network architectures. Experiments on ImageNet demonstrate that ViT-ResNAS achieves better accuracy-MACs and accuracy-throughput trade-offs than the original DeiT and other strong baselines of ViT. Code is available at https://github.com/yilunliao/vit-search.

The robustness of a model for real-world deployment is decided by how well it performs on unseen data and distinguishes between in-domain and out-of-domain samples. Visual document classifiers have shown impressive performance on in-distribution test sets. However, they tend to have a hard time correctly classifying and differentiating out-of-distribution examples. Image-based classifiers lack the text component, whereas multi-modality transformer-based models face the token serialization problem in visual documents due to their diverse layouts. They also require a lot of computing power during inference, making them impractical for many real-world applications. We propose, GVdoc, a graph-based document classification model that addresses both of these challenges. Our approach generates a document graph based on its layout, and then trains a graph neural network to learn node and graph embeddings. Through experiments, we show that our model, even with fewer parameters, outperforms state-of-the-art models on out-of-distribution data while retaining comparable performance on the in-distribution test set.

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

Graph neural networks (GNNs) have been demonstrated to be powerful in modeling graph-structured data. However, training GNNs usually requires abundant task-specific labeled data, which is often arduously expensive to obtain. One effective way to reduce the labeling effort is to pre-train an expressive GNN model on unlabeled data with self-supervision and then transfer the learned model to downstream tasks with only a few labels. In this paper, we present the GPT-GNN framework to initialize GNNs by generative pre-training. GPT-GNN introduces a self-supervised attributed graph generation task to pre-train a GNN so that it can capture the structural and semantic properties of the graph. We factorize the likelihood of the graph generation into two components: 1) Attribute Generation and 2) Edge Generation. By modeling both components, GPT-GNN captures the inherent dependency between node attributes and graph structure during the generative process. Comprehensive experiments on the billion-scale Open Academic Graph and Amazon recommendation data demonstrate that GPT-GNN significantly outperforms state-of-the-art GNN models without pre-training by up to 9.1% across various downstream tasks.

Information flows by routes inside the network via mechanisms implemented in the model. These routes can be represented as graphs where nodes correspond to token representations and edges to operations inside the network. We automatically build these graphs in a top-down manner, for each prediction leaving only the most important nodes and edges. In contrast to the existing workflows relying on activation patching, we do this through attribution: this allows us to efficiently uncover existing circuits with just a single forward pass. Additionally, the applicability of our method is far beyond patching: we do not need a human to carefully design prediction templates, and we can extract information flow routes for any prediction (not just the ones among the allowed templates). As a result, we can talk about model behavior in general, for specific types of predictions, or different domains. We experiment with Llama 2 and show that the role of some attention heads is overall important, e.g. previous token heads and subword merging heads. Next, we find similarities in Llama 2 behavior when handling tokens of the same part of speech. Finally, we show that some model components can be specialized on domains such as coding or multilingual texts.

The rise of transformers in vision tasks not only advances network backbone designs, but also starts a brand-new page to achieve end-to-end image recognition (e.g., object detection and panoptic segmentation). Originated from Natural Language Processing (NLP), transformer architectures, consisting of self-attention and cross-attention, effectively learn long-range interactions between elements in a sequence. However, we observe that most existing transformer-based vision models simply borrow the idea from NLP, neglecting the crucial difference between languages and images, particularly the extremely large sequence length of spatially flattened pixel features. This subsequently impedes the learning in cross-attention between pixel features and object queries. In this paper, we rethink the relationship between pixels and object queries and propose to reformulate the cross-attention learning as a clustering process. Inspired by the traditional k-means clustering algorithm, we develop a k-means Mask Xformer (kMaX-DeepLab) for segmentation tasks, which not only improves the state-of-the-art, but also enjoys a simple and elegant design. As a result, our kMaX-DeepLab achieves a new state-of-the-art performance on COCO val set with 58.0% PQ, Cityscapes val set with 68.4% PQ, 44.0% AP, and 83.5% mIoU, and ADE20K val set with 50.9% PQ and 55.2% mIoU without test-time augmentation or external dataset. We hope our work can shed some light on designing transformers tailored for vision tasks. TensorFlow code and models are available at https://github.com/google-research/deeplab2 A PyTorch re-implementation is also available at https://github.com/bytedance/kmax-deeplab

Transformers have become one of the dominant architectures in deep learning, particularly as a powerful alternative to convolutional neural networks (CNNs) in computer vision. However, Transformer training and inference in previous works can be prohibitively expensive due to the quadratic complexity of self-attention over a long sequence of representations, especially for high-resolution dense prediction tasks. To this end, we present a novel Less attention vIsion Transformer (LIT), building upon the fact that the early self-attention layers in Transformers still focus on local patterns and bring minor benefits in recent hierarchical vision Transformers. Specifically, we propose a hierarchical Transformer where we use pure multi-layer perceptrons (MLPs) to encode rich local patterns in the early stages while applying self-attention modules to capture longer dependencies in deeper layers. Moreover, we further propose a learned deformable token merging module to adaptively fuse informative patches in a non-uniform manner. The proposed LIT achieves promising performance on image recognition tasks, including image classification, object detection and instance segmentation, serving as a strong backbone for many vision tasks. Code is available at: https://github.com/zhuang-group/LIT

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

Transformers have achieved great success in many artificial intelligence fields, such as natural language processing, computer vision, and audio processing. Therefore, it is natural to attract lots of interest from academic and industry researchers. Up to the present, a great variety of Transformer variants (a.k.a. X-formers) have been proposed, however, a systematic and comprehensive literature review on these Transformer variants is still missing. In this survey, we provide a comprehensive review of various X-formers. We first briefly introduce the vanilla Transformer and then propose a new taxonomy of X-formers. Next, we introduce the various X-formers from three perspectives: architectural modification, pre-training, and applications. Finally, we outline some potential directions for future research.

Large language models (LLMs) have garnered significant attention in both the AI community and beyond. Among these, the Generative Pre-trained Transformer (GPT) has emerged as the dominant architecture, spawning numerous variants. However, these variants have undergone pre-training under diverse conditions, including variations in input data, data preprocessing, and training methodologies, resulting in a lack of controlled comparative studies. Here we meticulously examine two prominent open-sourced GPT architectures, GPT-NeoX and LLaMA, leveraging the computational power of Frontier, the world's first Exascale supercomputer. Employing the same materials science text corpus and a comprehensive end-to-end pipeline, we conduct a comparative analysis of their training and downstream performance. Our efforts culminate in achieving state-of-the-art performance on a challenging materials science benchmark. Furthermore, we investigate the computation and energy efficiency, and propose a computationally efficient method for architecture design. To our knowledge, these pre-trained models represent the largest available for materials science. Our findings provide practical guidance for building LLMs on HPC platforms.

Large language model inference is both memory-intensive and time-consuming, often requiring distributed algorithms to efficiently scale. Various model parallelism strategies are used in multi-gpu training and inference to partition computation across multiple devices, reducing memory load and computation time. However, using model parallelism necessitates communication of information between GPUs, which has been a major bottleneck and limits the gains obtained by scaling up the number of devices. We introduce Ladder Residual, a simple architectural modification applicable to all residual-based models that enables straightforward overlapping that effectively hides the latency of communication. Our insight is that in addition to systems optimization, one can also redesign the model architecture to decouple communication from computation. While Ladder Residual can allow communication-computation decoupling in conventional parallelism patterns, we focus on Tensor Parallelism in this paper, which is particularly bottlenecked by its heavy communication. For a Transformer model with 70B parameters, applying Ladder Residual to all its layers can achieve 30% end-to-end wall clock speed up at inference time with TP sharding over 8 devices. We refer the resulting Transformer model as the Ladder Transformer. We train a 1B and 3B Ladder Transformer from scratch and observe comparable performance to a standard dense transformer baseline. We also show that it is possible to convert parts of the Llama-3.1 8B model to our Ladder Residual architecture with minimal accuracy degradation by only retraining for 3B tokens.

GraphRAG addresses significant challenges in Retrieval-Augmented Generation (RAG) by leveraging graphs with embedded knowledge to enhance the reasoning capabilities of Large Language Models (LLMs). Despite its promising potential, the GraphRAG community currently lacks a unified framework for fine-grained decomposition of the graph-based knowledge retrieval process. Furthermore, there is no systematic categorization or evaluation of existing solutions within the retrieval process. In this paper, we present LEGO-GraphRAG, a modular framework that decomposes the retrieval process of GraphRAG into three interconnected modules: subgraph-extraction, path-filtering, and path-refinement. We systematically summarize and classify the algorithms and neural network (NN) models relevant to each module, providing a clearer understanding of the design space for GraphRAG instances. Additionally, we identify key design factors, such as Graph Coupling and Computational Cost, that influence the effectiveness of GraphRAG implementations. Through extensive empirical studies, we construct high-quality GraphRAG instances using a representative selection of solutions and analyze their impact on retrieval and reasoning performance. Our findings offer critical insights into optimizing GraphRAG instance design, ultimately contributing to the advancement of more accurate and contextually relevant LLM applications.

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.

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.

Transformer models have demonstrated high accuracy in numerous applications but have high complexity and lack sequential processing capability making them ill-suited for many streaming applications at the edge where devices are heavily resource-constrained. Thus motivated, many researchers have proposed reformulating the transformer models as RNN modules which modify the self-attention computation with explicit states. However, these approaches often incur significant performance degradation. The ultimate goal is to develop a model that has the following properties: parallel training, streaming and low-cost inference, and SOTA performance. In this paper, we propose a new direction to achieve this goal. We show how architectural modifications to a recurrent model can help push its performance toward Transformer models while retaining its sequential processing capability. Specifically, inspired by the recent success of Legendre Memory Units (LMU) in sequence learning tasks, we propose LMUFormer, which augments the LMU with convolutional patch embedding and convolutional channel mixer. Moreover, we present a spiking version of this architecture, which introduces the benefit of states within the patch embedding and channel mixer modules while simultaneously reducing the computing complexity. We evaluated our architectures on multiple sequence datasets. In comparison to SOTA transformer-based models within the ANN domain on the SCv2 dataset, our LMUFormer demonstrates comparable performance while necessitating a remarkable 53 times reduction in parameters and a substantial 65 times decrement in FLOPs. Additionally, owing to our model's proficiency in real-time data processing, we can achieve a 32.03% reduction in sequence length, all while incurring an inconsequential decline in performance. Our code is publicly available at https://github.com/zeyuliu1037/LMUFormer.git.

