Kunlun He

Yue Liu, Jun Xia, Sihang Zhou et al.

Graph clustering, which aims to divide nodes in the graph into several distinct clusters, is a fundamental yet challenging task. Benefiting from the powerful representation capability of deep learning, deep graph clustering methods have achieved great success in recent years. However, the corresponding survey paper is relatively scarce, and it is imminent to make a summary of this field. From this motivation, we conduct a comprehensive survey of deep graph clustering. Firstly, we introduce formulaic definition, evaluation, and development in this field. Secondly, the taxonomy of deep graph clustering methods is presented based on four different criteria, including graph type, network architecture, learning paradigm, and clustering method. Thirdly, we carefully analyze the existing methods via extensive experiments and summarize the challenges and opportunities from five perspectives, including graph data quality, stability, scalability, discriminative capability, and unknown cluster number. Besides, the applications of deep graph clustering methods in six domains, including computer vision, natural language processing, recommendation systems, social network analyses, bioinformatics, and medical science, are presented. Last but not least, this paper provides open resource supports, including 1) a collection (\url{https://github.com/yueliu1999/Awesome-Deep-Graph-Clustering}) of state-of-the-art deep graph clustering methods (papers, codes, and datasets) and 2) a unified framework (\url{https://github.com/Marigoldwu/A-Unified-Framework-for-Deep-Attribute-Graph-Clustering}) of deep graph clustering. We hope this work can serve as a quick guide and help researchers overcome challenges in this vibrant field.

Yawei Zhao, Qinghe Liu, Xinwang Liu et al.

Although data-driven methods usually have noticeable performance on disease diagnosis and treatment, they are suspected of leakage of privacy due to collecting data for model training. Recently, federated learning provides a secure and trustable alternative to collaboratively train model without any exchange of medical data among multiple institutes. Therefore, it has draw much attention due to its natural merit on privacy protection. However, when heterogenous medical data exists between different hospitals, federated learning usually has to face with degradation of performance. In the paper, we propose a new personalized framework of federated learning to handle the problem. It successfully yields personalized models based on awareness of similarity between local data, and achieves better tradeoff between generalization and personalization than existing methods. After that, we further design a differentially sparse regularizer to improve communication efficiency during procedure of model training. Additionally, we propose an effective method to reduce the computational cost, which improves computation efficiency significantly. Furthermore, we collect 5 real medical datasets, including 2 public medical image datasets and 3 private multi-center clinical diagnosis datasets, and evaluate its performance by conducting nodule classification, tumor segmentation, and clinical risk prediction tasks. Comparing with 13 existing related methods, the proposed method successfully achieves the best model performance, and meanwhile up to 60% improvement of communication efficiency. Source code is public, and can be accessed at: https://github.com/ApplicationTechnologyOfMedicalBigData/pFedNet-code.

Yuxiao Cheng, Runzhao Yang, Tingxiong Xiao et al. · tsinghua

Causal discovery from time-series data has been a central task in machine learning. Recently, Granger causality inference is gaining momentum due to its good explainability and high compatibility with emerging deep neural networks. However, most existing methods assume structured input data and degenerate greatly when encountering data with randomly missing entries or non-uniform sampling frequencies, which hampers their applications in real scenarios. To address this issue, here we present CUTS, a neural Granger causal discovery algorithm to jointly impute unobserved data points and build causal graphs, via plugging in two mutually boosting modules in an iterative framework: (i) Latent data prediction stage: designs a Delayed Supervision Graph Neural Network (DSGNN) to hallucinate and register unstructured data which might be of high dimension and with complex distribution; (ii) Causal graph fitting stage: builds a causal adjacency matrix with imputed data under sparse penalty. Experiments show that CUTS effectively infers causal graphs from unstructured time-series data, with significantly superior performance to existing methods. Our approach constitutes a promising step towards applying causal discovery to real applications with non-ideal observations.

