Daokun Zhang

Yixin Liu, Yizhen Zheng, Daokun Zhang et al.

Unsupervised graph representation learning (UGRL) has drawn increasing research attention and achieved promising results in several graph analytic tasks. Relying on the homophily assumption, existing UGRL methods tend to smooth the learned node representations along all edges, ignoring the existence of heterophilic edges that connect nodes with distinct attributes. As a result, current methods are hard to generalize to heterophilic graphs where dissimilar nodes are widely connected, and also vulnerable to adversarial attacks. To address this issue, we propose a novel unsupervised Graph Representation learning method with Edge hEterophily discriminaTing (GREET) which learns representations by discriminating and leveraging homophilic edges and heterophilic edges. To distinguish two types of edges, we build an edge discriminator that infers edge homophily/heterophily from feature and structure information. We train the edge discriminator in an unsupervised way through minimizing the crafted pivot-anchored ranking loss, with randomly sampled node pairs acting as pivots. Node representations are learned through contrasting the dual-channel encodings obtained from the discriminated homophilic and heterophilic edges. With an effective interplaying scheme, edge discriminating and representation learning can mutually boost each other during the training phase. We conducted extensive experiments on 14 benchmark datasets and multiple learning scenarios to demonstrate the superiority of GREET.

Qijie Ding, Daokun Zhang, Jie Yin

Entity alignment aims to discover unique equivalent entity pairs with the same meaning across different knowledge graphs (KGs). Existing models have focused on projecting KGs into a latent embedding space so that inherent semantics between entities can be captured for entity alignment. However, the adverse impacts of alignment conflicts have been largely overlooked during training, thereby limiting the entity alignment performance. To address this issue, we propose a novel Conflict-aware Pseudo Labeling via Optimal Transport model (CPL-OT) for entity alignment. The key idea is to iteratively pseudo-label alignment pairs empowered with conflict-aware optimal transport (OT) modeling to boost the precision of entity alignment. CPL-OT is composed of two key components -- entity embedding learning with global-local aggregation and iterative conflict-aware pseudo labeling -- that mutually reinforce each other. To mitigate alignment conflicts during pseudo labeling, we propose to use optimal transport as an effective means to warrant one-to-one entity alignment between two KGs with the minimal overall transport cost. Extensive experiments on benchmark datasets validate the superiority of CPL-OT over state-of-the-art baselines under both settings with and without prior alignment seeds.

Qijie Ding, Jie Yin, Daokun Zhang et al.

Entity alignment (EA) aims at identifying equivalent entity pairs across different knowledge graphs (KGs) that refer to the same real-world identity. To circumvent the shortage of seed alignments provided for training, recent EA models utilize pseudo-labeling strategies to iteratively add unaligned entity pairs predicted with high confidence to the seed alignments for model training. However, the adverse impact of confirmation bias during pseudo-labeling has been largely overlooked, thus hindering entity alignment performance. To systematically combat confirmation bias for pseudo-labeling-based entity alignment, we propose a Unified Pseudo-Labeling framework for Entity Alignment (UPL-EA) that explicitly eliminates pseudo-labeling errors to boost the accuracy of entity alignment. UPL-EA consists of two complementary components: (1) Optimal Transport (OT)-based pseudo-labeling uses discrete OT modeling as an effective means to determine entity correspondences and reduce erroneous matches across two KGs. An effective criterion is derived to infer pseudo-labeled alignments that satisfy one-to-one correspondences; (2) Parallel pseudo-label ensembling refines pseudo-labeled alignments by combining predictions over multiple models independently trained in parallel. The ensembled pseudo-labeled alignments are thereafter used to augment seed alignments to reinforce subsequent model training for alignment inference. The effectiveness of UPL-EA in eliminating pseudo-labeling errors is both theoretically supported and experimentally validated. Our extensive results and in-depth analyses demonstrate the superiority of UPL-EA over 15 competitive baselines and its utility as a general pseudo-labeling framework for entity alignment.

Daokun Zhang, Russell Tsuchida, Dino Sejdinovic

Label distribution learning (LDL) provides a framework wherein a distribution over categories rather than a single category is predicted, with the aim of addressing ambiguity in labeled data. Existing research on LDL mainly focuses on the task of point estimation, i.e., finding an optimal distribution in the probability simplex conditioned on the given sample. In this paper, we propose a novel label distribution learning model SNEFY-LDL, which estimates a probability distribution of all possible label distributions over the simplex, by unleashing the expressive power of the recently introduced Squared Neural Family (SNEFY), a new class of tractable probability models. As a way to summarize the fitted model, we derive the closed-form label distribution mean, variance and covariance conditioned on the given sample, which can be used to predict the ground-truth label distributions, construct label distribution confidence intervals, and measure the correlations between different labels. Moreover, more information about the label distribution prediction uncertainties can be acquired from the modeled probability density function. Extensive experiments on conformal prediction, active learning and ensemble learning are conducted, verifying SNEFY-LDL's great effectiveness in LDL uncertainty quantification. The source code of this paper is available at https://github.com/daokunzhang/SNEFY-LDL.