Graph Neural Networks (GNNs) are a powerful tool for machine learning on graphs.GNNs combine node feature information with the graph structure by recursively passing neural messages along edges of the input graph. However, incorporating both graph structure and feature information leads to complex models, and explaining predictions made by GNNs remains unsolved. Here we propose GNNExplainer, the first general, model-agnostic approach for providing interpretable explanations for predictions of any GNN-based model on any graph-based machine learning task. Given an instance, GNNExplainer identifies a compact subgraph structure and a small subset of node features that have a crucial role in GNN's prediction. Further, GNNExplainer can generate consistent and concise explanations for an entire class of instances. We formulate GNNExplainer as an optimization task that maximizes the mutual information between a GNN's prediction and distribution of possible subgraph structures. Experiments on synthetic and real-world graphs show that our approach can identify important graph structures as well as node features, and outperforms baselines by 17.1% on average. GNNExplainer provides a variety of benefits, from the ability to visualize semantically relevant structures to interpretability, to giving insights into errors of faulty GNNs.

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.

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

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-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.

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

Hypergraphs are a powerful abstraction for representing higher-order interactions between entities of interest. To exploit these relationships in making downstream predictions, a variety of hypergraph neural network architectures have recently been proposed, in large part building upon precursors from the more traditional graph neural network (GNN) literature. Somewhat differently, in this paper we begin by presenting an expressive family of parameterized, hypergraph-regularized energy functions. We then demonstrate how minimizers of these energies effectively serve as node embeddings that, when paired with a parameterized classifier, can be trained end-to-end via a supervised bilevel optimization process. Later, we draw parallels between the implicit architecture of the predictive models emerging from the proposed bilevel hypergraph optimization, and existing GNN architectures in common use. Empirically, we demonstrate state-of-the-art results on various hypergraph node classification benchmarks. Code is available at https://github.com/yxzwang/PhenomNN.

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

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

Graph neural networks (GNNs) learn the representation of graph-structured data, and their expressiveness can be further enhanced by inferring node relations for propagation. Attention-based GNNs infer neighbor importance to manipulate the weight of its propagation. Despite their popularity, the discussion on deep graph attention and its unique challenges has been limited. In this work, we investigate some problematic phenomena related to deep graph attention, including vulnerability to over-smoothed features and smooth cumulative attention. Through theoretical and empirical analyses, we show that various attention-based GNNs suffer from these problems. Motivated by our findings, we propose AEROGNN, a novel GNN architecture designed for deep graph attention. AERO-GNN provably mitigates the proposed problems of deep graph attention, which is further empirically demonstrated with (a) its adaptive and less smooth attention functions and (b) higher performance at deep layers (up to 64). On 9 out of 12 node classification benchmarks, AERO-GNN outperforms the baseline GNNs, highlighting the advantages of deep graph attention. Our code is available at https://github.com/syleeheal/AERO-GNN.

Transformer encoder architectures have recently achieved state-of-the-art results on monocular 3D human mesh reconstruction, but they require a substantial number of parameters and expensive computations. Due to the large memory overhead and slow inference speed, it is difficult to deploy such models for practical use. In this paper, we propose a novel transformer encoder-decoder architecture for 3D human mesh reconstruction from a single image, called FastMETRO. We identify the performance bottleneck in the encoder-based transformers is caused by the token design which introduces high complexity interactions among input tokens. We disentangle the interactions via an encoder-decoder architecture, which allows our model to demand much fewer parameters and shorter inference time. In addition, we impose the prior knowledge of human body's morphological relationship via attention masking and mesh upsampling operations, which leads to faster convergence with higher accuracy. Our FastMETRO improves the Pareto-front of accuracy and efficiency, and clearly outperforms image-based methods on Human3.6M and 3DPW. Furthermore, we validate its generalizability on FreiHAND.

This paper presents a new vision Transformer, called Swin Transformer, that capably serves as a general-purpose backbone for computer vision. Challenges in adapting Transformer from language to vision arise from differences between the two domains, such as large variations in the scale of visual entities and the high resolution of pixels in images compared to words in text. To address these differences, we propose a hierarchical Transformer whose representation is computed with Shifted windows. The shifted windowing scheme brings greater efficiency by limiting self-attention computation to non-overlapping local windows while also allowing for cross-window connection. This hierarchical architecture has the flexibility to model at various scales and has linear computational complexity with respect to image size. These qualities of Swin Transformer make it compatible with a broad range of vision tasks, including image classification (87.3 top-1 accuracy on ImageNet-1K) and dense prediction tasks such as object detection (58.7 box AP and 51.1 mask AP on COCO test-dev) and semantic segmentation (53.5 mIoU on ADE20K val). Its performance surpasses the previous state-of-the-art by a large margin of +2.7 box AP and +2.6 mask AP on COCO, and +3.2 mIoU on ADE20K, demonstrating the potential of Transformer-based models as vision backbones. The hierarchical design and the shifted window approach also prove beneficial for all-MLP architectures. The code and models are publicly available at~https://github.com/microsoft/Swin-Transformer.

Transformer model architectures have garnered immense interest lately due to their effectiveness across a range of domains like language, vision and reinforcement learning. In the field of natural language processing for example, Transformers have become an indispensable staple in the modern deep learning stack. Recently, a dizzying number of "X-former" models have been proposed - Reformer, Linformer, Performer, Longformer, to name a few - which improve upon the original Transformer architecture, many of which make improvements around computational and memory efficiency. With the aim of helping the avid researcher navigate this flurry, this paper characterizes a large and thoughtful selection of recent efficiency-flavored "X-former" models, providing an organized and comprehensive overview of existing work and models across multiple domains.

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

Transformer architectures have become a dominant paradigm for domains like language modeling but suffer in many inference settings due to their quadratic-time self-attention. Recently proposed subquadratic architectures, such as Mamba, have shown promise, but have been pretrained with substantially less computational resources than the strongest Transformer models. In this work, we present a method that is able to distill a pretrained Transformer architecture into alternative architectures such as state space models (SSMs). The key idea to our approach is that we can view both Transformers and SSMs as applying different forms of mixing matrices over the token sequences. We can thus progressively distill the Transformer architecture by matching different degrees of granularity in the SSM: first matching the mixing matrices themselves, then the hidden units at each block, and finally the end-to-end predictions. Our method, called MOHAWK, is able to distill a Mamba-2 variant based on the Phi-1.5 architecture (Phi-Mamba) using only 3B tokens and a hybrid version (Hybrid Phi-Mamba) using 5B tokens. Despite using less than 1% of the training data typically used to train models from scratch, Phi-Mamba boasts substantially stronger performance compared to all past open-source non-Transformer models. MOHAWK allows models like SSMs to leverage computational resources invested in training Transformer-based architectures, highlighting a new avenue for building such models.

The Transformer is an extremely powerful and prominent deep learning architecture. In this work, we challenge the commonly held belief in deep learning that going deeper is better, and show an alternative design approach that is building wider attention Transformers. We demonstrate that wide single layer Transformer models can compete with or outperform deeper ones in a variety of Natural Language Processing (NLP) tasks when both are trained from scratch. The impact of changing the model aspect ratio on Transformers is then studied systematically. This ratio balances the number of layers and the number of attention heads per layer while keeping the total number of attention heads and all other hyperparameters constant. On average, across 4 NLP tasks and 10 attention types, single layer wide models perform 0.3% better than their deep counterparts. We show an in-depth evaluation and demonstrate how wide models require a far smaller memory footprint and can run faster on commodity hardware, in addition, these wider models are also more interpretable. For example, a single layer Transformer on the IMDb byte level text classification has 3.1x faster inference latency on a CPU than its equally accurate deeper counterpart, and is half the size. We therefore put forward wider and shallower models as a viable and desirable alternative for small models on NLP tasks, and as an important area of research for domains beyond this.

Hyperspectral Imaging (HSI) plays an increasingly critical role in precise vision tasks within remote sensing, capturing a wide spectrum of visual data. Transformer architectures have significantly enhanced HSI task performance, while advancements in Transformer Architecture Search (TAS) have improved model discovery. To harness these advancements for HSI classification, we make the following contributions: i) We propose HyTAS, the first benchmark on transformer architecture search for Hyperspectral imaging, ii) We comprehensively evaluate 12 different methods to identify the optimal transformer over 5 different datasets, iii) We perform an extensive factor analysis on the Hyperspectral transformer search performance, greatly motivating future research in this direction. All benchmark materials are available at HyTAS.

Transformers are widely used for solving tasks in natural language processing, computer vision, speech, and music domains. In this paper, we talk about the efficiency of transformers in terms of memory (the number of parameters), computation cost (number of floating points operations), and performance of models, including accuracy, the robustness of the model, and fair \& bias-free features. We mainly discuss the vision transformer for the image classification task. Our contribution is to introduce an efficient 360 framework, which includes various aspects of the vision transformer, to make it more efficient for industrial applications. By considering those applications, we categorize them into multiple dimensions such as privacy, robustness, transparency, fairness, inclusiveness, continual learning, probabilistic models, approximation, computational complexity, and spectral complexity. We compare various vision transformer models based on their performance, the number of parameters, and the number of floating point operations (FLOPs) on multiple datasets.

Transformers have become an indispensable module for text generation models since their great success in machine translation. Previous works attribute the~success of transformers to the query-key-value dot-product attention, which provides a robust inductive bias by the fully connected token graphs. However, we found that self-attention has a severe limitation. When predicting the (i+1)-th token, self-attention only takes the i-th token as an information collector, and it tends to give a high attention weight to those tokens similar to itself. Therefore, most of the historical information that occurred before the i-th token is not taken into consideration. Based on this observation, in this paper, we propose a new architecture, called bird-eye transformer(BET), which goes one step further to improve the performance of transformers by reweighting self-attention to encourage it to focus more on important historical information. We have conducted experiments on multiple text generation tasks, including machine translation (2 datasets) and language models (3 datasets). These experimental~results show that our proposed model achieves a better performance than the baseline transformer architectures on~all~datasets. The code is released at: https://sites.google.com/view/bet-transformer/home.

