HackGAN: Harmonious Cross-Network Mapping Using CycleGAN With Wasserstein–Procrustes Learning for Unsupervised Network Alignment

Network alignment finds node correspondences across multiple networks, where the alignment accuracy is of crucial importance because of its profound impact on downstream applications. The vast majority of existing works focus on how to best utilize the topology and attribute information of the input networks as well as the anchor links when available. Nonetheless, it has not been well studied on how to boost the alignment performance through actively obtaining high-quality and informative anchor links, with a few exceptions. The sparse literature on active network alignment introduces the human in the loop to label some seed node correspondence (i.e., anchor links), which are informative from the perspective of querying the most uncertain node given few potential matchings. However, the direct influence of the intrinsic network attribute information on the alignment results has largely remained unknown. In this paper, we tackle this challenge and propose an active network alignment method (Attent) to identify the best nodes to query. The key idea of the proposed method is to leverage effective and efficient influence functions defined over the alignment solution to evaluate the goodness of the candidate nodes for query. Our proposed query strategy bears three distinct advantages, including (1) effectiveness, being able to accurately quantify the influence of the candidate nodes on the alignment results; (2) efficiency, scaling linearly with 15 − 17 × speed-up over the straight-forward implementation without any quality loss; (3) generality, consistently improving alignment performance of a variety of network alignment algorithms.

Network alignment is an important technique with applications in diverse domains, such as social network analysis, bioinformatics, and knowledge graph construction. Many of the alignment methods rely on predefined anchor nodes, which are often unavailable in real-world scenarios. To overcome this limitation, we propose MANNA (MAtched Neighbor consistency for Network Alignment), an unsupervised approach to network alignment that exploits the concept of Matched Neighborhood Consistency (MNC). The hypothesis of MANNA is that nodes with higher similarity within their local neighborhood structures are more likely to be aligned across different networks. To learn the structural and attribute features of networks, MANNA uses a Graph Neural Network (GNN). It extracts multi-order node embeddings to capture multi-scale neighborhood features, which are then used to construct similarity matrices for the alignment process. MANNA introduces a key innovation by using pseudo-anchor nodes identified by the MNC strategy to provide self-supervised learning signals in the absence of real anchor nodes. This approach enhances the model’s ability to learn accurate network representations and improve alignment accuracy. Alignment results are iteratively refined by applying the MNC strategy, which strengthens the consistency of neighborhood structures between matched nodes. Extensive experiments on three public datasets show that MANNA outperforms existing network alignment methods.

Nowadays, people are usually involved in multiple heterogeneous social networks simultaneously. Discovering the anchor links between the accounts owned by the same users across different social networks is crucial for many important inter-network applications, e.g., cross-network link transfer and cross-network recommendation. Many different supervised models have been proposed to predict anchor links so far, but they are effective only when the labeled anchor links are abundant. However, in real scenarios, such a requirement can hardly be met and most anchor links are unlabeled, since manually labeling the inter-network anchor links is quite costly and tedious. To overcome such a problem and utilize the numerous unlabeled anchor links in model building, in this paper, we introduce the active learning based anchor link prediction problem. Different from the traditional active learning problems, due to the one-to-one constraint on anchor links, if an unlabeled anchor link is identified as positive (i.e., existing), all the other unlabeled anchor links incident to account u or account v will be negative (i.e., non-existing) automatically. Viewed in such a perspective, asking for the labels of potential positive anchor links in the unlabeled set will be rewarding in the active anchor link prediction problem. Various novel anchor link information gain measures are defined in this paper, based on which several constraint active anchor link prediction methods are introduced. Extensive experiments have been done on real-world social network datasets to compare the performance of these methods with state-of-art anchor link prediction methods. The experimental results show that the proposed Mean-entropy-based Constrained Active Learning (MC) method can outperform other methods with significant advantages.

The online social network alignment problem aims at inferring the anchor links connecting the shared users across social networks, which are usually subject to the one-to-one cardinality constraint. Several existing social network alignment models have been proposed, many of which are based on the supervised learning setting. Given a set of labeled anchor links, a group of features can be extracted manually for the anchor links to build these models. Meanwhile, such methods may encounter great challenges in the application on real-world social network datasets, since manual feature extraction can be extremely expensive and tedious for the social networks involving heterogeneous information. In this paper, we propose to address the heterogeneous social network alignment problem with a deep learning model, namely DETA (Deep nETwork Alignment). Besides a small number of explicit features, DETA can automatically learn a set of latent features from the heterogeneous information. DETA models the anchor link one-to-one cardinality constraint as a mathematical constraint on the node degrees. Extensive experiments have been done on real-world aligned heterogeneous social network datasets, and the experimental results have demonstrated the effectiveness of the proposed model compared against the existing state-of-the-art baseline methods.

