scholarly journals Candidate gene prioritization using graph embedding

2020 ◽  
Author(s):  
Quan Do ◽  
Pierre Larmande
Keyword(s):  
Link Prediction ◽  
Graph Embedding ◽  
Prediction Performance ◽  
Knowledge Graph ◽  
Learning Techniques ◽  
Number Of Genes ◽  
Important Amount ◽  
Candidate Gene Prioritization ◽  
Gene Information ◽  
Embedding Methods

AbstractCandidate genes prioritization allows to rank among a large number of genes, those that are strongly associated with a phenotype or a disease. Due to the important amount of data that needs to be integrate and analyse, gene-to-phenotype association is still a challenging task. In this paper, we evaluated a knowledge graph approach combined with embedding methods to overcome these challenges. We first introduced a dataset of rice genes created from several open-access databases. Then, we used the Translating Embedding model and Convolution Knowledge Base model, to vectorize gene information. Finally, we evaluated the results using link prediction performance and vectors representation using some unsupervised learning techniques.

scholarly journals TransET: Knowledge Graph Embedding with Entity Types

Electronics ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1407
Author(s):  
Peng Wang ◽  
Jing Zhou ◽  
Yuzhang Liu ◽  
Xingchen Zhou
Keyword(s):  
Link Prediction ◽  
State Of The Art ◽  
Score Function ◽  
Graph Embedding ◽  
Vector Spaces ◽  
Knowledge Graph ◽  
Semantic Features ◽  
Knowledge Graphs ◽  
Real World Datasets ◽  
Low Dimensional

Knowledge graph embedding aims to embed entities and relations into low-dimensional vector spaces. Most existing methods only focus on triple facts in knowledge graphs. In addition, models based on translation or distance measurement cannot fully represent complex relations. As well-constructed prior knowledge, entity types can be employed to learn the representations of entities and relations. In this paper, we propose a novel knowledge graph embedding model named TransET, which takes advantage of entity types to learn more semantic features. More specifically, circle convolution based on the embeddings of entity and entity types is utilized to map head entity and tail entity to type-specific representations, then translation-based score function is used to learn the presentation triples. We evaluated our model on real-world datasets with two benchmark tasks of link prediction and triple classification. Experimental results demonstrate that it outperforms state-of-the-art models in most cases.

Hierarchical-Aware Relation Rotational Knowledge Graph Embedding For Link Prediction

2021 ◽  
Author(s):  
Shensi Wang ◽  
Kun Fu ◽  
Xian Sun ◽  
Zequn Zhang ◽  
Shuchao Li ◽  
...  
Keyword(s):  
Link Prediction ◽  
Graph Embedding ◽  
Knowledge Graph

scholarly journals Exploiting node metadata to predict interactions in large networks using graph embedding and neural networks

2021 ◽  
Author(s):  
Rogini Runghen ◽  
Daniel B Stouffer ◽  
Giulio Valentino Dalla Riva
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Link Prediction ◽  
Graph Embedding ◽  
Feature Space ◽  
Machine Learning Techniques ◽  
Large Networks ◽  
Data Set ◽  
Learning Techniques ◽  
Low Dimensional

Collecting network interaction data is difficult. Non-exhaustive sampling and complex hidden processes often result in an incomplete data set. Thus, identifying potentially present but unobserved interactions is crucial both in understanding the structure of large scale data, and in predicting how previously unseen elements will interact. Recent studies in network analysis have shown that accounting for metadata (such as node attributes) can improve both our understanding of how nodes interact with one another, and the accuracy of link prediction. However, the dimension of the object we need to learn to predict interactions in a network grows quickly with the number of nodes. Therefore, it becomes computationally and conceptually challenging for large networks. Here, we present a new predictive procedure combining a graph embedding method with machine learning techniques to predict interactions on the base of nodes' metadata. Graph embedding methods project the nodes of a network onto a---low dimensional---latent feature space. The position of the nodes in the latent feature space can then be used to predict interactions between nodes. Learning a mapping of the nodes' metadata to their position in a latent feature space corresponds to a classic---and low dimensional---machine learning problem. In our current study we used the Random Dot Product Graph model to estimate the embedding of an observed network, and we tested different neural networks architectures to predict the position of nodes in the latent feature space. Flexible machine learning techniques to map the nodes onto their latent positions allow to account for multivariate and possibly complex nodes' metadata. To illustrate the utility of the proposed procedure, we apply it to a large dataset of tourist visits to destinations across New Zealand. We found that our procedure accurately predicts interactions for both existing nodes and nodes newly added to the network, while being computationally feasible even for very large networks. Overall, our study highlights that by exploiting the properties of a well understood statistical model for complex networks and combining it with standard machine learning techniques, we can simplify the link prediction problem when incorporating multivariate node metadata. Our procedure can be immediately applied to different types of networks, and to a wide variety of data from different systems. As such, both from a network science and data science perspective, our work offers a flexible and generalisable procedure for link prediction.

