arXiv subjects

Carl Yang

Publications and source records attributed to Carl Yang.

At least 163 records · Page 9Linked to original sources

arXiv2022

A Bird's-Eye Tutorial of Graph Attention Architectures

Graph Neural Networks (GNNs) have shown tremendous strides in performance for graph-structured problems especially in the domains of natural language processing, computer vision and recommender systems. Inspired by the success of the transformer architecture, there has been an ever-growing body of work on attention variants of GNNs attempting to advance the state of the art in many of these problems. Incorporating "attention" into graph mining has been viewed as a way to overcome the noisiness, heterogenity and complexity associated with graph-structured data as well as to encode soft-inductive bias. It is hence crucial and advantageous to study these variants from a bird's-eye view to assess their strengths and weaknesses. We provide a systematic and focused tutorial centered around attention based GNNs in a hope to benefit researchers dealing with graph-structured problems. Our tutorial looks at GNN variants from the point of view of the attention function and iteratively builds the reader's understanding of different graph attention variants.

cs.LG↗

arXiv2022

FBNETGEN: Task-aware GNN-based fMRI Analysis via Functional Brain Network Generation

Functional magnetic resonance imaging (fMRI) is one of the most common imaging modalities to investigate brain functions. Recent studies in neuroscience stress the great potential of functional brain networks constructed from fMRI data for clinical predictions. Traditional functional brain networks, however, are noisy and unaware of downstream prediction tasks, while also incompatible with the deep graph neural network (GNN) models. In order to fully unleash the power of GNNs in network-based fMRI analysis, we develop FBNETGEN, a task-aware and interpretable fMRI analysis framework via deep brain network generation. In particular, we formulate (1) prominent region of interest (ROI) features extraction, (2) brain networks generation, and (3) clinical predictions with GNNs, in an end-to-end trainable model under the guidance of particular prediction tasks. Along with the process, the key novel component is the graph generator which learns to transform raw time-series features into task-oriented brain networks. Our learnable graphs also provide unique interpretations by highlighting prediction-related brain regions. Comprehensive experiments on two datasets, i.e., the recently released and currently largest publicly available fMRI dataset Adolescent Brain Cognitive Development (ABCD), and the widely-used fMRI dataset PNC, prove the superior effectiveness and interpretability of FBNETGEN. The implementation is available at https://github.com/Wayfear/FBNETGEN.

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arXiv2022

Joint Embedding of Structural and Functional Brain Networks with Graph Neural Networks for Mental Illness Diagnosis

Multimodal brain networks characterize complex connectivities among different brain regions from both structural and functional aspects and provide a new means for mental disease analysis. Recently, Graph Neural Networks (GNNs) have become a de facto model for analyzing graph-structured data. However, how to employ GNNs to extract effective representations from brain networks in multiple modalities remains rarely explored. Moreover, as brain networks provide no initial node features, how to design informative node attributes and leverage edge weights for GNNs to learn is left unsolved. To this end, we develop a novel multiview GNN for multimodal brain networks. In particular, we regard each modality as a view for brain networks and employ contrastive learning for multimodal fusion. Then, we propose a GNN model which takes advantage of the message passing scheme by propagating messages based on degree statistics and brain region connectivities. Extensive experiments on two real-world disease datasets (HIV and Bipolar) demonstrate the effectiveness of our proposed method over state-of-the-art baselines.

q-bio.NC↗

arXiv2022

SAIS: Supervising and Augmenting Intermediate Steps for Document-Level Relation Extraction

Stepping from sentence-level to document-level, the research on relation extraction (RE) confronts increasing text length and more complicated entity interactions. Consequently, it is more challenging to encode the key information sources--relevant contexts and entity types. However, existing methods only implicitly learn to model these critical information sources while being trained for RE. As a result, they suffer the problems of ineffective supervision and uninterpretable model predictions. In contrast, we propose to explicitly teach the model to capture relevant contexts and entity types by supervising and augmenting intermediate steps (SAIS) for RE. Based on a broad spectrum of carefully designed tasks, our proposed SAIS method not only extracts relations of better quality due to more effective supervision, but also retrieves the corresponding supporting evidence more accurately so as to enhance interpretability. By assessing model uncertainty, SAIS further boosts the performance via evidence-based data augmentation and ensemble inference while reducing the computational cost. Eventually, SAIS delivers state-of-the-art RE results on three benchmarks (DocRED, CDR, and GDA) and outperforms the runner-up by 5.04% relatively in F1 score in evidence retrieval on DocRED.

