Predicting enzyme-substrate interactions has long been a fundamental problem in biochemistry and metabolic engineering. While existing methods could leverage databases of expert-curated enzyme-substrate pairs for models to learn from known pair interactions, the databases are often sparse, i.e., there are only limited and incomplete examples of such pairs, and also labor-intensive to maintain. This lack of sufficient training data significantly hinders the ability of traditional enzyme prediction models to generalize to unseen interactions. In this work, we try to exploit chemical reaction equations from domain-specific databases, given their easier accessibility and denser, more abundant data. However, interactions of multiple compounds, e.g., educts and products, with the same enzymes create complex relational data patterns that traditional models cannot easily capture. To tackle that, we represent chemical reaction equations as triples of (educt, enzyme, product) within a knowledge graph, such that we can take advantage of knowledge graph embedding (KGE) to infer missing enzyme-substrate pairs for graph completion. Particularly, in order to capture intricate relationships among compounds, we propose our knowledge-enhanced hypergraph model for enzyme prediction, i.e., Hyper-Enz, which integrates a hypergraph transformer with a KGE model to learn representations of the hyper-edges that involve multiple educts and products. Also, a multi-expert paradigm is introduced to guide the learning of enzyme-substrate interactions with both the proposed model and chemical reaction equations. Experimental results show a significant improvement, with up to a 88% relative improvement in average enzyme retrieval accuracy and 30% improvement in pair-level prediction compared to traditional models, demonstrating the effectiveness of our approach.

One of many impediments to applying graph neural networks (GNNs) in processing large-volume real-world graph-structured data is that it disapproves of a centralized training scheme which involves gathering data belonging to different organizations due to privacy concerns. As a distributed data processing scheme, federated graph learning (FGL) enables learning GNN models collaboratively without sharing participants' private data. Though theoretically feasible, a core challenge in FGL systems is the variation of local training data distributions among clients, also known as the data heterogeneity problem. Most existing solutions suffer from two problems: (1) The typical optimizer based on empirical risk minimization tends to cause local models to fall into sharp valleys and weakens their generalization to out-of-distribution graph data. (2) The prevalent dimensional collapse in the learned representations of local graph data has an adverse impact on the classification capacity of the GNN model. To this end, we formulate a novel optimization objective that is aware of the sharpness (i.e., the curvature of the loss surface) of local GNN models. By minimizing the loss function and its sharpness simultaneously, we seek out model parameters in a flat region with uniformly low loss values, thus improving the generalization over heterogeneous data. By introducing a regularizer based on the correlation matrix of local representations, we relax the correlations of representations generated by individual local graph samples, so as to alleviate the dimensional collapse of the learned model. The proposed Sharpness-aware fEderated grAph Learning (SEAL) algorithm can enhance the classification accuracy and generalization ability of local GNN models in federated graph learning. Experimental studies on several graph classification benchmarks show that SEAL consistently outperforms SOTA FGL baselines and provides gains for more participants.

Federated Learning (FL) is increasingly adopted in edge computing scenarios, where a large number of heterogeneous clients operate under constrained or sufficient resources. The iterative training process of FL incurs considerable computation and communication overhead, which is unfriendly for resource-constrained devices. One-shot FL is a promising approach to addressing communication issues inherent in conventional FL, and model-heterogeneous FL solves the problem of diverse computing resources across clients. However, existing methods face challenges in effectively managing model-heterogeneous one-shot FL, often leading to unsatisfactory global model performance or reliance on auxiliary datasets. To address these challenges, we propose a novel FL framework named FedMHO, which leverages deep classification models on resource-sufficient clients and lightweight generative models on resource-constrained devices. On the server side, FedMHO involves a two-stage process that includes data generation and knowledge fusion. Furthermore, we introduce FedMHO-MD and FedMHO-SD to mitigate the knowledge-forgetting problem during the knowledge fusion stage, and an unsupervised data optimization solution to improve the quality of synthetic samples. Comprehensive experiments demonstrate the effectiveness of our methods, as they outperform state-of-the-art baselines in various experimental setups.

One-shot federated learning (FL) has gained traction due to its communication efficiency and scalability. However, unlike traditional FL, which can frequently align client models through multiple rounds of client training and server aggregation, one-shot FL allows only a single communication round, causing each client to easily overfit its local data and leading to divergent objectives. Without any chance to iteratively correct these biases or mitigate heterogeneity, the aggregated model significantly deviates from the optimum achieved under dataset centralized training. To address this challenge, we propose OFedED, a one-shot FL framework that preserves privacy and fully exploits client data by combining local data distillation with server-side ensemble learning. Each client distills its own dataset into an ultracompact coreset that retains essential distributional characteristics; the server aggregates these coresets to guide ensemble training that captures inter-client heterogeneity, harnesses complementary knowledge, corrects local bias, and drives performance close to centralized training. In addition, we theoretically show that, under mild assumptions for local data distillations, the server can simulate a centralized optimization process by finetuning on the aggregated distilled data, effectively bypassing the need for multiple communication rounds, showing that properly distilled data can encode sufficient task-relevant information to support centralized-level optimization. Extensive experiments reveal that OFedED consistently and significantly outperforms SOTA methods, achieving an improvement of up to 9.17% on MNIST and 3.97% on CIFAR-10, the robustness being verified also by experiments using ResNet and various server-client architectures.