Large transformer models display promising performance on a wide range of natural language processing (NLP) tasks. Although the AI community has expanded the model scale to the trillion parameter level, the practical deployment of 10-100 billion parameter models is still uncertain due to the latency, throughput, and memory constraints. In this paper, we proposed EnergonAI to solve the challenges of the efficient deployment of 10-100 billion parameter transformer models on single- or multi-GPU systems. EnergonAI adopts a hierarchy-controller system architecture to coordinate multiple devices and efficiently support different parallel patterns. It delegates the execution of sub-models to multiple workers in the single-controller style and applies tensor parallelism and pipeline parallelism among the workers in a multi-controller style. Upon the novel architecture, we propose three techniques, i.e. non-blocking pipeline parallelism, distributed redundant computation elimination, and peer memory pooling. EnergonAI enables the users to program complex parallel code the same as a serial one. Compared with the FasterTransformer, we have proven that EnergonAI has superior performance on latency and throughput. In our experiments, EnergonAI can achieve 37% latency reduction in tensor parallelism, 10% scalability improvement in pipeline parallelism, and it improves the model scale inferred on a single GPU by using a larger heterogeneous memory space at cost of limited performance reduction.

Very recently, a variety of vision transformer architectures for dense prediction tasks have been proposed and they show that the design of spatial attention is critical to their success in these tasks. In this work, we revisit the design of the spatial attention and demonstrate that a carefully-devised yet simple spatial attention mechanism performs favourably against the state-of-the-art schemes. As a result, we propose two vision transformer architectures, namely, Twins-PCPVT and Twins-SVT. Our proposed architectures are highly-efficient and easy to implement, only involving matrix multiplications that are highly optimized in modern deep learning frameworks. More importantly, the proposed architectures achieve excellent performance on a wide range of visual tasks, including image level classification as well as dense detection and segmentation. The simplicity and strong performance suggest that our proposed architectures may serve as stronger backbones for many vision tasks. Our code is released at https://github.com/Meituan-AutoML/Twins .

Recent progress in natural language processing has been driven by advances in both model architecture and model pretraining. Transformer architectures have facilitated building higher-capacity models and pretraining has made it possible to effectively utilize this capacity for a wide variety of tasks. Transformers is an open-source library with the goal of opening up these advances to the wider machine learning community. The library consists of carefully engineered state-of-the art Transformer architectures under a unified API. Backing this library is a curated collection of pretrained models made by and available for the community. Transformers is designed to be extensible by researchers, simple for practitioners, and fast and robust in industrial deployments. The library is available at https://github.com/huggingface/transformers.

We present Simplified Text-Attributed Graph Embeddings (STAGE), a straightforward yet effective method for enhancing node features in Graph Neural Network (GNN) models that encode Text-Attributed Graphs (TAGs). Our approach leverages Large-Language Models (LLMs) to generate embeddings for textual attributes. STAGE achieves competitive results on various node classification benchmarks while also maintaining a simplicity in implementation relative to current state-of-the-art (SoTA) techniques. We show that utilizing pre-trained LLMs as embedding generators provides robust features for ensemble GNN training, enabling pipelines that are simpler than current SoTA approaches which require multiple expensive training and prompting stages. We also implement diffusion-pattern GNNs in an effort to make this pipeline scalable to graphs beyond academic benchmarks.

Recently, subgraph GNNs have emerged as an important direction for developing expressive graph neural networks (GNNs). While numerous architectures have been proposed, so far there is still a limited understanding of how various design paradigms differ in terms of expressive power, nor is it clear what design principle achieves maximal expressiveness with minimal architectural complexity. To address these fundamental questions, this paper conducts a systematic study of general node-based subgraph GNNs through the lens of Subgraph Weisfeiler-Lehman Tests (SWL). Our central result is to build a complete hierarchy of SWL with strictly growing expressivity. Concretely, we prove that any node-based subgraph GNN falls into one of the six SWL equivalence classes, among which SSWL achieves the maximal expressive power. We also study how these equivalence classes differ in terms of their practical expressiveness such as encoding graph distance and biconnectivity. Furthermore, we give a tight expressivity upper bound of all SWL algorithms by establishing a close relation with localized versions of WL and Folklore WL (FWL) tests. Our results provide insights into the power of existing subgraph GNNs, guide the design of new architectures, and point out their limitations by revealing an inherent gap with the 2-FWL test. Finally, experiments demonstrate that SSWL-inspired subgraph GNNs can significantly outperform prior architectures on multiple benchmarks despite great simplicity.

In recent years, there has been a trend in the field of Reinforcement Learning (RL) towards large action models trained offline on large-scale datasets via sequence modeling. Existing models are primarily based on the Transformer architecture, which result in powerful agents. However, due to slow inference times, Transformer-based approaches are impractical for real-time applications, such as robotics. Recently, modern recurrent architectures, such as xLSTM and Mamba, have been proposed that exhibit parallelization benefits during training similar to the Transformer architecture while offering fast inference. In this work, we study the aptitude of these modern recurrent architectures for large action models. Consequently, we propose a Large Recurrent Action Model (LRAM) with an xLSTM at its core that comes with linear-time inference complexity and natural sequence length extrapolation abilities. Experiments on 432 tasks from 6 domains show that LRAM compares favorably to Transformers in terms of performance and speed.

Recurrent neural network (RNN) and self-attention mechanism (SAM) are the de facto methods to extract spatial-temporal information for temporal graph learning. Interestingly, we found that although both RNN and SAM could lead to a good performance, in practice neither of them is always necessary. In this paper, we propose GraphMixer, a conceptually and technically simple architecture that consists of three components: (1) a link-encoder that is only based on multi-layer perceptrons (MLP) to summarize the information from temporal links, (2) a node-encoder that is only based on neighbor mean-pooling to summarize node information, and (3) an MLP-based link classifier that performs link prediction based on the outputs of the encoders. Despite its simplicity, GraphMixer attains an outstanding performance on temporal link prediction benchmarks with faster convergence and better generalization performance. These results motivate us to rethink the importance of simpler model architecture.

AutoML has demonstrated remarkable success in finding an effective neural architecture for a given machine learning task defined by a specific dataset and an evaluation metric. However, most present AutoML techniques consider each task independently from scratch, which requires exploring many architectures, leading to high computational cost. Here we propose AutoTransfer, an AutoML solution that improves search efficiency by transferring the prior architectural design knowledge to the novel task of interest. Our key innovation includes a task-model bank that captures the model performance over a diverse set of GNN architectures and tasks, and a computationally efficient task embedding that can accurately measure the similarity among different tasks. Based on the task-model bank and the task embeddings, we estimate the design priors of desirable models of the novel task, by aggregating a similarity-weighted sum of the top-K design distributions on tasks that are similar to the task of interest. The computed design priors can be used with any AutoML search algorithm. We evaluate AutoTransfer on six datasets in the graph machine learning domain. Experiments demonstrate that (i) our proposed task embedding can be computed efficiently, and that tasks with similar embeddings have similar best-performing architectures; (ii) AutoTransfer significantly improves search efficiency with the transferred design priors, reducing the number of explored architectures by an order of magnitude. Finally, we release GNN-Bank-101, a large-scale dataset of detailed GNN training information of 120,000 task-model combinations to facilitate and inspire future research.

We present a neat yet effective recursive operation on vision transformers that can improve parameter utilization without involving additional parameters. This is achieved by sharing weights across the depth of transformer networks. The proposed method can obtain a substantial gain (~2%) simply using naive recursive operation, requires no special or sophisticated knowledge for designing principles of networks, and introduces minimal computational overhead to the training procedure. To reduce the additional computation caused by recursive operation while maintaining the superior accuracy, we propose an approximating method through multiple sliced group self-attentions across recursive layers which can reduce the cost consumption by 10~30% with minimal performance loss. We call our model Sliced Recursive Transformer (SReT), a novel and parameter-efficient vision transformer design that is compatible with a broad range of other designs for efficient ViT architectures. Our best model establishes significant improvement on ImageNet-1K over state-of-the-art methods while containing fewer parameters. The proposed weight sharing mechanism by sliced recursion structure allows us to build a transformer with more than 100 or even 1000 shared layers with ease while keeping a compact size (13~15M), to avoid optimization difficulties when the model is too large. The flexible scalability has shown great potential for scaling up models and constructing extremely deep vision transformers. Code is available at https://github.com/szq0214/SReT.

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.

The recent boom of linear forecasting models questions the ongoing passion for architectural modifications of Transformer-based forecasters. These forecasters leverage Transformers to model the global dependencies over temporal tokens of time series, with each token formed by multiple variates of the same timestamp. However, Transformers are challenged in forecasting series with larger lookback windows due to performance degradation and computation explosion. Besides, the embedding for each temporal token fuses multiple variates that represent potential delayed events and distinct physical measurements, which may fail in learning variate-centric representations and result in meaningless attention maps. In this work, we reflect on the competent duties of Transformer components and repurpose the Transformer architecture without any modification to the basic components. We propose iTransformer that simply applies the attention and feed-forward network on the inverted dimensions. Specifically, the time points of individual series are embedded into variate tokens which are utilized by the attention mechanism to capture multivariate correlations; meanwhile, the feed-forward network is applied for each variate token to learn nonlinear representations. The iTransformer model achieves state-of-the-art on challenging real-world datasets, which further empowers the Transformer family with promoted performance, generalization ability across different variates, and better utilization of arbitrary lookback windows, making it a nice alternative as the fundamental backbone of time series forecasting. Code is available at this repository: https://github.com/thuml/iTransformer.

