Graph Domain Research Articles

Multi-source Selective Graph Domain Adaptation Network for cross-subject EEG emotion recognition

Affective brain-computer interface is an important part of realizing emotional human–computer interaction. However, existing objective individual differences among subjects significantly hinder the application of electroencephalography (EEG) emotion recognition. Existing methods still lack the complete extraction of subject-invariant representations for EEG and the ability to fuse valuable information from multiple subjects to facilitate the emotion recognition of the target subject. To address the above challenges, we propose a Multi-source Selective Graph Domain Adaptation Network (MSGDAN), which can better utilize data from different source subjects and perform more robust emotion recognition on the target subject. The proposed network extracts and selects the individual information specific to each subject, where public information refers to subject-invariant components from multi-source subjects. Moreover, the graph domain adaptation network captures both functional connectivity and regional states of the brain via a dynamic graph network and then integrates graph domain adaptation to ensure the invariance of both functional connectivity and regional states. To evaluate our method, we conduct cross-subject emotion recognition experiments on the SEED, SEED-IV, and DEAP datasets. The results demonstrate that the MSGDAN has superior classification performance.

Graph domain adaptation-based framework for gene expression enhancement and cell type identification in large-scale spatially resolved transcriptomics.

Spatially resolved transcriptomics (SRT) technologies facilitate gene expression profiling with spatial resolution in a naïve state. Nevertheless, current SRT technologies exhibit limitations, manifesting as either low transcript detection sensitivity or restricted gene throughput. These constraints result in diminished precision and coverage in gene measurement. In response, we introduce SpaGDA, a sophisticated deep learning-based graph domain adaptation framework for both scenarios of gene expression imputation and cell type identification in spatially resolved transcriptomics data by impartially transferring knowledge from reference scRNA-seq data. Systematic benchmarking analyses across several SRT datasets generated from different technologies have demonstrated SpaGDA's superior effectiveness compared to state-of-the-art methods in both scenarios. Further applied to three SRT datasets of different biological contexts, SpaGDA not only better recovers the well-established knowledge sourced from public atlases and existing scientific literature but also yields a more informative spatial expression pattern of genes. Together, these results demonstrate that SpaGDA can be used to overcome the challenges of current SRT data and provide more accurate insights into biological processes or disease development. The SpaGDA is available in https://github.com/shenrb/SpaGDA.

Learning Graph Representations Through Learning and Propagating Edge Features.

Graph convolutional networks have achieved considerable success in various graph domain tasks. Recently, numerous types of graph convolutional networks have been developed. A typical rule for learning a node's feature in these graph convolutional networks is to aggregate node features from the node's local neighborhood. However, in these models, the interrelation information between adjacent nodes is not well-considered. This information could be helpful to learn improved node embeddings. In this article, we present a graph representation learning framework that generates node embeddings through learning and propagating edge features. Instead of aggregating node features from a local neighborhood, we learn a feature for each edge and update a node's representation by aggregating local edge features. The edge feature is learned from the concatenation of the edge's starting node feature, the input edge feature, and the edge's end node feature. Unlike node feature propagation-based graph networks, our model propagates different features from a node to its neighbors. In addition, we learn an attention vector for each edge in aggregation, enabling the model to focus on important information in each feature dimension. By learning and aggregating edge features, the interrelation between a node and its neighboring nodes is integrated in the aggregated feature, which helps learn improved node embeddings in graph representation learning. Our model is evaluated on graph classification, node classification, graph regression, and multitask binary graph classification on eight popular datasets. The experimental results demonstrate that our model achieves improved performance compared with a wide variety of baseline models.

Graph Kernel Neural Networks.

The convolution operator at the core of many modern neural architectures can effectively be seen as performing a dot product between an input matrix and a filter. While this is readily applicable to data such as images, which can be represented as regular grids in the Euclidean space, extending the convolution operator to work on graphs proves more challenging, due to their irregular structure. In this article, we propose to use graph kernels, i.e., kernel functions that compute an inner product on graphs, to extend the standard convolution operator to the graph domain. This allows us to define an entirely structural model that does not require computing the embedding of the input graph. Our architecture allows to plug-in any type of graph kernels and has the added benefit of providing some interpretability in terms of the structural masks that are learned during the training process, similar to what happens for convolutional masks in traditional convolutional neural networks (CNNs). We perform an extensive ablation study to investigate the model hyperparameters' impact and show that our model achieves competitive performance on standard graph classification and regression datasets.