Yuxiao Cheng, Ziqian Wang, Tingxiong Xiao et al. · tsinghua

Time-series causal discovery (TSCD) is a fundamental problem of machine learning. However, existing synthetic datasets cannot properly evaluate or predict the algorithms' performance on real data. This study introduces the CausalTime pipeline to generate time-series that highly resemble the real data and with ground truth causal graphs for quantitative performance evaluation. The pipeline starts from real observations in a specific scenario and produces a matching benchmark dataset. Firstly, we harness deep neural networks along with normalizing flow to accurately capture realistic dynamics. Secondly, we extract hypothesized causal graphs by performing importance analysis on the neural network or leveraging prior knowledge. Thirdly, we derive the ground truth causal graphs by splitting the causal model into causal term, residual term, and noise term. Lastly, using the fitted network and the derived causal graph, we generate corresponding versatile time-series proper for algorithm assessment. In the experiments, we validate the fidelity of the generated data through qualitative and quantitative experiments, followed by a benchmarking of existing TSCD algorithms using these generated datasets. CausalTime offers a feasible solution to evaluating TSCD algorithms in real applications and can be generalized to a wide range of fields. For easy use of the proposed approach, we also provide a user-friendly website, hosted on www.causaltime.cc.

Meng Liu, Ke Liang, Yawei Zhao et al.

Temporal graph learning aims to generate high-quality representations for graph-based tasks with dynamic information, which has recently garnered increasing attention. In contrast to static graphs, temporal graphs are typically organized as node interaction sequences over continuous time rather than an adjacency matrix. Most temporal graph learning methods model current interactions by incorporating historical neighborhood. However, such methods only consider first-order temporal information while disregarding crucial high-order structural information, resulting in suboptimal performance. To address this issue, we propose a self-supervised method called S2T for temporal graph learning, which extracts both temporal and structural information to learn more informative node representations. Notably, the initial node representations combine first-order temporal and high-order structural information differently to calculate two conditional intensities. An alignment loss is then introduced to optimize the node representations, narrowing the gap between the two intensities and making them more informative. Concretely, in addition to modeling temporal information using historical neighbor sequences, we further consider structural knowledge at both local and global levels. At the local level, we generate structural intensity by aggregating features from high-order neighbor sequences. At the global level, a global representation is generated based on all nodes to adjust the structural intensity according to the active statuses on different nodes. Extensive experiments demonstrate that the proposed model S2T achieves at most 10.13% performance improvement compared with the state-of-the-art competitors on several datasets.

Xin Zou, Ruimeng Liu, Chang Tang et al.

Multi-View Clustering (MVC) has gained significant attention for its ability to leverage complementary information across diverse views. However, existing deep MVC methods often struggle with view-distribution entanglement during cross-view fusion, which hampers the quality of the shared latent space and leads to suboptimal Figures. To address this issue, we propose the Generalized Multi-view Auto-Encoder (GMAE), a framework designed to preserve cross-view complementarity through disentangled representation learning. Specifically, GMAE employs dual-path autoencoders to decouple source features into view-specific and view-common embeddings, facilitating the discovery of clearer clustering structures. We further construct cross-view adversarial discriminators to guide view-specific encoders in capturing more discriminative features. By strategically modulating mutual information, GMAE effectively aligns distributions and prevents representation collapse, ensuring the generation of robust, non-trivial embeddings. Comprehensive experiments on 13 benchmark datasets demonstrate that GMAE consistently outperforms state-of-the-art methods in both complete and incomplete MVC tasks. Our code implementation is available at the repository: https://github.com/obananas/GMAE.

Jiyuan Liu, Xinwang Liu, Siqi Wang et al.

Vertical federated learning is a natural and elegant approach to integrate multi-view data vertically partitioned across devices (clients) while preserving their privacies. Apart from the model training, existing methods requires the collaboration of all clients in the model inference. However, the model inference is probably maintained for service in a long time, while the collaboration, especially when the clients belong to different organizations, is unpredictable in real-world scenarios, such as concellation of contract, network unavailablity, etc., resulting in the failure of them. To address this issue, we, at the first attempt, propose a flexible Active-Passive Federated learning (APFed) framework. Specifically, the active client is the initiator of a learning task and responsible to build the complete model, while the passive clients only serve as assistants. Once the model built, the active client can make inference independently. In addition, we instance the APFed framework into two classification methods with employing the reconstruction loss and the contrastive loss on passive clients, respectively. Meanwhile, the two methods are tested in a set of experiments and achieves desired results, validating their effectiveness.

Pan Liu, Xin Yang Lu, Kunlun He

Loss function are an essential part in modern data-driven approach, such as bi-level training scheme and machine learnings. In this paper we propose a loss function consisting of a $r$-order (an)-isotropic total variation semi-norms $TV^r$, $r\in \mathbb{R}^+$, defined via the Riemann-Liouville (R-L) fractional derivative. We focus on studying key theoretical properties, such as the lower semi-continuity and compactness with respect to both the function and the order of derivative $r$, of such loss functions.