As acquiring pixel-wise annotations of real-world images for semantic segmentation is a costly process, a model can instead be trained with more accessible synthetic data and adapted to real images without requiring their annotations. This process is studied in unsupervised domain adaptation (UDA). Even though a large number of methods propose new adaptation strategies, they are mostly based on outdated network architectures. As the influence of recent network architectures has not been systematically studied, we first benchmark different network architectures for UDA and newly reveal the potential of Transformers for UDA semantic segmentation. Based on the findings, we propose a novel UDA method, DAFormer. The network architecture of DAFormer consists of a Transformer encoder and a multi-level context-aware feature fusion decoder. It is enabled by three simple but crucial training strategies to stabilize the training and to avoid overfitting to the source domain: While (1) Rare Class Sampling on the source domain improves the quality of the pseudo-labels by mitigating the confirmation bias of self-training toward common classes, (2) a Thing-Class ImageNet Feature Distance and (3) a learning rate warmup promote feature transfer from ImageNet pretraining. DAFormer represents a major advance in UDA. It improves the state of the art by 10.8 mIoU for GTA-to-Cityscapes and 5.4 mIoU for Synthia-to-Cityscapes and enables learning even difficult classes such as train, bus, and truck well. The implementation is available at https://github.com/lhoyer/DAFormer.

Graph generation has been dominated by autoregressive models due to their simplicity and effectiveness, despite their sensitivity to ordering. Yet diffusion models have garnered increasing attention, as they offer comparable performance while being permutation-invariant. Current graph diffusion models generate graphs in a one-shot fashion, but they require extra features and thousands of denoising steps to achieve optimal performance. We introduce PARD, a Permutation-invariant Auto Regressive Diffusion model that integrates diffusion models with autoregressive methods. PARD harnesses the effectiveness and efficiency of the autoregressive model while maintaining permutation invariance without ordering sensitivity. Specifically, we show that contrary to sets, elements in a graph are not entirely unordered and there is a unique partial order for nodes and edges. With this partial order, PARD generates a graph in a block-by-block, autoregressive fashion, where each block's probability is conditionally modeled by a shared diffusion model with an equivariant network. To ensure efficiency while being expressive, we further propose a higher-order graph transformer, which integrates transformer with PPGN. Like GPT, we extend the higher-order graph transformer to support parallel training of all blocks. Without any extra features, PARD achieves state-of-the-art performance on molecular and non-molecular datasets, and scales to large datasets like MOSES containing 1.9M molecules.

Transformers have shown great potential in computer vision tasks. A common belief is their attention-based token mixer module contributes most to their competence. However, recent works show the attention-based module in Transformers can be replaced by spatial MLPs and the resulted models still perform quite well. Based on this observation, we hypothesize that the general architecture of the Transformers, instead of the specific token mixer module, is more essential to the model's performance. To verify this, we deliberately replace the attention module in Transformers with an embarrassingly simple spatial pooling operator to conduct only basic token mixing. Surprisingly, we observe that the derived model, termed as PoolFormer, achieves competitive performance on multiple computer vision tasks. For example, on ImageNet-1K, PoolFormer achieves 82.1% top-1 accuracy, surpassing well-tuned Vision Transformer/MLP-like baselines DeiT-B/ResMLP-B24 by 0.3%/1.1% accuracy with 35%/52% fewer parameters and 50%/62% fewer MACs. The effectiveness of PoolFormer verifies our hypothesis and urges us to initiate the concept of "MetaFormer", a general architecture abstracted from Transformers without specifying the token mixer. Based on the extensive experiments, we argue that MetaFormer is the key player in achieving superior results for recent Transformer and MLP-like models on vision tasks. This work calls for more future research dedicated to improving MetaFormer instead of focusing on the token mixer modules. Additionally, our proposed PoolFormer could serve as a starting baseline for future MetaFormer architecture design. Code is available at https://github.com/sail-sg/poolformer.

While Language Models have become workhorses for NLP, their interplay with textual knowledge graphs (KGs) - structured memories of general or domain knowledge - is actively researched. Current embedding methodologies for such graphs typically either (i) linearize graphs for embedding them using sequential Language Models (LMs), which underutilize structural information, or (ii) use Graph Neural Networks (GNNs) to preserve graph structure, while GNNs cannot represent textual features as well as a pre-trained LM could. In this work we introduce a novel language model, the Graph Language Model (GLM), that integrates the strengths of both approaches, while mitigating their weaknesses. The GLM parameters are initialized from a pretrained LM, to facilitate nuanced understanding of individual concepts and triplets. Simultaneously, its architectural design incorporates graph biases, thereby promoting effective knowledge distribution within the graph. Empirical evaluations on relation classification tasks on ConceptNet subgraphs reveal that GLM embeddings surpass both LM- and GNN-based baselines in supervised and zero-shot settings.

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.

In order to reduce the computational complexity of large language models, great efforts have been made to to improve the efficiency of transformer models such as linear attention and flash-attention. However, the model size and corresponding computational complexity are constantly scaled up in pursuit of higher performance. In this work, we present MemoryFormer, a novel transformer architecture which significantly reduces the computational complexity (FLOPs) from a new perspective. We eliminate nearly all the computations of the transformer model except for the necessary computation required by the multi-head attention operation. This is made possible by utilizing an alternative method for feature transformation to replace the linear projection of fully-connected layers. Specifically, we first construct a group of in-memory lookup tables that store a large amount of discrete vectors to replace the weight matrix used in linear projection. We then use a hash algorithm to retrieve a correlated subset of vectors dynamically based on the input embedding. The retrieved vectors combined together will form the output embedding, which provides an estimation of the result of matrix multiplication operation in a fully-connected layer. Compared to conducting matrix multiplication, retrieving data blocks from memory is a much cheaper operation which requires little computations. We train MemoryFormer from scratch and conduct extensive experiments on various benchmarks to demonstrate the effectiveness of the proposed model.

Vision transformer based models bring significant improvements for image segmentation tasks. Although these architectures offer powerful capabilities irrespective of specific segmentation tasks, their use of computational resources can be taxing on deployed devices. One way to overcome this challenge is by adapting the computation level to the specific needs of the input image rather than the current one-size-fits-all approach. To this end, we introduce ECO-M2F or EffiCient TransfOrmer Encoders for Mask2Former-style models. Noting that the encoder module of M2F-style models incur high resource-intensive computations, ECO-M2F provides a strategy to self-select the number of hidden layers in the encoder, conditioned on the input image. To enable this self-selection ability for providing a balance between performance and computational efficiency, we present a three step recipe. The first step is to train the parent architecture to enable early exiting from the encoder. The second step is to create an derived dataset of the ideal number of encoder layers required for each training example. The third step is to use the aforementioned derived dataset to train a gating network that predicts the number of encoder layers to be used, conditioned on the input image. Additionally, to change the computational-accuracy tradeoff, only steps two and three need to be repeated which significantly reduces retraining time. Experiments on the public datasets show that the proposed approach reduces expected encoder computational cost while maintaining performance, adapts to various user compute resources, is flexible in architecture configurations, and can be extended beyond the segmentation task to object detection.

We present a framework for using transformer networks as universal computers by programming them with specific weights and placing them in a loop. Our input sequence acts as a punchcard, consisting of instructions and memory for data read/writes. We demonstrate that a constant number of encoder layers can emulate basic computing blocks, including embedding edit operations, non-linear functions, function calls, program counters, and conditional branches. Using these building blocks, we emulate a small instruction-set computer. This allows us to map iterative algorithms to programs that can be executed by a looped, 13-layer transformer. We show how this transformer, instructed by its input, can emulate a basic calculator, a basic linear algebra library, and in-context learning algorithms that employ backpropagation. Our work highlights the versatility of the attention mechanism, and demonstrates that even shallow transformers can execute full-fledged, general-purpose programs.

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.

Hierarchical structures are popular in recent vision transformers, however, they require sophisticated designs and massive datasets to work well. In this paper, we explore the idea of nesting basic local transformers on non-overlapping image blocks and aggregating them in a hierarchical way. We find that the block aggregation function plays a critical role in enabling cross-block non-local information communication. This observation leads us to design a simplified architecture that requires minor code changes upon the original vision transformer. The benefits of the proposed judiciously-selected design are threefold: (1) NesT converges faster and requires much less training data to achieve good generalization on both ImageNet and small datasets like CIFAR; (2) when extending our key ideas to image generation, NesT leads to a strong decoder that is 8times faster than previous transformer-based generators; and (3) we show that decoupling the feature learning and abstraction processes via this nested hierarchy in our design enables constructing a novel method (named GradCAT) for visually interpreting the learned model. Source code is available https://github.com/google-research/nested-transformer.

The design choices in Transformer feed-forward neural networks have resulted in significant computational and parameter overhead. In this work, we emphasize the importance of hidden dimension in designing lightweight FFNs, a factor often overlooked in previous architectures. Guided by this principle, we introduce PartialFormer, a parameter-efficient Transformer architecture utilizing multiple smaller FFNs to reduce parameters and computation while maintaining essential hidden dimensions. These smaller FFNs are integrated into a multi-head attention system to enable effective collaboration. We also propose a tailored head scaling strategy to enhance PartialFormer's capabilities. Furthermore, we present a residual-like attention calculation to improve depth scaling within PartialFormer. Extensive experiments on 9 translation tasks and 1 abstractive summarization task validate the effectiveness of our PartialFormer approach. Our code would be available at: https://github.com/zhengkid/PartialFormer.

Diffusion Transformers (DiTs) introduce the transformer architecture to diffusion tasks for latent-space image generation. With an isotropic architecture that chains a series of transformer blocks, DiTs demonstrate competitive performance and good scalability; but meanwhile, the abandonment of U-Net by DiTs and their following improvements is worth rethinking. To this end, we conduct a simple toy experiment by comparing a U-Net architectured DiT with an isotropic one. It turns out that the U-Net architecture only gain a slight advantage amid the U-Net inductive bias, indicating potential redundancies within the U-Net-style DiT. Inspired by the discovery that U-Net backbone features are low-frequency-dominated, we perform token downsampling on the query-key-value tuple for self-attention and bring further improvements despite a considerable amount of reduction in computation. Based on self-attention with downsampled tokens, we propose a series of U-shaped DiTs (U-DiTs) in the paper and conduct extensive experiments to demonstrate the extraordinary performance of U-DiT models. The proposed U-DiT could outperform DiT-XL/2 with only 1/6 of its computation cost. Codes are available at https://github.com/YuchuanTian/U-DiT.