Jiaxuan Li, Qing Xu, Xiangjian He et al.

Medical image segmentation plays an important role in computer-aided diagnosis. Existing methods mainly utilize spatial attention to highlight the region of interest. However, due to limitations of medical imaging devices, medical images exhibit significant heterogeneity, posing challenges for segmentation. Ultrasound images, for instance, often suffer from speckle noise, low resolution, and poor contrast between target tissues and background, which may lead to inaccurate boundary delineation. To address these challenges caused by heterogeneous image quality, we propose a hybrid CNN-Transformer model,called CFFormer, which leverages effective channel feature extraction to enhance the model' s ability to accurately identify tissue regions by capturing rich contextual information. The proposed architecture contains two key components: the Cross Feature Channel Attention (CFCA) module and the X-Spatial Feature Fusion (XFF) module. The model incorporates dual encoders, with the CNN encoder focusing on capturing local features and the Transformer encoder modeling global features. The CFCA module filters and facilitates interactions between the channel features from the two encoders, while the XFF module effectively reduces the significant semantic information differences in spatial features, enabling a smooth and cohesive spatial feature fusion. We evaluate our model across eight datasets covering five modalities to test its generalization capability. Experimental results demonstrate that our model outperforms current state-of-the-art methods and maintains accurate tissue region segmentation across heterogeneous medical image datasets. The code is available at https://github.com/JiaxuanFelix/CFFormer.

Daokun Zhang, Jie Yin, Xingquan Zhu et al.

Traditional network embedding primarily focuses on learning a continuous vector representation for each node, preserving network structure and/or node content information, such that off-the-shelf machine learning algorithms can be easily applied to the vector-format node representations for network analysis. However, the learned continuous vector representations are inefficient for large-scale similarity search, which often involves finding nearest neighbors measured by distance or similarity in a continuous vector space. In this paper, we propose a search efficient binary network embedding algorithm called BinaryNE to learn a binary code for each node, by simultaneously modeling node context relations and node attribute relations through a three-layer neural network. BinaryNE learns binary node representations through a stochastic gradient descent based online learning algorithm. The learned binary encoding not only reduces memory usage to represent each node, but also allows fast bit-wise comparisons to support faster node similarity search than using Euclidean distance or other distance measures. Extensive experiments and comparisons demonstrate that BinaryNE not only delivers more than 25 times faster search speed, but also provides comparable or better search quality than traditional continuous vector based network embedding methods. The binary codes learned by BinaryNE also render competitive performance on node classification and node clustering tasks. The source code of this paper is available at https://github.com/daokunzhang/BinaryNE.

Daokun Zhang, Jie Yin, Xingquan Zhu et al.

Network embedding aims to learn a latent, low-dimensional vector representations of network nodes, effective in supporting various network analytic tasks. While prior arts on network embedding focus primarily on preserving network topology structure to learn node representations, recently proposed attributed network embedding algorithms attempt to integrate rich node content information with network topological structure for enhancing the quality of network embedding. In reality, networks often have sparse content, incomplete node attributes, as well as the discrepancy between node attribute feature space and network structure space, which severely deteriorates the performance of existing methods. In this paper, we propose a unified framework for attributed network embedding-attri2vec-that learns node embeddings by discovering a latent node attribute subspace via a network structure guided transformation performed on the original attribute space. The resultant latent subspace can respect network structure in a more consistent way towards learning high-quality node representations. We formulate an optimization problem which is solved by an efficient stochastic gradient descent algorithm, with linear time complexity to the number of nodes. We investigate a series of linear and non-linear transformations performed on node attributes and empirically validate their effectiveness on various types of networks. Another advantage of attri2vec is its ability to solve out-of-sample problems, where embeddings of new coming nodes can be inferred from their node attributes through the learned mapping function. Experiments on various types of networks confirm that attri2vec is superior to state-of-the-art baselines for node classification, node clustering, as well as out-of-sample link prediction tasks. The source code of this paper is available at https://github.com/daokunzhang/attri2vec.

Daokun Zhang, Jie Yin, Xingquan Zhu et al.