Zhifeng Wang, Renjiao Yi, Xin Wen et al.

Vascular diseases pose a significant threat to human health, with X-ray angiography established as the gold standard for diagnosis, allowing for detailed observation of blood vessels. However, angiographic X-rays expose personnel and patients to higher radiation levels than non-angiographic X-rays, which are unwanted. Thus, modality translation from non-angiographic to angiographic X-rays is desirable. Data-driven deep approaches are hindered by the lack of paired large-scale X-ray angiography datasets. While making high-quality vascular angiography synthesis crucial, it remains challenging. We find that current medical image synthesis primarily operates at pixel level and struggles to adapt to the complex geometric structure of blood vessels, resulting in unsatisfactory quality of blood vessel image synthesis, such as disconnections or unnatural curvatures. To overcome this issue, we propose a self-supervised method via diffusion models to transform non-angiographic X-rays into angiographic X-rays, mitigating data shortages for data-driven approaches. Our model comprises a diffusion model that learns the distribution of vascular data from diffusion latent, a generator for vessel synthesis, and a mask-based adversarial module. To enhance geometric accuracy, we propose a parametric vascular model to fit the shape and distribution of blood vessels. The proposed method contributes a pipeline and a synthetic dataset for X-ray angiography. We conducted extensive comparative and ablation experiments to evaluate the Angio-Diff. The results demonstrate that our method achieves state-of-the-art performance in synthetic angiography image quality and more accurately synthesizes the geometric structure of blood vessels. The code is available at https://github.com/zfw-cv/AngioDiff.

Muhao Xu, Zhenfeng Zhu, Youru Li et al.

Multimodal electronic health record (EHR) data can offer a holistic assessment of a patient's health status, supporting various predictive healthcare tasks. Recently, several studies have embraced the multitask learning approach in the healthcare domain, exploiting the inherent correlations among clinical tasks to predict multiple outcomes simultaneously. However, existing methods necessitate samples to possess complete labels for all tasks, which places heavy demands on the data and restricts the flexibility of the model. Meanwhile, within a multitask framework with multimodal inputs, how to comprehensively consider the information disparity among modalities and among tasks still remains a challenging problem. To tackle these issues, a unified healthcare prediction model, also named by \textbf{FlexCare}, is proposed to flexibly accommodate incomplete multimodal inputs, promoting the adaption to multiple healthcare tasks. The proposed model breaks the conventional paradigm of parallel multitask prediction by decomposing it into a series of asynchronous single-task prediction. Specifically, a task-agnostic multimodal information extraction module is presented to capture decorrelated representations of diverse intra- and inter-modality patterns. Taking full account of the information disparities between different modalities and different tasks, we present a task-guided hierarchical multimodal fusion module that integrates the refined modality-level representations into an individual patient-level representation. Experimental results on multiple tasks from MIMIC-IV/MIMIC-CXR/MIMIC-NOTE datasets demonstrate the effectiveness of the proposed method. Additionally, further analysis underscores the feasibility and potential of employing such a multitask strategy in the healthcare domain. The source code is available at https://github.com/mhxu1998/FlexCare.

Jiaqi Jin, Siwei Wang, Zhibin Dong et al.

Multi-view clustering leverages complementary representations from diverse sources to enhance performance. However, real-world data often suffer incomplete cases due to factors like privacy concerns and device malfunctions. A key challenge is effectively utilizing available instances to recover missing views. Existing methods frequently overlook the heterogeneity among views during recovery, leading to significant distribution discrepancies between recovered and true data. Additionally, many approaches focus on cross-view correlations, neglecting insights from intra-view reliable structure and cross-view clustering structure. To address these issues, we propose BURG, a novel method for incomplete multi-view clustering with distriBution dUal-consistency Recovery Guidance. We treat each sample as a distinct category and perform cross-view distribution transfer to predict the distribution space of missing views. To compensate for the lack of reliable category information, we design a dual-consistency guided recovery strategy that includes intra-view alignment guided by neighbor-aware consistency and cross-view alignment guided by prototypical consistency. Extensive experiments on benchmarks demonstrate the superiority of BURG in the incomplete multi-view scenario.

Xihong Yang, Siwei Wang, Jiaqi Jin et al.