Existing geometric knowledge graph embedding methods employ various relational transformations, such as translation, rotation, and projection, to model different relation patterns, which aims to enhance the expressiveness of models. In contrast to current approaches that treat the expressiveness of the model as a binary issue, we aim to delve deeper into analyzing the level of difficulty in which geometric knowledge graph embedding models can represent relation patterns. In this paper, we provide a theoretical analysis framework that measures the expressiveness of the model in relation patterns by quantifying the size of the solution space of linear equation systems. Additionally, we propose a mechanism for imposing relational constraints on geometric knowledge graph embedding models by setting “traps” near relational optimal solutions, which enables the model to better converge to the optimal solution. Empirically, we analyze and compare several typical knowledge graph embedding models with different geometric algebras, revealing that some models have insufficient solution space due to their design, which leads to performance weaknesses. We also demonstrate that the proposed relational constraint operations can improve the performance of certain relation patterns. The experimental results on public benchmarks and relation pattern specified dataset are consistent with our theoretical analysis.

Spatio-temporal forecasting of future values of spatially correlated time series is important across many cyber-physical systems (CPS). Recent studies offer evidence that the use of graph neural networks to capture latent correlations between time series holds a potential for enhanced forecasting. However, most existing methods rely on predefined or self-learning graphs, which are either static or unintentionally dynamic, and thus cannot model the time-varying correlations that exhibit trends and periodicities caused by the regularity of the underlying processes in CPS. To tackle such limitation, we propose Time-aware Graph Structure Learning (TagSL), which extracts time-aware correlations among time series by measuring the interaction of node and time representations in high-dimensional spaces. Notably, we introduce time discrepancy learning that utilizes contrastive learning with distance-based regularization terms to constrain learned spatial correlations to a trend sequence. Additionally, we propose a periodic discriminant function to enable the capture of periodic changes from the state of nodes. Next, we present a Graph Convolution-based Gated Recurrent Unit (GCGRU) that jointly captures spatial and temporal dependencies while learning time-aware and node-specific patterns. Finally, we introduce a unified framework named Time-aware Graph Convolutional Recurrent Network (TGCRN), combining TagSL, and GCGRU in an encoder-decoder architecture for multi-step spatiotemporal forecasting. We report on experiments with TGCRN and popular existing approaches on five real-world datasets, thus providing evidence that TGCRN is capable of advancing the state-of-the-art. We also cover a detailed ablation study and visualization analysis, offering detailed insight into the effectiveness of time-aware structure learning.

Graphs in real-world applications usually evolve constantly presenting dynamic behaviors such as social networks and transportation networks. Hence, dynamic graph embedding has gained much attention recently. In dynamic graphs, both the topology and node attributes could change over time, which pose great challenges for developing effective embedding models. Typically, the evolution process of a dynamic graph can be recorded as a series of snapshots. We observe that the evolution process inherently provides both prior information (previous snapshots) and validation information (the next snapshot). The prior information can be used to fit the evolution process, while the validation information can be used to improve the generalization ability of a graph embedding model. However, existing dynamic graph embedding models only utilize the prior information, but overlook the validation information. To tackle this issue, this paper proposes a novel dynamic graph embedding method via Model-Agnostic Meta-Learning, which utilizes both kinds of information to obtain better graph representation. The extensive experiments on eight real-world datasets demonstrate the superiority of our proposed method over state-of-the-art methods on various graph analysis tasks.

Capturing the relatedness of different domains is a key challenge in transferring knowledge across domains. In this paper, we propose an effective and efficient Gaussian process (GP) modelling framework, mTGPmk, that can explicitly model domain relatedness and adaptively control the space as well as the strength of knowledge transfer. mTGPmk takes both the discrepancy of input feature space and the discrepancy of predictive function into account in the transfer procedure. Specifically, mTGPmk adaptively selects a good latent manifold shared by different domains, and utilizes a parametric similarity coefficient to measure the predictive function covariance of different domains in this manifold. The latent shared manifold and the similarity coefficient are jointly learned in a coupled manner. By doing so, mTGPmk maximizes the strength of the shared knowledge transfer by choosing the transfer space with the best transfer capacity. More importantly, mTGPmk exploits a succinct and computationally efficient manifold learning approach so that it can be well trained with scarce target training data. Extensive experimental studies using 36 synthetic transfer tasks and 10 real-world transfer tasks show the effectiveness of mTGPmk on capturing the relatedness and the transfer adaptiveness.