cs.CL↗

arXiv2022

Shift-Robust Node Classification via Graph Adversarial Clustering

Graph Neural Networks (GNNs) are de facto node classification models in graph structured data. However, during testing-time, these algorithms assume no data shift, i.e., $\Pr_\text{train}(X,Y) = \Pr_\text{test}(X,Y)$. Domain adaption methods can be adopted for data shift, yet most of them are designed to only encourage similar feature distribution between source and target data. Conditional shift on classes can still affect such adaption. Fortunately, graph yields graph homophily across different data distributions. In response, we propose Shift-Robust Node Classification (SRNC) to address these limitations. We introduce an unsupervised cluster GNN on target graph to group the similar nodes by graph homophily. An adversarial loss with label information on source graph is used upon clustering objective. Then a shift-robust classifier is optimized on training graph and adversarial samples on target graph, which are generated by cluster GNN. We conduct experiments on both open-set shift and representation-shift, which demonstrates the superior accuracy of SRNC on generalizing to test graph with data shift. SRNC is consistently better than previous SoTA domain adaption algorithm on graph that progressively use model predictions on target graph for training.

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arXiv2022

Structure-Preserving Graph Kernel for Brain Network Classification

This paper presents a novel graph-based kernel learning approach for connectome analysis. Specifically, we demonstrate how to leverage the naturally available structure within the graph representation to encode prior knowledge in the kernel. We first proposed a matrix factorization to directly extract structural features from natural symmetric graph representations of connectome data. We then used them to derive a structure-persevering graph kernel to be fed into the support vector machine. The proposed approach has the advantage of being clinically interpretable. Quantitative evaluations on challenging HIV disease classification (DTI- and fMRI-derived connectome data) and emotion recognition (EEG-derived connectome data) tasks demonstrate the superior performance of our proposed methods against the state-of-the-art. Results showed that relevant EEG-connectome information is primarily encoded in the alpha band during the emotion regulation task.

eess.IV↗

arXiv2022

Graph Auto-Encoder Via Neighborhood Wasserstein Reconstruction

Graph neural networks (GNNs) have drawn significant research attention recently, mostly under the setting of semi-supervised learning. When task-agnostic representations are preferred or supervision is simply unavailable, the auto-encoder framework comes in handy with a natural graph reconstruction objective for unsupervised GNN training. However, existing graph auto-encoders are designed to reconstruct the direct links, so GNNs trained in this way are only optimized towards proximity-oriented graph mining tasks, and will fall short when the topological structures matter. In this work, we revisit the graph encoding process of GNNs which essentially learns to encode the neighborhood information of each node into an embedding vector, and propose a novel graph decoder to reconstruct the entire neighborhood information regarding both proximity and structure via Neighborhood Wasserstein Reconstruction (NWR). Specifically, from the GNN embedding of each node, NWR jointly predicts its node degree and neighbor feature distribution, where the distribution prediction adopts an optimal-transport loss based on the Wasserstein distance. Extensive experiments on both synthetic and real-world network datasets show that the unsupervised node representations learned with NWR have much more advantageous in structure-oriented graph mining tasks, while also achieving competitive performance in proximity-oriented ones.

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arXiv2022

A Survey on Graph Structure Learning: Progress and Opportunities

Graphs are widely used to describe real-world objects and their interactions. Graph Neural Networks (GNNs) as a de facto model for analyzing graphstructured data, are highly sensitive to the quality of the given graph structures. Therefore, noisy or incomplete graphs often lead to unsatisfactory representations and prevent us from fully understanding the mechanism underlying the system. In pursuit of an optimal graph structure for downstream tasks, recent studies have sparked an effort around the central theme of Graph Structure Learning (GSL), which aims to jointly learn an optimized graph structure and corresponding graph representations. In the presented survey, we broadly review recent progress in GSL methods. Specifically, we first formulate a general pipeline of GSL and review state-of-the-art methods classified by the way of modeling graph structures, followed by applications of GSL across domains. Finally, we point out some issues in current studies and discuss future directions.

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arXiv2022

Exploiting Data Sparsity in Secure Cross-Platform Social Recommendation

Social recommendation has shown promising improvements over traditional systems since it leverages social correlation data as an additional input. Most existing work assumes that all data are available to the recommendation platform. However, in practice, user-item interaction data (e.g.,rating) and user-user social data are usually generated by different platforms, and both of which contain sensitive information. Therefore, "How to perform secure and efficient social recommendation across different platforms, where the data are highly-sparse in nature" remains an important challenge. In this work, we bring secure computation techniques into social recommendation, and propose S3Rec, a sparsity-aware secure cross-platform social recommendation framework. As a result, our model can not only improve the recommendation performance of the rating platform by incorporating the sparse social data on the social platform, but also protect data privacy of both platforms. Moreover, to further improve model training efficiency, we propose two secure sparse matrix multiplication protocols based on homomorphic encryption and private information retrieval. Our experiments on two benchmark datasets demonstrate the effectiveness of S3Rec.

