Collaborating Authors

Construct a biomedical knowledge graph with NLP


I have already demonstrated how to create a knowledge graph out of a Wikipedia page. However, since the post got a lot of attention, I've decided to explore other domains where using NLP techniques to construct a knowledge graph makes sense. In my opinion, the biomedical field is a prime example where representing the data as a graph makes sense as you are often analyzing interactions and relations between genes, diseases, drugs, proteins, and more. In the above visualization, we have ascorbic acid, also known as vitamin C, and some of its relations to other concepts. For example, it shows that vitamin C could be used to treat chronic gastritis.

KACC: A Multi-task Benchmark for Knowledge Abstraction, Concretization and Completion Artificial Intelligence

A comprehensive knowledge graph (KG) contains an instance-level entity graph and an ontology-level concept graph. The two-view KG provides a testbed for models to "simulate" human's abilities on knowledge abstraction, concretization, and completion (KACC), which are crucial for human to recognize the world and manage learned knowledge. Existing studies mainly focus on partial aspects of KACC. In order to promote thorough analyses for KACC abilities of models, we propose a unified KG benchmark by improving existing benchmarks in terms of dataset scale, task coverage, and difficulty. Specifically, we collect new datasets that contain larger concept graphs, abundant cross-view links as well as dense entity graphs. Based on the datasets, we propose novel tasks such as multi-hop knowledge abstraction (MKA), multi-hop knowledge concretization (MKC) and then design a comprehensive benchmark. For MKA and MKC tasks, we further annotate multi-hop hierarchical triples as harder samples. The experimental results of existing methods demonstrate the challenges of our benchmark. The resource is available at

Quaternion Knowledge Graph Embeddings

Neural Information Processing Systems

In this work, we move beyond the traditional complex-valued representations, introducing more expressive hypercomplex representations to model entities and relations for knowledge graph embeddings. More specifically, quaternion embeddings, hypercomplex-valued embeddings with three imaginary components, are utilized to represent entities. Relations are modelled as rotations in the quaternion space. The advantages of the proposed approach are: (1) Latent inter-dependencies (between all components) are aptly captured with Hamilton product, encouraging a more compact interaction between entities and relations; (2) Quaternions enable expressive rotation in four-dimensional space and have more degree of freedom than rotation in complex plane; (3) The proposed framework is a generalization of ComplEx on hypercomplex space while offering better geometrical interpretations, concurrently satisfying the key desiderata of relational representation learning (i.e., modeling symmetry, anti-symmetry and inversion). Experimental results demonstrate that our method achieves state-of-the-art performance on four well-established knowledge graph completion benchmarks.

Context-Enhanced Entity and Relation Embedding for Knowledge Graph Completion Artificial Intelligence

Most researches for knowledge graph completion learn representations of entities and relations to predict missing links in incomplete knowledge graphs. However, these methods fail to take full advantage of both the contextual information of entity and relation. Here, we extract contexts of entities and relations from the triplets which they compose. We propose a model named AggrE, which conducts efficient aggregations respectively on entity context and relation context in multi-hops, and learns context-enhanced entity and relation embeddings for knowledge graph completion. The experiment results show that AggrE is competitive to existing models.

Learning Knowledge Representation Across Knowledge Graphs

AAAI Conferences

Distributed knowledge representation learning (KRL) methods encode both entities and relations in knowledge graphs (KG) in a lower-dimensional semantic space, which model relatively dense knowledge graphs well and greatly improve the performance of knowledge graph completion and knowledge reasoning. However, existing KRL methods including Trans(E, H, R, D and Sparse) hardly obtain comparative performances on sparse KGs where most of entities and relations have very low frequencies. Furthermore, all existing methods target at KRL on one knowledge graph independently. The embeddings of different KGs are independent with each other. In this paper, we propose a novel cross-knowledge-graph (cross-KG) KRL method which learns embeddings for two different KGs simultaneously. Through projecting semantic related entities and relations in two KGs to a uniform semantic space, our method could learn better embeddings for sparse KGs by incorporating information from another relatively larger and denser KG. The learned embeddings are also helpful for downstream cross-KGs or cross-linguals tasks like ontology alignment. The experiment results show that our method could significantly outperform corresponding baseline methods on knowledge graph completion on single KG and cross-KG entity prediction and mapping tasks.