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.

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.

Vision-Language models (VLMs) pre-trained on large corpora have demonstrated notable success across a range of downstream tasks. In light of the rapidly increasing size of pre-trained VLMs, parameter-efficient transfer learning (PETL) has garnered attention as a viable alternative to full fine-tuning. One such approach is the adapter, which introduces a few trainable parameters into the pre-trained models while preserving the original parameters during adaptation. In this paper, we present a novel modeling framework that recasts adapter tuning after attention as a graph message passing process on attention graphs, where the projected query and value features and attention matrix constitute the node features and the graph adjacency matrix, respectively. Within this framework, tuning adapters in VLMs necessitates handling heterophilic graphs, owing to the disparity between the projected query and value space. To address this challenge, we propose a new adapter architecture, p-adapter, which employs p-Laplacian message passing in Graph Neural Networks (GNNs). Specifically, the attention weights are re-normalized based on the features, and the features are then aggregated using the calibrated attention matrix, enabling the dynamic exploitation of information with varying frequencies in the heterophilic attention graphs. We conduct extensive experiments on different pre-trained VLMs and multi-modal tasks, including visual question answering, visual entailment, and image captioning. The experimental results validate our method's significant superiority over other PETL methods.

The transformer is a neural network component that can be used to learn useful representations of sequences or sets of data-points. The transformer has driven recent advances in natural language processing, computer vision, and spatio-temporal modelling. There are many introductions to transformers, but most do not contain precise mathematical descriptions of the architecture and the intuitions behind the design choices are often also missing. Moreover, as research takes a winding path, the explanations for the components of the transformer can be idiosyncratic. In this note we aim for a mathematically precise, intuitive, and clean description of the transformer architecture. We will not discuss training as this is rather standard. We assume that the reader is familiar with fundamental topics in machine learning including multi-layer perceptrons, linear transformations, softmax functions and basic probability.

Complex Logical Query Answering (CLQA) over incomplete knowledge graphs is a challenging task. Recently, Query Embedding (QE) methods are proposed to solve CLQA by performing multi-hop logical reasoning. However, most of them only consider historical query context information while ignoring future information, which leads to their failure to capture the complex dependencies behind the elements of a query. In recent years, the transformer architecture has shown a strong ability to model long-range dependencies between words. The bidirectional attention mechanism proposed by the transformer can solve the limitation of these QE methods regarding query context. Still, as a sequence model, it is difficult for the transformer to model complex logical queries with branch structure computation graphs directly. To this end, we propose a neural one-point embedding method called Pathformer based on the tree-like computation graph, i.e., query computation tree. Specifically, Pathformer decomposes the query computation tree into path query sequences by branches and then uses the transformer encoder to recursively encode these path query sequences to obtain the final query embedding. This allows Pathformer to fully utilize future context information to explicitly model the complex interactions between various parts of the path query. Experimental results show that Pathformer outperforms existing competitive neural QE methods, and we found that Pathformer has the potential to be applied to non-one-point embedding space.

This work introduces DiGress, a discrete denoising diffusion model for generating graphs with categorical node and edge attributes. Our model utilizes a discrete diffusion process that progressively edits graphs with noise, through the process of adding or removing edges and changing the categories. A graph transformer network is trained to revert this process, simplifying the problem of distribution learning over graphs into a sequence of node and edge classification tasks. We further improve sample quality by introducing a Markovian noise model that preserves the marginal distribution of node and edge types during diffusion, and by incorporating auxiliary graph-theoretic features. A procedure for conditioning the generation on graph-level features is also proposed. DiGress achieves state-of-the-art performance on molecular and non-molecular datasets, with up to 3x validity improvement on a planar graph dataset. It is also the first model to scale to the large GuacaMol dataset containing 1.3M drug-like molecules without the use of molecule-specific representations.

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

We explore a new class of diffusion models based on the transformer architecture. We train latent diffusion models of images, replacing the commonly-used U-Net backbone with a transformer that operates on latent patches. We analyze the scalability of our Diffusion Transformers (DiTs) through the lens of forward pass complexity as measured by Gflops. We find that DiTs with higher Gflops -- through increased transformer depth/width or increased number of input tokens -- consistently have lower FID. In addition to possessing good scalability properties, our largest DiT-XL/2 models outperform all prior diffusion models on the class-conditional ImageNet 512x512 and 256x256 benchmarks, achieving a state-of-the-art FID of 2.27 on the latter.

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.

We show that Transformer encoder architectures can be sped up, with limited accuracy costs, by replacing the self-attention sublayers with simple linear transformations that "mix" input tokens. These linear mixers, along with standard nonlinearities in feed-forward layers, prove competent at modeling semantic relationships in several text classification tasks. Most surprisingly, we find that replacing the self-attention sublayer in a Transformer encoder with a standard, unparameterized Fourier Transform achieves 92-97% of the accuracy of BERT counterparts on the GLUE benchmark, but trains 80% faster on GPUs and 70% faster on TPUs at standard 512 input lengths. At longer input lengths, our FNet model is significantly faster: when compared to the "efficient" Transformers on the Long Range Arena benchmark, FNet matches the accuracy of the most accurate models, while outpacing the fastest models across all sequence lengths on GPUs (and across relatively shorter lengths on TPUs). Finally, FNet has a light memory footprint and is particularly efficient at smaller model sizes; for a fixed speed and accuracy budget, small FNet models outperform Transformer counterparts.

Transformers have demonstrated effectiveness in in-context solving data-fitting problems from various (latent) models, as reported by Garg et al. However, the absence of an inherent iterative structure in the transformer architecture presents a challenge in emulating the iterative algorithms, which are commonly employed in traditional machine learning methods. To address this, we propose the utilization of looped transformer architecture and its associated training methodology, with the aim of incorporating iterative characteristics into the transformer architectures. Experimental results suggest that the looped transformer achieves performance comparable to the standard transformer in solving various data-fitting problems, while utilizing less than 10\% of the parameter count.

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.

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

The transformer model has gained widespread adoption in computer vision tasks in recent times. However, due to the quadratic time and memory complexity of self-attention, which is proportional to the number of input tokens, most existing Vision Transformers (ViTs) encounter challenges in achieving efficient performance in practical industrial deployment scenarios, such as TensorRT and CoreML, where traditional CNNs excel. Although some recent attempts have been made to design CNN-Transformer hybrid architectures to tackle this problem, their overall performance has not met expectations. To tackle these challenges, we propose an efficient hybrid ViT architecture named FMViT. This approach enhances the model's expressive power by blending high-frequency features and low-frequency features with varying frequencies, enabling it to capture both local and global information effectively. Additionally, we introduce deploy-friendly mechanisms such as Convolutional Multigroup Reparameterization (gMLP), Lightweight Multi-head Self-Attention (RLMHSA), and Convolutional Fusion Block (CFB) to further improve the model's performance and reduce computational overhead. Our experiments demonstrate that FMViT surpasses existing CNNs, ViTs, and CNNTransformer hybrid architectures in terms of latency/accuracy trade-offs for various vision tasks. On the TensorRT platform, FMViT outperforms Resnet101 by 2.5% (83.3% vs. 80.8%) in top-1 accuracy on the ImageNet dataset while maintaining similar inference latency. Moreover, FMViT achieves comparable performance with EfficientNet-B5, but with a 43% improvement in inference speed. On CoreML, FMViT outperforms MobileOne by 2.6% in top-1 accuracy on the ImageNet dataset, with inference latency comparable to MobileOne (78.5% vs. 75.9%). Our code can be found at https://github.com/tany0699/FMViT.

This paper presents the FlowTransformer framework, a novel approach for implementing transformer-based Network Intrusion Detection Systems (NIDSs). FlowTransformer leverages the strengths of transformer models in identifying the long-term behaviour and characteristics of networks, which are often overlooked by most existing NIDSs. By capturing these complex patterns in network traffic, FlowTransformer offers a flexible and efficient tool for researchers and practitioners in the cybersecurity community who are seeking to implement NIDSs using transformer-based models. FlowTransformer allows the direct substitution of various transformer components, including the input encoding, transformer, classification head, and the evaluation of these across any flow-based network dataset. To demonstrate the effectiveness and efficiency of the FlowTransformer framework, we utilise it to provide an extensive evaluation of various common transformer architectures, such as GPT 2.0 and BERT, on three commonly used public NIDS benchmark datasets. We provide results for accuracy, model size and speed. A key finding of our evaluation is that the choice of classification head has the most significant impact on the model performance. Surprisingly, Global Average Pooling, which is commonly used in text classification, performs very poorly in the context of NIDS. In addition, we show that model size can be reduced by over 50\%, and inference and training times improved, with no loss of accuracy, by making specific choices of input encoding and classification head instead of other commonly used alternatives.

In recent years, the use of multi-modal pre-trained Transformers has led to significant advancements in visually-rich document understanding. However, existing models have mainly focused on features such as text and vision while neglecting the importance of layout relationship between text nodes. In this paper, we propose GraphLayoutLM, a novel document understanding model that leverages the modeling of layout structure graph to inject document layout knowledge into the model. GraphLayoutLM utilizes a graph reordering algorithm to adjust the text sequence based on the graph structure. Additionally, our model uses a layout-aware multi-head self-attention layer to learn document layout knowledge. The proposed model enables the understanding of the spatial arrangement of text elements, improving document comprehension. We evaluate our model on various benchmarks, including FUNSD, XFUND and CORD, and achieve state-of-the-art results among these datasets. Our experimental results demonstrate that our proposed method provides a significant improvement over existing approaches and showcases the importance of incorporating layout information into document understanding models. We also conduct an ablation study to investigate the contribution of each component of our model. The results show that both the graph reordering algorithm and the layout-aware multi-head self-attention layer play a crucial role in achieving the best performance.