Graph domain adaptation with localized graph signal representations

In this paper we propose a domain adaptation algorithm designed for graph domains. Given a source graph with many labeled nodes and a target graph with few or no labeled nodes, we aim to estimate the target labels by making use of the similarity between the characteristics of the variation of the label functions on the two graphs. Our assumption about the source and the target domains is that the local behavior of the label function, such as its spread and speed of variation on the graph, bears resemblance between the two graphs. We estimate the unknown target labels by solving an optimization problem where the label information is transferred from the source graph to the target graph based on the prior that the projections of the label functions onto localized graph bases be similar between the source and the target graphs. In order to efficiently capture the local variation of the label functions on the graphs, spectral graph wavelets are used as the graph bases. Experimentation on various data sets shows that the proposed method yields quite satisfactory classification accuracy compared to reference domain adaptation methods.

GTE: a graph learning framework for prediction of T-cell receptors and epitopes binding specificity.

The interaction between T-cell receptors (TCRs) and peptides (epitopes) presented by major histocompatibility complex molecules (MHC) is fundamental to the immune response. Accurate prediction of TCR-epitope interactions is crucial for advancing the understanding of various diseases and their prevention and treatment. Existing methods primarily rely on sequence-based approaches, overlooking the inherent topology structure of TCR-epitope interaction networks. In this study, we present $GTE$, a novel heterogeneous Graph neural network model based on inductive learning to capture the topological structure between TCRs and Epitopes. Furthermore, we address the challenge of constructing negative samples within the graph by proposing a dynamic edge update strategy, enhancing model learning with the nonbinding TCR-epitope pairs. Additionally, to overcome data imbalance, we adapt the Deep AUC Maximization strategy to the graph domain. Extensive experiments are conducted on four public datasets to demonstrate the superiority of exploring underlying topological structures in predicting TCR-epitope interactions, illustrating the benefits of delving into complex molecular networks. The implementation code and data are available at https://github.com/uta-smile/GTE.

BrainDAS: Structure-aware domain adaptation network for multi-site brain network analysis

In the medical field, datasets are mostly integrated across sites due to difficult data acquisition and insufficient data at a single site. The domain shift problem caused by the heterogeneous distribution among multi-site data makes autism spectrum disorder (ASD) hard to identify. Recently, domain adaptation has received considerable attention as a promising solution. However, domain adaptation on graph data like brain networks has not been fully studied. It faces two major challenges: (1) complex graph structure; and (2) multiple source domains. To overcome the issues, we propose an end-to-end structure-aware domain adaptation framework for brain network analysis (BrainDAS) using resting-state functional magnetic resonance imaging (rs-fMRI). The proposed approach contains two stages: supervision-guided multi-site graph domain adaptation with dynamic kernel generation and graph classification with attention-based graph pooling. We evaluate our BrainDAS on a public dataset provided by Autism Brain Imaging Data Exchange (ABIDE) which includes 871 subjects from 17 different sites, surpassing state-of-the-art algorithms in several different evaluation settings. Furthermore, our promising results demonstrate the interpretability and generalization of the proposed method. Our code is available at https://github.com/songruoxian/BrainDAS.

Structure enhanced prototypical alignment for unsupervised cross-domain node classification

Graph Neural Networks (GNNs) have demonstrated remarkable success in graph node classification task. However, their performance heavily relies on the availability of high-quality labeled data, which can be time-consuming and labor-intensive to acquire for graph-structured data. Therefore, the task of transferring knowledge from a label-rich graph (source domain) to a completely unlabeled graph (target domain) becomes crucial. In this paper, we propose a novel unsupervised graph domain adaptation framework called Structure Enhanced Prototypical Alignment (SEPA), which aims to learn domain-invariant representations on non-IID (non-independent and identically distributed) data. Specifically, SEPA captures class-wise semantics by constructing a prototype-based graph and introduces an explicit domain discrepancy metric to align the source and target domains. The proposed SEPA framework is optimized in an end-to-end manner, which could be incorporated into various GNN architectures. Experimental results on several real-world datasets demonstrate that our proposed framework outperforms recent state-of-the-art baselines with different gains.

Geometric Multimodal Deep Learning With Multiscaled Graph Wavelet Convolutional Network.

