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Qiaoyu Tan

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GiGaMAE: Generalizable Graph Masked Autoencoder via Collaborative Latent Space Reconstruction

Aug 18, 2023
Yucheng Shi, Yushun Dong, Qiaoyu Tan, Jundong Li, Ninghao Liu

Self-supervised learning with masked autoencoders has recently gained popularity for its ability to produce effective image or textual representations, which can be applied to various downstream tasks without retraining. However, we observe that the current masked autoencoder models lack good generalization ability on graph data. To tackle this issue, we propose a novel graph masked autoencoder framework called GiGaMAE. Different from existing masked autoencoders that learn node presentations by explicitly reconstructing the original graph components (e.g., features or edges), in this paper, we propose to collaboratively reconstruct informative and integrated latent embeddings. By considering embeddings encompassing graph topology and attribute information as reconstruction targets, our model could capture more generalized and comprehensive knowledge. Furthermore, we introduce a mutual information based reconstruction loss that enables the effective reconstruction of multiple targets. This learning objective allows us to differentiate between the exclusive knowledge learned from a single target and common knowledge shared by multiple targets. We evaluate our method on three downstream tasks with seven datasets as benchmarks. Extensive experiments demonstrate the superiority of GiGaMAE against state-of-the-art baselines. We hope our results will shed light on the design of foundation models on graph-structured data. Our code is available at: https://github.com/sycny/GiGaMAE.

* Accepted by CIKM 2023 
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Homophily-enhanced Structure Learning for Graph Clustering

Aug 11, 2023
Ming Gu, Gaoming Yang, Sheng Zhou, Ning Ma, Jiawei Chen, Qiaoyu Tan, Meihan Liu, Jiajun Bu

Graph clustering is a fundamental task in graph analysis, and recent advances in utilizing graph neural networks (GNNs) have shown impressive results. Despite the success of existing GNN-based graph clustering methods, they often overlook the quality of graph structure, which is inherent in real-world graphs due to their sparse and multifarious nature, leading to subpar performance. Graph structure learning allows refining the input graph by adding missing links and removing spurious connections. However, previous endeavors in graph structure learning have predominantly centered around supervised settings, and cannot be directly applied to our specific clustering tasks due to the absence of ground-truth labels. To bridge the gap, we propose a novel method called \textbf{ho}mophily-enhanced structure \textbf{le}arning for graph clustering (HoLe). Our motivation stems from the observation that subtly enhancing the degree of homophily within the graph structure can significantly improve GNNs and clustering outcomes. To realize this objective, we develop two clustering-oriented structure learning modules, i.e., hierarchical correlation estimation and cluster-aware sparsification. The former module enables a more accurate estimation of pairwise node relationships by leveraging guidance from latent and clustering spaces, while the latter one generates a sparsified structure based on the similarity matrix and clustering assignments. Additionally, we devise a joint optimization approach alternating between training the homophily-enhanced structure learning and GNN-based clustering, thereby enforcing their reciprocal effects. Extensive experiments on seven benchmark datasets of various types and scales, across a range of clustering metrics, demonstrate the superiority of HoLe against state-of-the-art baselines.

* 11 pages with 7 figures. Accepted by CIKM'23 
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Collaborative Graph Neural Networks for Attributed Network Embedding

Jul 22, 2023
Qiaoyu Tan, Xin Zhang, Xiao Huang, Hao Chen, Jundong Li, Xia Hu

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Graph neural networks (GNNs) have shown prominent performance on attributed network embedding. However, existing efforts mainly focus on exploiting network structures, while the exploitation of node attributes is rather limited as they only serve as node features at the initial layer. This simple strategy impedes the potential of node attributes in augmenting node connections, leading to limited receptive field for inactive nodes with few or even no neighbors. Furthermore, the training objectives (i.e., reconstructing network structures) of most GNNs also do not include node attributes, although studies have shown that reconstructing node attributes is beneficial. Thus, it is encouraging to deeply involve node attributes in the key components of GNNs, including graph convolution operations and training objectives. However, this is a nontrivial task since an appropriate way of integration is required to maintain the merits of GNNs. To bridge the gap, in this paper, we propose COllaborative graph Neural Networks--CONN, a tailored GNN architecture for attribute network embedding. It improves model capacity by 1) selectively diffusing messages from neighboring nodes and involved attribute categories, and 2) jointly reconstructing node-to-node and node-to-attribute-category interactions via cross-correlation. Experiments on real-world networks demonstrate that CONN excels state-of-the-art embedding algorithms with a great margin.