Graph neural networks induced by concept lattices for classification

DSSGNN-PPI: A Protein–Protein Interactions prediction model based on Double Structure and Sequence graph neural networks

BackgroundIn the last decade, a considerable amount of research has been devoted to investigating the phylogenetic properties of organisms from a systems-level perspective. Most studies have focused on the classification of organisms based on structural comparison and local alignment of metabolic pathways. In contrast, global alignment of multiple metabolic networks complements sequence-based phylogenetic analyses and provides more comprehensive information.ResultsWe explored the phylogenetic relationships between microorganisms through global alignment of multiple metabolic networks. The proposed approach integrates sequence homology data with topological information of metabolic networks. In general, compared to recent studies, the resulting trees reflect the living style of organisms as well as classical taxa. Moreover, for phylogenetically closely related organisms, the classification results are consistent with specific metabolic characteristics, such as the light-harvesting systems, fermentation types, and sources of electrons in photosynthesis.ConclusionsWe demonstrate the usefulness of global alignment of multiple metabolic networks to infer phylogenetic relationships between species. In addition, our exhaustive analysis of microbial metabolic pathways reveals differences in metabolic features between phylogenetically closely related organisms. With the ongoing increase in the number of genomic sequences and metabolic annotations, the proposed approach will help identify phenotypic variations that may not be apparent based solely on sequence-based classification.

BackgroundThe discovery of functionally conserved proteins is a tough and important task in system biology. Global network alignment provides a systematic framework to search for these proteins from multiple protein-protein interaction (PPI) networks. Although there exist many web servers for network alignment, no one allows to perform global multiple network alignment tasks on users’ test datasets.ResultsHere, we developed a web server WebNetcoffee based on the algorithm of NetCoffee to search for a global network alignment from multiple networks. To build a series of online test datasets, we manually collected 218,339 proteins, 4,009,541 interactions and many other associated protein annotations from several public databases. All these datasets and alignment results are available for download, which can support users to perform algorithm comparison and downstream analyses.ConclusionWebNetCoffee provides a versatile, interactive and user-friendly interface for easily running alignment tasks on both online datasets and users’ test datasets, managing submitted jobs and visualizing the alignment results through a web browser. Additionally, our web server also facilitates graphical visualization of induced subnetworks for a given protein and its neighborhood. To the best of our knowledge, it is the first web server that facilitates the performing of global alignment for multiple PPI networks.Availabilityhttp://www.nwpu-bioinformatics.com/WebNetCoffee

Network alignment is the matching of two networks with corresponding nodes that belong to the same user or entity. The most common application is to analyze which accounts belong to the same user in two social networks. Most of existing techniques rely on matrix factorization so that they cannot be scaled to large-scale networks, are constrained by strict constraints, and cannot learn node embedding without a training set. In this paper, we propose an unsupervised network alignment model based on multi-level graph attention networks. The model uses multi-level graph attention network to learn the embedded representation of nodes, satisfying attribute and structure constraints of alignment. Augmented learning process is proposed to simulate attribute noise and structural noise to improve adaptability of the model. Extensive experiments on real datasets show that the proposed model performs better than the state-of-the-art network alignment model. We also demonstrate the robustness of the proposed model.

In the era of information data explosion, accurately classifying massive text data and mining emotional tendencies play an important role in purifying the network environment. A sentiment classification model that combines the advantages of BERT and graph neural networks is proposed to address the shortcomings of a single traditional classification model in terms of classification accuracy and efficiency. It is recommended to combine the transformer based BERT model with graph neural networks, using the text embedding technology in BERT to leverage its powerful feature extraction ability and the advantage of graph neural networks in aggregating semantic features of text structure information. This will advance the semantic information of the entire text and then pass the semantic features to the combined model for classification. At the same time, in text sequence processing, it is proposed to construct an emotional dependency tree and obtain a leading matrix based on dependency relationships, which can improve the model's understanding of text semantic and structural information. The model was tested on English datasets such as 20NG and R8, as well as the Weibo 100k dataset, with a particularly high rate of 93.7% on the Weibo 100k dataset. Comparative experiments were conducted with other models.The results indicate that compared with other segmentation models, our model has better segmentation performance and can effectively aggregate semantic information of comment texts.

