Transformer and Snowball Graph Convolution Learning for Biomedical Graph Classification

Graph or network has been widely used for describing and modeling complex systems in biomedicine. Deep learning methods, especially graph neural networks (GNNs), have been developed to learn and predict with such structured data. In this paper, we proposed a novel transformer and snowball encoding networks (TSEN) for biomedical graph classification, which introduced transformer architecture with graph snowball connection into GNNs for learning whole-graph representation. TSEN combined graph snowball connection with graph transformer by snowball encoding layers, which enhanced the power to capture multi-scale information and global patterns to learn the whole-graph features. On the other hand, TSEN also used snowball graph convolution as position embedding in transformer structure, which was a simple yet effective method for capturing local patterns naturally. Results of experiments using four graph classification datasets demonstrated that TSEN outperformed the state-of-the-art typical GNN models and the graph-transformer based GNN models.Comment: Prepared for submitting to TB

Transformers over Directed Acyclic Graphs

Transformer models have recently gained popularity in graph representation learning as they have the potential to learn complex relationships beyond the ones captured by regular graph neural networks. The main research question is how to inject the structural bias of graphs into the transformer architecture, and several proposals have been made for undirected molecular graphs and, recently, also for larger network graphs. In this paper, we study transformers over directed acyclic graphs (DAGs) and propose architecture adaptations tailored to DAGs: (1) An attention mechanism that is considerably more efficient than the regular quadratic complexity of transformers and at the same time faithfully captures the DAG structure, and (2) a positional encoding of the DAG's partial order, complementing the former. We rigorously evaluate our approach over various types of tasks, ranging from classifying source code graphs to nodes in citation networks, and show that it is effective in two important aspects: in making graph transformers generally outperform graph neural networks tailored to DAGs and in improving SOTA graph transformer performance in terms of both quality and efficiency

Long Range Graph Benchmark

Graph Neural Networks (GNNs) that are based on the message passing (MP) paradigm generally exchange information between 1-hop neighbors to build node representations at each layer. In principle, such networks are not able to capture long-range interactions (LRI) that may be desired or necessary for learning a given task on graphs. Recently, there has been an increasing interest in development of Transformer-based methods for graphs that can consider full node connectivity beyond the original sparse structure, thus enabling the modeling of LRI. However, MP-GNNs that simply rely on 1-hop message passing often fare better in several existing graph benchmarks when combined with positional feature representations, among other innovations, hence limiting the perceived utility and ranking of Transformer-like architectures. Here, we present the Long Range Graph Benchmark (LRGB) with 5 graph learning datasets: PascalVOC-SP, COCO-SP, PCQM-Contact, Peptides-func and Peptides-struct that arguably require LRI reasoning to achieve strong performance in a given task. We benchmark both baseline GNNs and Graph Transformer networks to verify that the models which capture long-range dependencies perform significantly better on these tasks. Therefore, these datasets are suitable for benchmarking and exploration of MP-GNNs and Graph Transformer architectures that are intended to capture LRI.Comment: Added reference to T\"onshoff et al., 2023 in Sec. 4.1; NeurIPS 2022 Track on D&B; Open-sourced at: https://github.com/vijaydwivedi75/lrg

Dynamic Graph Representation Learning via Graph Transformer Networks

Dynamic graph representation learning is an important task with widespread applications. Previous methods on dynamic graph learning are usually sensitive to noisy graph information such as missing or spurious connections, which can yield degenerated performance and generalization. To overcome this challenge, we propose a Transformer-based dynamic graph learning method named Dynamic Graph Transformer (DGT) with spatial-temporal encoding to effectively learn graph topology and capture implicit links. To improve the generalization ability, we introduce two complementary self-supervised pre-training tasks and show that jointly optimizing the two pre-training tasks results in a smaller Bayesian error rate via an information-theoretic analysis. We also propose a temporal-union graph structure and a target-context node sampling strategy for efficient and scalable training. Extensive experiments on real-world datasets illustrate that DGT presents superior performance compared with several state-of-the-art baselines

GTNet: Graph Transformer Network for 3D Point Cloud Classification and Semantic Segmentation

