Graph neural networks (GNNs) have enabled the automation of many web applications that entail node classification on graphs, such as scam detection in social media and event prediction in service networks. Nevertheless, recent studies revealed that the GNNs are vulnerable to adversarial attacks, where feeding GNNs with poisoned data at training time can lead them to yield catastrophically devastative test accuracy. This finding heats up the frontier of attacks and defenses against GNNs. However, the prior studies mainly posit that the adversaries can enjoy free access to manipulate the original graph, while obtaining such access could be too costly in practice. To fill this gap, we propose a novel attacking paradigm, named Generative Adversarial Fake Node Camouflaging (GAFNC), with its crux lying in crafting a set of fake nodes in a generative-adversarial regime. These nodes carry camouflaged malicious features and can poison the victim GNN by passing their malicious messages to the original graph via learned topological structures, such that they 1) maximize the devastation of classification accuracy (i.e., global attack) or 2) enforce the victim GNN to misclassify a targeted node set into prescribed classes (i.e., target attack). We benchmark our experiments on four real-world graph datasets, and the results substantiate the viability, effectiveness, and stealthiness of our proposed poisoning attack approach. Code is released in github.com/chao92/GAFNC.

Leveraging on-site renewable sources like solar and wind provides ample opportunities on developing environmental friendly and energy-efficient data centers. Evidence shows that renewable-aware job schedulers conserve energy by adjusting the arrangement of non-urgent workload according to renewable energy states. We propose an energy management system with a renewable-aware scheduler called REDUX3, which offers a smart way of managing the energy supply of data centers powered by the grid and renewable energy. Due to the intermittent nature of renewable energy resources, REDUX3 judiciously back-fills workload when renewable energy is sufficient, and defer workload to the next time slot if renewable energy is at outage state. As an integrated and smarter update from our previous work [1], [2] and [3], REDUX3 also orchestrates distribute UPS devices (i.e., recharge or discharge) to allocate energy resources when (1) grid price is at low or high states or (2) renewable energy generation is at a low or fluctuating level. Compared with the existing strategies, REDUX3 demonstrates a prominent capacity of boosting renewable energy utilization.

Internal validation is the most popular evaluation strategy used for drug-target predictive models. The simple random shuffling in the cross-validation, however, is not always ideal to handle large, diverse and copious datasets as it could potentially introduce bias. Hence, these predictive models cannot be comprehensively evaluated to provide insight into their general performance on a variety of use-cases (e.g. permutations of different levels of connectiveness and categories in drug and target space, as well as validations based on different data sources). In this work, we introduce a benchmark, BETA, that aims to address this gap by (i) providing an extensive multipartite network consisting of 0.97 million biomedical concepts and 8.5 million associations, in addition to 62 million drug-drug and protein-protein similarities and (ii) presenting evaluation strategies that reflect seven cases (i.e. general, screening with different connectivity, target and drug screening based on categories, searching for specific drugs and targets and drug repurposing for specific diseases), a total of seven Tests (consisting of 344 Tasks in total) across multiple sampling and validation strategies. Six state-of-the-art methods covering two broad input data types (chemical structure- and gene sequence-based and network-based) were tested across all the developed Tasks. The best-worst performing cases have been analyzed to demonstrate the ability of the proposed benchmark to identify limitations of the tested methods for running over the benchmark tasks. The results highlight BETA as a benchmark in the selection of computational strategies for drug repurposing and target discovery.

