Ziqi Gao

Jianheng Tang, Fengrui Hua, Ziqi Gao et al.

With a long history of traditional Graph Anomaly Detection (GAD) algorithms and recently popular Graph Neural Networks (GNNs), it is still not clear (1) how they perform under a standard comprehensive setting, (2) whether GNNs can outperform traditional algorithms such as tree ensembles, and (3) how about their efficiency on large-scale graphs. In response, we introduce GADBench -- a benchmark tool dedicated to supervised anomalous node detection in static graphs. GADBench facilitates a detailed comparison across 29 distinct models on ten real-world GAD datasets, encompassing thousands to millions ($\sim$6M) nodes. Our main finding is that tree ensembles with simple neighborhood aggregation can outperform the latest GNNs tailored for the GAD task. We shed light on the current progress of GAD, setting a robust groundwork for subsequent investigations in this domain. GADBench is open-sourced at https://github.com/squareRoot3/GADBench.

Lanqing Li, Liang Zeng, Ziqi Gao et al.

The last decade has witnessed a prosperous development of computational methods and dataset curation for AI-aided drug discovery (AIDD). However, real-world pharmaceutical datasets often exhibit highly imbalanced distribution, which is overlooked by the current literature but may severely compromise the fairness and generalization of machine learning applications. Motivated by this observation, we introduce ImDrug, a comprehensive benchmark with an open-source Python library which consists of 4 imbalance settings, 11 AI-ready datasets, 54 learning tasks and 16 baseline algorithms tailored for imbalanced learning. It provides an accessible and customizable testbed for problems and solutions spanning a broad spectrum of the drug discovery pipeline such as molecular modeling, drug-target interaction and retrosynthesis. We conduct extensive empirical studies with novel evaluation metrics, to demonstrate that the existing algorithms fall short of solving medicinal and pharmaceutical challenges in the data imbalance scenario. We believe that ImDrug opens up avenues for future research and development, on real-world challenges at the intersection of AIDD and deep imbalanced learning.

Jianheng Tang, Jiajin Li, Ziqi Gao et al.

Graph Neural Networks (GNNs) are widely applied for graph anomaly detection. As one of the key components for GNN design is to select a tailored spectral filter, we take the first step towards analyzing anomalies via the lens of the graph spectrum. Our crucial observation is the existence of anomalies will lead to the `right-shift' phenomenon, that is, the spectral energy distribution concentrates less on low frequencies and more on high frequencies. This fact motivates us to propose the Beta Wavelet Graph Neural Network (BWGNN). Indeed, BWGNN has spectral and spatial localized band-pass filters to better handle the `right-shift' phenomenon in anomalies. We demonstrate the effectiveness of BWGNN on four large-scale anomaly detection datasets. Our code and data are released at https://github.com/squareRoot3/Rethinking-Anomaly-Detection

Liang Zeng, Lanqing Li, Ziqi Gao et al.

Graph contrastive learning (GCL) has attracted a surge of attention due to its superior performance for learning node/graph representations without labels. However, in practice, the underlying class distribution of unlabeled nodes for the given graph is usually imbalanced. This highly imbalanced class distribution inevitably deteriorates the quality of learned node representations in GCL. Indeed, we empirically find that most state-of-the-art GCL methods cannot obtain discriminative representations and exhibit poor performance on imbalanced node classification. Motivated by this observation, we propose a principled GCL framework on Imbalanced node classification (ImGCL), which automatically and adaptively balances the representations learned from GCL without labels. Specifically, we first introduce the online clustering based progressively balanced sampling (PBS) method with theoretical rationale, which balances the training sets based on pseudo-labels obtained from learned representations in GCL. We then develop the node centrality based PBS method to better preserve the intrinsic structure of graphs, by upweighting the important nodes of the given graph. Extensive experiments on multiple imbalanced graph datasets and imbalanced settings demonstrate the effectiveness of our proposed framework, which significantly improves the performance of the recent state-of-the-art GCL methods. Further experimental ablations and analyses show that the ImGCL framework consistently improves the representation quality of nodes in under-represented (tail) classes.

Ziqi Gao, Yifan Niu, Jiashun Cheng et al.