Exploring the Runtime Performance of Knowledge Graph Embedding Methods

2021 ◽  
Author(s):  
Angelica S. Valeriani ◽  
Guido Walter Di Donato ◽  
Marco D. Santambrogio
Keyword(s):  
Graph Embedding ◽  
Knowledge Graph ◽  
Runtime Performance ◽  
Embedding Methods

scholarly journals Unsupervised Embedding Enhancements of Knowledge Graphs using Textual Associations

2019 ◽  
Author(s):  
Neil Veira ◽  
Brian Keng ◽  
Kanchana Padmanabhan ◽  
Andreas Veneris
Keyword(s):  
Link Prediction ◽  
Graph Embedding ◽  
Structured Data ◽  
Knowledge Graph ◽  
Sources Of Information ◽  
Textual Information ◽  
Text Document ◽  
First Case ◽  
Textual Data ◽  
Unsupervised Approach

Knowledge graph embeddings are instrumental for representing and learning from multi-relational data, with recent embedding models showing high effectiveness for inferring new facts from existing databases. However, such precisely structured data is usually limited in quantity and in scope. Therefore, to fully optimize the embeddings it is important to also consider more widely available sources of information such as text. This paper describes an unsupervised approach to incorporate textual information by augmenting entity embeddings with embeddings of associated words. The approach does not modify the optimization objective for the knowledge graph embedding, which allows it to be integrated with existing embedding models. Two distinct forms of textual data are considered, with different embedding enhancements proposed for each case. In the first case, each entity has an associated text document that describes it. In the second case, a text document is not available, and instead entities occur as words or phrases in an unstructured corpus of text fragments. Experiments show that both methods can offer improvement on the link prediction task when applied to many different knowledge graph embedding models.

scholarly journals Adaptive Network Automata Modelling of Complex Networks

2021 ◽  
Author(s):  
Alessandro Muscoloni ◽  
Umberto Michieli ◽  
Carlo Vittorio Cannistraci
Keyword(s):  
Complex Networks ◽  
Link Prediction ◽  
Network Science ◽  
Fundamental Problem ◽  
Graph Embedding ◽  
Prediction Performance ◽  
Self Organization ◽  
Deterministic Models ◽  
Adaptive Network ◽  
Wide Range

Many complex networks have a connectivity that might be only partially detected or that tends to grow over time, hence the prediction of non-observed links is a fundamental problem in network science. The aim of topological link prediction is to forecast these non-observed links by only exploiting features intrinsic to the network topology. It has a wide range of real applications, like suggesting friendships in social networks or predicting interactions in biological networks.The Cannistraci-Hebb theory is a recent achievement in network science that includes a theoretical framework to understand local-based link prediction on paths of length n. In this study we introduce two innovations: theory of modelling (science) and theory of realization (engineering). For the theory of modelling we first recall a definition of network automata as a general framework for modelling the growth of connectivity in complex networks. We then show that several deterministic models previously developed fall within this framework and we introduce novel network automata following the Cannistraci-Hebb rule. For the theory of realization, we present how to build adaptive network automata for link prediction, which incorporate multiple deterministic models of self-organization and automatically choose the rule that better explains the patterns of connectivity in the network under investigation. We compare Cannistraci-Hebb adaptive (CHA) network automaton against state-of-the-art link prediction methods such as structural perturbation method (SPM), stochastic block models (SBM) and artificial intelligence algorithms for graph embedding. CHA displays an overall higher link prediction performance across different evaluation frameworks on 1386 networks. Finally, we highlight that CHA offers the key advantage to explicitly explain the mechanistic rule of self-organization which leads to the link prediction performance, whereas SPM and graph embedding not. In comparison to CHA, SBM unfortunately shows irrelevant and unsatisfactory performance demonstrating that SBM modelling is not adequate for link prediction in real networks.

scholarly journals Learning Hierarchy-Aware Knowledge Graph Embeddings for Link Prediction

2020 ◽  
Vol 34 (03) ◽  
pp. 3065-3072 ◽  
Author(s):  
Zhanqiu Zhang ◽  
Jianyu Cai ◽  
Yongdong Zhang ◽  
Jie Wang
Keyword(s):  
Coordinate System ◽  
Link Prediction ◽  
Graph Embedding ◽  
Knowledge Graph ◽  
Polar Coordinate System ◽  
Radial Coordinate ◽  
Polar Coordinate ◽  
Benchmark Datasets ◽  
Knowledge Graphs ◽  
Semantic Hierarchies

Knowledge graph embedding, which aims to represent entities and relations as low dimensional vectors (or matrices, tensors, etc.), has been shown to be a powerful technique for predicting missing links in knowledge graphs. Existing knowledge graph embedding models mainly focus on modeling relation patterns such as symmetry/antisymmetry, inversion, and composition. However, many existing approaches fail to model semantic hierarchies, which are common in real-world applications. To address this challenge, we propose a novel knowledge graph embedding model—namely, Hierarchy-Aware Knowledge Graph Embedding (HAKE)—which maps entities into the polar coordinate system. HAKE is inspired by the fact that concentric circles in the polar coordinate system can naturally reflect the hierarchy. Specifically, the radial coordinate aims to model entities at different levels of the hierarchy, and entities with smaller radii are expected to be at higher levels; the angular coordinate aims to distinguish entities at the same level of the hierarchy, and these entities are expected to have roughly the same radii but different angles. Experiments demonstrate that HAKE can effectively model the semantic hierarchies in knowledge graphs, and significantly outperforms existing state-of-the-art methods on benchmark datasets for the link prediction task.

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