With the widespread use of information technologies, information networks are becoming increasingly popular to capture complex relationships across various disciplines, such as social networks, citation networks, telecommunication networks, and biological networks. Analyzing these networks sheds light on different aspects of social life such as the structure of societies, information diffusion, and communication patterns. In reality, however, the large scale of information networks often makes network analytic tasks computationally expensive or intractable. Network representation learning has been recently proposed as a new learning paradigm to embed network vertices into a low-dimensional vector space, by preserving network topology structure, vertex content, and other side information. This facilitates the original network to be easily handled in the new vector space for further analysis. In this survey, we perform a comprehensive review of the current literature on network representation learning in the data mining and machine learning field. We propose new taxonomies to categorize and summarize the state-of-the-art network representation learning techniques according to the underlying learning mechanisms, the network information intended to preserve, as well as the algorithmic designs and methodologies. We summarize evaluation protocols used for validating network representation learning including published benchmark datasets, evaluation methods, and open source algorithms. We also perform empirical studies to compare the performance of representative algorithms on common datasets, and analyze their computational complexity. Finally, we suggest promising research directions to facilitate future study.

Jiaxuan Li, Qing Xu, Xiangjian He et al.

Masked Autoencoders (MAE) achieve self-supervised learning of image representations by randomly removing a portion of visual tokens and reconstructing the original image as a pretext task, thereby significantly enhancing pretraining efficiency and yielding excellent adaptability across downstream tasks. However, MAE and other MAE-style paradigms that adopt random masking generally require more pre-training epochs to maintain adaptability. Meanwhile, ViT in MAE suffers from inefficient parameter use due to fixed spatial resolution across layers. To overcome these limitations, we propose the Complementary Masked Autoencoders (CoMA), which employ a complementary masking strategy to ensure uniform sampling across all pixels, thereby improving effective learning of all features and enhancing the model's adaptability. Furthermore, we introduce DyViT, a hierarchical vision transformer that employs a Dynamic Multi-Window Self-Attention (DM-MSA), significantly reducing the parameters and FLOPs while improving fine-grained feature learning. Pre-trained on ImageNet-1K with CoMA, DyViT matches the downstream performance of MAE using only 12% of the pre-training epochs, demonstrating more effective learning. It also attains a 10% reduction in pre-training time per epoch, further underscoring its superior pre-training efficiency.

Teng Jiek See, Daokun Zhang, Mario Boley et al.

Graph Neural Networks (GNNs) are the currently most effective methods for predicting molecular properties but there remains a need for more accurate models. GNN accuracy can be improved by increasing the model complexity but this also increases the computational cost and memory requirement during training and inference. In this study, we develop Layer-to-Layer Knowledge Mixing (LKM), a novel self-knowledge distillation method that increases the accuracy of state-of-the-art GNNs while adding negligible computational complexity during training and inference. By minimizing the mean absolute distance between pre-existing hidden embeddings of GNN layers, LKM efficiently aggregates multi-hop and multi-scale information, enabling improved representation of both local and global molecular features. We evaluated LKM using three diverse GNN architectures (DimeNet++, MXMNet, and PAMNet) using datasets of quantum chemical properties (QM9, MD17 and Chignolin). We found that the LKM method effectively reduces the mean absolute error of quantum chemical and biophysical property predictions by up to 9.8% (QM9), 45.3% (MD17 Energy), and 22.9% (Chignolin). This work demonstrates the potential of LKM to significantly improve the accuracy of GNNs for chemical property prediction without any substantial increase in training and inference cost.

Huan Zhang, Daokun Zhang, Kexin Meng et al.

Bayesian network classifiers provide a feasible solution to tabular data classification, with a number of merits like high time and memory efficiency, and great explainability. However, due to the parameter explosion and data sparsity issues, Bayesian network classifiers are restricted to low-order feature dependency modeling, making them struggle in extrapolating the occurrence probabilities of complex real-world data. In this paper, we propose a novel paradigm to design high-order Bayesian network classifiers, by learning distributional representations for feature values, as what has been done in word embedding and graph representation learning. The learned distributional representations are encoded with the semantic relatedness between different features through their observed co-occurrence patterns in training data, which then serve as a hallmark to extrapolate the occurrence probabilities of new test samples. As a classifier design realization, we remake the K-dependence Bayesian classifier (KDB) by extending it into a neural version, i.e., NeuralKDB, where a novel neural network architecture is designed to learn distributional representations of feature values and parameterize the conditional probabilities between interdependent features. A stochastic gradient descent based algorithm is designed to train the NeuralKDB model efficiently. Extensive classification experiments on 60 UCI datasets demonstrate that the proposed NeuralKDB classifier excels in capturing high-order feature dependencies and significantly outperforms the conventional Bayesian network classifiers, as well as other competitive classifiers, including two neural network based classifiers without distributional representation learning.

Xinheng Lyu, Yuci Liang, Wenting Chen et al.