Networked data, notably social network data, often comes with a rich set of annotations, or attributes, such as documents (e.g., tweets) and locations (e.g., check-ins). Community search in such attributed networks has been studied intensively due to its many applications in friends recommendation, event organization, advertising, etc. We study the problem of attribute-constrained co-located community (ACOC) search, which returns a community that satisfies three properties: i) structural cohesiveness: the members in the community are densely connected; ii) spatial co-location: the members are close to each other; and iii) attribute constraint: a set of attributes are covered by the attributes associated with the members. The ACOC problem is shown to be NP-hard. We develop four efficient approximation algorithms with guaranteed error bounds in addition to an exact solution that works on relatively small graphs. Extensive experiments conducted with both real and synthetic data offer insight into the efficiency and effectiveness of the proposed methods, showing that they outperform three adapted state-of-the-art algorithms by an order of magnitude. We also find that the approximation algorithms are much faster than the exact solution and yet offer high accuracy.

Given a set of server points (e.g., locations) P and a set of client points (e.g., users) O, the problem of maximizing bichromatic reverse k-nearest neighbor (MaxBRkNN) aims to find a region for setting up a new service site such that it can influence the most clients, i.e., it is in the kNN results of most client points. All existing studies first compute the kNN of client points and then perform the MaxBRkNN search. However, computing kNN for all clients is extremely time consuming especially on large datasets. Observing this, we develop an approach which computes kNN for only promising clients by utilising a two-level grid index (ADPGI) to reduce the cost substantially. Empirical studies on both real and synthetic datasets show that our proposed exact algorithm is 3 to 5 times faster than two state-of-the-art MaxBRkNN algorithms.

Clustering text and link data, as an important task in text and link analysis, aims at finding communities of linked documents by leveraging the information from both domains. Due to its improved performance over the single domain counterpart, it has attracted increasing attention from practitioners in recent years. Despite its popularity, all existing algorithms on clustering text and link data overlook the existence of domain-specific distinctions and thus result in unsatisfactory clustering quality. In this paper, we address this limitation by explicitly modeling the domain-specific distinctions in the clustering process. Specifically, we extend the idea of consensus and domain-specific subspace decomposition from flat data to graph data. Such a modeling, when coupled with a regularization to further sharpen the information distinction, makes the consensus information between text and link more accurate for clustering with both domains. The final model is cast into the spectral clustering model by imposing the subspace orthogonality. To eschew the costly eigen-decomposition required for spectral clustering and further speed-up the optimization, we take advantage of the data sparsity and the low dimensionality of subspaces, and deploy a constraint-preserving gradient method to efficiently solve the model. The experimental study on three real datasets shows that our algorithm consistently and significantly outperforms the state-of-the-art relevant algorithms in terms of both quality and efficiency.

Stochastic block model is a widely used statistical tool for modeling graphs and networks. Despite its popularity, the development on efficient inference algorithms for this model is surprisingly inadequate. The existing solutions are either too slow to handle large networks, or suffer from convergence issues. In this paper, we propose a fast and principled inference algorithm for stochastic block model. The algorithm is based on the variational Bayesian framework, and deploys the natural conjugate gradient method to accelerate the optimization of the variational bound. Leveraging upon the power of both conjugate and natural gradients, it converges super linearly and produces high quality solutions in practice. In particular, we apply our algorithm to the community detection task and compare it with the state-of-the-art variational Bayesian algorithms. We show that it can achieve up to two orders of magnitude speedup without significantly compromising the quality of solutions.

Graph clustering, also known as community detection, is a long-standing problem in data mining. In recent years, with the proliferation of rich attribute information available for objects in real-world graphs, how to leverage not only structural but also attribute information for clustering attributed graphs becomes a new challenge. Most existing works took a distance-based approach. They proposed various distance measures to fuse structural and attribute information and then applied standard techniques for graph clustering based on these distance measures. In this article, we take an alternative view and propose a novel Bayesian framework for attributed graph clustering. Our framework provides a general and principled solution to modeling both the structural and the attribute aspects of a graph. It avoids the artificial design of a distance measure in existing methods and, furthermore, can seamlessly handle graphs with different types of edges and vertex attributes. We develop an efficient variational method for graph clustering under this framework and derive two concrete algorithms for clustering unweighted and weighted attributed graphs. Experimental results on large real-world datasets show that our algorithms significantly outperform the state-of-the-art distance-based method, in terms of both effectiveness and efficiency.

Graph clustering, also known as community detection, is a long-standing problem in data mining. However, with the proliferation of rich attribute information available for objects in real-world graphs, how to leverage structural and attribute information for clustering attributed graphs becomes a new challenge. Most existing works take a distance-based approach. They proposed various distance measures to combine structural and attribute information. In this paper, we consider an alternative view and propose a model-based approach to attributed graph clustering. We develop a Bayesian probabilistic model for attributed graphs. The model provides a principled and natural framework for capturing both structural and attribute aspects of a graph, while avoiding the artificial design of a distance measure. Clustering with the proposed model can be transformed into a probabilistic inference problem, for which we devise an efficient variational algorithm. Experimental results on large real-world datasets demonstrate that our method significantly outperforms the state-of-art distance-based attributed graph clustering method.