Multi-view clustering (MVC) aims to explore the common clustering structure across multiple views. Many existing MVC methods heavily rely on the assumption of view consistency, where alignments for corresponding samples across different views are ordered in advance. However, real-world scenarios often present a challenge as only partial data is consistently aligned across different views, restricting the overall clustering performance. In this work, we consider the model performance decreasing phenomenon caused by data order shift (i.e., from fully to partially aligned) as a generalized multi-view clustering problem. To tackle this problem, we design a causal multi-view clustering network, termed CauMVC. We adopt a causal modeling approach to understand multi-view clustering procedure. To be specific, we formulate the partially aligned data as an intervention and multi-view clustering with partially aligned data as an post-intervention inference. However, obtaining invariant features directly can be challenging. Thus, we design a Variational Auto-Encoder for causal learning by incorporating an encoder from existing information to estimate the invariant features. Moreover, a decoder is designed to perform the post-intervention inference. Lastly, we design a contrastive regularizer to capture sample correlations. To the best of our knowledge, this paper is the first work to deal generalized multi-view clustering via causal learning. Empirical experiments on both fully and partially aligned data illustrate the strong generalization and effectiveness of CauMVC.

Yeyu Yan, Shuai Zheng, Wenjun Hui et al.

Graph condensation (GC) aims to distill the original graph into a small-scale graph, mitigating redundancy and accelerating GNN training. However, conventional GC approaches heavily rely on rigid GNNs and task-specific supervision. Such a dependency severely restricts their reusability and generalization across various tasks and architectures. In this work, we revisit the goal of ideal GC from the perspective of GNN optimization consistency, and then a generalized GC optimization objective is derived, by which those traditional GC methods can be viewed nicely as special cases of this optimization paradigm. Based on this, Pre-trained Graph Condensation (PreGC) via optimal transport is proposed to transcend the limitations of task- and architecture-dependent GC methods. Specifically, a hybrid-interval graph diffusion augmentation is presented to suppress the weak generalization ability of the condensed graph on particular architectures by enhancing the uncertainty of node states. Meanwhile, the matching between optimal graph transport plan and representation transport plan is tactfully established to maintain semantic consistencies across source graph and condensed graph spaces, thereby freeing graph condensation from task dependencies. To further facilitate the adaptation of condensed graphs to various downstream tasks, a traceable semantic harmonizer from source nodes to condensed nodes is proposed to bridge semantic associations through the optimized representation transport plan in pre-training. Extensive experiments verify the superiority and versatility of PreGC, demonstrating its task-independent nature and seamless compatibility with arbitrary GNNs.

Xinhang Wan, Jiyuan Liu, Qian Qu et al.

In this paper, we address the problem of novel class discovery (NCD), which aims to cluster novel classes by leveraging knowledge from disjoint known classes. While recent advances have made significant progress in this area, existing NCD methods face two major limitations. First, they primarily focus on single-view data (e.g., images), overlooking the increasingly common multi-view data, such as multi-omics datasets used in disease diagnosis. Second, their reliance on pseudo-labels to supervise novel class clustering often results in unstable performance, as pseudo-label quality is highly sensitive to factors such as data noise and feature dimensionality. To address these challenges, we propose a novel framework named Intra-view and Inter-view Correlation Guided Multi-view Novel Class Discovery (IICMVNCD), which is the first attempt to explore NCD in multi-view setting so far. Specifically, at the intra-view level, leveraging the distributional similarity between known and novel classes, we employ matrix factorization to decompose features into view-specific shared base matrices and factor matrices. The base matrices capture distributional consistency among the two datasets, while the factor matrices model pairwise relationships between samples. At the inter-view level, we utilize view relationships among known classes to guide the clustering of novel classes. This includes generating predicted labels through the weighted fusion of factor matrices and dynamically adjusting view weights of known classes based on the supervision loss, which are then transferred to novel class learning. Experimental results validate the effectiveness of our proposed approach.

Dong Chen, Shuai Zheng, Yeyu Yan et al.