Multimodal data provide complementary information of a natural phenomenon by integrating data from various domains with very different statistical properties. Capturing the intramodality and cross-modality information of multimodal data is the essential capability of multimodal learning methods. The geometry-aware data analysis approaches provide these capabilities by implicitly representing data in various modalities based on their geometric underlying structures. Also, in many applications, data are explicitly defined on an intrinsic geometric structure. Generalizing deep learning methods to the non-Euclidean domains is an emerging research field, which has recently been investigated in many studies. Most of those popular methods are developed for unimodal data. In this article, a multimodal graph wavelet convolutional network (M-GWCN) is proposed as an end-to-end network. M-GWCN simultaneously finds intramodality representation by applying the multiscale graph wavelet transform to provide helpful localization properties in the graph domain of each modality and cross-modality representation by learning permutations that encode correlations among various modalities. M-GWCN is not limited to either the homogeneous modalities with the same number of data or any prior knowledge indicating correspondences between modalities. Several semisupervised node classification experiments have been conducted on three popular unimodal explicit graph-based datasets and five multimodal implicit ones. The experimental results indicate the superiority and effectiveness of the proposed methods compared with both spectral graph domain convolutional neural networks and state-of-the-art multimodal methods.

Identification of rail cracks based on path graph features and SVM

In order to improve the accuracy of rail crack identification, a new method based on path graph feature and support vector machine is proposed. This method uses graph signal processing and graph theory to transform the magnetic flux leakage signal of rail crack, calculates the “time domain” and “frequency domain” statistics of the path graph signal, and effectively identifies rail cracks with different defect parameters by SVM classifier. The measured data verify the effectiveness of this method, which shows that the method of identifying rail cracks by using path graph features has higher accuracy and stability. The innovation of this method is that it draws on the idea of transform domain features to extract the graph domain features that can best represent the MFL signal. Compared with the 31 features used by the traditional method, this method only needs 22 features to achieve better recognition results and has shorter training time. For the recognition rate of 18 kinds of cracks, the average recognition rate of this method is more than 83.51%, and the highest recognition rate is 95.34%. Therefore, this study provides a new way for magnetic leakage analysis and treatment of rail crack detection, has important practical value, and provides beneficial enlightenment for further research in related fields.

TO-UGDA: target-oriented unsupervised graph domain adaptation

Graph domain adaptation (GDA) aims to address the challenge of limited label data in the target graph domain. Existing methods such as UDAGCN, GRADE, DEAL, and COCO for different-level (node-level, graph-level) adaptation tasks exhibit variations in domain feature extraction, and most of them solely rely on representation alignment to transfer label information from a labeled source domain to an unlabeled target domain. However, this approach can be influenced by irrelevant information and usually ignores the conditional shift of the downstream predictor. To effectively address this issue, we introduce a target-oriented unsupervised graph domain adaptive framework for graph adaptation called TO-UGDA. Particularly, domain-invariant feature representations are extracted using graph information bottleneck. The discrepancy between two domains is minimized using an adversarial alignment strategy to obtain a unified feature distribution. Additionally, the meta pseudo-label is introduced to enhance downstream adaptation and improve the model’s generalizability. Through extensive experimentation on real-world graph datasets, it is proved that the proposed framework achieves excellent performance across various node-level and graph-level adaptation tasks.

Information filtering and interpolating for semi-supervised graph domain adaptation

Graph domain adaptation, which falls under the umbrella of graph transfer learning, involves transferring knowledge from a labeled source graph to improve prediction accuracy on an unlabeled target graph, where both graphs have identical label spaces but exhibit distribution discrepancies due to temporal data shifts or distinct data collection methods. This adaptation is complicated by the challenges of graph-specific domain discrepancies and cross-graph label scarcity. This paper proposes a semi-supervised Graph domain adaptation method via Information Filtering and Interpolating (GIFI). Specifically, GIFI utilizes a parameterized graph reduction module and a variational information bottleneck to adequately filter out irrelevant information from the source and target graphs to eliminate distribution discrepancy. GIFI also introduces an interpolation-enhanced pseudo-labeling strategy for cross-graph semi-supervised learning, which can mitigate model over-fitting on domain-specific features and limited labeled nodes, thus improving the model’s adaptation and discriminative capability. Experimental results on various graph domain adaptation benchmarks demonstrate GIFI’s superior performance over state-of-the-art methods. Our code is available at https://github.com/joe817/GIFI.

