Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, where genome dynamics such as horizontal gene transfer, gene duplication, and gene loss/gain complicate accurate genome assembly from metagenomic communities. Detecting repeats is a crucial first step in overcoming these challenges. To address this issue, we propose GraSSRep, a novel approach that leverages the assembly graph's structure through graph neural networks (GNNs) within a self-supervised learning framework to classify DNA sequences into repetitive and non-repetitive categories. Specifically, we frame this problem as a node classification task within a metagenomic assembly graph. In a self-supervised fashion, we rely on a high-precision (but low-recall) heuristic to generate pseudo-labels for a small proportion of the nodes. We then use those pseudo-labels to train a GNN embedding and a random forest classifier to propagate the labels to the remaining nodes. In this way, GraSSRep combines sequencing features with pre-defined and learned graph features to achieve state-of-the-art performance in repeat detection. We evaluate our method using simulated and synthetic metagenomic datasets. The results on the simulated data highlight our GraSSRep's robustness to repeat attributes, demonstrating its effectiveness in handling the complexity of repeated sequences. Additionally, our experiments with synthetic metagenomic datasets reveal that incorporating the graph structure and the GNN enhances our detection performance. Finally, in comparative analyses, GraSSRep outperforms existing repeat detection tools with respect to precision and recall.
Graph Neural Networks (GNNs) have demonstrated significant success in learning from graph-structured data across various domains. Despite their great successful, one critical challenge is often overlooked by existing works, i.e., the learning of message propagation that can generalize effectively to underrepresented graph regions. These minority regions often exhibit irregular homophily/heterophily patterns and diverse neighborhood class distributions, resulting in ambiguity. In this work, we investigate the ambiguity problem within GNNs, its impact on representation learning, and the development of richer supervision signals to fight against this problem. We conduct a fine-grained evaluation of GNN, analyzing the existence of ambiguity in different graph regions and its relation with node positions. To disambiguate node embeddings, we propose a novel method, {\method}, which exploits additional optimization guidance to enhance representation learning, particularly for nodes in ambiguous regions. {\method} identifies ambiguous nodes based on temporal inconsistency of predictions and introduces a disambiguation regularization by employing contrastive learning in a topology-aware manner. {\method} promotes discriminativity of node representations and can alleviating semantic mixing caused by message propagation, effectively addressing the ambiguity problem. Empirical results validate the efficiency of {\method} and highlight its potential to improve GNN performance in underrepresented graph regions.
Graph Neural Networks (GNNs) have demonstrated their effectiveness in various graph learning tasks, yet their reliance on neighborhood aggregation during inference poses challenges for deployment in latency-sensitive applications, such as real-time financial fraud detection. To address this limitation, recent studies have proposed distilling knowledge from teacher GNNs into student Multi-Layer Perceptrons (MLPs) trained on node content, aiming to accelerate inference. However, these approaches often inadequately explore structural information when inferring unseen nodes. To this end, we introduce SimMLP, a Self-supervised framework for learning MLPs on graphs, designed to fully integrate rich structural information into MLPs. Notably, SimMLP is the first MLP-learning method that can achieve equivalence to GNNs in the optimal case. The key idea is to employ self-supervised learning to align the representations encoded by graph context-aware GNNs and neighborhood dependency-free MLPs, thereby fully integrating the structural information into MLPs. We provide a comprehensive theoretical analysis, demonstrating the equivalence between SimMLP and GNNs based on mutual information and inductive bias, highlighting SimMLP's advanced structural learning capabilities. Additionally, we conduct extensive experiments on 20 benchmark datasets, covering node classification, link prediction, and graph classification, to showcase SimMLP's superiority over state-of-the-art baselines, particularly in scenarios involving unseen nodes (e.g., inductive and cold-start node classification) where structural insights are crucial. Our codes are available at: https://github.com/Zehong-Wang/SimMLP.