Recent research on deep graph learning has shifted from static to dynamic graphs, motivated by the evolving behaviors observed in complex real-world systems. However, the temporal extension in dynamic graphs poses significant data efficiency challenges, including increased data volume, high spatiotemporal redundancy, and reliance on costly dynamic graph neural networks (DGNNs). To alleviate the concerns, we pioneer the study of dynamic graph condensation (DGC), which aims to substantially reduce the scale of dynamic graphs for data-efficient DGNN training. Accordingly, we propose DyGC, a novel framework that condenses the real dynamic graph into a compact version while faithfully preserving the inherent spatiotemporal characteristics. Specifically, to endow synthetic graphs with realistic evolving structures, a novel spiking structure generation mechanism is introduced. It draws on the dynamic behavior of spiking neurons to model temporally-aware connectivity in dynamic graphs. Given the tightly coupled spatiotemporal dependencies, DyGC proposes a tailored distribution matching approach that first constructs a semantically rich state evolving field for dynamic graphs, and then performs fine-grained spatiotemporal state alignment to guide the optimization of the condensed graph. Experiments across multiple dynamic graph datasets and representative DGNN architectures demonstrate the effectiveness of DyGC. Notably, our method retains up to 96.2% DGNN performance with only 0.5% of the original graph size, and achieves up to 1846 times training speedup.

Yuxiao Cheng, Xinxin Song, Ziqian Wang et al. · tsinghua

Recent advances in deep learning (DL) have prompted the development of high-performing early warning score (EWS) systems, predicting clinical deteriorations such as acute kidney injury, acute myocardial infarction, or circulatory failure. DL models have proven to be powerful tools for various tasks but come with the cost of lacking interpretability and limited generalizability, hindering their clinical applications. To develop a practical EWS system applicable to various outcomes, we propose causally-informed explainable early prediction model, which leverages causal discovery to identify the underlying causal relationships of prediction and thus owns two unique advantages: demonstrating the explicit interpretation of the prediction while exhibiting decent performance when applied to unfamiliar environments. Benefiting from these features, our approach achieves superior accuracy for 6 different critical deteriorations and achieves better generalizability across different patient groups, compared to various baseline algorithms. Besides, we provide explicit causal pathways to serve as references for assistant clinical diagnosis and potential interventions. The proposed approach enhances the practical application of deep learning in various medical scenarios.

Minfeng Xu, Chen-Chen Fan, Yan-Jie Zhou et al.

Cardiovascular diseases (CVD) remain a leading health concern and contribute significantly to global mortality rates. While clinical advancements have led to a decline in CVD mortality, accurately identifying individuals who could benefit from preventive interventions remains an unsolved challenge in preventive cardiology. Current CVD risk prediction models, recommended by guidelines, are based on limited traditional risk factors or use CT imaging to acquire quantitative biomarkers, and still have limitations in predictive accuracy and applicability. On the other hand, end-to-end trained CVD risk prediction methods leveraging deep learning on CT images often fail to provide transparent and explainable decision grounds for assisting physicians. In this work, we proposed a novel joint representation that integrates discrete quantitative biomarkers and continuous deep features extracted from chest CT scans. Our approach initiated with a deep CVD risk classification model by capturing comprehensive continuous deep learning features while jointly obtaining currently clinical-established quantitative biomarkers via segmentation models. In the feature joint representation stage, we use an instance-wise feature-gated mechanism to align the continuous and discrete features, followed by a soft instance-wise feature interaction mechanism fostering independent and effective feature interaction for the final CVD risk prediction. Our method substantially improves CVD risk predictive performance and offers individual contribution analysis of each biomarker, which is important in assisting physicians' decision-making processes. We validated our method on a public chest low-dose CT dataset and a private external chest standard-dose CT patient cohort of 17,207 CT volumes from 6,393 unique subjects, and demonstrated superior predictive performance, achieving AUCs of 0.875 and 0.843, respectively.

Yuxiao Cheng, Lianglong Li, Tingxiong Xiao et al.

Causal discovery in time-series is a fundamental problem in the machine learning community, enabling causal reasoning and decision-making in complex scenarios. Recently, researchers successfully discover causality by combining neural networks with Granger causality, but their performances degrade largely when encountering high-dimensional data because of the highly redundant network design and huge causal graphs. Moreover, the missing entries in the observations further hamper the causal structural learning. To overcome these limitations, We propose CUTS+, which is built on the Granger-causality-based causal discovery method CUTS and raises the scalability by introducing a technique called Coarse-to-fine-discovery (C2FD) and leveraging a message-passing-based graph neural network (MPGNN). Compared to previous methods on simulated, quasi-real, and real datasets, we show that CUTS+ largely improves the causal discovery performance on high-dimensional data with different types of irregular sampling.