Augmenting optimization-based molecular design with graph neural networks

Computer-aided molecular design (CAMD) studies quantitative structure–property relationships and discovers desired molecules using optimization algorithms. With the emergence of machine learning models, CAMD score functions may be replaced by various surrogates to automatically learn the structure–property relationships. Due to their outstanding performance on graph domains, graph neural networks (GNNs) have recently appeared frequently in CAMD. But using GNNs introduces new optimization challenges. This paper formulates GNNs using mixed-integer programming and then integrates this GNN formulation into the optimization and machine learning toolkit OMLT. To characterize and formulate molecules, we inherit the well-established mixed-integer optimization formulation for CAMD and propose symmetry-breaking constraints to remove symmetric solutions caused by graph isomorphism. In two case studies, we investigate fragment-based odorant molecular design with more practical requirements to test the compatibility and performance of our approaches.

Prototype-Based Interpretable Graph Neural Networks

Graph neural networks have proved to be a key tool for dealing with many problems and domains such as chemistry, natural language processing and social networks. While the structure of the layers is simple, it is difficult to identify the patterns learned by the graph neural network. Several works propose post-hoc methods to explain graph predictions, but few of them try to generate interpretable models. Conversely, the topic of the interpretable models is highly investigated in image recognition. Given the similarity between image and graph domains, we analyze the adaptability of prototype-based neural networks for graph and node classification. In particular, we investigate the use of two interpretable networks, ProtoPNet and TesNet, in the graph domain. We show that the adapted networks manage to reach better or higher accuracy scores than their respective black-box models and comparable performances with state-of-the-art self-explainable models. Showing how to extract ProtoPNet and TesNet explanations on graph neural networks, we further study how to obtain global and local explanations for the trained models. We then evaluate the explanations of the interpretable models by comparing them with post-hoc approaches and self-explainable models. Our findings show that the application of TesNet and ProtoPNet to the graph domain produces qualitative predictions while improving their reliability and transparency.

Rethinking Propagation for Unsupervised Graph Domain Adaptation

Unsupervised Graph Domain Adaptation (UGDA) aims to transfer knowledge from a labelled source graph to an unlabelled target graph in order to address the distribution shifts between graph domains. Previous works have primarily focused on aligning data from the source and target graph in the representation space learned by graph neural networks (GNNs). However, the inherent generalization capability of GNNs has been largely overlooked. Motivated by our empirical analysis, we reevaluate the role of GNNs in graph domain adaptation and uncover the pivotal role of the propagation process in GNNs for adapting to different graph domains. We provide a comprehensive theoretical analysis of UGDA and derive a generalization bound for multi-layer GNNs. By formulating GNN Lipschitz for k-layer GNNs, we show that the target risk bound can be tighter by removing propagation layers in source graph and stacking multiple propagation layers in target graph. Based on the empirical and theoretical analysis mentioned above, we propose a simple yet effective approach called A2GNN for graph domain adaptation. Through extensive experiments on real-world datasets, we demonstrate the effectiveness of our proposed A2GNN framework.

Open-Set Graph Domain Adaptation via Separate Domain Alignment

Domain adaptation has become an attractive learning paradigm, as it can leverage source domains with rich labels to deal with classification tasks in an unlabeled target domain. A few recent studies develop domain adaptation approaches for graph-structured data. In the case of node classification task, current domain adaptation methods only focus on the closed-set setting, where source and target domains share the same label space. A more practical assumption is that the target domain may contain new classes that are not included in the source domain. Therefore, in this paper, we introduce a novel and challenging problem for graphs, i.e., open-set domain adaptive node classification, and propose a new approach to solve it. Specifically, we develop an algorithm for efficient knowledge transfer from a labeled source graph to an unlabeled target graph under a separate domain alignment (SDA) strategy, in order to learn discriminative feature representations for the target graph. Our goal is to not only correctly classify target nodes into the known classes, but also classify unseen types of nodes into an unknown class. Experimental results on real-world datasets show that our method outperforms existing methods on graph domain adaptation.

Utilizing signal flow graph on multiple feedback amplifiers of NMC and DACFC with emphasis on design space exploration and conversion

SummaryOver a long time, different methods of frequency compensation of multistage amplifiers have been exploited for improvement in the behavior of stabilizing. In the present paper, the step‐by‐step conversion process of the dual active capacitive feedback compensation (DACFC) three‐stage amplifier into the nested Miller compensation (NMC) three‐stage amplifier is presented by a systematic approach and signal flow graphs (SFGs) based on the graph theory rules in graph domain. Also, according to graph rules, the conversion of the multiple feedback amplifier NMC into the multiple feedback amplifier DACFC is investigated in detail in the graph domain. During the conversion process, the difference in the gain‐bandwidth product (GBW) in the two mentioned case study's amplifiers is examined in terms of the graph at the system level. The elimination of two branches in one step of the conversion process of the SFG of the NMC into the SFG of the DACFC leads to a significant improvement in the behavior of GBW. This paper also conducts verification of the design of conventional NMC and DACFC amplifier circuits in HSPICE using 0.35‐μm CMOS technology and compares the circuit simulation results to SFG simulation results. In order to show the correctness of the idea, they are redesigned in HSPICE using 0.18‐μm CMOS technology, and appropriate results are obtained.

