Knowledge graphs are an increasingly common data structure for representing biomedical information. These knowledge graphs can easily represent heterogeneous types of information, and many algorithms and tools exist for querying and analyzing graphs. Biomedical knowledge graphs have been used in a variety of applications, including drug repurposing, identification of drug targets, prediction of drug side effects, and clinical decision support. Typically, knowledge graphs are constructed by centralization and integration of data from multiple disparate sources. Here, we describe BioThings Explorer, an application that can query a virtual, federated knowledge graph derived from the aggregated information in a network of biomedical web services. BioThings Explorer leverages semantically precise annotations of the inputs and outputs for each resource, and automates the chaining of web service calls to execute multi-step graph queries. Because there is no large, centralized knowledge graph to maintain, BioThing Explorer is distributed as a lightweight application that dynamically retrieves information at query time. More information can be found at https://explorer.biothings.io, and code is available at https://github.com/biothings/biothings_explorer.

The determinantal point process (DPP) is an elegant probabilistic model of repulsion with applications in various machine learning tasks including summarization and search. However, the maximum a posteriori (MAP) inference for DPP which plays an important role in many applications is NP-hard, and even the popular greedy algorithm can still be too computationally expensive to be used in large-scale real-time scenarios. To overcome the computational challenge, in this paper, we propose a novel algorithm to greatly accelerate the greedy MAP inference for DPP. In addition, our algorithm also adapts to scenarios where the repulsion is only required among nearby few items in the result sequence. We apply the proposed algorithm to generate relevant and diverse recommendations. Experimental results show that our proposed algorithm is significantly faster than state-of-the-art competitors, and provides a better relevance-diversity trade-off on several public datasets, which is also confirmed in an online A/B test.