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Register a new userBenchmark and Best Practices for Biomedical Knowledge Graph Embeddings
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Added by
David Chang
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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Much of biomedical and healthcare data is encoded in discrete, symbolic form such as text and medical codes. There is a wealth of expert-curated biomedical domain knowledge stored in knowledge bases and ontologies, but the lack of reliable methods for learning knowledge representation has limited their usefulness in machine learning applications. While text-based representation learning has significantly improved in recent years through advances in natural language processing, attempts to learn biomedical concept embeddings so far have been lacking. A recent family of models called knowledge graph embeddings have shown promising results on general domain knowledge graphs, and we explore their capabilities in the biomedical domain. We train several state-of-the-art knowledge graph embedding models on the SNOMED-CT knowledge graph, provide a benchmark with comparison to existing methods and in-depth discussion on best practices, and make a case for the importance of leveraging the multi-relational nature of knowledge graphs for learning biomedical knowledge representation. The embeddings, code, and materials will be made available to the communitY.
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Knowledge graph embeddings are now a widely adopted approach to knowledge representation in which entities and relationships are embedded in vector spaces. In this chapter, we introduce the reader to the concept of knowledge graph embeddings by explaining what they are, how they can be generated and how they can be evaluated. We summarize the state-of-the-art in this field by describing the approaches that have been introduced to represent knowledge in the vector space. In relation to knowledge representation, we consider the problem of explainability, and discuss models and methods for explaining predictions obtained via knowledge graph embeddings.
Learning knowledge graph embedding from an existing knowledge graph is very important to knowledge graph completion. For a fact $(h,r,t)$ with the head entity $h$ having a relation $r$ with the tail entity $t$, the current approaches aim to learn low dimensional representations $(mathbf{h},mathbf{r},mathbf{t})$, each of which corresponds to the elements in $(h, r, t)$, respectively. As $(mathbf{h},mathbf{r},mathbf{t})$ is learned from the existing facts within a knowledge graph, these representations can not be used to detect unknown facts (if the entities or relations never occur in the knowledge graph). This paper proposes a new approach called TransW, aiming to go beyond the current work by composing knowledge graph embeddings using word embeddings. Given the fact that an entity or a relation contains one or more words (quite often), it is sensible to learn a mapping function from word embedding spaces to knowledge embedding spaces, which shows how entities are constructed using human words. More importantly, composing knowledge embeddings using word embeddings makes it possible to deal with the emerging new facts (either new entities or relations). Experimental results using three public datasets show the consistency and outperformance of the proposed TransW.
Knowledge-based biomedical data science (KBDS) involves the design and implementation of computer systems that act as if they knew about biomedicine. Such systems depend on formally represented knowledge in computer systems, often in the form of knowledge graphs. Here we survey the progress in the last year in systems that use formally represented knowledge to address data science problems in both clinical and biological domains, as well as on approaches for creating knowledge graphs. Major themes include the relationships between knowledge graphs and machine learning, the use of natural language processing, and the expansion of knowledge-based approaches to novel domains, such as Chinese Traditional Medicine and biodiversity.
Learning knowledge graph (KG) embeddings has received increasing attention in recent years. Most embedding models in literature interpret relations as linear or bilinear mapping functions to operate on entity embeddings. However, we find that such relation-level modeling cannot capture the diverse relational structures of KGs well. In this paper, we propose a novel edge-centric embedding model TransEdge, which contextualizes relation representations in terms of specific head-tail entity pairs. We refer to such contextualized representations of a relation as edge embeddings and interpret them as translations between entity embeddings. TransEdge achieves promising performance on different prediction tasks. Our experiments on benchmark datasets indicate that it obtains the state-of-the-art results on embedding-based entity alignment. We also show that TransEdge is complementary with conventional entity alignment methods. Moreover, it shows very competitive performance on link prediction.
Embedding entities and relations into a continuous multi-dimensional vector space have become the dominant method for knowledge graph embedding in representation learning. However, most existing models ignore to represent hierarchical knowledge, such as the similarities and dissimilarities of entities in one domain. We proposed to learn a Domain Representations over existing knowledge graph embedding models, such that entities that have similar attributes are organized into the same domain. Such hierarchical knowledge of domains can give further evidence in link prediction. Experimental results show that domain embeddings give a significant improvement over the most recent state-of-art baseline knowledge graph embedding models.
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