Weisfeiler–Lehman goes dynamic: An analysis of the expressive power of Graph Neural Networks for attributed and dynamic graphs

Graph Neural Networks (GNNs) are a large class of relational models for graph processing. Recent theoretical studies on the expressive power of GNNs have focused on two issues. On the one hand, it has been proven that GNNs are as powerful as the Weisfeiler–Lehman test (1-WL) in their ability to distinguish graphs. Moreover, it has been shown that the equivalence enforced by 1-WL equals unfolding equivalence. On the other hand, GNNs turned out to be universal approximators on graphs modulo the constraints enforced by 1-WL/unfolding equivalence. However, these results only apply to Static Attributed Undirected Homogeneous Graphs (SAUHG) with node attributes. In contrast, real-life applications often involve a much larger variety of graph types. In this paper, we conduct a theoretical analysis of the expressive power of GNNs for two other graph domains that are particularly interesting in practical applications, namely dynamic graphs and SAUGHs with edge attributes. Dynamic graphs are widely used in modern applications; hence, the study of the expressive capability of GNNs in this domain is essential for practical reasons and, in addition, it requires a new analyzing approach due to the difference in the architecture of dynamic GNNs compared to static ones. On the other hand, the examination of SAUHGs is of particular relevance since they act as a standard form for all graph types: it has been shown that all graph types can be transformed without loss of information to SAUHGs with both attributes on nodes and edges. This paper considers generic GNN models and appropriate 1-WL tests for those domains. Then, the known results on the expressive power of GNNs are extended to the mentioned domains: it is proven that GNNs have the same capability as the 1-WL test, the 1-WL equivalence equals unfolding equivalence and that GNNs are universal approximators modulo 1-WL/unfolding equivalence. Moreover, the proof of the approximation capability is mostly constructive and allows us to deduce hints on the architecture of GNNs that can achieve the desired approximation.

Digital twin-driven graph domain adaptation neural network for remaining useful life prediction of rolling bearing

Remaining useful life (RUL) prediction is significant for the healthy operation of machinery. In order to accurately identify the bearing degeneration states, it is necessary to collect massive full lifecycle data. However, the bearing lifecycle data is insufficient for effectively training a RUL prediction model in engineering practice. In this paper, a digital twin-driven graph domain adaptation method is proposed. First, a full lifecycle dynamic twin model of bearings is constructed to generate abundant twin data, in which the surface morphology evolution and roller relative slip at different stages are simulated to generate vibration responses. Second, a novel multi-layered cross-domain gated graph convolutional network (MGGCN) is developed, in which a new graph domain adaptation model is designed to solve the problem that traditional domain adaptation methods are not effective in processing the non-Euclidean data. The spatial and temporal features are extracted by multiple nonlinear transformations and previous time-step hidden state incorporation, respectively. In addition, a graph Laplacian regularized maximum mean discrepancy (GLMMD) is designed and applied in the training of model to enhance the capability of discerning graph domain differences. The experimental results confirm that the proposed method can achieve effective performance even in scenarios with limited actual data.

How graph features from message passing affect graph classification and regression?

Graph neural networks (GNNs) have been applied to various graph domains. However, GNNs based on the message passing scheme, which iteratively aggregates information from neighboring nodes, have difficulty learning to represent larger subgraph structures because of the nature of the scheme. We investigate the prediction performance of GNNs when the number of message passing iteration increases to capture larger subgraph structures on classification and regression tasks using various real-world graph datasets. Our empirical results show that the averaged features over nodes obtained by the message passing scheme in GNNs are likely to converge to a certain value, which significantly deteriorates the resulting prediction performance. This is in contrast to the state-of-the-art Weisfeiler–Lehman graph kernel, which has been used actively in machine learning for graphs, as it can comparably learn the large subgraph structures and its performance does not usually drop significantly drop from the first couple of rounds of iterations. Moreover, we report that when we apply node features obtained via GNNs to SVMs, the performance of the Weisfeiler-Lehman kernel can be superior to that of the graph convolutional model, which is a typically employed approach in GNNs.