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OpenGSL: A Comprehensive Benchmark for Graph Structure Learning

Jun 17, 2023
Zhiyao Zhou, Sheng Zhou, Bochao Mao, Xuanyi Zhou, Jiawei Chen, Qiaoyu Tan, Daochen Zha, Can Wang, Yan Feng, Chun Chen

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Graph Neural Networks (GNNs) have emerged as the de facto standard for representation learning on graphs, owing to their ability to effectively integrate graph topology and node attributes. However, the inherent suboptimal nature of node connections, resulting from the complex and contingent formation process of graphs, presents significant challenges in modeling them effectively. To tackle this issue, Graph Structure Learning (GSL), a family of data-centric learning approaches, has garnered substantial attention in recent years. The core concept behind GSL is to jointly optimize the graph structure and the corresponding GNN models. Despite the proposal of numerous GSL methods, the progress in this field remains unclear due to inconsistent experimental protocols, including variations in datasets, data processing techniques, and splitting strategies. In this paper, we introduce OpenGSL, the first comprehensive benchmark for GSL, aimed at addressing this gap. OpenGSL enables a fair comparison among state-of-the-art GSL methods by evaluating them across various popular datasets using uniform data processing and splitting strategies. Through extensive experiments, we observe that existing GSL methods do not consistently outperform vanilla GNN counterparts. However, we do observe that the learned graph structure demonstrates a strong generalization ability across different GNN backbones, despite its high computational and space requirements. We hope that our open-sourced library will facilitate rapid and equitable evaluation and inspire further innovative research in the field of GSL. The code of the benchmark can be found in https://github.com/OpenGSL/OpenGSL.

* 9 pages, 4 figures 
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Multi-Task Learning for Post-transplant Cause of Death Analysis: A Case Study on Liver Transplant

Mar 30, 2023
Sirui Ding, Qiaoyu Tan, Chia-yuan Chang, Na Zou, Kai Zhang, Nathan R. Hoot, Xiaoqian Jiang, Xia Hu

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Organ transplant is the essential treatment method for some end-stage diseases, such as liver failure. Analyzing the post-transplant cause of death (CoD) after organ transplant provides a powerful tool for clinical decision making, including personalized treatment and organ allocation. However, traditional methods like Model for End-stage Liver Disease (MELD) score and conventional machine learning (ML) methods are limited in CoD analysis due to two major data and model-related challenges. To address this, we propose a novel framework called CoD-MTL leveraging multi-task learning to model the semantic relationships between various CoD prediction tasks jointly. Specifically, we develop a novel tree distillation strategy for multi-task learning, which combines the strength of both the tree model and multi-task learning. Experimental results are presented to show the precise and reliable CoD predictions of our framework. A case study is conducted to demonstrate the clinical importance of our method in the liver transplant.

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Towards Fair Patient-Trial Matching via Patient-Criterion Level Fairness Constraint

Mar 24, 2023
Chia-Yuan Chang, Jiayi Yuan, Sirui Ding, Qiaoyu Tan, Kai Zhang, Xiaoqian Jiang, Xia Hu, Na Zou

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Clinical trials are indispensable in developing new treatments, but they face obstacles in patient recruitment and retention, hindering the enrollment of necessary participants. To tackle these challenges, deep learning frameworks have been created to match patients to trials. These frameworks calculate the similarity between patients and clinical trial eligibility criteria, considering the discrepancy between inclusion and exclusion criteria. Recent studies have shown that these frameworks outperform earlier approaches. However, deep learning models may raise fairness issues in patient-trial matching when certain sensitive groups of individuals are underrepresented in clinical trials, leading to incomplete or inaccurate data and potential harm. To tackle the issue of fairness, this work proposes a fair patient-trial matching framework by generating a patient-criterion level fairness constraint. The proposed framework considers the inconsistency between the embedding of inclusion and exclusion criteria among patients of different sensitive groups. The experimental results on real-world patient-trial and patient-criterion matching tasks demonstrate that the proposed framework can successfully alleviate the predictions that tend to be biased.

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Towards Personalized Preprocessing Pipeline Search

Feb 28, 2023
Diego Martinez, Daochen Zha, Qiaoyu Tan, Xia Hu

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Feature preprocessing, which transforms raw input features into numerical representations, is a crucial step in automated machine learning (AutoML) systems. However, the existing systems often have a very small search space for feature preprocessing with the same preprocessing pipeline applied to all the numerical features. This may result in sub-optimal performance since different datasets often have various feature characteristics, and features within a dataset may also have their own preprocessing preferences. To bridge this gap, we explore personalized preprocessing pipeline search, where the search algorithm is allowed to adopt a different preprocessing pipeline for each feature. This is a challenging task because the search space grows exponentially with more features. To tackle this challenge, we propose ClusterP3S, a novel framework for Personalized Preprocessing Pipeline Search via Clustering. The key idea is to learn feature clusters such that the search space can be significantly reduced by using the same preprocessing pipeline for the features within a cluster. To this end, we propose a hierarchical search strategy to jointly learn the clusters and search for the optimal pipelines, where the upper-level search optimizes the feature clustering to enable better pipelines built upon the clusters, and the lower-level search optimizes the pipeline given a specific cluster assignment. We instantiate this idea with a deep clustering network that is trained with reinforcement learning at the upper level, and random search at the lower level. Experiments on benchmark classification datasets demonstrate the effectiveness of enabling feature-wise preprocessing pipeline search.