Given a node-attributed graph, and a graph task (link prediction or node classification), can we tell if a graph neural network (GNN) will perform well? More specifically, do the graph structure and the node features carry enough usable information for the task? Our goals are (1) to develop a fast tool to measure how much information is in the graph structure and in the node features, and (2) to exploit the information to solve the task, if there is enough. We propose NetInfoF, a framework including NetInfoF_Probe and NetInfoF_Act, for the measurement and the exploitation of network usable information (NUI), respectively. Given a graph data, NetInfoF_Probe measures NUI without any model training, and NetInfoF_Act solves link prediction and node classification, while two modules share the same backbone. In summary, NetInfoF has following notable advantages: (a) General, handling both link prediction and node classification; (b) Principled, with theoretical guarantee and closed-form solution; (c) Effective, thanks to the proposed adjustment to node similarity; (d) Scalable, scaling linearly with the input size. In our carefully designed synthetic datasets, NetInfoF correctly identifies the ground truth of NUI and is the only method being robust to all graph scenarios. Applied on real-world datasets, NetInfoF wins in 11 out of 12 times on link prediction compared to general GNN baselines.
Hypergraphs are characterized by complex topological structure, representing higher-order interactions among multiple entities through hyperedges. Lately, hypergraph-based deep learning methods to learn informative data representations for the problem of node classification on text-attributed hypergraphs have garnered increasing research attention. However, existing methods struggle to simultaneously capture the full extent of hypergraph structural information and the rich linguistic attributes inherent in the nodes attributes, which largely hampers their effectiveness and generalizability. To overcome these challenges, we explore ways to further augment a pretrained BERT model with specialized hypergraph-aware layers for the task of node classification. Such layers introduce higher-order structural inductive bias into the language model, thus improving the model's capacity to harness both higher-order context information from the hypergraph structure and semantic information present in text. In this paper, we propose a new architecture, HyperBERT, a mixed text-hypergraph model which simultaneously models hypergraph relational structure while maintaining the high-quality text encoding capabilities of a pre-trained BERT. Notably, HyperBERT presents results that achieve a new state-of-the-art on five challenging text-attributed hypergraph node classification benchmarks.
Large language models (LLMs) like ChatGPT, exhibit powerful zero-shot and instruction-following capabilities, have catalyzed a revolutionary transformation across diverse fields, especially for open-ended tasks. While the idea is less explored in the graph domain, despite the availability of numerous powerful graph models (GMs), they are restricted to tasks in a pre-defined form. Although several methods applying LLMs to graphs have been proposed, they fail to simultaneously handle the pre-defined and open-ended tasks, with LLM as a node feature enhancer or as a standalone predictor. To break this dilemma, we propose to bridge the pretrained GM and LLM by a Translator, named GraphTranslator, aiming to leverage GM to handle the pre-defined tasks effectively and utilize the extended interface of LLMs to offer various open-ended tasks for GM. To train such Translator, we propose a Producer capable of constructing the graph-text alignment data along node information, neighbor information and model information. By translating node representation into tokens, GraphTranslator empowers an LLM to make predictions based on language instructions, providing a unified perspective for both pre-defined and open-ended tasks. Extensive results demonstrate the effectiveness of our proposed GraphTranslator on zero-shot node classification. The graph question answering experiments reveal our GraphTranslator potential across a broad spectrum of open-ended tasks through language instructions. Our code is available at: https://github.com/alibaba/GraphTranslator.
Scalable graph neural networks (GNNs) have emerged as a promising technique, which exhibits superior predictive performance and high running efficiency across numerous large-scale graph-based web applications. However, (i) Most scalable GNNs tend to treat all nodes in graphs with the same propagation rules, neglecting their topological uniqueness; (ii) Existing node-wise propagation optimization strategies are insufficient on web-scale graphs with intricate topology, where a full portrayal of nodes' local properties is required. Intuitively, different nodes in web-scale graphs possess distinct topological roles, and therefore propagating them indiscriminately or neglect local contexts may compromise the quality of node representations. This intricate topology in web-scale graphs cannot be matched by small-scale scenarios. To address the above issues, we propose \textbf{A}daptive \textbf{T}opology-aware \textbf{P}ropagation (ATP), which reduces potential high-bias propagation and extracts structural patterns of each node in a scalable manner to improve running efficiency and predictive performance. Remarkably, ATP is crafted to be a plug-and-play node-wise propagation optimization strategy, allowing for offline execution independent of the graph learning process in a new perspective. Therefore, this approach can be seamlessly integrated into most scalable GNNs while remain orthogonal to existing node-wise propagation optimization strategies. Extensive experiments on 12 datasets, including the most representative large-scale ogbn-papers100M, have demonstrated the effectiveness of ATP. Specifically, ATP has proven to be efficient in improving the performance of prevalent scalable GNNs for semi-supervised node classification while addressing redundant computational costs.