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arXiv2022

How Can Graph Neural Networks Help Document Retrieval: A Case Study on CORD19 with Concept Map Generation

Graph neural networks (GNNs), as a group of powerful tools for representation learning on irregular data, have manifested superiority in various downstream tasks. With unstructured texts represented as concept maps, GNNs can be exploited for tasks like document retrieval. Intrigued by how can GNNs help document retrieval, we conduct an empirical study on a large-scale multi-discipline dataset CORD-19. Results show that instead of the complex structure-oriented GNNs such as GINs and GATs, our proposed semantics-oriented graph functions achieve better and more stable performance based on the BM25 retrieved candidates. Our insights in this case study can serve as a guideline for future work to develop effective GNNs with appropriate semantics-oriented inductive biases for textual reasoning tasks like document retrieval and classification. All code for this case study is available at https://github.com/HennyJie/GNN-DocRetrieval.

cs.IR↗

arXiv2021

Federated Graph Classification over Non-IID Graphs

Federated learning has emerged as an important paradigm for training machine learning models in different domains. For graph-level tasks such as graph classification, graphs can also be regarded as a special type of data samples, which can be collected and stored in separate local systems. Similar to other domains, multiple local systems, each holding a small set of graphs, may benefit from collaboratively training a powerful graph mining model, such as the popular graph neural networks (GNNs). To provide more motivation towards such endeavors, we analyze real-world graphs from different domains to confirm that they indeed share certain graph properties that are statistically significant compared with random graphs. However, we also find that different sets of graphs, even from the same domain or same dataset, are non-IID regarding both graph structures and node features. To handle this, we propose a graph clustered federated learning (GCFL) framework that dynamically finds clusters of local systems based on the gradients of GNNs, and theoretically justify that such clusters can reduce the structure and feature heterogeneity among graphs owned by the local systems. Moreover, we observe the gradients of GNNs to be rather fluctuating in GCFL which impedes high-quality clustering, and design a gradient sequence-based clustering mechanism based on dynamic time warping (GCFL+). Extensive experimental results and in-depth analysis demonstrate the effectiveness of our proposed frameworks.

cs.LG↗

arXiv2021

Subgraph Federated Learning with Missing Neighbor Generation

Graphs have been widely used in data mining and machine learning due to their unique representation of real-world objects and their interactions. As graphs are getting bigger and bigger nowadays, it is common to see their subgraphs separately collected and stored in multiple local systems. Therefore, it is natural to consider the subgraph federated learning setting, where each local system holds a small subgraph that may be biased from the distribution of the whole graph. Hence, the subgraph federated learning aims to collaboratively train a powerful and generalizable graph mining model without directly sharing their graph data. In this work, towards the novel yet realistic setting of subgraph federated learning, we propose two major techniques: (1) FedSage, which trains a GraphSage model based on FedAvg to integrate node features, link structures, and task labels on multiple local subgraphs; (2) FedSage+, which trains a missing neighbor generator along FedSage to deal with missing links across local subgraphs. Empirical results on four real-world graph datasets with synthesized subgraph federated learning settings demonstrate the effectiveness and efficiency of our proposed techniques. At the same time, consistent theoretical implications are made towards their generalization ability on the global graphs.

cs.LG↗

arXiv2021

Transfer Learning of Graph Neural Networks with Ego-graph Information Maximization

Graph neural networks (GNNs) have achieved superior performance in various applications, but training dedicated GNNs can be costly for large-scale graphs. Some recent work started to study the pre-training of GNNs. However, none of them provide theoretical insights into the design of their frameworks, or clear requirements and guarantees towards their transferability. In this work, we establish a theoretically grounded and practically useful framework for the transfer learning of GNNs. Firstly, we propose a novel view towards the essential graph information and advocate the capturing of it as the goal of transferable GNN training, which motivates the design of EGI (Ego-Graph Information maximization) to analytically achieve this goal. Secondly, when node features are structure-relevant, we conduct an analysis of EGI transferability regarding the difference between the local graph Laplacians of the source and target graphs. We conduct controlled synthetic experiments to directly justify our theoretical conclusions. Comprehensive experiments on two real-world network datasets show consistent results in the analyzed setting of direct-transfering, while those on large-scale knowledge graphs show promising results in the more practical setting of transfering with fine-tuning.

