Knowledge Guided Feature Aggregation for the Prediction of Chronic Obstructive Pulmonary Disease With Chinese EMRs

Abstract

The automatic disease diagnosis utilizing clinical data has been suffering from the issues of feature sparse and high probability of missing values. Since the graph neural network is a effective tool to model the structural information and infer the missing values, it is becoming the dominant method for the predictive model construction from electronic medical records. Existing graph neural network based solutions usually adopt the medical concepts (e.g., symptoms) the feature representation of clinical data without considering their underlying semantic relations. The limited discriminative capability of the medical concept cannot provide sufficient indicative information about the disease. This article proposes a knowledge-guided graph attention network for the disease prediction. Beside extracting the attribute-value structure as a large-size medical concept, the mutual information between multiple medical concepts mentioned in the electronic medical records are taken into account in the graph construction. Meanwhile, the defined diseases and their associations with the medical concepts in the medical knowledge graph are incorporated into the graph, which provides the potentials to enhance the indicative impacts of the medical concepts directly related to a target disease. Then, the spatial and attention based graph encoders are employed to aggregate information from directly neighbor nodes to generate node embeddings as the compact features to be used for disease diagnosis. The approach itself is a general one that can utilized to build the predictive model using Chinese EMRs for different diseases. The empirical experiments for its performance evaluation are conducted on the real-world COPD EMR dataset. The comparison study results show that the proposed model outperforms baseline methods, which illustrates the effectiveness of our proposed model.