Graph neural networks (GNNs) are the dominant paradigm for classifying nodes in a graph, but they have several undesirable attributes stemming from their message passing architecture. Recently, distillation methods succeeded in eliminating the use of GNNs at test time but they still require them during training. We perform a careful analysis of the role that GNNs play in distillation methods. This analysis leads us to propose a fully GNN-free approach for node classification, not requiring them at train or test time. Our method consists of three key components: smoothness constraints, pseudo-labeling iterations and neighborhood-label histograms. Our final approach can match the state-of-the-art accuracy on standard popular benchmarks such as citation and co-purchase networks, without training a GNN.
Masked graph autoencoders have emerged as a powerful graph self-supervised learning method that has yet to be fully explored. In this paper, we unveil that the existing discrete edge masking and binary link reconstruction strategies are insufficient to learn topologically informative representations, from the perspective of message propagation on graph neural networks. These limitations include blocking message flows, vulnerability to over-smoothness, and suboptimal neighborhood discriminability. Inspired by these understandings, we explore non-discrete edge masks, which are sampled from a continuous and dispersive probability distribution instead of the discrete Bernoulli distribution. These masks restrict the amount of output messages for each edge, referred to as "bandwidths". We propose a novel, informative, and effective topological masked graph autoencoder using bandwidth masking and a layer-wise bandwidth prediction objective. We demonstrate its powerful graph topological learning ability both theoretically and empirically. Our proposed framework outperforms representative baselines in both self-supervised link prediction (improving the discrete edge reconstructors by at most 20%) and node classification on numerous datasets, solely with a structure-learning pretext. Our implementation is available at https://github.com/Newiz430/Bandana.
Text-attributed graphs (TAGs) present unique challenges for direct processing by Language Learning Models (LLMs), yet their extensive commonsense knowledge and robust reasoning capabilities offer great promise for node classification in TAGs. Prior research in this field has grappled with issues such as over-squashing, heterophily, and ineffective graph information integration, further compounded by inconsistencies in dataset partitioning and underutilization of advanced LLMs. To address these challenges, we introduce Similarity-based Neighbor Selection (SNS). Using SimCSE and advanced neighbor selection techniques, SNS effectively improves the quality of selected neighbors, thereby improving graph representation and alleviating issues like over-squashing and heterophily. Besides, as an inductive and training-free approach, SNS demonstrates superior generalization and scalability over traditional GNN methods. Our comprehensive experiments, adhering to standard dataset partitioning practices, demonstrate that SNS, through simple prompt interactions with LLMs, consistently outperforms vanilla GNNs and achieves state-of-the-art results on datasets like PubMed in node classification, showcasing LLMs' potential in graph structure understanding. Our research further underscores the significance of graph structure integration in LLM applications and identifies key factors for their success in node classification. Code is available at https://github.com/ruili33/SNS.
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.
Temporal graph representation learning (TGRL) is essential for modeling dynamic systems in real-world networks. However, traditional TGRL methods, despite their effectiveness, often face significant computational challenges and inference delays due to the inefficient sampling of temporal neighbors. Conventional sampling methods typically involve backtracking through the interaction history of each node. In this paper, we propose a novel TGRL framework, No-Looking-Back (NLB), which overcomes these challenges by introducing a forward recent sampling strategy. This strategy eliminates the need to backtrack through historical interactions by utilizing a GPU-executable, size-constrained hash table for each node. The hash table records a down-sampled set of recent interactions, enabling rapid query responses with minimal inference latency. The maintenance of this hash table is highly efficient, operating with $O(1)$ complexity. Fully compatible with GPU processing, NLB maximizes programmability, parallelism, and power efficiency. Empirical evaluations demonstrate that NLB not only matches or surpasses state-of-the-art methods in accuracy for tasks like link prediction and node classification across six real-world datasets but also achieves 1.32-4.40x faster training, 1.2-7.94x greater energy efficiency, and 1.63-12.95x lower inference latency compared to competitive baselines. The link to the code: https://github.com/Graph-COM/NLB.