MOTIVATION: The generalized linear mixed model (GLMM) is an extension of the generalized linear model (GLM) in which the linear predictor takes random effects into account. Given its power of precisely modeling the mixed effects from multiple sources of random variations, the method has been widely used in biomedical computation, for instance in the genome-wide association studies (GWASs) that aim to detect genetic variance significantly associated with phenotypes such as human diseases. Collaborative GWAS on large cohorts of patients across multiple institutions is often impeded by the privacy concerns of sharing personal genomic and other health data. To address such concerns, we present in this paper a privacy-preserving Expectation-Maximization (EM) algorithm to build GLMM collaboratively when input data are distributed to multiple participating parties and cannot be transferred to a central server. We assume that the data are horizontally partitioned among participating parties: i.e. each party holds a subset of records (including observational values of fixed effect variables and their corresponding outcome), and for all records, the outcome is regulated by the same set of known fixed effects and random effects. RESULTS: Our collaborative EM algorithm is mathematically equivalent to the original EM algorithm commonly used in GLMM construction. The algorithm also runs efficiently when tested on simulated and real human genomic data, and thus can be practically used for privacy-preserving GLMM construction. We implemented the algorithm for collaborative GLMM (cGLMM) construction in R. The data communication was implemented using the rsocket package. AVAILABILITY AND IMPLEMENTATION: The software is released in open source at https://github.com/huthvincent/cGLMM. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Network embedding techniques aim to encode each vertex/edge as a low-dimensional vector, enabling easy integration with existing graph mining algorithms. This paper presents a novel network embedding framework, VEEMBEDCLASS, that combines local vertex/edge embedding with deep matrix fusion and Siamese multi-label classification for facilitating classification-based local network embedding. First, we propose to perform the embeddings of each vertex/edge on K local vertex/edge embedding models respectively, with the joint optimization by considering both intra-class and inter-class correlations, to learn their latent local features on each class. The deep matrix fusion technique is developed to preserve the first-order and second-order proximity of vertices and edges on each of K classes simultaneously. Second, a Student t-distribution based Siamese multi-label classification method is designed to train associated vertices and edges with similar local characteristics together and learn their class membership probabilities, in response to the power-law vertex degree distribution widespread in real graphs. A principle of vertex-edge homophily is introduced to guarantee that the common edge/vertex shared by two associated vertices/edges and themselves are similar in terms of both structural correlations and class memberships. Finally, we integrate local vertex/edge embedding and Siamese multi-label classification into a unified model by mutually enhancing each other.

Network embedding aims to learn latent low dimensional representation of vertices in graphs while preserving the intrinsic characteristics of graph data. In this paper, we propose a density-aware local autoencoder embedding architecture, DAL-SAE, with three features. First, we develop a flexible density-aware local deep autoencoder embedding method to perform local embedding on each of K clustering-based subgraphs with the optimization at both vertex and subgraph levels, in response to imbalanced density-based local characteristics of vertices and subgraphs. We design K local autoencoder embedding models, each with individual parameters and structure, to jointly train K subgraphs and optimize the loss functions within and across clusters. Second, we design an autoencoder graph clustering method to optimize local embedding and graph clustering simultaneously and capture local, clustering, and global network structure in the learning process. Third but last, a density-aware local Siamese autoencoder embedding approach can be utilized to train multiple clustering-based subgraphs with similar local characteristics on the common Siamese networks, to save the memory consumption of multiple local embedding models as well as maintain the similar embedding features.

Traditional network representation learning techniques aim to learn latent low-dimensional representation of vertices in graphs. This paper presents a novel edge representation learning framework, GANDLERL, that combines generative adversarial network based multi-label classification with density-adaptive local edge representation learning for producing high-quality low-dimensional edge representations. First, we design a generative adversarial network based multi-label edge classification model to classify rarely labeled edges in graphs with a large amount of noise data into K classes. A four-player zero-sum game model, with the mixed training of true and real-looking fake edges as well as a contrastive loss containing a similar-loss and a dissimilar-loss, is proposed to improve the classification quality of unlabeled edges. Second, a local autoencoder edge representation learning method is developed to design K local representation learning models, each with individual parameters and structure to perform local representation learning on each of K classification-based subgraphs with unique local characteristics and jointly optimize the loss functions within and across classes. Third but last, we propose a density-adaptive edge representation learning method with the optimization at both edge and subgraph levels to address the representation learning of graph data with highly imbalanced vertex degree and edge distribution.

Biomedical Informatics is a growing interdisciplinary field in which research topics and citation trends have been evolving rapidly in recent years. To analyze these data in a fast, reproducible manner, automation of certain processes is needed. JAMIA is a "generalist" journal for biomedical informatics. Its articles reflect the wide range of topics in informatics. In this study, we retrieved Medical Subject Headings (MeSH) terms and citations of JAMIA articles published between 2009 and 2014. We use tensors (i.e., multidimensional arrays) to represent the interaction among topics, time and citations, and applied tensor decomposition to automate the analysis. The trends represented by tensors were then carefully interpreted and the results were compared with previous findings based on manual topic analysis. A list of most cited JAMIA articles, their topics, and publication trends over recent years is presented. The analyses confirmed previous studies and showed that, from 2012 to 2014, the number of articles related to MeSH terms Methods, Organization & Administration, and Algorithms increased significantly both in number of publications and citations. Citation trends varied widely by topic, with Natural Language Processing having a large number of citations in particular years, and Medical Record Systems, Computerized remaining a very popular topic in all years.