In recent years, Transformers have become the de-facto architecture for sequence modeling on text and a variety of multi-dimensional data, such as images and video. However, the use of self-attention layers in a Transformer incurs prohibitive compute and memory complexity that scales quadratically w.r.t. the sequence length. A recent architecture, Mamba, based on state space models has been shown to achieve comparable performance for modeling text sequences, while scaling linearly with the sequence length. In this work, we present Mamba-ND, a generalized design extending the Mamba architecture to arbitrary multi-dimensional data. Our design alternatively unravels the input data across different dimensions following row-major orderings. We provide a systematic comparison of Mamba-ND with several other alternatives, based on prior multi-dimensional extensions such as Bi-directional LSTMs and S4ND. Empirically, we show that Mamba-ND demonstrates performance competitive with the state-of-the-art on a variety of multi-dimensional benchmarks, including ImageNet-1K classification, HMDB-51 action recognition, and ERA5 weather forecasting.

Transformer architectures are the backbone of the modern AI revolution. However, they are based on simply stacking the same blocks in dozens of layers and processing information sequentially from one block to another. In this paper, we propose to challenge this and introduce adaptive computations for LLM-like setups, which allow the final layer to attend to all of the intermediate layers as it deems fit through the attention mechanism, thereby introducing computational attention shortcuts. These shortcuts can thus make the architecture depth and context adaptive. We showcase four different datasets, namely acoustic tokens, natural language, and symbolic music, and we achieve superior performance for GPT-like architecture. We give evidence via attention maps that the models learn complex dependencies across layers that are adaptive in context and depth depending on the input tokens.

This work presents an analysis of the effectiveness of using standard shallow feed-forward networks to mimic the behavior of the attention mechanism in the original Transformer model, a state-of-the-art architecture for sequence-to-sequence tasks. We substitute key elements of the attention mechanism in the Transformer with simple feed-forward networks, trained using the original components via knowledge distillation. Our experiments, conducted on the IWSLT2017 dataset, reveal the capacity of these "attentionless Transformers" to rival the performance of the original architecture. Through rigorous ablation studies, and experimenting with various replacement network types and sizes, we offer insights that support the viability of our approach. This not only sheds light on the adaptability of shallow feed-forward networks in emulating attention mechanisms but also underscores their potential to streamline complex architectures for sequence-to-sequence tasks.

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.

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

Transformer-based models have emerged as one of the most widely used architectures for natural language processing, natural language generation, and image generation. The size of the state-of-the-art models has increased steadily reaching billions of parameters. These huge models are memory hungry and incur significant inference latency even on cutting edge AI-accelerators, such as GPUs. Specifically, the time and memory complexity of the attention operation is quadratic in terms of the total context length, i.e., prompt and output tokens. Thus, several optimizations such as key-value tensor caching and FlashAttention computation have been proposed to deliver the low latency demands of applications relying on such large models. However, these techniques do not cater to the computationally distinct nature of different phases during inference. To that end, we propose LeanAttention, a scalable technique of computing self-attention for the token-generation phase (decode-phase) of decoder-only transformer models. LeanAttention enables scaling the attention mechanism implementation for the challenging case of long context lengths by re-designing the execution flow for the decode-phase. We identify that the associative property of online softmax can be treated as a reduction operation thus allowing us to parallelize the attention computation over these large context lengths. We extend the "stream-K" style reduction of tiled calculation to self-attention to enable parallel computation resulting in an average of 2.6x attention execution speedup over FlashAttention-2 and up to 8.33x speedup for 512k context lengths.

The vision community is witnessing a modeling shift from CNNs to Transformers, where pure Transformer architectures have attained top accuracy on the major video recognition benchmarks. These video models are all built on Transformer layers that globally connect patches across the spatial and temporal dimensions. In this paper, we instead advocate an inductive bias of locality in video Transformers, which leads to a better speed-accuracy trade-off compared to previous approaches which compute self-attention globally even with spatial-temporal factorization. The locality of the proposed video architecture is realized by adapting the Swin Transformer designed for the image domain, while continuing to leverage the power of pre-trained image models. Our approach achieves state-of-the-art accuracy on a broad range of video recognition benchmarks, including on action recognition (84.9 top-1 accuracy on Kinetics-400 and 86.1 top-1 accuracy on Kinetics-600 with ~20x less pre-training data and ~3x smaller model size) and temporal modeling (69.6 top-1 accuracy on Something-Something v2). The code and models will be made publicly available at https://github.com/SwinTransformer/Video-Swin-Transformer.

We propose SAM-Road, an adaptation of the Segment Anything Model (SAM) for extracting large-scale, vectorized road network graphs from satellite imagery. To predict graph geometry, we formulate it as a dense semantic segmentation task, leveraging the inherent strengths of SAM. The image encoder of SAM is fine-tuned to produce probability masks for roads and intersections, from which the graph vertices are extracted via simple non-maximum suppression. To predict graph topology, we designed a lightweight transformer-based graph neural network, which leverages the SAM image embeddings to estimate the edge existence probabilities between vertices. Our approach directly predicts the graph vertices and edges for large regions without expensive and complex post-processing heuristics, and is capable of building complete road network graphs spanning multiple square kilometers in a matter of seconds. With its simple, straightforward, and minimalist design, SAM-Road achieves comparable accuracy with the state-of-the-art method RNGDet++, while being 40 times faster on the City-scale dataset. We thus demonstrate the power of a foundational vision model when applied to a graph learning task. The code is available at https://github.com/htcr/sam_road.

Transformer is a deep neural network that employs a self-attention mechanism to comprehend the contextual relationships within sequential data. Unlike conventional neural networks or updated versions of Recurrent Neural Networks (RNNs) such as Long Short-Term Memory (LSTM), transformer models excel in handling long dependencies between input sequence elements and enable parallel processing. As a result, transformer-based models have attracted substantial interest among researchers in the field of artificial intelligence. This can be attributed to their immense potential and remarkable achievements, not only in Natural Language Processing (NLP) tasks but also in a wide range of domains, including computer vision, audio and speech processing, healthcare, and the Internet of Things (IoT). Although several survey papers have been published highlighting the transformer's contributions in specific fields, architectural differences, or performance evaluations, there is still a significant absence of a comprehensive survey paper encompassing its major applications across various domains. Therefore, we undertook the task of filling this gap by conducting an extensive survey of proposed transformer models from 2017 to 2022. Our survey encompasses the identification of the top five application domains for transformer-based models, namely: NLP, Computer Vision, Multi-Modality, Audio and Speech Processing, and Signal Processing. We analyze the impact of highly influential transformer-based models in these domains and subsequently classify them based on their respective tasks using a proposed taxonomy. Our aim is to shed light on the existing potential and future possibilities of transformers for enthusiastic researchers, thus contributing to the broader understanding of this groundbreaking technology.

Vision transformers have gained popularity recently, leading to the development of new vision backbones with improved features and consistent performance gains. However, these advancements are not solely attributable to novel feature transformation designs; certain benefits also arise from advanced network-level and block-level architectures. This paper aims to identify the real gains of popular convolution and attention operators through a detailed study. We find that the key difference among these feature transformation modules, such as attention or convolution, lies in their spatial feature aggregation approach, known as the "spatial token mixer" (STM). To facilitate an impartial comparison, we introduce a unified architecture to neutralize the impact of divergent network-level and block-level designs. Subsequently, various STMs are integrated into this unified framework for comprehensive comparative analysis. Our experiments on various tasks and an analysis of inductive bias show a significant performance boost due to advanced network-level and block-level designs, but performance differences persist among different STMs. Our detailed analysis also reveals various findings about different STMs, such as effective receptive fields and invariance tests. All models and codes used in this study are publicly available at https://github.com/OpenGVLab/STM-Evaluation.

The self-attention-based model, transformer, is recently becoming the leading backbone in the field of computer vision. In spite of the impressive success made by transformers in a variety of vision tasks, it still suffers from heavy computation and intensive memory costs. To address this limitation, this paper presents an Interpretability-Aware REDundancy REDuction framework (IA-RED^2). We start by observing a large amount of redundant computation, mainly spent on uncorrelated input patches, and then introduce an interpretable module to dynamically and gracefully drop these redundant patches. This novel framework is then extended to a hierarchical structure, where uncorrelated tokens at different stages are gradually removed, resulting in a considerable shrinkage of computational cost. We include extensive experiments on both image and video tasks, where our method could deliver up to 1.4x speed-up for state-of-the-art models like DeiT and TimeSformer, by only sacrificing less than 0.7% accuracy. More importantly, contrary to other acceleration approaches, our method is inherently interpretable with substantial visual evidence, making vision transformer closer to a more human-understandable architecture while being lighter. We demonstrate that the interpretability that naturally emerged in our framework can outperform the raw attention learned by the original visual transformer, as well as those generated by off-the-shelf interpretation methods, with both qualitative and quantitative results. Project Page: http://people.csail.mit.edu/bpan/ia-red/.

The Transformer architecture is shown to provide a powerful machine transduction framework for online handwritten gestures corresponding to glyph strokes of natural language sentences. The attention mechanism is successfully used to create latent representations of an end-to-end encoder-decoder model, solving multi-level segmentation while also learning some language features and syntax rules. The additional use of a large decoding space with some learned Byte-Pair-Encoding (BPE) is shown to provide robustness to ablated inputs and syntax rules. The encoder stack was directly fed with spatio-temporal data tokens potentially forming an infinitely large input vocabulary, an approach that finds applications beyond that of this work. Encoder transfer learning capabilities is also demonstrated on several languages resulting in faster optimisation and shared parameters. A new supervised dataset of online handwriting gestures suitable for generic handwriting recognition tasks was used to successfully train a small transformer model to an average normalised Levenshtein accuracy of 96% on English or German sentences and 94% in French.

Vision Transformers (ViT) have marked a paradigm shift in computer vision, outperforming state-of-the-art models across diverse tasks. However, their practical deployment is hampered by high computational and memory demands. This study addresses the challenge by evaluating four primary model compression techniques: quantization, low-rank approximation, knowledge distillation, and pruning. We methodically analyze and compare the efficacy of these techniques and their combinations in optimizing ViTs for resource-constrained environments. Our comprehensive experimental evaluation demonstrates that these methods facilitate a balanced compromise between model accuracy and computational efficiency, paving the way for wider application in edge computing devices.