Large Language Models (LLMs) are increasingly used for various tasks with graph structures. Though LLMs can process graph information in a textual format, they overlook the rich vision modality, which is an intuitive way for humans to comprehend structural information and conduct general graph reasoning. The potential benefits and capabilities of representing graph structures as visual images (i.e., $\textit{visual graph}$) are still unexplored. To fill the gap, we innovatively propose an end-to-end framework, called $\textbf{G}$raph to v$\textbf{I}$sual and $\textbf{T}$extual Integr$\textbf{A}$tion (GITA), which firstly incorporates visual graphs into general graph reasoning. Besides, we establish $\textbf{G}$raph-based $\textbf{V}$ision-$\textbf{L}$anguage $\textbf{Q}$uestion $\textbf{A}$nswering (GVLQA) dataset from existing graph data, which is the first vision-language dataset for general graph reasoning purposes. Extensive experiments on the GVLQA dataset and five real-world datasets show that GITA outperforms mainstream LLMs in terms of general graph reasoning capabilities. Moreover, We highlight the effectiveness of the layout augmentation on visual graphs and pretraining on the GVLQA dataset.
Deep graph models (e.g., graph neural networks and graph transformers) have become important techniques for leveraging knowledge across various types of graphs. Yet, the neural scaling laws on graphs, i.e., how the performance of deep graph models changes with model and dataset sizes, have not been systematically investigated, casting doubts on the feasibility of achieving large graph models. To fill this gap, we benchmark many graph datasets from different tasks and make an attempt to establish the neural scaling laws on graphs from both model and data perspectives. The model size we investigated is up to 100 million parameters, and the dataset size investigated is up to 50 million samples. We first verify the validity of such laws on graphs, establishing proper formulations to describe the scaling behaviors. For model scaling, we identify that despite the parameter numbers, the model depth also plays an important role in affecting the model scaling behaviors, which differs from observations in other domains such as CV and NLP. For data scaling, we suggest that the number of graphs can not effectively measure the graph data volume in scaling law since the sizes of different graphs are highly irregular. Instead, we reform the data scaling law with the number of nodes or edges as the metric to address the irregular graph sizes. We further demonstrate that the reformed law offers a unified view of the data scaling behaviors for various fundamental graph tasks including node classification, link prediction, and graph classification. This work provides valuable insights into neural scaling laws on graphs, which can serve as an important tool for collecting new graph data and developing large graph models.
For analysing real-world networks, graph representation learning is a popular tool. These methods, such as a graph autoencoder (GAE), typically rely on low-dimensional representations, also called embeddings, which are obtained through minimising a loss function; these embeddings are used with a decoder for downstream tasks such as node classification and edge prediction. While GAEs tend to be fairly accurate, they suffer from scalability issues. For improved speed, a Local2Global approach, which combines graph patch embeddings based on eigenvector synchronisation, was shown to be fast and achieve good accuracy. Here we propose L2G2G, a Local2Global method which improves GAE accuracy without sacrificing scalability. This improvement is achieved by dynamically synchronising the latent node representations, while training the GAEs. It also benefits from the decoder computing an only local patch loss. Hence, aligning the local embeddings in each epoch utilises more information from the graph than a single post-training alignment does, while maintaining scalability. We illustrate on synthetic benchmarks, as well as real-world examples, that L2G2G achieves higher accuracy than the standard Local2Global approach and scales efficiently on the larger data sets. We find that for large and dense networks, it even outperforms the slow, but assumed more accurate, GAEs.
Developing computational tools for integrative analysis across multiple types of omics data has been of immense importance in cancer molecular biology and precision medicine research. While recent advancements have yielded integrative prediction solutions for multi-omics data, these methods lack a comprehensive and cohesive understanding of the rationale behind their specific predictions. To shed light on personalized medicine and unravel previously unknown characteristics within integrative analysis of multi-omics data, we introduce a novel integrative neural network approach for cancer molecular subtype and biomedical classification applications, named Integrative Graph Convolutional Networks (IGCN). IGCN can identify which types of omics receive more emphasis for each patient to predict a certain class. Additionally, IGCN has the capability to pinpoint significant biomarkers from a range of omics data types. To demonstrate the superiority of IGCN, we compare its performance with other state-of-the-art approaches across different cancer subtype and biomedical classification tasks.