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Bring Your Own View: Graph Neural Networks for Link Prediction with Personalized Subgraph Selection

Dec 23, 2022
Qiaoyu Tan, Xin Zhang, Ninghao Liu, Daochen Zha, Li Li, Rui Chen, Soo-Hyun Choi, Xia Hu

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Graph neural networks (GNNs) have received remarkable success in link prediction (GNNLP) tasks. Existing efforts first predefine the subgraph for the whole dataset and then apply GNNs to encode edge representations by leveraging the neighborhood structure induced by the fixed subgraph. The prominence of GNNLP methods significantly relies on the adhoc subgraph. Since node connectivity in real-world graphs is complex, one shared subgraph is limited for all edges. Thus, the choices of subgraphs should be personalized to different edges. However, performing personalized subgraph selection is nontrivial since the potential selection space grows exponentially to the scale of edges. Besides, the inference edges are not available during training in link prediction scenarios, so the selection process needs to be inductive. To bridge the gap, we introduce a Personalized Subgraph Selector (PS2) as a plug-and-play framework to automatically, personally, and inductively identify optimal subgraphs for different edges when performing GNNLP. PS2 is instantiated as a bi-level optimization problem that can be efficiently solved differently. Coupling GNNLP models with PS2, we suggest a brand-new angle towards GNNLP training: by first identifying the optimal subgraphs for edges; and then focusing on training the inference model by using the sampled subgraphs. Comprehensive experiments endorse the effectiveness of our proposed method across various GNNLP backbones (GCN, GraphSage, NGCF, LightGCN, and SEAL) and diverse benchmarks (Planetoid, OGB, and Recommendation datasets). Our code is publicly available at \url{https://github.com/qiaoyu-tan/PS2}

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DreamShard: Generalizable Embedding Table Placement for Recommender Systems

Oct 05, 2022
Daochen Zha, Louis Feng, Qiaoyu Tan, Zirui Liu, Kwei-Herng Lai, Bhargav Bhushanam, Yuandong Tian, Arun Kejariwal, Xia Hu

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We study embedding table placement for distributed recommender systems, which aims to partition and place the tables on multiple hardware devices (e.g., GPUs) to balance the computation and communication costs. Although prior work has explored learning-based approaches for the device placement of computational graphs, embedding table placement remains to be a challenging problem because of 1) the operation fusion of embedding tables, and 2) the generalizability requirement on unseen placement tasks with different numbers of tables and/or devices. To this end, we present DreamShard, a reinforcement learning (RL) approach for embedding table placement. DreamShard achieves the reasoning of operation fusion and generalizability with 1) a cost network to directly predict the costs of the fused operation, and 2) a policy network that is efficiently trained on an estimated Markov decision process (MDP) without real GPU execution, where the states and the rewards are estimated with the cost network. Equipped with sum and max representation reductions, the two networks can directly generalize to any unseen tasks with different numbers of tables and/or devices without fine-tuning. Extensive experiments show that DreamShard substantially outperforms the existing human expert and RNN-based strategies with up to 19% speedup over the strongest baseline on large-scale synthetic tables and our production tables. The code is available at https://github.com/daochenzha/dreamshard

* Accepted by NeurIPS 2022 
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Graph Contrastive Learning with Personalized Augmentation

Sep 15, 2022
Xin Zhang, Qiaoyu Tan, Xiao Huang, Bo Li

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Graph contrastive learning (GCL) has emerged as an effective tool for learning unsupervised representations of graphs. The key idea is to maximize the agreement between two augmented views of each graph via data augmentation. Existing GCL models mainly focus on applying \textit{identical augmentation strategies} for all graphs within a given scenario. However, real-world graphs are often not monomorphic but abstractions of diverse natures. Even within the same scenario (e.g., macromolecules and online communities), different graphs might need diverse augmentations to perform effective GCL. Thus, blindly augmenting all graphs without considering their individual characteristics may undermine the performance of GCL arts.To deal with this, we propose the first principled framework, termed as \textit{G}raph contrastive learning with \textit{P}ersonalized \textit{A}ugmentation (GPA), to advance conventional GCL by allowing each graph to choose its own suitable augmentation operations.In essence, GPA infers tailored augmentation strategies for each graph based on its topology and node attributes via a learnable augmentation selector, which is a plug-and-play module and can be effectively trained with downstream GCL models end-to-end. Extensive experiments across 11 benchmark graphs from different types and domains demonstrate the superiority of GPA against state-of-the-art competitors.Moreover, by visualizing the learned augmentation distributions across different types of datasets, we show that GPA can effectively identify the most suitable augmentations for each graph based on its characteristics.

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