Graph embedding and ensemble learning for predicting gene-disease associations

In this paper, we present a model which incorporates biomedical knowledge graph, graph embedding and deep learning methods for literature-based discovery. Firstly, the relations between entities are extracted from biomedical abstracts and then a knowledge graph is constructed by using these obtained relations. Secondly, the graph embedding technologies are applied to convert the entities and relations in the knowledge graph into a low-dimensional vector space. Thirdly, a bidirectional Long Short-Term Memory network is trained based on the entity associations represented by the pre-trained graph embeddings. Finally, the learned model is used for open and closed literature-based discovery tasks. The experimental results show that our method could not only effectively discover hidden associations between entities, but also reveal the corresponding mechanism of interactions. It suggests that incorporating knowledge graph and deep learning methods is an effective way for capturing the underlying complex associations between entities hidden in the literature.

Perturbation analysis on PCA plus graph embedding methods and PCA plus exponential graph embedding methods

PeerRemove: An adaptive node removal strategy for P2P botnet based on deep reinforcement learning

Reliable Internet of Things (IoT) service discovery is a significant task in intelligent service-oriented IoT systems. Collaborative filtering (CF) turns out to be an effective solution to IoT service discovery. However, the traditional CF framework is facing the following challenges: inefficiency in learning the high-order interactions between users and IoT services and ineffectively making use of geographical location information. Moreover, deploying a CF framework in real-world distributed IoT systems poses another significant challenge in terms of reliability assurance and privacy protection. For bridging this gap, we propose an innovative integrated collaborative filtering framework (ICF) with incorporating the location-aware quality of IoT services into a heterogeneous graph embedding model. Meanwhile, a Geohash-based privacy-preservation mechanism is introduced to encoding the location information into a short string for protecting the sensitive location information. The proposed ICF framework is an integrated architecture combining advanced graph embedding learning and heterogeneous side information. And a joint objective optimization function is designed in the graph embedding learning to qualify automatic IoT service features. In this way, the hidden user-service interaction information and location-aware quality semantic features can be explored in an effective and reliable way. Furthermore, the learned location-aware quality embedding vector is incorporated to discover the reliable services among all IoT services with the mini-batch online clustering-based CF algorithm. The experimental findings illustrate the significant efficacy and reliability of our proposed ICF framework in large scale IoT service discovery scenarios.

Emerging technologies for drug repurposing: Harnessing the potential of text and graph embedding approaches

On connections between Rényi entropy Principal Component Analysis, kernel learning and graph embedding

The study of protein–protein interaction and the determination of protein functions are important parts of proteomics. Computational methods are used to study the similarity between proteins based on Gene Ontology (GO) to explore their functions and possible interactions. GO is a series of standardized terms that describe gene products from molecular functions, biological processes, and cell components. Previous studies on assessing the similarity of GO terms were primarily based on Information Content (IC) between GO terms to measure the similarity of proteins. However, these methods tend to ignore the structural information between GO terms. Therefore, considering the structural information of GO terms, we systematically analyze the performance of the GO graph and GO Annotation (GOA) graph in calculating the similarity of proteins using different graph embedding methods. When applied to the actual Human and Yeast datasets, the feature vectors of GO terms and proteins are learned based on different graph embedding methods. To measure the similarity of the proteins annotated by different GO numbers, we used Dynamic Time Warping (DTW) and cosine to calculate protein similarity in GO graph and GOA graph, respectively. Link prediction experiments were then performed to evaluate the reliability of protein similarity networks constructed by different methods. It is shown that graph embedding methods have obvious advantages over the traditional IC-based methods. We found that random walk graph embedding methods, in particular, showed excellent performance in calculating the similarity of proteins. By comparing link prediction experiment results from GO(DTW) and GOA(cosine) methods, it is shown that GO(DTW) features provide highly effective information for analyzing the similarity among proteins.

Graph embedding is becoming widely adopted as an efficient way to learn graph representations required to solve graph analytics problems. However, most existing graph embedding methods, owing to computation-efficiency challenges for large-scale graphs, generally employ a one-size-fits-all strategy to extract information, resulting in a large amount of redundant or inaccurate representations. In this work, we propose HuGE, an efficient and scalable graph embedding method enabled by an entropy-driven mechanism. Specifically, HuGE leverages hybrid-property heuristic random walk to capture node features, which considers both node degree and the number of common neighbors in each walking step. More importantly, to guarantee information effectiveness of sampling, HuGE adopts two heuristic methods to decide the random walk length and the number of walks per node, respectively. Extensive experiments on real-world graphs demonstrate that HuGE achieves both efficiency and performance advantages over recent popular graph embedding approaches. For link prediction and multi-label classification, our approach not only offers >10% average gains, but also exhibits 22×–126× speedup compared with existing sampling-based methods.