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arXiv2021

Understanding Structural Vulnerability in Graph Convolutional Networks

Recent studies have shown that Graph Convolutional Networks (GCNs) are vulnerable to adversarial attacks on the graph structure. Although multiple works have been proposed to improve their robustness against such structural adversarial attacks, the reasons for the success of the attacks remain unclear. In this work, we theoretically and empirically demonstrate that structural adversarial examples can be attributed to the non-robust aggregation scheme (i.e., the weighted mean) of GCNs. Specifically, our analysis takes advantage of the breakdown point which can quantitatively measure the robustness of aggregation schemes. The key insight is that weighted mean, as the basic design of GCNs, has a low breakdown point and its output can be dramatically changed by injecting a single edge. We show that adopting the aggregation scheme with a high breakdown point (e.g., median or trimmed mean) could significantly enhance the robustness of GCNs against structural attacks. Extensive experiments on four real-world datasets demonstrate that such a simple but effective method achieves the best robustness performance compared to state-of-the-art models.

cs.LG↗

arXiv2021

FedGraphNN: A Federated Learning System and Benchmark for Graph Neural Networks

Graph Neural Network (GNN) research is rapidly growing thanks to the capacity of GNNs in learning distributed representations from graph-structured data. However, centralizing a massive amount of real-world graph data for GNN training is prohibitive due to privacy concerns, regulation restrictions, and commercial competitions. Federated learning (FL), a trending distributed learning paradigm, provides possibilities to solve this challenge while preserving data privacy. Despite recent advances in vision and language domains, there is no suitable platform for the FL of GNNs. To this end, we introduce FedGraphNN, an open FL benchmark system that can facilitate research on federated GNNs. FedGraphNN is built on a unified formulation of graph FL and contains a wide range of datasets from different domains, popular GNN models, and FL algorithms, with secure and efficient system support. Particularly for the datasets, we collect, preprocess, and partition 36 datasets from 7 domains, including both publicly available ones and specifically obtained ones such as hERG and Tencent. Our empirical analysis showcases the utility of our benchmark system, while exposing significant challenges in graph FL: federated GNNs perform worse in most datasets with a non-IID split than centralized GNNs; the GNN model that attains the best result in the centralized setting may not maintain its advantage in the FL setting. These results imply that more research efforts are needed to unravel the mystery behind federated GNNs. Moreover, our system performance analysis demonstrates that the FedGraphNN system is computationally efficient and secure to large-scale graphs datasets. We maintain the source code at https://github.com/FedML-AI/FedGraphNN.

cs.LG↗

arXiv2021

Graph Entropy Guided Node Embedding Dimension Selection for Graph Neural Networks

Graph representation learning has achieved great success in many areas, including e-commerce, chemistry, biology, etc. However, the fundamental problem of choosing the appropriate dimension of node embedding for a given graph still remains unsolved. The commonly used strategies for Node Embedding Dimension Selection (NEDS) based on grid search or empirical knowledge suffer from heavy computation and poor model performance. In this paper, we revisit NEDS from the perspective of minimum entropy principle. Subsequently, we propose a novel Minimum Graph Entropy (MinGE) algorithm for NEDS with graph data. To be specific, MinGE considers both feature entropy and structure entropy on graphs, which are carefully designed according to the characteristics of the rich information in them. The feature entropy, which assumes the embeddings of adjacent nodes to be more similar, connects node features and link topology on graphs. The structure entropy takes the normalized degree as basic unit to further measure the higher-order structure of graphs. Based on them, we design MinGE to directly calculate the ideal node embedding dimension for any graph. Finally, comprehensive experiments with popular Graph Neural Networks (GNNs) on benchmark datasets demonstrate the effectiveness and generalizability of our proposed MinGE.

cs.LG↗

arXiv2021

Structure-Aware Hard Negative Mining for Heterogeneous Graph Contrastive Learning

Recently, heterogeneous Graph Neural Networks (GNNs) have become a de facto model for analyzing HGs, while most of them rely on a relative large number of labeled data. In this work, we investigate Contrastive Learning (CL), a key component in self-supervised approaches, on HGs to alleviate the label scarcity problem. We first generate multiple semantic views according to metapaths and network schemas. Then, by pushing node embeddings corresponding to different semantic views close to each other (positives) and pulling other embeddings apart (negatives), one can obtain informative representations without human annotations. However, this CL approach ignores the relative hardness of negative samples, which may lead to suboptimal performance. Considering the complex graph structure and the smoothing nature of GNNs, we propose a structure-aware hard negative mining scheme that measures hardness by structural characteristics for HGs. By synthesizing more negative nodes, we give larger weights to harder negatives with limited computational overhead to further boost the performance. Empirical studies on three real-world datasets show the effectiveness of our proposed method. The proposed method consistently outperforms existing state-of-the-art methods and notably, even surpasses several supervised counterparts.

cs.LG↗

arXiv2021

Effective and Interpretable fMRI Analysis via Functional Brain Network Generation

Recent studies in neuroscience show great potential of functional brain networks constructed from fMRI data for popularity modeling and clinical predictions. However, existing functional brain networks are noisy and unaware of downstream prediction tasks, while also incompatible with recent powerful machine learning models of GNNs. In this work, we develop an end-to-end trainable pipeline to extract prominent fMRI features, generate brain networks, and make predictions with GNNs, all under the guidance of downstream prediction tasks. Preliminary experiments on the PNC fMRI data show the superior effectiveness and unique interpretability of our framework.

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