Graph Community Infomax

Graph representation learning aims at learning low-dimension representations for nodes in graphs, and has been proven very useful in several downstream tasks. In this article, we propose a new model, Graph Community Infomax (GCI), that can adversarial learn representations for nodes in attributed networks. Different from other adversarial network embedding models, which would assume that the data follow some prior distributions and generate fake examples, GCI utilizes the community information of networks, using nodes as positive(or real) examples and negative(or fake) examples at the same time. An autoencoder is applied to learn the embedding vectors for nodes and reconstruct the adjacency matrix, and a discriminator is used to maximize the mutual information between nodes and communities. Experiments on several real-world and synthetic networks have shown that GCI outperforms various network embedding methods on community detection tasks.

Protein–Protein Interactions Prediction Base on Multiple Information Fusion via Graph Representation Learning

It is a critical impact on the processing of biological cells to protein–protein interactions (PPIs) in nature. Traditional PPIs predictive biological experiments consume a lot of human and material costs and time. Therefore, there is a great need to use computational methods to forecast PPIs. Most of the existing calculation methods are based on the sequence characteristics or internal structural characteristics of proteins, and most of them have the singleness of features. Therefore, we propose a novel method to predict PPIs base on multiple information fusion through graph representation learning. Specifically, firstly, the known protein sequences are calculated, and the properties of each protein are obtained by k-mer. Then, the known protein relationship pairs were constructed into an adjacency graph, and the graph representation learning method–graph convolution network was used to fuse the attributes of each protein with the graph structure information to obtain the features containing a variety of information. Finally, we put the multi-information features into the random forest classifier species for prediction and classification. Experimental results indicate that our method has high accuracy and AUC of 78.83% and 86.10%, respectively. In conclusion, our method has an excellent application prospect for predicting unknown PPIs.

An Adaptive Application Framework with Customizable Quality Metrics

Many embedded environments require applications to produce outcomes under different, potentially changing, resource constraints. Relaxing application semantics through approximations enables trading off resource usage for outcome quality. Although quality is a highly subjective notion, previous work assumes given, fixed low-level quality metrics that often lack a strong correlation to a user’s higher-level quality experience. Users may also change their minds with respect to their quality expectations depending on the resource budgets they are willing to dedicate to an execution. This motivates the need for an adaptive application framework where users provide execution budgets and a customized quality notion. This article presents a novel adaptive program graph representation that enables user-level, customizable quality based on basic quality aspects defined by application developers. Developers also define application configuration spaces, with possible customization to eliminate undesirable configurations. At runtime, the graph enables the dynamic selection of the configuration with maximal customized quality within the user-provided resource budget. An adaptive application framework based on our novel graph representation has been implemented on Android and Linux platforms and evaluated on eight benchmark programs, four with fully customizable quality. Using custom quality instead of the default quality, users may improve their subjective quality experience value by up to 3.59×, with 1.76× on average under different resource constraints. Developers are able to exploit their application structure knowledge to define configuration spaces that are on average 68.7% smaller as compared to existing, structure-oblivious approaches. The overhead of dynamic reconfiguration averages less than 1.84% of the overall application execution time.

Erasure-Resilient Sublinear-Time Graph Algorithms

We investigate sublinear-time algorithms that take partially erased graphs represented by adjacency lists as input. Our algorithms make degree and neighbor queries to the input graph and work with a specified fraction of adversarial erasures in adjacency entries. We focus on two computational tasks: testing if a graph is connected or ε-far from connected and estimating the average degree. For testing connectedness, we discover a threshold phenomenon: when the fraction of erasures is less than ε, this property can be tested efficiently (in time independent of the size of the graph); when the fraction of erasures is at least ε, then a number of queries linear in the size of the graph representation is required. Our erasure-resilient algorithm (for the special case with no erasures) is an improvement over the previously known algorithm for connectedness in the standard property testing model and has optimal dependence on the proximity parameter ε. For estimating the average degree, our results provide an “interpolation” between the query complexity for this computational task in the model with no erasures in two different settings: with only degree queries, investigated by Feige (SIAM J. Comput. ‘06), and with degree queries and neighbor queries, investigated by Goldreich and Ron (Random Struct. Algorithms ‘08) and Eden et al. (ICALP ‘17). We conclude with a discussion of our model and open questions raised by our work.

Multi-Scale Graph Representation Learning for Autism Identification With Functional MRI

Resting-state functional MRI (rs-fMRI) has been widely used for the early diagnosis of autism spectrum disorder (ASD). With rs-fMRI, the functional connectivity networks (FCNs) are usually constructed for representing each subject, with each element representing the pairwise relationship between brain region-of-interests (ROIs). Previous studies often first extract handcrafted network features (such as node degree and clustering coefficient) from FCNs and then construct a prediction model for ASD diagnosis, which largely requires expert knowledge. Graph convolutional networks (GCNs) have recently been employed to jointly perform FCNs feature extraction and ASD identification in a data-driven manner. However, existing studies tend to focus on the single-scale topology of FCNs by using one single atlas for ROI partition, thus ignoring potential complementary topology information of FCNs at different spatial scales. In this paper, we develop a multi-scale graph representation learning (MGRL) framework for rs-fMRI based ASD diagnosis. The MGRL consists of three major components: (1) multi-scale FCNs construction using multiple brain atlases for ROI partition, (2) FCNs representation learning via multi-scale GCNs, and (3) multi-scale feature fusion and classification for ASD diagnosis. The proposed MGRL is evaluated on 184 subjects from the public Autism Brain Imaging Data Exchange (ABIDE) database with rs-fMRI scans. Experimental results suggest the efficacy of our MGRL in FCN feature extraction and ASD identification, compared with several state-of-the-art methods.

An effective drug-disease associations prediction model based on graphic representation learning over multi-biomolecular network

Background Drug-disease associations (DDAs) can provide important information for exploring the potential efficacy of drugs. However, up to now, there are still few DDAs verified by experiments. Previous evidence indicates that the combination of information would be conducive to the discovery of new DDAs. How to integrate different biological data sources and identify the most effective drugs for a certain disease based on drug-disease coupled mechanisms is still a challenging problem. Results In this paper, we proposed a novel computation model for DDA predictions based on graph representation learning over multi-biomolecular network (GRLMN). More specifically, we firstly constructed a large-scale molecular association network (MAN) by integrating the associations among drugs, diseases, proteins, miRNAs, and lncRNAs. Then, a graph embedding model was used to learn vector representations for all drugs and diseases in MAN. Finally, the combined features were fed to a random forest (RF) model to predict new DDAs. The proposed model was evaluated on the SCMFDD-S data set using five-fold cross-validation. Experiment results showed that GRLMN model was very accurate with the area under the ROC curve (AUC) of 87.9%, which outperformed all previous works in terms of both accuracy and AUC in benchmark dataset. To further verify the high performance of GRLMN, we carried out two case studies for two common diseases. As a result, in the ranking of drugs that were predicted to be related to certain diseases (such as kidney disease and fever), 15 of the top 20 drugs have been experimentally confirmed. Conclusions The experimental results show that our model has good performance in the prediction of DDA. GRLMN is an effective prioritization tool for screening the reliable DDAs for follow-up studies concerning their participation in drug reposition.