A major challenge lies in discovering, emphasizing, and characterizing human gene-disease and gene-gene associations. The limitations of data on the role of human gene products in substance use disorder (SUD) makes it challenging to transition from genetic associations to actionable insights. The integration of data from multiple diverse sources, including information-dense studies in model organisms, has the potential to address this gap. We demonstrate a modified performance of the Random Walk with Restart algorithm when multi-species data is integrated in the heterogeneous network within the context of SUD. Additionally, our approach distinguishes among disparate pathways derived from the Kyoto Encyclopedia of Genes and Genomes. Thus, we conclude that direct incorporation of multi-species data to an aggregated heterogeneous knowledge graph can adjust RWR’s performance and enables users to discover new gene-disease and gene-gene associations.

Steiner tree problem (STP) in graphs aims to find a tree of minimum weight in the graph that connects a given set of vertices. It is a classic NP-hard combinatorial optimization problem and has many applications in real world. Many approximate algorithms have been developed for STP, but they suffer from high computational complexity and weak worst-case solution guarantees, respectively. Heuristic algorithms are also developed. But each of them requires application domain knowledge to design and is only suitable for specific scenarios. In this paper, we design a novel framework Cherrypick based on novel graph embedding and deep reinforcement learning to tackle the STP. Given an STP instance, Cherrypick uses this embedding to encode its path-related information and sends the encoded graph to a deep reinforcement learning component based on deep Q network (DQN) to find solutions. We implement the Cherrypick and demonstrate its efficacy and efficiency with extensive experiments using real-world and synthetic datasets.

Author response for "Graph embedding and transfer learning can help predict potential species interaction networks despite data limitations"

Abstract. Intermodal transportation, using multiple modes in a single journey, promotes sustainable logistics. This paper addresses the Intermodal Vehicle Routing Problem and proposes GAGE-Q, which integrates graph embedding and Reinforcement Learning into a Genetic Algorithm. Our method models cities and their multi-modal connections as a graph, leveraging embedding for spatial dependencies and RL-based crossover for faster convergence and better solutions. Experiments on synthetic and real-world data show that GAGE-Q outperforms state-of-the-art methods, offering improved solution quality and efficiency in intermodal route planning.

The innovative concept of Video Extract-Transform-Load (V-ETL), recently proposed in Skyscraper, reinterprets large-scale video analytics as a data warehousing problem. In this study, we aim at enabling real-time and high-throughput ingestion of hundreds of video streams and maximizing the overall accuracy, by constructing a proper ingestion plan for each video stream. To achieve the goal, we construct a comprehensive configuration space that takes into account the configurable components in the entire ingestion pipeline, including numeric parameters and categorical options such as visual inference model selection. The new space is 10 7 times larger than existing approaches, rendering them as sub-optimal points in our space. To effectively explore the huge and heterogeneous configuration space, we devise an accuracy-aware search strategy based on graph embedding and reinforcement learning to establish the runtime-quality Pareto frontier. To reduce the configuration exploration cost for all video streams, we cluster video streams with similar contexts and adopt mixed integer programming to maximize the overall ingestion accuracy while ensuring the real-time ingestion requirement. In the experimental evaluation with one NVIDIA GeForce RTX 4090 GPU card, our Hippo can support real-time ingestion with 300 video streams and secures an ingestion accuracy that exceeds its competitors by more than 30%.

Graph embedding aims to learn the low-dimensional representation of nodes in the network, which has been paid more and more attention in many graph-based tasks recently. Graph Convolution Network (GCN) is a typical deep semisupervised graph embedding model, which can acquire node representation from the complex network. However, GCN usually needs to use a lot of labeled data and additional expressive features in the graph embedding learning process, so the model cannot be effectively applied to undirected graphs with only network structure information. In this paper, we propose a novel unsupervised graph embedding method via hierarchical graph convolution network (HGCN). Firstly, HGCN builds the initial node embedding and pseudo-labels for the undirected graphs, and then further uses GCNs to learn the node embedding and update labels, finally combines HGCN output representation with the initial embedding to get the graph embedding. Furthermore, we improve the model to match the different undirected networks according to the number of network node label types. Comprehensive experiments demonstrate that our proposed HGCN and HGCN∗ can significantly enhance the performance of the node classification task.

Identifying disease-related genes provides essential information for physiology, pathology and pharmacology. With the rapid growth of high-throughput sequencing technology and genome-wide association studies, a large number of gene-disease associations have been accumulated. These associations, coupled with the existing gene-related and disease-related databases, enable prediction of unknown associations by computational approaches. In this article, we proposed a new graph-based machine learning framework to predict the disease related genes. We first constructed a heterogeneous gene-disease association graph by integrating multiple biomedical knowledge bases, and subsequently processed the graph by a method that utilizes graph embedding representation and graph convolutional networks to learn the gene-disease associations. In our method, we defined a novel cluster loss function and a dropout mechanism to improve the generalization ability. We conducted experiments on DisGeNet dataset in 10-fold cross validation. The experimental results suggested that our method significantly outperformed the existing methods according to the performance of gene prioritization. The performance comparison of the variations of our method showed the efficacy of each module in our method.