Graph neural networks (GNNs) demonstrate a robust capability for representation learning on graphs with complex structures, showcasing superior performance in various applications. The majority of existing GNNs employ a graph convolution operation by using both attribute and structure information through coupled learning. In essence, GNNs, from an optimization perspective, seek to learn a consensus and compromise embedding representation that balances attribute and graph information, selectively exploring and retaining valid information. To obtain a more comprehensive embedding representation of nodes, a novel GNNs framework, dubbed Decoupled Graph Neural Networks (DGNN), is introduced. DGNN explores distinctive embedding representations from the attribute and graph spaces by decoupled terms. Considering that semantic graph, constructed from attribute feature space, consists of different node connection information and provides enhancement for the topological graph, both topological and semantic graphs are combined for the embedding representation learning. Further, structural consistency among attribute embedding and graph embeddings is promoted to effectively remove redundant information and establish soft connection. This involves promoting factor sharing for adjacency reconstruction matrices, facilitating the exploration of a consensus and high-level correlation. Finally, a more powerful and complete representation is achieved through the concatenation of these embeddings. Experimental results conducted on several graph benchmark datasets verify its superiority in node classification task.
In recent years, spectral graph neural networks, characterized by polynomial filters, have garnered increasing attention and have achieved remarkable performance in tasks such as node classification. These models typically assume that eigenvalues for the normalized Laplacian matrix are distinct from each other, thus expecting a polynomial filter to have a high fitting ability. However, this paper empirically observes that normalized Laplacian matrices frequently possess repeated eigenvalues. Moreover, we theoretically establish that the number of distinguishable eigenvalues plays a pivotal role in determining the expressive power of spectral graph neural networks. In light of this observation, we propose an eigenvalue correction strategy that can free polynomial filters from the constraints of repeated eigenvalue inputs. Concretely, the proposed eigenvalue correction strategy enhances the uniform distribution of eigenvalues, thus mitigating repeated eigenvalues, and improving the fitting capacity and expressive power of polynomial filters. Extensive experimental results on both synthetic and real-world datasets demonstrate the superiority of our method. The code is available at: https://github.com/Lukangkang123/EC-GNN
The vanilla Graph Convolutional Network (GCN) uses a low-pass filter to extract low-frequency signals from graph topology, which may lead to the over-smoothing problem when GCN goes deep. To this end, various methods have been proposed to create an adaptive filter by incorporating an extra filter (e.g., a high-pass filter) extracted from the graph topology. However, these methods heavily rely on topological information and ignore the node attribute space, which severely sacrifices the expressive power of the deep GCNs, especially when dealing with disassortative graphs. In this paper, we propose a cross-space adaptive filter, called CSF, to produce the adaptive-frequency information extracted from both the topology and attribute spaces. Specifically, we first derive a tailored attribute-based high-pass filter that can be interpreted theoretically as a minimizer for semi-supervised kernel ridge regression. Then, we cast the topology-based low-pass filter as a Mercer's kernel within the context of GCNs. This serves as a foundation for combining it with the attribute-based filter to capture the adaptive-frequency information. Finally, we derive the cross-space filter via an effective multiple-kernel learning strategy, which unifies the attribute-based high-pass filter and the topology-based low-pass filter. This helps to address the over-smoothing problem while maintaining effectiveness. Extensive experiments demonstrate that CSF not only successfully alleviates the over-smoothing problem but also promotes the effectiveness of the node classification task.
In the web era, graph machine learning has been widely used on ubiquitous graph-structured data. As a pivotal component for bolstering web security and enhancing the robustness of graph-based applications, the significance of graph anomaly detection is continually increasing. While Graph Neural Networks (GNNs) have demonstrated efficacy in supervised and semi-supervised graph anomaly detection, their performance is contingent upon the availability of sufficient ground truth labels. The labor-intensive nature of identifying anomalies from complex graph structures poses a significant challenge in real-world applications. Despite that, the indirect supervision signals from other tasks (e.g., node classification) are relatively abundant. In this paper, we propose a novel MultItask acTIve Graph Anomaly deTEction framework, namely MITIGATE. Firstly, by coupling node classification tasks, MITIGATE obtains the capability to detect out-of-distribution nodes without known anomalies. Secondly, MITIGATE quantifies the informativeness of nodes by the confidence difference across tasks, allowing samples with conflicting predictions to provide informative yet not excessively challenging information for subsequent training. Finally, to enhance the likelihood of selecting representative nodes that are distant from known patterns, MITIGATE adopts a masked aggregation mechanism for distance measurement, considering both inherent features of nodes and current labeled status. Empirical studies on four datasets demonstrate that MITIGATE significantly outperforms the state-of-the-art methods for anomaly detection. Our code is publicly available at: https://github.com/AhaChang/MITIGATE.