This paper proposes an algorithm named as PrTransH to learn embedding vectors from real world EMR data based medical knowledge. The unique challenge in embedding medical knowledge graph from real world EMR data is that the uncertainty of knowledge triplets blurs the border between correct triplet and wrong triplet, changing the fundamental assumption of many existing algorithms. To address the challenge, some enhancements are made to existing TransH algorithm, including: 1) involve probability of medical knowledge triplet into training objective; 2) replace the margin-based ranking loss with unified loss calculation considering both valid and corrupted triplets; 3) augment training data set with medical background knowledge. Verifications on real world EMR data based medical knowledge graph prove that PrTransH outperforms TransH in link prediction task. To the best of our survey, this paper is the first one to learn and verify knowledge embedding on probabilistic knowledge graphs.
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