Gating-Enhanced Hierarchical Structure Learning in Hyperbolic Space and Multi-scale Neighbor Topology Learning in Euclidean Space for Prediction of Microbe-Drug Associations

Identifying drug-related microbes may help us explore how the microbes affect the functions of drugs by promoting or inhibiting their effects. Most previous methods for the prediction of microbe-drug associations focused on integrating the attributes and topologies of microbe and drug nodes in Euclidean space. The heterogeneous network composed of microbes and drugs has a hierarchical structure, and the hyperbolic space is helpful for reflecting the structure. However, the previous methods did not fully exploit the structure. We propose a multi-space feature learning enhanced microbe-drug association prediction method, MFLP, to fuse the hierarchical structure of microbe and drug nodes in hyperbolic space and the multiscale neighbor topologies in Euclidean space. First, we project the nodes of the microbe-drug heterogeneous network on the sphere in hyperbolic space and then construct a topology which implies hierarchical structure and forms a hierarchical attribute embedding. The node information from multiple types of neighbor nodes with the new topological structure in the tangent plane space of a sphere is aggregated by the designed gating-enhanced hyperbolic graph neural network. Second, the gate at the node feature level is constructed to adaptively fuse the hierarchical features of microbe and drug nodes from two adjacent graph neural encoding layers. Third, multiple neighbor topological embeddings for each microbe and drug node are formed by neighborhood random walks on the microbe-drug heterogeneous network, and they cover neighborhood topologies with multiple scales, respectively. Finally, as each scale of topological embedding contains its specific neighborhood topology, we establish an independent graph convolutional neural network for the topology and form the topological representations of microbe and drug nodes in Euclidean space. The comparison experiments based on cross validation showed that MFLP outperformed several advanced prediction methods, and the ablation experiments verified the effectiveness of MFLP’s major innovations. The case studies on three drugs further demonstrated MFLP’s ability in being applied to discover potential candidate microbes for the given drugs.