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).

Differentiable architecture search (DARTS) is successfully applied in many vision tasks. However, directly using DARTS for Transformers is memory-intensive, which renders the search process infeasible. To this end, we propose a multi-split reversible network and combine it with DARTS. Specifically, we devise a backpropagation-with-reconstruction algorithm so that we only need to store the last layer's outputs. By relieving the memory burden for DARTS, it allows us to search with larger hidden size and more candidate operations. We evaluate the searched architecture on three sequence-to-sequence datasets, i.e., WMT'14 English-German, WMT'14 English-French, and WMT'14 English-Czech. Experimental results show that our network consistently outperforms standard Transformers across the tasks. Moreover, our method compares favorably with big-size Evolved Transformers, reducing search computation by an order of magnitude.

Transformers, which are popular for language modeling, have been explored for solving vision tasks recently, e.g., the Vision Transformer (ViT) for image classification. The ViT model splits each image into a sequence of tokens with fixed length and then applies multiple Transformer layers to model their global relation for classification. However, ViT achieves inferior performance to CNNs when trained from scratch on a midsize dataset like ImageNet. We find it is because: 1) the simple tokenization of input images fails to model the important local structure such as edges and lines among neighboring pixels, leading to low training sample efficiency; 2) the redundant attention backbone design of ViT leads to limited feature richness for fixed computation budgets and limited training samples. To overcome such limitations, we propose a new Tokens-To-Token Vision Transformer (T2T-ViT), which incorporates 1) a layer-wise Tokens-to-Token (T2T) transformation to progressively structurize the image to tokens by recursively aggregating neighboring Tokens into one Token (Tokens-to-Token), such that local structure represented by surrounding tokens can be modeled and tokens length can be reduced; 2) an efficient backbone with a deep-narrow structure for vision transformer motivated by CNN architecture design after empirical study. Notably, T2T-ViT reduces the parameter count and MACs of vanilla ViT by half, while achieving more than 3.0\% improvement when trained from scratch on ImageNet. It also outperforms ResNets and achieves comparable performance with MobileNets by directly training on ImageNet. For example, T2T-ViT with comparable size to ResNet50 (21.5M parameters) can achieve 83.3\% top1 accuracy in image resolution 384times384 on ImageNet. (Code: https://github.com/yitu-opensource/T2T-ViT)

Rationale discovery is defined as finding a subset of the input data that maximally supports the prediction of downstream tasks. In graph machine learning context, graph rationale is defined to locate the critical subgraph in the given graph topology, which fundamentally determines the prediction results. In contrast to the rationale subgraph, the remaining subgraph is named the environment subgraph. Graph rationalization can enhance the model performance as the mapping between the graph rationale and prediction label is viewed as invariant, by assumption. To ensure the discriminative power of the extracted rationale subgraphs, a key technique named "intervention" is applied. The core idea of intervention is that given any changing environment subgraphs, the semantics from the rationale subgraph is invariant, which guarantees the correct prediction result. However, most, if not all, of the existing rationalization works on graph data develop their intervention strategies on the graph level, which is coarse-grained. In this paper, we propose well-tailored intervention strategies on graph data. Our idea is driven by the development of Transformer models, whose self-attention module provides rich interactions between input nodes. Based on the self-attention module, our proposed invariant graph Transformer (IGT) can achieve fine-grained, more specifically, node-level and virtual node-level intervention. Our comprehensive experiments involve 7 real-world datasets, and the proposed IGT shows significant performance advantages compared to 13 baseline methods.

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.

This paper studies how to keep a vision backbone effective while removing token mixers in its basic building blocks. Token mixers, as self-attention for vision transformers (ViTs), are intended to perform information communication between different spatial tokens but suffer from considerable computational cost and latency. However, directly removing them will lead to an incomplete model structure prior, and thus brings a significant accuracy drop. To this end, we first develop an RepIdentityFormer base on the re-parameterizing idea, to study the token mixer free model architecture. And we then explore the improved learning paradigm to break the limitation of simple token mixer free backbone, and summarize the empirical practice into 5 guidelines. Equipped with the proposed optimization strategy, we are able to build an extremely simple vision backbone with encouraging performance, while enjoying the high efficiency during inference. Extensive experiments and ablative analysis also demonstrate that the inductive bias of network architecture, can be incorporated into simple network structure with appropriate optimization strategy. We hope this work can serve as a starting point for the exploration of optimization-driven efficient network design. Project page: https://techmonsterwang.github.io/RIFormer/.

Transformers are central to recent successes in natural language processing and computer vision. Transformers have a mostly uniform backbone where layers alternate between feed-forward and self-attention in order to build a deep network. Here we investigate this design choice and find that more complex blocks that have different permutations of layer primitives can be more efficient. Using this insight, we develop a complex block, named Brainformer, that consists of a diverse sets of layers such as sparsely gated feed-forward layers, dense feed-forward layers, attention layers, and various forms of layer normalization and activation functions. Brainformer consistently outperforms the state-of-the-art dense and sparse Transformers, in terms of both quality and efficiency. A Brainformer model with 8 billion activated parameters per token demonstrates 2x faster training convergence and 5x faster step time compared to its GLaM counterpart. In downstream task evaluation, Brainformer also demonstrates a 3% higher SuperGLUE score with fine-tuning compared to GLaM with a similar number of activated parameters. Finally, Brainformer largely outperforms a Primer dense model derived with NAS with similar computation per token on fewshot evaluations.

When predicting the next token in a sequence, vanilla transformers compute attention over all previous tokens, resulting in quadratic scaling of compute with sequence length. State-space models compress the entire sequence of tokens into a fixed-dimensional representation to improve efficiency, while other architectures achieve sub-quadratic complexity via low-rank projections or sparse attention patterns over the sequence. In this paper, we introduce Attamba, a novel architecture that uses state-space models to compress chunks of tokens and applies attention on these compressed key-value representations. We find that replacing key and value projections in a transformer with SSMs can improve model quality and enable flexible token chunking, resulting in 24% improved perplexity with transformer of similar KV-Cache and attention footprint, and ~4 times smaller KV-Cache and Attention FLOPs for 5% perplexity trade-off. Attamba can perform attention on chunked-sequences of variable length, enabling a smooth transition between quadratic and linear scaling, offering adaptable efficiency gains.

Transformer models have revolutionized natural language processing with their unparalleled ability to grasp complex contextual relationships. However, the vast number of parameters in these models has raised concerns regarding computational efficiency, environmental impact, and deployability on resource-limited platforms. To address these challenges, this paper investigates the application of weight pruning-a strategic reduction of model parameters based on their significance-as an optimization strategy for Transformer architectures. Through extensive experimentation, we explore various pruning methodologies, highlighting their impact on model performance, size, and computational demands. Our findings suggest that with judicious selection of pruning hyperparameters, significant reductions in model size are attainable without considerable compromise on performance. Moreover, when coupled with post-pruning fine-tuning strategies, some pruned models even exhibit enhanced generalization capabilities. This work seeks to bridge the gap between model efficiency and performance, paving the way for more scalable and environmentally responsible deep learning applications.

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.

Transformer models are deployed in a wide range of settings, from multi-accelerator clusters to standalone mobile phones. The diverse inference constraints in these scenarios necessitate practitioners to train foundation models such as PaLM 2, Llama, & ViTs as a series of models of varying sizes. Due to significant training costs, only a select few model sizes are trained and supported, limiting more fine-grained control over relevant tradeoffs, including latency, cost, and accuracy. This work introduces MatFormer, a nested Transformer architecture designed to offer elasticity in a variety of deployment constraints. Each Feed Forward Network (FFN) block of a MatFormer model is jointly optimized with a few nested smaller FFN blocks. This training procedure allows for the Mix'n'Match of model granularities across layers -- i.e., a trained universal MatFormer model enables extraction of hundreds of accurate smaller models, which were never explicitly optimized. We empirically demonstrate MatFormer's effectiveness across different model classes (decoders & encoders), modalities (language & vision), and scales (up to 2.6B parameters). We find that a 2.6B decoder-only MatFormer language model (MatLM) allows us to extract smaller models spanning from 1.5B to 2.6B, each exhibiting comparable validation loss and one-shot downstream evaluations to their independently trained counterparts. Furthermore, we observe that smaller encoders extracted from a universal MatFormer-based ViT (MatViT) encoder preserve the metric-space structure for adaptive large-scale retrieval. Finally, we showcase that speculative decoding with the accurate and consistent submodels extracted from MatFormer can further reduce inference latency.

Transformers have become foundational architectures for both natural language and computer vision tasks. However, the high computational cost makes it quite challenging to deploy on resource-constraint devices. This paper investigates the computational bottleneck modules of efficient transformer, i.e., normalization layers and attention modules. LayerNorm is commonly used in transformer architectures but is not computational friendly due to statistic calculation during inference. However, replacing LayerNorm with more efficient BatchNorm in transformer often leads to inferior performance and collapse in training. To address this problem, we propose a novel method named PRepBN to progressively replace LayerNorm with re-parameterized BatchNorm in training. Moreover, we propose a simplified linear attention (SLA) module that is simple yet effective to achieve strong performance. Extensive experiments on image classification as well as object detection demonstrate the effectiveness of our proposed method. For example, our SLAB-Swin obtains 83.6% top-1 accuracy on ImageNet-1K with 16.2ms latency, which is 2.4ms less than that of Flatten-Swin with 0.1% higher accuracy. We also evaluated our method for language modeling task and obtain comparable performance and lower latency.Codes are publicly available at https://github.com/xinghaochen/SLAB and https://github.com/mindspore-lab/models/tree/master/research/huawei-noah/SLAB.