Graph neural networks (GNNs) are popular weapons for modeling relational data. Existing GNNs are not specified for attribute-incomplete graphs, making missing attribute imputation a burning issue. Until recently, many works notice that GNNs are coupled with spectral concentration, which means the spectrum obtained by GNNs concentrates on a local part in spectral domain, e.g., low-frequency due to oversmoothing issue. As a consequence, GNNs may be seriously flawed for reconstructing graph attributes as graph spectral concentration tends to cause a low imputation precision. In this work, we present a regularized graph autoencoder for graph attribute imputation, named MEGAE, which aims at mitigating spectral concentration problem by maximizing the graph spectral entropy. Notably, we first present the method for estimating graph spectral entropy without the eigen-decomposition of Laplacian matrix and provide the theoretical upper error bound. A maximum entropy regularization then acts in the latent space, which directly increases the graph spectral entropy. Extensive experiments show that MEGAE outperforms all the other state-of-the-art imputation methods on a variety of benchmark datasets.

Ziqi Gao, S. Kevin Zhou

Undersampled MRI reconstruction is crucial for accelerating clinical scanning. Dual-domain reconstruction network is performant among SoTA deep learning methods. In this paper, we rethink dual-domain model design from the perspective of the receptive field, which is needed for image recovery and K-space interpolation problems. Further, we introduce domain-specific modules for dual-domain reconstruction, namely k-space global initialization and image-domain parallel local detail enhancement. We evaluate our modules by translating a SoTA method DuDoRNet under different conventions of MRI reconstruction including image-domain, dual-domain, and reference-guided reconstruction on the public IXI dataset. Our model DuDoRNet+ achieves significant improvements over competing deep learning methods.

Ziqi Gao, Yuntao Wang, Jianguo Chen et al.

Multimodal sensors provide complementary information to develop accurate machine-learning methods for human activity recognition (HAR), but introduce significantly higher computational load, which reduces efficiency. This paper proposes an efficient multimodal neural architecture for HAR using an RGB camera and inertial measurement units (IMUs) called Multimodal Temporal Segment Attention Network (MMTSA). MMTSA first transforms IMU sensor data into a temporal and structure-preserving gray-scale image using the Gramian Angular Field (GAF), representing the inherent properties of human activities. MMTSA then applies a multimodal sparse sampling method to reduce data redundancy. Lastly, MMTSA adopts an inter-segment attention module for efficient multimodal fusion. Using three well-established public datasets, we evaluated MMTSA's effectiveness and efficiency in HAR. Results show that our method achieves superior performance improvements 11.13% of cross-subject F1-score on the MMAct dataset than the previous state-of-the-art (SOTA) methods. The ablation study and analysis suggest that MMTSA's effectiveness in fusing multimodal data for accurate HAR. The efficiency evaluation on an edge device showed that MMTSA achieved significantly better accuracy, lower computational load, and lower inference latency than SOTA methods.

Ziqi Gao, S. Kevin Zhou

Implicit visual knowledge in a large latent diffusion model (LLDM) pre-trained on natural images is rich and hypothetically universal to natural and medical images. To test this hypothesis from a practical perspective, we propose a novel framework for undersampled MRI Reconstruction by Prompting a large latent Diffusion model (MRPD). While the existing methods trained on MRI datasets are typically of limited generalizability toward diverse data acquisition scenarios, MRPD supports unsupervised and universally adaptive MRI reconstruction. For unsupervised reconstruction, MRSampler guides LLDM with a random-phase-modulated hard-to-soft control. With any single- or multiple-source MRI dataset, MRPD's performance is boosted universally by a lightweight MRAdapter that only finetunes the LLDM's autoencoder. Experiments on FastMRI and IXI show that MRPD is the only model that supports both MRI database-free and database-available scenarios and attains the best generalizability towards out-of-domain (OOD) samplings, contrasts, and organs among compared unsupervised, supervised, and MRI diffusion methods. To our knowledge, MRPD is the first method that empirically shows the universal prowess of an LLDM pre-trained on vast natural images for MRI. Our official implementation is at https://github.com/Z7Gao/MRPD.