Whole slide images (WSIs) are vital in digital pathology, enabling gigapixel tissue analysis across various pathological tasks. While recent advancements in multi-modal large language models (MLLMs) allow multi-task WSI analysis through natural language, they often underperform compared to task-specific models. Collaborative multi-agent systems have emerged as a promising solution to balance versatility and accuracy in healthcare, yet their potential remains underexplored in pathology-specific domains. To address these issues, we propose WSI-Agents, a novel collaborative multi-agent system for multi-modal WSI analysis. WSI-Agents integrates specialized functional agents with robust task allocation and verification mechanisms to enhance both task-specific accuracy and multi-task versatility through three components: (1) a task allocation module assigning tasks to expert agents using a model zoo of patch and WSI level MLLMs, (2) a verification mechanism ensuring accuracy through internal consistency checks and external validation using pathology knowledge bases and domain-specific models, and (3) a summary module synthesizing the final summary with visual interpretation maps. Extensive experiments on multi-modal WSI benchmarks show WSI-Agents's superiority to current WSI MLLMs and medical agent frameworks across diverse tasks.

Guangsi Shi, Daokun Zhang, Ming Jin et al.

The great learning ability of deep learning models facilitates us to comprehend the real physical world, making learning to simulate complicated particle systems a promising endeavour. However, the complex laws of the physical world pose significant challenges to the learning based simulations, such as the varying spatial dependencies between interacting particles and varying temporal dependencies between particle system states in different time stamps, which dominate particles' interacting behaviour and the physical systems' evolution patterns. Existing learning based simulation methods fail to fully account for the complexities, making them unable to yield satisfactory simulations. To better comprehend the complex physical laws, this paper proposes a novel learning based simulation model- Graph Networks with Spatial-Temporal neural Ordinary Equations (GNSTODE)- that characterizes the varying spatial and temporal dependencies in particle systems using a united end-to-end framework. Through training with real-world particle-particle interaction observations, GNSTODE is able to simulate any possible particle systems with high precisions. We empirically evaluate GNSTODE's simulation performance on two real-world particle systems, Gravity and Coulomb, with varying levels of spatial and temporal dependencies. The results show that the proposed GNSTODE yields significantly better simulations than state-of-the-art learning based simulation methods, which proves that GNSTODE can serve as an effective solution to particle simulations in real-world application.

Daokun Zhang, Jie Yin, Philip S. Yu

Link prediction aims to infer the link existence between pairs of nodes in networks/graphs. Despite their wide application, the success of traditional link prediction algorithms is hindered by three major challenges -- link sparsity, node attribute noise and dynamic changes -- that are faced by many real-world networks. To address these challenges, we propose a Contextualized Self-Supervised Learning (CSSL) framework that fully exploits structural context prediction for link prediction. The proposed CSSL framework learns a link encoder to infer the link existence probability from paired node embeddings, which are constructed via a transformation on node attributes. To generate informative node embeddings for link prediction, structural context prediction is leveraged as a self-supervised learning task to boost the link prediction performance. Two types of structural context are investigated, i.e., context nodes collected from random walks vs. context subgraphs. The CSSL framework can be trained in an end-to-end manner, with the learning of model parameters supervised by both the link prediction and self-supervised learning tasks. The proposed CSSL is a generic and flexible framework in the sense that it can handle both attributed and non-attributed networks, and operate under both transductive and inductive link prediction settings. Extensive experiments and ablation studies on seven real-world benchmark networks demonstrate the superior performance of the proposed self-supervision based link prediction algorithm over state-of-the-art baselines, on different types of networks under both transductive and inductive settings. The proposed CSSL also yields competitive performance in terms of its robustness to node attribute noise and scalability over large-scale networks.

Yixin Liu, Yu Zheng, Daokun Zhang et al.

In recent years, graph neural networks (GNNs) have emerged as a successful tool in a variety of graph-related applications. However, the performance of GNNs can be deteriorated when noisy connections occur in the original graph structures; besides, the dependence on explicit structures prevents GNNs from being applied to general unstructured scenarios. To address these issues, recently emerged deep graph structure learning (GSL) methods propose to jointly optimize the graph structure along with GNN under the supervision of a node classification task. Nonetheless, these methods focus on a supervised learning scenario, which leads to several problems, i.e., the reliance on labels, the bias of edge distribution, and the limitation on application tasks. In this paper, we propose a more practical GSL paradigm, unsupervised graph structure learning, where the learned graph topology is optimized by data itself without any external guidance (i.e., labels). To solve the unsupervised GSL problem, we propose a novel StrUcture Bootstrapping contrastive LearnIng fraMEwork (SUBLIME for abbreviation) with the aid of self-supervised contrastive learning. Specifically, we generate a learning target from the original data as an "anchor graph", and use a contrastive loss to maximize the agreement between the anchor graph and the learned graph. To provide persistent guidance, we design a novel bootstrapping mechanism that upgrades the anchor graph with learned structures during model learning. We also design a series of graph learners and post-processing schemes to model the structures to learn. Extensive experiments on eight benchmark datasets demonstrate the significant effectiveness of our proposed SUBLIME and high quality of the optimized graphs.