Deep learning, as a vital technique, has sparked a notable revolution in artificial intelligence. As the most representative architecture, Transformers have empowered numerous advanced models, especially the large language models that comprise billions of parameters, becoming a cornerstone in deep learning. Despite the impressive achievements, Transformers still face inherent limitations, particularly the time-consuming inference resulting from the quadratic computation complexity of attention calculation. Recently, a novel architecture named Mamba, drawing inspiration from classical state space models, has emerged as a promising alternative for building foundation models, delivering comparable modeling abilities to Transformers while preserving near-linear scalability concerning sequence length. This has sparked an increasing number of studies actively exploring Mamba's potential to achieve impressive performance across diverse domains. Given such rapid evolution, there is a critical need for a systematic review that consolidates existing Mamba-empowered models, offering a comprehensive understanding of this emerging model architecture. In this survey, we therefore conduct an in-depth investigation of recent Mamba-associated studies, covering from three main aspects: the advancements of Mamba-based models, the techniques of adapting Mamba to diverse data, and the applications where Mamba can excel. Specifically, we first recall the foundational knowledge of various representative deep learning models and the details of Mamba as preliminaries. Then, to showcase the significance of Mamba, we comprehensively review the related studies focusing on Mamba models' architecture design, data adaptability, and applications. Finally, we present an discussion of current limitations and explore various promising research directions to provide deeper insights for future investigations.

Transformer-based architectures are the model of choice for natural language understanding, but they come at a significant cost, as they have quadratic complexity in the input length, require a lot of training data, and can be difficult to tune. In the pursuit of lower costs, we investigate simple MLP-based architectures. We find that existing architectures such as MLPMixer, which achieves token mixing through a static MLP applied to each feature independently, are too detached from the inductive biases required for natural language understanding. In this paper, we propose a simple variant, HyperMixer, which forms the token mixing MLP dynamically using hypernetworks. Empirically, we demonstrate that our model performs better than alternative MLP-based models, and on par with Transformers. In contrast to Transformers, HyperMixer achieves these results at substantially lower costs in terms of processing time, training data, and hyperparameter tuning.

The crystallization of modeling methods around the Transformer architecture has been a boon for practitioners. Simple, well-motivated architectural variations can transfer across tasks and scale, increasing the impact of modeling research. However, with the emergence of state-of-the-art 100B+ parameters models, large language models are increasingly expensive to accurately design and train. Notably, it can be difficult to evaluate how modeling decisions may impact emergent capabilities, given that these capabilities arise mainly from sheer scale alone. In the process of building BLOOM--the Big Science Large Open-science Open-access Multilingual language model--our goal is to identify an architecture and training setup that makes the best use of our 1,000,000 A100-GPU-hours budget. Specifically, we perform an ablation study at the billion-parameter scale comparing different modeling practices and their impact on zero-shot generalization. In addition, we study the impact of various popular pre-training corpora on zero-shot generalization. We also study the performance of a multilingual model and how it compares to the English-only one. Finally, we consider the scaling behaviour of Transformers to choose the target model size, shape, and training setup. All our models and code are open-sourced at https://huggingface.co/bigscience .

Attention-based transformers have become the standard architecture in many deep learning fields, primarily due to their ability to model long-range dependencies and handle variable-length input sequences. However, the attention mechanism with its quadratic complexity is a significant bottleneck in the transformer architecture. This algorithm is only uni-directional in the decoder and converges to a static pattern in over-parametrized decoder-only models. I address this issue by developing a generative function as attention or activation replacement. It still has the auto-regressive character by comparing each token with the previous one. In my test setting with nanoGPT this yields a smaller loss while having a smaller model. The loss further drops by incorporating an average context vector. This concept of attention replacement is distributed under the GNU AGPL v3 license at https://gitlab.com/Bachstelze/causal_generation.

In this paper, we present DevFormer, a novel transformer-based architecture for addressing the complex and computationally demanding problem of hardware design optimization. Despite the demonstrated efficacy of transformers in domains including natural language processing and computer vision, their use in hardware design has been limited by the scarcity of offline data. Our approach addresses this limitation by introducing strong inductive biases such as relative positional embeddings and action-permutation symmetricity that effectively capture the hardware context and enable efficient design optimization with limited offline data. We apply DevFoemer to the problem of decoupling capacitor placement and show that it outperforms state-of-the-art methods in both simulated and real hardware, leading to improved performances while reducing the number of components by more than 30%. Finally, we show that our approach achieves promising results in other offline contextual learning-based combinatorial optimization tasks.

The Transformer architecture is shown to provide a powerful framework as an end-to-end model for building expression trees from online handwritten gestures corresponding to glyph strokes. In particular, the attention mechanism was successfully used to encode, learn and enforce the underlying syntax of expressions creating latent representations that are correctly decoded to the exact mathematical expression tree, providing robustness to ablated inputs and unseen glyphs. For the first time, the encoder is fed with spatio-temporal data tokens potentially forming an infinitely large vocabulary, which finds applications beyond that of online gesture recognition. A new supervised dataset of online handwriting gestures is provided for training models on generic handwriting recognition tasks and a new metric is proposed for the evaluation of the syntactic correctness of the output expression trees. A small Transformer model suitable for edge inference was successfully trained to an average normalised Levenshtein accuracy of 94%, resulting in valid postfix RPN tree representation for 94% of predictions.

This paper investigates the key role of Feed-Forward Networks (FFNs) in transformer models by utilizing the Parallel Attention and Feed-Forward Net Design (PAF) architecture, and comparing it to their Series Attention and Feed-Forward Net Design (SAF) counterparts. Central to the effectiveness of PAF are two main assumptions regarding the FFN block and the attention block within a layer: 1) the primary function of the FFN block is to maintain isotropy among token embeddings and prevent their degeneration, and 2) the residual norm computed in the attention block is substantially smaller than the input token embedding norm. To empirically validate these assumptions, we train PAF variants of two large language models (RoBERTa-large and bert-large-uncased). Our results demonstrate that both assumptions hold true in the PAF design. This study contributes to a deeper understanding of the roles and interactions between FFNs and self-attention mechanisms in transformer architectures.

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.

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.

Graph Neural Networks (GNNs) have already been widely applied in various graph mining tasks. However, they suffer from the shallow architecture issue, which is the key impediment that hinders the model performance improvement. Although several relevant approaches have been proposed, none of the existing studies provides an in-depth understanding of the root causes of performance degradation in deep GNNs. In this paper, we conduct the first systematic experimental evaluation to present the fundamental limitations of shallow architectures. Based on the experimental results, we answer the following two essential questions: (1) what actually leads to the compromised performance of deep GNNs; (2) when we need and how to build deep GNNs. The answers to the above questions provide empirical insights and guidelines for researchers to design deep and well-performed GNNs. To show the effectiveness of our proposed guidelines, we present Deep Graph Multi-Layer Perceptron (DGMLP), a powerful approach (a paradigm in its own right) that helps guide deep GNN designs. Experimental results demonstrate three advantages of DGMLP: 1) high accuracy -- it achieves state-of-the-art node classification performance on various datasets; 2) high flexibility -- it can flexibly choose different propagation and transformation depths according to graph size and sparsity; 3) high scalability and efficiency -- it supports fast training on large-scale graphs. Our code is available in https://github.com/zwt233/DGMLP.

GNN-to-MLP distillation aims to utilize knowledge distillation (KD) to learn computationally-efficient multi-layer perceptron (student MLP) on graph data by mimicking the output representations of teacher GNN. Existing methods mainly make the MLP to mimic the GNN predictions over a few class labels. However, the class space may not be expressive enough for covering numerous diverse local graph structures, thus limiting the performance of knowledge transfer from GNN to MLP. To address this issue, we propose to learn a new powerful graph representation space by directly labeling nodes' diverse local structures for GNN-to-MLP distillation. Specifically, we propose a variant of VQ-VAE to learn a structure-aware tokenizer on graph data that can encode each node's local substructure as a discrete code. The discrete codes constitute a codebook as a new graph representation space that is able to identify different local graph structures of nodes with the corresponding code indices. Then, based on the learned codebook, we propose a new distillation target, namely soft code assignments, to directly transfer the structural knowledge of each node from GNN to MLP. The resulting framework VQGraph achieves new state-of-the-art performance on GNN-to-MLP distillation in both transductive and inductive settings across seven graph datasets. We show that VQGraph with better performance infers faster than GNNs by 828x, and also achieves accuracy improvement over GNNs and stand-alone MLPs by 3.90% and 28.05% on average, respectively. Code: https://github.com/YangLing0818/VQGraph.

Transformer-based architectures have become the de-facto standard models for diverse vision tasks owing to their superior performance. As the size of the models continues to scale up, model distillation becomes extremely important in various real applications, particularly on devices limited by computational resources. However, prevailing knowledge distillation methods exhibit diminished efficacy when confronted with a large capacity gap between the teacher and the student, e.g, 10x compression rate. In this paper, we present a novel approach named Automatic Multi-step Distillation (AMD) for large-scale vision model compression. In particular, our distillation process unfolds across multiple steps. Initially, the teacher undergoes distillation to form an intermediate teacher-assistant model, which is subsequently distilled further to the student. An efficient and effective optimization framework is introduced to automatically identify the optimal teacher-assistant that leads to the maximal student performance. We conduct extensive experiments on multiple image classification datasets, including CIFAR-10, CIFAR-100, and ImageNet. The findings consistently reveal that our approach outperforms several established baselines, paving a path for future knowledge distillation methods on large-scale vision models.

Transformers, as a fundamental deep learning architecture, have demonstrated remarkable capabilities in reasoning. This paper investigates the generalizable first-order logical reasoning ability of transformers with their parameterized knowledge and explores ways to improve it. The first-order reasoning capability of transformers is assessed through their ability to perform first-order logical entailment, which is quantitatively measured by their performance in answering knowledge graph queries. We establish connections between (1) two types of distribution shifts studied in out-of-distribution generalization and (2) the unseen knowledge and query settings discussed in the task of knowledge graph query answering, enabling a characterization of fine-grained generalizability. Results on our comprehensive dataset show that transformers outperform previous methods specifically designed for this task and provide detailed empirical evidence on the impact of input query syntax, token embedding, and transformer architectures on the reasoning capability of transformers. Interestingly, our findings reveal a mismatch between positional encoding and other design choices in transformer architectures employed in prior practices. This discovery motivates us to propose a more sophisticated, logic-aware architecture, TEGA, to enhance the capability for generalizable first-order logical entailment in transformers.