Answering complex queries in knowledge graphs with bidirectional sequence encoders usable to support decision making and having medical use applications

Abstract

A method of encoding a query graph having m root nodes and n leaf nodes includes receiving m×n path queries representing the query graph, where each path query starts with a root node and ends with a leaf node, and where the query graph includes one or more missing nodes or edges between nodes. Positions of each node and edge within each path query are encoded independently, where the encoded positions include a positional order, and positional counter values that are reset at a start position of each path query. The missing nodes or edges are masked to produce a masked query that is fed to a transformer encoder. The method can be used for, but is not limited to, medical uses, such as for predicting protein-drug interactions or medical conditions, as well as other applications, to support decision making or optimizing processes or predictions.