Advances in machine learning and deep learning methods, together with the increasing availability of large-scale pharmacological, genomic, and chemical datasets, have created opportunities for identifying potentially useful relationships within biochemical networks. Knowledge embedding models have been found to have value in detecting knowledge-based correlations among entities, but little effort has been made to apply them to networks of biochemical entities. This is because such networks tend to be unbalanced and sparse, and knowledge embedding models do not work well on them. However, to some extent, the shortcomings of knowledge embedding models can be compensated for if they are used in association with graph embedding. In this paper, we combine knowledge embedding and graph embedding to represent biochemical entities and their relations as dense and low-dimensional vectors. We build a cascade learning framework which incorporates semantic features from the knowledge embedding model, and graph features from the graph embedding model, to score the probability of linking. The proposed method performs noticeably better than the models with which it is compared. It predicted links and entities with an accuracy of 93%, and its average hits@10 score has an average of 8.6% absolute improvement compared with original knowledge embedding model, 1.1% to 9.7% absolute improvement compared with other knowledge and graph embedding algorithm. In addition, we designed a meta-path algorithm to detect path relations in the biomedical network. Case studies further verify the value of the proposed model in finding potential relationships between diseases, drugs, genes, treatments, etc. Amongst the findings of the proposed model are the suggestion that VDR (vitamin D receptor) may be linked to prostate cancer. This is backed by evidence from medical databases and published research, supporting the suggestion that our proposed model could be of value to biomedical researchers.

No abstract

No abstract

We present a multi-filtering Graph Convolution Neural Network (GCN) framework for network embedding task. It uses multiple local GCN filters to do feature extraction in every propagation layer. We show this approach could capture different important aspects of node features against the existing attribute embedding based method. We also show that with multi-filtering GCN approach, we can achieve significant improvement against baseline methods when training data is limited. We also perform many empirical experiments and demonstrate the benefit of using multiple filters against single filter as well as most current existing network embedding methods for both the link prediction and node classification tasks.1. We introduce a novel approach called MF-GCN based

Attributed network embedding (ANE) attempts to represent a network in short code, while retaining information about node topological structures and node attributes. A node's feature and topological structure information could be divided into different local aspects, while in many cases, not all the information but part of the information contained in several local aspects determine the relations among different nodes. Most of the existing works barely concern and identify the aspect influence from network embedding to our knowledge. We attempt to use local embeddings to represent local aspect information and propose InfomaxANE which encodes both global and local embeddings from the perspective of mutual information. The local aspect embeddings are forced to learn and extract different aspect information from nodes' features and topological structures by using orthogonal constraint. A theoretical analysis is also provided to further confirm its correctness and rationality. Besides, to provide complete and refined information for local encoders, we also optimize feature aggregation in SAGE with different structures: feature similarities are concerned and aggregator is seperated from encoder. InfomaxANE is evaluated on both node clustering and node classification tasks (including both transductive and inductive settings) with several benchmark datasets, the results show the outperformance of InfomaxANE over competitive baselines. We also verify the significance of each module in our proposed InfomaxANE in the additional experiment.