Path-aware multi-hop graph towards improving graph learning

Recently, Graph Neural Networks (GNNs) have been widely used for fraud detection. GNNs first generate node embedding by aggregating neighboring information under different relations, and then use the final node embedding to detect the node’s suspiciousness. However, traditional GNNs employing only a single type of aggregator fail to capture neighbor information from multiple perspectives and treating different relations equally inevitably weakens the semantic information of heterogeneous graphs. Meanwhile, expressive ability of GNNs is limited by using conventional concatenating or averaging operations to update the center node. Also, camouflaged entities could damage GNN-based models. To handle these problems, a novel heterogeneous GNN model called <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Multiple Aggregators and Feature Interactions Network</i> (MAFI) is proposed in this paper to conduct fraud detection tasks. Concretely, multiple types of aggregators are applied on different relations to aggregate neighbor information and aggregator-level attention is utilized to learn the importance of different aggregators. Also, relation-level attention is leveraged to learn the importance of each relation. Besides, conventional update operations are replaced with vector-wise implicit and explicit feature interactions. Moreover, a trainable neighbor sampler is employed to filter camouflaged fraudsters. Comprehensive experiments on two real-world fraud datasets indicate that the proposed MAFI outperforms existing GNN-based fraud detectors.

Network alignment aims at finding a bijective mapping between nodes of two networks. Due to its wide application in various fields (e.g., Computer Vision, Data Management, Bioinformatics, and Privacy Protection), researchers have proposed many network alignment algorithms, most of which rely on a set of pre-mapped seeds. However, it is challenging to identify an initial credible set of seeds solely with structural information. In this paper, by exploiting the observation that a true mapping leads to a large portion of consistent edges among the mapped nodes, we formally define the credibility of a mapping as its deviation from a random one. This enables us to measure the credibility of an initial set of seeds. We also present DeepMatching which is a seed identification framework for social network alignment. First, we represent the nodes of the two mapping networks with their structural feature vectors by employing graph embedding techniques. Second, we obtain an initial mapping of the nodes based on the obtained vectors by leveraging point set registration methods. Third, we develop a heuristic algorithm to extract a credible set of seed from the initial mapping. Finally, we utilize the extracted seed set as input of an efficient propagation-based algorithm for large scale network alignment. We conduct extensive experiments to evaluate the performance of DeepMatching, and the results clearly demonstrate its effectiveness and the efficiency.

Research of Protein-Protein Interaction (PPI) Network Alignment is playing an important role in understanding the crucial underlying biological knowledge such as functionally homologous proteins and conserved evolutionary pathways across different species. Existing methods of PPI network alignment often try to improve the coverage ratio of the alignment result by aligning all proteins from different species. However, there is a fundamental biological premise that needs to be considered carefully: not every protein in a species can, nor should, find its homologous proteins in other species. In this work, we propose a novel alignment method to map only those proteins with the most similarity throughout the PPI networks of multiple species. For the similarity features of the protein in the networks, we integrate both topological features with biological characteristics to provide enhanced supports for the alignment procedures. For topological features, we apply a representation learning method on the networks and generate a low dimensional vector embedding with its surrounding structural features for each protein. The topological similarity of proteins from different PPI networks can thus be transferred as the similarity of their corresponding vector representations, which provides a new way to comprehensively quantify the topological similarities between proteins. We also propose a new measure for the topological evaluation of the alignment results which better uncover the structural quality of the alignment across multiple networks. Both biological and topological evaluations on the alignment results of real datasets demonstrate our approach is promising and preferable against previous multiple alignment methods.

In this paper we introduce an efficient algorithm for alignment of multiple large-scale biological networks. In this scheme, we first compute a probabilistic similarity measure between nodes that belong to different networks using a semi-Markov random walk model. The estimated probabilities are further enhanced by incorporating the local and the cross-species network similarity information through the use of two different types of probabilistic consistency transformations. The transformed alignment probabilities are used to predict the alignment of multiple networks based on a greedy approach. We demonstrate that the proposed algorithm, called SMETANA, outperforms many state-of-the-art network alignment techniques, in terms of computational efficiency, alignment accuracy, and scalability. Our experiments show that SMETANA can easily align tens of genome-scale networks with thousands of nodes on a personal computer without any difficulty. The source code of SMETANA is available upon request. The source code of SMETANA can be downloaded from http://www.ece.tamu.edu/~bjyoon/SMETANA/.