Recently, graph-based and Transformer-based deep learning networks have demonstrated excellent performances on various point cloud tasks. Most of the existing graph methods are based on static graph, which take a fixed input to establish graph relations. Moreover, many graph methods apply maximization and averaging to aggregate neighboring features, so that only a single neighboring point affects the feature of centroid or different neighboring points have the same influence on the centroid's feature, which ignoring the correlation and difference between points. Most Transformer-based methods extract point cloud features based on global attention and lack the feature learning on local neighbors. To solve the problems of these two types of models, we propose a new feature extraction block named Graph Transformer and construct a 3D point point cloud learning network called GTNet to learn features of point clouds on local and global patterns. Graph Transformer integrates the advantages of graph-based and Transformer-based methods, and consists of Local Transformer and Global Transformer modules. Local Transformer uses a dynamic graph to calculate all neighboring point weights by intra-domain cross-attention with dynamically updated graph relations, so that every neighboring point could affect the features of centroid with different weights; Global Transformer enlarges the receptive field of Local Transformer by a global self-attention. In addition, to avoid the disappearance of the gradient caused by the increasing depth of network, we conduct residual connection for centroid features in GTNet; we also adopt the features of centroid and neighbors to generate the local geometric descriptors in Local Transformer to strengthen the local information learning capability of the model. Finally, we use GTNet for shape classification, part segmentation and semantic segmentation tasks in this paper

NAR-Former V2: Rethinking Transformer for Universal Neural Network Representation Learning

As more deep learning models are being applied in real-world applications, there is a growing need for modeling and learning the representations of neural networks themselves. An efficient representation can be used to predict target attributes of networks without the need for actual training and deployment procedures, facilitating efficient network deployment and design. Recently, inspired by the success of Transformer, some Transformer-based representation learning frameworks have been proposed and achieved promising performance in handling cell-structured models. However, graph neural network (GNN) based approaches still dominate the field of learning representation for the entire network. In this paper, we revisit Transformer and compare it with GNN to analyse their different architecture characteristics. We then propose a modified Transformer-based universal neural network representation learning model NAR-Former V2. It can learn efficient representations from both cell-structured networks and entire networks. Specifically, we first take the network as a graph and design a straightforward tokenizer to encode the network into a sequence. Then, we incorporate the inductive representation learning capability of GNN into Transformer, enabling Transformer to generalize better when encountering unseen architecture. Additionally, we introduce a series of simple yet effective modifications to enhance the ability of the Transformer in learning representation from graph structures. Our proposed method surpasses the GNN-based method NNLP by a significant margin in latency estimation on the NNLQP dataset. Furthermore, regarding accuracy prediction on the NASBench101 and NASBench201 datasets, our method achieves highly comparable performance to other state-of-the-art methods.Comment: 9 pages, 2 figures, 6 tables. Code is available at https://github.com/yuny220/NAR-Former-V

Transforming Graphs for Enhanced Attribute Clustering: An Innovative Graph Transformer-Based Method

Graph Representation Learning (GRL) is an influential methodology, enabling a more profound understanding of graph-structured data and aiding graph clustering, a critical task across various domains. The recent incursion of attention mechanisms, originally an artifact of Natural Language Processing (NLP), into the realm of graph learning has spearheaded a notable shift in research trends. Consequently, Graph Attention Networks (GATs) and Graph Attention Auto-Encoders have emerged as preferred tools for graph clustering tasks. Yet, these methods primarily employ a local attention mechanism, thereby curbing their capacity to apprehend the intricate global dependencies between nodes within graphs. Addressing these impediments, this study introduces an innovative method known as the Graph Transformer Auto-Encoder for Graph Clustering (GTAGC). By melding the Graph Auto-Encoder with the Graph Transformer, GTAGC is adept at capturing global dependencies between nodes. This integration amplifies the graph representation and surmounts the constraints posed by the local attention mechanism. The architecture of GTAGC encompasses graph embedding, integration of the Graph Transformer within the autoencoder structure, and a clustering component. It strategically alternates between graph embedding and clustering, thereby tailoring the Graph Transformer for clustering tasks, whilst preserving the graph's global structural information. Through extensive experimentation on diverse benchmark datasets, GTAGC has exhibited superior performance against existing state-of-the-art graph clustering methodologies